OLOBO: Ontology for Linking and Integrating Open Biological and Biomedical Ontologies
type: Ontology
date: 06-01-2017
subject: An ontology for linking and integrating open biological and biomedical ontologies
editor note: Development version
creator: Edison Ong
description: OLOBO is a biomedical ontology that aims to link and integrate open biological and biomediacl ontologies (OBO),.
format: OWL-DL
version info: Vision Release: 1.0.01
creator: Yongqun "Oliver" He

BFO OWL specification label
type: AnnotationProperty
term from ontology: bfo.owl
term from ontology: obi.owl
editor preferred label: BFO OWL specification label
curator notes: Really of interest to developers only
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.
sub property of: label

BFO CLIF specification label
type: AnnotationProperty
term from ontology: bfo.owl
term from ontology: obi.owl
definition source: Person:Alan Ruttenberg
editor preferred label: BFO CLIF specification label
curator notes: Really of interest to developers only
definition: Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
sub property of: label

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

example of usage
type: AnnotationProperty
term from ontology: bfo.owl
term from ontology: obi.owl
definition: A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
definition: 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.
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Daniel Schober
editor preferred label: example
editor preferred label: example of usage
has curation status: IAO_0000122

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

definition
type: AnnotationProperty
label: textual definition
term from ontology: bfo.owl
term from ontology: chebi.owl
term from ontology: doid.owl
term from ontology: go.owl
term from ontology: obi.owl
term from ontology: pato.owl
term from ontology: po.owl
term from ontology: pro.owl
term from ontology: xao.owl
term from ontology: zfa.owl
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.
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Daniel Schober
definition: The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor preferred label: definition
has curation status: IAO_0000122

editor note
type: AnnotationProperty
has db xref: IAO:0000116
term from ontology: bfo.owl
id: editor_note
shorthand: editor_note
term from ontology: obi.owl
is metadata tag: true
has OBO namespace: uberon
definition: An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
term editor: PERSON:Daniel Schober
editor preferred label: editor note
has curation status: IAO_0000122

term editor
type: AnnotationProperty
term from ontology: bfo.owl
term from ontology: obi.owl
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.
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition: Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
term editor: PERSON:Daniel Schober
editor preferred label: term editor
has curation status: IAO_0000122

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

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

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

curator notes
type: AnnotationProperty
label: curator note
has db xref: IAO:0000232
term from ontology: bfo.owl
shorthand: curator_notes
id: curator_notes
term from ontology: obi.owl
is metadata tag: true
has OBO namespace: uberon
definition: An administrative note of use for a curator but of no use for a user
term editor: PERSON:Alan Ruttenberg
editor preferred label: curator note
has curation status: IAO_0000122

imported from
type: AnnotationProperty
term from ontology: bfo.owl
term from ontology: obi.owl
definition: For external terms/classes, the ontology from which the term was imported
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot
editor preferred label: imported from
has curation status: IAO_0000125

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

OBO foundry unique label
type: AnnotationProperty
editor note: The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
term from ontology: go.owl
term from ontology: obi.owl
definition: An alternative name for a class or property which is unique across the OBO Foundry.
definition source: GROUP:OBO Foundry <http://obofoundry.org/>
editor preferred label: OBO foundry unique label
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bjoern Peters
term editor: PERSON:Chris Mungall
term editor: PERSON:Melanie Courtot
has curation status: IAO_0000125

elucidation
type: AnnotationProperty
term from ontology: bfo.owl
term from ontology: obi.owl
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
editor preferred label: elucidation
term editor: person:Alan Ruttenberg

has associated axiom(nl)
type: AnnotationProperty
term from ontology: bfo.owl
term from ontology: obi.owl
elucidation: An axiom associated with a term expressed using natural language
definition source: Person:Alan Ruttenberg
term editor: Person:Alan Ruttenberg
editor preferred label: has associated axiom(nl)

has associated axiom(fol)
type: AnnotationProperty
term from ontology: bfo.owl
term from ontology: obi.owl
elucidation: An axiom expressed in first order logic using CLIF syntax
definition source: Person:Alan Ruttenberg
term editor: Person:Alan Ruttenberg
editor preferred label: has associated axiom(fol)

has axiom label
type: AnnotationProperty
term from ontology: bfo.owl
term from ontology: obi.owl
elucidation: A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI
definition source: Person:Alan Ruttenberg
term editor: Person:Alan Ruttenberg
editor preferred label: has axiom id

term replaced by
type: AnnotationProperty
term from ontology: go.owl
term from ontology: obi.owl
term from ontology: pato.owl
term from ontology: po.owl
term from ontology: pro.owl
term from ontology: xao.owl
term from ontology: zfa.owl
definition: Add as annotation triples in the granting ontology
definition source: Person:Alan Ruttenberg
term editor: Person:Alan Ruttenberg
definition: Use on obsolete terms, relating the term to another term that can be used as a substitute
editor preferred label: term replaced by
has curation status: IAO_0000125

term from ontology

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: RO_0002422

is opposite_of
type: AnnotationProperty
has db xref: RO:0002604
id: is_opposite_of
shorthand: is_opposite_of
has OBO namespace: quality
is metadata tag: true
is class level: true

external_definition
type: AnnotationProperty
IAO_0000115: An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class.
comment: This annotation property may be replaced with an annotation property from an external ontology such as IAO
has db xref: UBPROP:0000001
id: external_definition
shorthand: external_definition
is metadata tag: true
has OBO namespace: uberon

axiom_lost_from_external_ontology
type: AnnotationProperty
IAO_0000115: A textual description of an axiom loss in this ontology compared to an external ontology.
comment: This annotation property may be replaced with an annotation property from an external ontology such as IAO
has db xref: UBPROP:0000002
id: axiom_lost_from_external_ontology
shorthand: axiom_lost_from_external_ontology
is metadata tag: true
has OBO namespace: uberon

homology_notes
type: AnnotationProperty
IAO_0000115: Notes on the homology status of this class.
comment: This annotation property may be replaced with an annotation property from an external ontology such as IAO
has db xref: UBPROP:0000003
id: homology_notes
shorthand: homology_notes
is metadata tag: true
has OBO namespace: uberon

has_relational_adjective
type: AnnotationProperty
has db xref: UBPROP:0000007
IAO_0000232: Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'.
shorthand: has_relational_adjective
id: has_relational_adjective
is metadata tag: true
has OBO namespace: uberon

taxon_notes
type: AnnotationProperty
IAO_0000115: Notes on the how instances of this class vary across species.
has db xref: UBPROP:0000008
id: taxon_notes
shorthand: taxon_notes
is metadata tag: true
has OBO namespace: uberon

function_notes
type: AnnotationProperty
IAO_0000115: Notes on the evolved function of instances of this class.
IAO_0000116: This annotation property may be replaced with an annotation property from an external ontology such as IAO
has db xref: UBPROP:0000009
shorthand: function_notes
id: function_notes
is metadata tag: true
has OBO namespace: uberon

external_ontology_notes
type: AnnotationProperty
IAO_0000115: Notes on how similar or equivalent classes are represented in other ontologies.
IAO_0000116: This annotation property may be replaced with an annotation property from an external ontology such as IAO
has db xref: UBPROP:0000012
shorthand: external_ontology_notes
id: external_ontology_notes
is metadata tag: true
has OBO namespace: uberon

fma_set_term
type: AnnotationProperty
UBPROP_0000012: FMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set term
has db xref: UBPROP:0000202
id: fma_set_term
shorthand: fma_set_term
is metadata tag: true
has OBO namespace: uberon

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
term from ontology: bfo.owl
shorthand: dc-contributor
id: dc-contributor
term from ontology: obi.owl
is metadata tag: true
has OBO namespace: uberon

creator
type: AnnotationProperty
term from ontology: go.owl
term from ontology: obi.owl
term from ontology: po.owl

date
type: AnnotationProperty
term from ontology: go.owl
term from ontology: obi.owl
term from ontology: po.owl

member
type: AnnotationProperty
term from ontology: bfo.owl
term from ontology: obi.owl

subset_property
type: AnnotationProperty
term from ontology: chebi.owl
term from ontology: doid.owl
term from ontology: go.owl
term from ontology: pato.owl
term from ontology: po.owl
term from ontology: xao.owl
term from ontology: zfa.owl

synonym_type_property
type: AnnotationProperty
term from ontology: chebi.owl
term from ontology: go.owl
term from ontology: po.owl
term from ontology: pro.owl
term from ontology: xao.owl
term from ontology: zfa.owl

auto-generated-by
type: AnnotationProperty
term from ontology: doid.owl
term from ontology: pato.owl
term from ontology: pro.owl
term from ontology: xao.owl
term from ontology: zfa.owl

consider
type: AnnotationProperty
term from ontology: go.owl
term from ontology: pato.owl
term from ontology: po.owl
term from ontology: pro.owl
term from ontology: xao.owl
term from ontology: zfa.owl

created by
type: AnnotationProperty
term from ontology: doid.owl
term from ontology: go.owl
term from ontology: pato.owl
term from ontology: po.owl
term from ontology: xao.owl
term from ontology: zfa.owl

creation date
type: AnnotationProperty
term from ontology: doid.owl
term from ontology: go.owl
term from ontology: pato.owl
term from ontology: po.owl
term from ontology: xao.owl
term from ontology: zfa.owl

date
type: AnnotationProperty
term from ontology: chebi.owl
term from ontology: doid.owl
term from ontology: pato.owl
term from ontology: pro.owl
term from ontology: xao.owl
term from ontology: zfa.owl

default-namespace
type: AnnotationProperty
term from ontology: chebi.owl
term from ontology: doid.owl
term from ontology: go.owl
term from ontology: pato.owl
term from ontology: po.owl
term from ontology: pro.owl
term from ontology: xao.owl
term from ontology: zfa.owl

has_alternative_id
type: AnnotationProperty
term from ontology: chebi.owl
term from ontology: doid.owl
term from ontology: go.owl
term from ontology: pato.owl
term from ontology: po.owl
term from ontology: pro.owl
term from ontology: xao.owl
term from ontology: zfa.owl

has_broad_synonym
type: AnnotationProperty
term from ontology: go.owl
term from ontology: pato.owl
term from ontology: po.owl
term from ontology: pro.owl
term from ontology: xao.owl
term from ontology: zfa.owl

database_cross_reference
type: AnnotationProperty
term from ontology: chebi.owl
term from ontology: doid.owl
term from ontology: go.owl
term from ontology: pato.owl
term from ontology: po.owl
term from ontology: pro.owl
term from ontology: xao.owl
term from ontology: zfa.owl

has_exact_synonym
type: AnnotationProperty
term from ontology: chebi.owl
term from ontology: doid.owl
term from ontology: go.owl
term from ontology: pato.owl
term from ontology: po.owl
term from ontology: pro.owl
term from ontology: xao.owl
term from ontology: zfa.owl

has_narrow_synonym
type: AnnotationProperty
term from ontology: doid.owl
term from ontology: go.owl
term from ontology: pato.owl
term from ontology: po.owl
term from ontology: pro.owl
term from ontology: xao.owl
term from ontology: zfa.owl

has_obo_format_version
type: AnnotationProperty
term from ontology: chebi.owl
term from ontology: doid.owl
term from ontology: go.owl
term from ontology: pato.owl
term from ontology: po.owl
term from ontology: pro.owl
term from ontology: xao.owl
term from ontology: zfa.owl

has_obo_namespace
type: AnnotationProperty
term from ontology: chebi.owl
term from ontology: doid.owl
term from ontology: go.owl
term from ontology: pato.owl
term from ontology: po.owl
term from ontology: pro.owl
term from ontology: xao.owl
term from ontology: zfa.owl

has_related_synonym
type: AnnotationProperty
term from ontology: chebi.owl
term from ontology: doid.owl
term from ontology: go.owl
term from ontology: pato.owl
term from ontology: po.owl
term from ontology: pro.owl
term from ontology: xao.owl
term from ontology: zfa.owl

has_scope
type: AnnotationProperty
term from ontology: go.owl
term from ontology: po.owl
term from ontology: pro.owl

has_synonym_type
type: AnnotationProperty
term from ontology: chebi.owl
term from ontology: go.owl
term from ontology: po.owl
term from ontology: pro.owl
term from ontology: xao.owl
term from ontology: zfa.owl

id
type: AnnotationProperty
term from ontology: chebi.owl
term from ontology: doid.owl
term from ontology: go.owl
term from ontology: pato.owl
term from ontology: po.owl
term from ontology: pro.owl
term from ontology: xao.owl
term from ontology: zfa.owl

in_subset
type: AnnotationProperty
term from ontology: chebi.owl
term from ontology: doid.owl
term from ontology: go.owl
term from ontology: pato.owl
term from ontology: po.owl
term from ontology: xao.owl
term from ontology: zfa.owl

is class level
type: AnnotationProperty
term from ontology: go.owl
term from ontology: pato.owl

is metadata tag
type: AnnotationProperty
term from ontology: go.owl
term from ontology: pato.owl

is transitive
type: AnnotationProperty
term from ontology: chebi.owl
term from ontology: pro.owl

saved-by
type: AnnotationProperty
term from ontology: chebi.owl
term from ontology: doid.owl
term from ontology: pato.owl
term from ontology: po.owl
term from ontology: pro.owl
term from ontology: xao.owl
term from ontology: zfa.owl

shorthand
type: AnnotationProperty
term from ontology: chebi.owl
term from ontology: go.owl
term from ontology: obi.owl
term from ontology: pato.owl
term from ontology: po.owl
term from ontology: xao.owl
term from ontology: zfa.owl

treat-xrefs-as-genus-differentia
type: AnnotationProperty
term from ontology: po.owl
term from ontology: xao.owl
term from ontology: zfa.owl

comment
type: AnnotationProperty
term from ontology: bfo.owl
term from ontology: chebi.owl
term from ontology: doid.owl
term from ontology: go.owl
term from ontology: obi.owl
term from ontology: pato.owl
term from ontology: po.owl
term from ontology: pro.owl
term from ontology: xao.owl
term from ontology: zfa.owl

isDefinedBy
type: AnnotationProperty
term from ontology: bfo.owl
term from ontology: obi.owl

label
type: AnnotationProperty
term from ontology: bfo.owl
term from ontology: chebi.owl
term from ontology: doid.owl
term from ontology: go.owl
term from ontology: obi.owl
term from ontology: pato.owl
term from ontology: po.owl
term from ontology: pro.owl
term from ontology: xao.owl
term from ontology: zfa.owl

seeAlso
type: AnnotationProperty
term from ontology: bfo.owl
term from ontology: obi.owl

deprecated
type: AnnotationProperty
term from ontology: chebi.owl
term from ontology: doid.owl
term from ontology: go.owl
term from ontology: obi.owl
term from ontology: pato.owl
term from ontology: po.owl
term from ontology: pro.owl
term from ontology: xao.owl
term from ontology: zfa.owl

homepage
type: AnnotationProperty
term from ontology: bfo.owl
term from ontology: obi.owl

part of
type: ObjectProperty
type: TransitiveProperty
term from ontology: go.owl
term from ontology: obi.owl
term from ontology: pato.owl
term from ontology: po.owl
term from ontology: pro.owl
term from ontology: xao.owl
term from ontology: zfa.owl
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 https://code.google.com/p/obo-relations/wiki/ROAndTime
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'.
definition: a core relation that holds between a part and its whole
editor preferred label: 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)
alternative term: part_of
example of usage: this day is part of this year (occurrent parthood)
inverse of: has part
temporal interpretation: RO_0001901
imported from: ro.owl

has part
type: ObjectProperty
type: TransitiveProperty
term from ontology: chebi.owl
term from ontology: go.owl
term from ontology: obi.owl
term from ontology: pato.owl
term from ontology: po.owl
term from ontology: pro.owl
term from ontology: zfa.owl
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 https://code.google.com/p/obo-relations/wiki/ROAndTime
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'.
definition: a core relation that holds between a whole and its part
editor preferred label: has part
alternative 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)
temporal interpretation: RO_0001901
imported from: ro.owl

preceded by
type: ObjectProperty
type: TransitiveProperty
term from ontology: obi.owl
term from ontology: po.owl
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.
source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
alternative term: is preceded by
editor preferred label: preceded by
alternative 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.
domain: occurrent
range: occurrent
inverse of: precedes
imported from: ro.owl
in subset: ro-eco

precedes
type: ObjectProperty
type: TransitiveProperty
term from ontology: obi.owl
term from ontology: po.owl
editor preferred label: 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.
domain: occurrent
range: occurrent
imported from: ro.owl
in subset: ro-eco

occurs in
type: ObjectProperty
term from ontology: go.owl
term from ontology: obi.owl
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
definition: b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
editor preferred label: occurs in
alternative term: occurs_in
alternative term: unfolds in
alternative term: unfolds_in
domain: occurrent
range: independent continuant
imported from: ro.owl
property chain axiom: part of

participates in
type: ObjectProperty
term from ontology: obi.owl
term from ontology: pro.owl
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
editor preferred label: participates in
alternative term: participates_in
example of usage: this blood clot participates in this blood coagulation
example of usage: this input material (or this output material) participates in this process
example of usage: this investigator participates in this investigation
domain: continuant
range: occurrent
imported from: ro.owl

has quality
type: ObjectProperty
term from ontology: obi.owl
term from ontology: pro.owl
editor note: A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
alternative term: has_quality
example of usage: this apple has quality this red color
range: quality
imported from: ro.owl

has role
type: ObjectProperty
term from ontology: chebi.owl
term from ontology: obi.owl
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.
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
alternative term: has_role
example of usage: this person has role this investigator role (more colloquially: this person has this role of investigator)
domain: independent continuant
range: role
imported from: ro.owl

derives from
type: ObjectProperty
type: TransitiveProperty
term from ontology: obi.owl
term from ontology: pro.owl
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
curator notes: This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations.
definition: a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
alternative term: derives_from
example of usage: this cell derives from this parent cell (cell division)
example of usage: this nucleus derives from this parent nucleus (nuclear division)
domain: independent continuant
range: independent continuant
has curation status: IAO_0000125
imported from: ro.owl
in subset: ro-eco

located in
type: ObjectProperty
type: TransitiveProperty
term from ontology: doid.owl
term from ontology: obi.owl
term from ontology: po.owl
term from ontology: pro.owl
source: http://www.obofoundry.org/ro/#OBO_REL:located_in
editor note: Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
editor note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
definition: a relation between two independent continuants, the target and the location, in which the target is entirely within the location
editor preferred label: located in
alternative term: located_in
example of usage: my brain is located in my head
example of usage: this rat is located in this cage
temporal interpretation: RO_0001901
imported from: ro.owl

only in taxon
type: ObjectProperty
term from ontology: po.owl
term from ontology: pro.owl
example of usage: lactation SubClassOf 'only in taxon' some 'Mammalia'
definition: x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
editor note: The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria
term editor: Chris Mungall
has curation status: IAO_0000125
imported from: ro.owl
definition source: http://www.ncbi.nlm.nih.gov/pubmed/17921072
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20973947

develops from
type: ObjectProperty
type: TransitiveProperty
term from ontology: po.owl
term from ontology: xao.owl
term from ontology: zfa.owl
term editor: Melissa Haendel
term editor: David Osumi-Sutherland
term editor: Terry Meehan
definition: x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
comment: This is the transitive form of the develops from relation
term editor: Chris Mungall
has curation status: IAO_0000125
imported from: ro.owl
property chain axiom: part of

adjacent to
type: ObjectProperty
term from ontology: obi.owl
term from ontology: po.owl
definition: x adjacent to y if and only if x and y share a boundary.
example of usage: A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
example of usage: The epidermis layer of a vertebrate is adjacent to the dermis.
editor note: This relation acts as a join point with BSPO
term editor: Chris Mungall
example of usage: The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
example of usage: The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
has curation status: IAO_0000125
temporal interpretation: RO_0001901
imported from: ro.owl

entity
type: Class
term from ontology: bfo.owl
term from ontology: obi.owl
BFO OWL specification label: entity
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
BFO CLIF specification label: Entity
elucidation: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
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
example of usage: Julius Caesar
example of usage: Verdi’s Requiem
editor preferred label: entity
example of usage: the Second World War
example of usage: your body mass index
imported from: bfo.owl
imported from: obi.owl

continuant
type: Class
subclass of: entity
disjoint with: occurrent
term from ontology: bfo.owl
term from ontology: obi.owl
BFO OWL specification label: continuant
BFO CLIF specification label: Continuant
has associated axiom(fol): (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
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) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
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]
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])
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
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])
imported from: bfo.owl

occurrent
type: Class
subclass of: entity
term from ontology: bfo.owl
term from ontology: obi.owl
has associated axiom(fol): (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
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.
has associated axiom(fol): (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
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])
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.
BFO CLIF specification label: Occurrent
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.
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])
BFO OWL specification label: occurrent
has associated axiom(nl): Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
imported from: bfo.owl

independent continuant
type: Class
subclass of: continuant
disjoint with: specifically dependent continuant
disjoint with: generically dependent continuant
term from ontology: bfo.owl
term from ontology: obi.owl
BFO CLIF specification label: IndependentContinuant
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]
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(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])
example of usage: a heart
example of usage: a spatial region
BFO OWL specification label: ic
example of usage: a chair
example of usage: a leg
example of usage: a molecule
example of usage: an atom
example of usage: an orchestra.
example of usage: an organism
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])
example of usage: the bottom right portion of a human torso
example of usage: the interior of your mouth
imported from: bfo.owl

spatial region
type: Class
subclass of: immaterial entity
disjoint with: site
disjoint with: continuant fiat boundary
term from ontology: bfo.owl
term from ontology: obi.owl
has associated axiom(fol): (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
has associated axiom(nl): All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
BFO OWL specification label: s-region
BFO CLIF specification label: SpatialRegion
has associated axiom(fol): (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
elucidation: A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
editor note: BFO 2 Reference: Spatial regions do not participate in processes.
editor note: Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
imported from: bfo.owl

temporal region
type: Class
subclass of: occurrent
disjoint with: spatiotemporal region
disjoint with: process
disjoint with: process boundary
term from ontology: bfo.owl
term from ontology: obi.owl
has associated axiom(fol): (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
has associated axiom(nl): Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
BFO CLIF specification label: TemporalRegion
BFO OWL specification label: t-region
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]
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])
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

two-dimensional spatial region
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region
term from ontology: bfo.owl
term from ontology: obi.owl
BFO OWL specification label: 2d-s-region
BFO CLIF specification label: TwoDimensionalSpatialRegion
has associated axiom(fol): (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
elucidation: A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
example of usage: an infinitely thin plane in space.
example of usage: the surface of a sphere-shaped part of space
imported from: bfo.owl

spatiotemporal region
type: Class
subclass of: occurrent
term from ontology: bfo.owl
term from ontology: obi.owl
has associated axiom(fol): (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
has associated axiom(fol): (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
elucidation: A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
BFO OWL specification label: st-region
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
BFO CLIF specification label: SpatiotemporalRegion
has associated axiom(fol): (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
has associated axiom(nl): All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
has associated axiom(nl): Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
has associated axiom(nl): Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
has associated axiom(nl): Every spatiotemporal region occupies_spatiotemporal_region itself.
has associated axiom(nl): Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
example of usage: the spatiotemporal region occupied by a human life
example of usage: the spatiotemporal region occupied by a process of cellular meiosis.
example of usage: the spatiotemporal region occupied by the development of a cancer tumor
imported from: bfo.owl

process
type: Class
subclass of: occurrent
term from ontology: bfo.owl
term from ontology: obi.owl
BFO CLIF specification label: Process
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]
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)
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
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])
BFO OWL specification label: process
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.
imported from: bfo.owl

disposition
type: Class
subclass of: realizable entity
disjoint with: role
term from ontology: bfo.owl
term from ontology: obi.owl
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]
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.
BFO CLIF specification label: Disposition
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]
example of usage: an atom of element X has the disposition to decay to an atom of element Y
BFO OWL specification label: disposition
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])
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])
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
imported from: bfo.owl

realizable entity
type: Class
subclass of: specifically dependent continuant
disjoint with: quality
term from ontology: bfo.owl
term from ontology: obi.owl
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]
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(nl): All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
BFO CLIF specification label: RealizableEntity
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])
BFO OWL specification label: realizable
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

zero-dimensional spatial region
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region
term from ontology: bfo.owl
term from ontology: obi.owl
BFO OWL specification label: 0d-s-region
BFO CLIF specification label: ZeroDimensionalSpatialRegion
has associated axiom(fol): (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
elucidation: A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
imported from: bfo.owl

quality
type: Class
subclass of: specifically dependent continuant
term from ontology: bfo.owl
term from ontology: obi.owl
term from ontology: pro.owl
has associated axiom(fol): (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
BFO OWL specification label: quality
BFO CLIF specification label: Quality
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]
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])
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])
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

specifically dependent continuant
type: Class
subclass of: continuant
term from ontology: bfo.owl
term from ontology: obi.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]
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
BFO CLIF specification label: SpecificallyDependentContinuant
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.
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])
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.
BFO OWL specification label: sdc
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
imported from: bfo.owl

role
type: Class
subclass of: realizable entity
term from ontology: bfo.owl
term from ontology: obi.owl
BFO CLIF specification label: Role
BFO OWL specification label: role
has associated axiom(fol): (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
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.
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.
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])
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
imported from: bfo.owl

fiat object part
type: Class
subclass of: material entity
term from ontology: bfo.owl
term from ontology: obi.owl
term from ontology: pro.owl
BFO OWL specification label: fiat-object-part
BFO CLIF specification label: FiatObjectPart
has associated axiom(fol): (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
editor note: BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
elucidation: b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
example of usage: or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
example of usage: the FMA:regional parts of an intact human body.
example of usage: the Western hemisphere of the Earth
example of usage: the division of the brain into regions
example of usage: the division of the planet into hemispheres
example of usage: the dorsal and ventral surfaces of the body
example of usage: the upper and lower lobes of the left lung
imported from: bfo.owl

one-dimensional spatial region
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region
term from ontology: bfo.owl
term from ontology: obi.owl
has associated axiom(fol): (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
BFO CLIF specification label: OneDimensionalSpatialRegion
BFO OWL specification label: 1d-s-region
elucidation: A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
example of usage: an edge of a cube-shaped portion of space.
imported from: bfo.owl

object aggregate
type: Class
subclass of: material entity
term from ontology: bfo.owl
term from ontology: obi.owl
BFO CLIF specification label: ObjectAggregate
editor note: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
definition source: ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
has associated axiom(fol): (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
editor note: BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
example of usage: a collection of cells in a blood biobank.
example of usage: a swarm of bees is an aggregate of members who are linked together through natural bonds
example of usage: a symphony orchestra
example of usage: defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
BFO OWL specification label: object-aggregate
example of usage: an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
elucidation: b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
example of usage: defined by fiat: the aggregate of members of an organization
example of usage: defined through physical attachment: the aggregate of atoms in a lump of granite
example of usage: defined via attributive delimitations such as: the patients in this hospital
example of usage: the aggregate of bearings in a constant velocity axle joint
example of usage: the aggregate of blood cells in your body
example of usage: the nitrogen atoms in the atmosphere
example of usage: the restaurants in Palo Alto
example of usage: your collection of Meissen ceramic plates.
imported from: bfo.owl

three-dimensional spatial region
type: Class
subclass of: spatial region
term from ontology: bfo.owl
term from ontology: obi.owl
BFO OWL specification label: 3d-s-region
has associated axiom(fol): (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
elucidation: A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
BFO CLIF specification label: ThreeDimensionalSpatialRegion
example of usage: a cube-shaped region of space
example of usage: a sphere-shaped region of space,
imported from: bfo.owl

site
type: Class
subclass of: immaterial entity
term from ontology: bfo.owl
term from ontology: obi.owl
has associated axiom(fol): (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
example of usage: Manhattan Canyon)
example of usage: a rabbit hole
BFO OWL specification label: site
BFO CLIF specification label: Site
example of usage: a hole in the interior of a portion of cheese
example of usage: an air traffic control region defined in the airspace above an airport
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])
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

object
type: Class
subclass of: material entity
term from ontology: bfo.owl
term from ontology: obi.owl
term from ontology: pro.owl
BFO OWL specification label: object
editor note: BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
BFO CLIF specification label: Object
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
example of usage: atom
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])
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
imported from: bfo.owl

generically dependent continuant
type: Class
subclass of: continuant
term from ontology: bfo.owl
term from ontology: obi.owl
BFO OWL specification label: gdc
has associated axiom(fol): (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
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.
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])
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.
imported from: bfo.owl

function
type: Class
subclass of: disposition
term from ontology: bfo.owl
term from ontology: obi.owl
has associated axiom(fol): (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
BFO CLIF specification label: Function
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])
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.
BFO OWL 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
imported from: bfo.owl

process boundary
type: Class
subclass of: occurrent
term from ontology: bfo.owl
term from ontology: obi.owl
has associated axiom(fol): (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
has associated axiom(fol): (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
has associated axiom(nl): Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
BFO OWL specification label: p-boundary
BFO CLIF specification label: ProcessBoundary
definition: p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
example of usage: the boundary between the 2nd and 3rd year of your life.
imported from: bfo.owl

one-dimensional temporal region
type: Class
subclass of: temporal region
disjoint with: zero-dimensional temporal region
term from ontology: bfo.owl
term from ontology: obi.owl
BFO CLIF specification label: OneDimensionalTemporalRegion
BFO OWL specification label: 1d-t-region
has associated axiom(fol): (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
elucidation: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
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).
example of usage: the temporal region during which a process occurs.
imported from: bfo.owl

material entity
type: Class
subclass of: independent continuant
disjoint with: immaterial entity
id: BFO:0000040
has OBO namespace: bfo
term from ontology: bfo.owl
term from ontology: obi.owl
term from ontology: pro.owl
BFO OWL specification label: material
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 y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
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]
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])
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.
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])
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
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])
example of usage: the undetached arm of a human being
imported from: bfo.owl
imported from: pr.owl

continuant fiat boundary
type: Class
subclass of: immaterial entity
term from ontology: bfo.owl
term from ontology: obi.owl
BFO CLIF specification label: ContinuantFiatBoundary
has associated axiom(fol): (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
editor note: BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions.
editor note: BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29
has associated axiom(nl): Every continuant fiat boundary is located at some spatial region at every time at which it exists
BFO OWL specification label: cf-boundary
editor note: Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
definition: b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
imported from: bfo.owl

immaterial entity
type: Class
subclass of: independent continuant
term from ontology: bfo.owl
term from ontology: obi.owl
BFO OWL specification label: immaterial
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
BFO CLIF specification label: ImmaterialEntity
imported from: bfo.owl

one-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
disjoint with: two-dimensional continuant fiat boundary
disjoint with: zero-dimensional continuant fiat boundary
term from ontology: bfo.owl
term from ontology: obi.owl
BFO CLIF specification label: OneDimensionalContinuantFiatBoundary
has associated axiom(fol): (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
BFO OWL specification label: 1d-cf-boundary
example of usage: The Equator
elucidation: a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
example of usage: all geopolitical boundaries
example of usage: all lines of latitude and longitude
example of usage: the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
example of usage: the median sulcus of your tongue
imported from: bfo.owl

process profile
type: Class
subclass of: process
disjoint with: history
term from ontology: bfo.owl
term from ontology: obi.owl
BFO OWL specification label: process-profile
has associated axiom(fol): (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
has associated axiom(fol): (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
example of usage: On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
example of usage: One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
BFO CLIF specification label: ProcessProfile
example of usage: The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
definition: b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
elucidation: b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
imported from: bfo.owl

relational quality
type: Class
subclass of: quality
term from ontology: bfo.owl
term from ontology: obi.owl
BFO OWL specification label: r-quality
has associated axiom(fol): (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]
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.
BFO CLIF specification label: RelationalQuality
example of usage: a marriage bond, an instance of love, an obligation between one person and another.
definition: b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
imported from: bfo.owl

two-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
term from ontology: bfo.owl
term from ontology: obi.owl
has associated axiom(fol): (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
BFO CLIF specification label: TwoDimensionalContinuantFiatBoundary
BFO OWL specification label: 2d-cf-boundary
elucidation: a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
imported from: bfo.owl

zero-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
term from ontology: bfo.owl
term from ontology: obi.owl
has associated axiom(fol): (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
BFO OWL specification label: 0d-cf-boundary
BFO CLIF specification label: ZeroDimensionalContinuantFiatBoundary
elucidation: a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
example of usage: the geographic North Pole
example of usage: the point of origin of some spatial coordinate system.
example of usage: the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
editor note: zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
imported from: bfo.owl

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

history
type: Class
subclass of: process
term from ontology: bfo.owl
term from ontology: obi.owl
BFO OWL specification label: history
elucidation: A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
BFO CLIF specification label: History
imported from: bfo.owl

water
type: Class
subclass of: hydrides
subclass of: oxygen hydride
subclass of: inorganic hydroxy compound
has related synonym: 0
has related synonym: 18.011
has related synonym: 18.01530
definition: An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms.
has related synonym: BOUND WATER
has db xref: Beilstein:3587155
has db xref: CAS:7732-18-5
has alternative id: CHEBI:10743
has alternative id: CHEBI:13352
id: CHEBI:15377
has alternative id: CHEBI:27313
has alternative id: CHEBI:42043
has alternative id: CHEBI:42857
has alternative id: CHEBI:43228
has alternative id: CHEBI:44292
has alternative id: CHEBI:44701
has alternative id: CHEBI:44819
has alternative id: CHEBI:5585
has db xref: Gmelin:117
has related synonym: H2O
has db xref: HMDB:HMDB02111
has related synonym: HOH
has related synonym: InChI=1S/H2O/h1H2
has db xref: KEGG:C00001
has db xref: KEGG:D00001
has db xref: MetaCyc:WATER
has db xref: MolBase:1
has db xref: PDBeChem:HOH
has db xref: PDBeChem:MTO
has db xref: Reaxys:3587155
has exact synonym: WATER
has related synonym: Wasser
has exact synonym: Water
has db xref: Wikipedia:Water
has related synonym: XLYOFNOQVPJJNP-UHFFFAOYSA-N
has related synonym: [H]O[H]
has related synonym: [OH2]
has related synonym: acqua
has related synonym: agua
has related synonym: aqua
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has related synonym: dihydridooxygen
has related synonym: dihydrogen oxide
has related synonym: eau
has related synonym: hydrogen hydroxide
term from ontology: obi.owl
has exact synonym: oxidane
has exact synonym: water
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

hydron
type: Class
subclass of: monoatomic cation
subclass of: monoatomic hydrogen
subclass of: nuclear particle
subclass of: inorganic cation
has related synonym: +1
has related synonym: 1.00794
has related synonym: 1.008
has alternative id: CHEBI:10744
has alternative id: CHEBI:13357
id: CHEBI:15378
has alternative id: CHEBI:5584
has related synonym: GPRLSGONYQIRFK-UHFFFAOYSA-N
has related synonym: H
has related synonym: H(+)
has related synonym: H+
has exact synonym: Hydron
has related synonym: InChI=1S/p+1
has db xref: KEGG:C00080
definition: The general name for the hydrogen nucleus, to be used without regard to the hydrogen nuclear mass (either for hydrogen in its natural abundance or where it is not desired to distinguish between the isotopes).
has related synonym: [H+]
has OBO namespace: chebi_ontology
has exact synonym: hydrogen(1+)
has exact synonym: hydron
imported from: chebi.owl
in subset: 3 STAR

biotin
type: Class
subclass of: biotins
has related synonym: (+)-cis-Hexahydro-2-oxo-1H-thieno[3,4]imidazole-4-valeric acid
has related synonym: (3aS,4S,6aR)-Hexahydro-2-oxo-1H-thieno[3,4-d]imidazole-4-valeric acid
has related synonym: 0
has related synonym: 244.088
has related synonym: 244.31172
has related synonym: 5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanoic acid
has exact synonym: 5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid
definition: An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins.
has exact synonym: BIOTIN
has db xref: Beilstein:86838
has exact synonym: Biotin
has related synonym: C10H16N2O3S
has db xref: CAS:58-85-5
has alternative id: CHEBI:13905
id: CHEBI:15956
has alternative id: CHEBI:22882
has alternative id: CHEBI:22884
has alternative id: CHEBI:3108
has alternative id: CHEBI:41236
has db xref: COMe:MOL000144
has related synonym: Coenzyme R
has related synonym: D-(+)-biotin
has related synonym: D-Biotin
has db xref: DrugBank:DB00121
has db xref: Drug_Central:373
has db xref: Gmelin:1918703
has db xref: HMDB:HMDB00030
has related synonym: InChI=1S/C10H16N2O3S/c13-8(14)4-2-1-3-7-9-6(5-16-7)11-10(15)12-9/h6-7,9H,1-5H2,(H,13,14)(H2,11,12,15)/t6-,7-,9-/m0/s1
has db xref: KEGG:C00120
has db xref: KEGG:D00029
has db xref: KNApSAcK:C00000756
has db xref: LINCS:LSM-3994
has db xref: MetaCyc:BIOTIN
has db xref: PDBeChem:BTN
has db xref: PMID:11435506
has db xref: PMID:11800048
has db xref: PMID:12055344
has db xref: PMID:12803839
has db xref: PMID:15012185
has db xref: PMID:15202718
has db xref: PMID:15272000
has db xref: PMID:15899401
has db xref: PMID:16419467
has db xref: PMID:16676358
has db xref: PMID:16677798
has db xref: PMID:16769720
has db xref: PMID:17297119
has db xref: PMID:18452485
has db xref: PMID:18509457
has db xref: PMID:19319844
has db xref: PMID:19727438
has db xref: PMID:19928962
has db xref: PMID:20967359
has db xref: PMID:20974274
has db xref: PMID:21248194
has db xref: PMID:21356565
has db xref: PMID:21373679
has db xref: PMID:21596550
has db xref: PMID:21871906
has db xref: PMID:25515858
has db xref: Reaxys:86838
has related synonym: Vitamin H
has db xref: Wikipedia:Biotin
has related synonym: YBJHBAHKTGYVGT-ZKWXMUAHSA-N
has related synonym: biotina
has related synonym: biotine
has related synonym: biotinum
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has related synonym: cis-(+)-Tetrahydro-2-oxothieno[3,4]imidazoline-4-valeric acid
has related synonym: cis-Hexahydro-2-oxo-1H-thieno(3,4)imidazole-4-valeric acid
has related synonym: cis-Tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid
term from ontology: obi.owl
has related synonym: vitamin B7
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

polynucleotide
type: Class
subclass of: biomacromolecule
subclass of: nucleobase-containing molecular entity
has related synonym: (C5H8O6PR)n.C10H17O10PR2
has related synonym: 0
has related synonym: 0.0
definition: A nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues.
has related synonym: C10H17O10PR2(C5H8O6PR)n
has alternative id: CHEBI:13672
has alternative id: CHEBI:14859
id: CHEBI:15986
has alternative id: CHEBI:8312
has db xref: KEGG:C00419
has exact synonym: Polynucleotide
has OBO namespace: chebi_ontology
has related synonym: polynucleotides
imported from: chebi.owl
in subset: 3 STAR

GTP
type: Class
subclass of: purine ribonucleoside 5'-triphosphate
subclass of: guanosine 5'-phosphate
has related synonym: 0
has related synonym: 5'-GTP
has related synonym: 522.991
has related synonym: 523.18062
has db xref: Beilstein:1201437
has db xref: Beilstein:74004
has related synonym: C10H16N5O14P3
has db xref: CAS:86-01-1
has alternative id: CHEBI:13342
id: CHEBI:15996
has alternative id: CHEBI:24451
has alternative id: CHEBI:42934
has alternative id: CHEBI:5234
has db xref: DrugBank:DB04137
has exact synonym: GTP
has related synonym: GUANOSINE-5'-TRIPHOSPHATE
has related synonym: Guanosine 5'-triphosphate
has related synonym: H4gtp
has db xref: KEGG:C00044
has db xref: KNApSAcK:C00007223
has db xref: PDBeChem:GTP
has related synonym: XKMLYUALXHKNFT-UUOKFMHZSA-N
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has exact synonym: guanosine 5'-(tetrahydrogen triphosphate)
has related synonym: guanosine 5'-triphosphoric acid
has related synonym: guanosine triphosphate
term from ontology: pro.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

phospholipid
type: Class
subclass of: lipid
subclass of: organic phosphate
subclass of: phosphoric ester
definition: A lipid containing phosphoric acid as a mono- or di-ester. The term encompasses phosphatidic acids and phosphoglycerides.
has related synonym: C5H6O8PR3
has alternative id: CHEBI:14816
id: CHEBI:16247
has alternative id: CHEBI:26063
has alternative id: CHEBI:8150
has db xref: KEGG:C00865
has exact synonym: Phospholipid
has OBO namespace: chebi_ontology
has related synonym: phospholipid derivative
has related synonym: phospholipids
imported from: chebi.owl
in subset: 3 STAR

indole-3-acetic acid
type: Class
subclass of: monocarboxylic acid
subclass of: indolyl carboxylic acid
has related synonym: (Indol-3-yl)acetate
has related synonym: (indol-3-yl)acetic acid
has related synonym: 0
has related synonym: 175.063
has related synonym: 175.18400
has exact synonym: 1H-indol-3-ylacetic acid
has related synonym: 2-(indol-3-yl)ethanoic acid
has related synonym: 3-Indolylessigsaeure
definition: A monocarboxylic acid that is acetic acid in which one of the methyl hydrogens has been replaced by a 1H-indol-3-yl group.
has db xref: Beilstein:143358
has related synonym: C10H9NO2
has db xref: CAS:87-51-4
id: CHEBI:16411
has alternative id: CHEBI:24802
has alternative id: CHEBI:5905
has db xref: DrugBank:DB07950
has db xref: Gmelin:143197
has db xref: HMDB:HMDB00197
has related synonym: IAA
has related synonym: IES
has related synonym: InChI=1S/C10H9NO2/c12-10(13)5-7-6-11-9-4-2-1-3-8(7)9/h1-4,6,11H,5H2,(H,12,13)
has exact synonym: Indole-3-acetic acid
has related synonym: Indoleacetic acid
has db xref: KEGG:C00954
has db xref: KNApSAcK:C00000100
has related synonym: OC(=O)Cc1c[nH]c2ccccc12
has db xref: PDBeChem:IAC
has db xref: PMID:13610897
has db xref: PMID:23545355
has db xref: PMID:24285754
has db xref: Reaxys:143358
has related synonym: SEOVTRFCIGRIMH-UHFFFAOYSA-N
has db xref: Wikipedia:Indole-3-acetic_acid
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has related synonym: heteroauxin
term from ontology: pro.owl
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

lipopolysaccharide
type: Class
subclass of: liposaccharide
subclass of: polysaccharide derivative
has alternative id: CHEBI:14520
id: CHEBI:16412
has alternative id: CHEBI:25062
has alternative id: CHEBI:6494
has db xref: KEGG:C00338
has related synonym: LPS
has exact synonym: Lipopolysaccharide
definition: Liposaccharide natural compounds consisting of a trisaccharide repeating unit (two heptose units and octulosonic acid) with oligosaccharide side chains and 3-hydroxytetradecanoic acid units (they are a major constituent of the cell walls of Gram-negative bacteria).
has db xref: PMID:15589368
has db xref: PMID:24186868
has db xref: PMID:24506665
has db xref: PMID:24642373
has db xref: PMID:24659348
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has related synonym: lipopolysaccharides
term from ontology: pro.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

peptide
type: Class
subclass of: carboxamide
subclass of: organic amino compound
has related synonym: (C2H2NOR)nC2H3NOR
has related synonym: 0
definition: Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
has alternative id: CHEBI:14753
id: CHEBI:16670
has alternative id: CHEBI:25906
has alternative id: CHEBI:7990
has db xref: KEGG:C00012
has related synonym: Peptid
has exact synonym: Peptide
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
has exact synonym: peptides
has related synonym: peptido
has related synonym: peptidos
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

acyl monophosphate
type: Class
subclass of: organic phosphate
subclass of: acyclic mixed acid anhydride
has related synonym: 0
has related synonym: 124.964
has related synonym: 124.99730
has related synonym: Acyl phosphate
definition: An organic phosphate ester or anhydride formed by condensation of phosphoric acid with a carboxylic acid.
has related synonym: CH2O5PR
has alternative id: CHEBI:13246
has alternative id: CHEBI:13725
id: CHEBI:16826
has alternative id: CHEBI:22222
has alternative id: CHEBI:2454
has db xref: KEGG:C02133
has related synonym: OP(O)(=O)OC([*])=O
has related synonym: acyl monophosphate ester
has related synonym: acyl monophosphate esters
has related synonym: acyl monophosphates
has related synonym: acyl phosphates
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

deoxyribonucleic acid
type: Class
subclass of: nucleic acid
has related synonym: (Deoxyribonucleotide)m
has related synonym: (Deoxyribonucleotide)n
has related synonym: (Deoxyribonucleotide)n+m
has db xref: CAS:9007-49-2
has alternative id: CHEBI:13302
id: CHEBI:16991
has alternative id: CHEBI:21123
has alternative id: CHEBI:33698
has alternative id: CHEBI:4291
has related synonym: DNA
has related synonym: DNAn
has related synonym: DNAn+1
has related synonym: DNS
has exact synonym: Deoxyribonucleic acid
has related synonym: Desoxyribonukleinsaeure
definition: High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
has db xref: KEGG:C00039
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has exact synonym: deoxyribonucleic acids
has related synonym: deoxyribonucleic acids
has related synonym: desoxyribose nucleic acid
term from ontology: obi.owl
has related synonym: thymus nucleic acid
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

hydrogensulfite
type: Class
subclass of: sulfur oxoanion
has related synonym: -1
has related synonym: 80.965
has related synonym: 81.07214
has related synonym: Bisulfite
has db xref: CAS:15181-46-1
has alternative id: CHEBI:13367
id: CHEBI:17137
has alternative id: CHEBI:5598
has db xref: Gmelin:1455
has related synonym: HO3S
has related synonym: HSO3(-)
has related synonym: HSO3-
has related synonym: Hydrogen sulfite
has related synonym: InChI=1S/H2O3S/c1-4(2)3/h(H2,1,2,3)/p-1
has db xref: KEGG:C11481
has related synonym: LSNNMFCWUKXFEE-UHFFFAOYSA-M
has related synonym: OS([O-])=O
has db xref: PDBeChem:SO3
has related synonym: [SO2(OH)](-)
has related synonym: bisulfite
has related synonym: bisulphite
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has related synonym: hydrogen sulfite(1-)
has exact synonym: hydrogen(trioxidosulfate)(1-)
has exact synonym: hydrogensulfite(1-)
has exact synonym: hydrogentrioxosulfate(1-)
has exact synonym: hydrogentrioxosulfate(IV)
has related synonym: hydrosulfite anion
has exact synonym: hydroxidodioxidosulfate(1-)
has exact synonym: monohydrogentrioxosulfate
term from ontology: obi.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

nucleoside 5'-monophosphate
type: Class
subclass of: nucleoside phosphate
has related synonym: 0
has related synonym: 213.016
has related synonym: C5H10O7PR
has alternative id: CHEBI:14676
id: CHEBI:17188
has alternative id: CHEBI:25607
has alternative id: CHEBI:7439
has alternative id: CHEBI:7653
has alternative id: CHEBI:7654
has db xref: KEGG:C01329
has db xref: KEGG:C02520
has related synonym: NMP
has related synonym: Nucleoside monophosphate
has related synonym: Nucleoside phosphate
has OBO namespace: chebi_ontology
has related synonym: nucleoside monophosphate
has related synonym: nucleoside monophosphates
imported from: chebi.owl
in subset: 3 STAR

glucose
type: Class
subclass of: carbohydrates and carbohydrate derivatives
has related synonym: 0
has related synonym: 180.15588
definition: An aldohexose used as a source of energy and metabolic intermediate.
has related synonym: C6H12O6
has db xref: CAS:50-99-7
has alternative id: CHEBI:14313
id: CHEBI:17234
has alternative id: CHEBI:24277
has alternative id: CHEBI:33929
has alternative id: CHEBI:5418
has related synonym: DL-glucose
has related synonym: Glc
has exact synonym: Glucose
has related synonym: Glukose
has db xref: KEGG:C00293
has db xref: Wikipedia:Glucose
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has exact synonym: gluco-hexose
has exact synonym: glucose
term from ontology: obi.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

GDP
type: Class
subclass of: purine ribonucleoside 5'-diphosphate
subclass of: guanosine 5'-phosphate
has related synonym: 0
has related synonym: 443.024
has related synonym: 443.20072
has related synonym: C10H15N5O11P2
has db xref: CAS:146-91-8
has alternative id: CHEBI:13327
has alternative id: CHEBI:14379
id: CHEBI:17552
has alternative id: CHEBI:24448
has alternative id: CHEBI:42738
has alternative id: CHEBI:5212
has db xref: DrugBank:DB04315
has exact synonym: GDP
has related synonym: Guanosine 5'-diphosphate
has related synonym: Guanosine diphosphate
has db xref: KEGG:C00035
has db xref: KEGG:G10620
has related synonym: QGWNDRXFNXRZMB-UUOKFMHZSA-N
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has exact synonym: guanosine 5'-(trihydrogen diphosphate)
term from ontology: pro.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

5'-adenylyl sulfate
type: Class
subclass of: acyl monophosphate
subclass of: adenosine 5'-phosphate
subclass of: acyl sulfate
has related synonym: 0
has related synonym: 427.020
has related synonym: 427.28562
has exact synonym: 5'-Adenylyl sulfate
has exact synonym: 5'-adenylyl hydrogen sulfate
has related synonym: ADENOSINE-5'-PHOSPHOSULFATE
has related synonym: APS
has related synonym: Adenosine 5'-phosphosulfate
has related synonym: Adenylylsulfate
definition: An adenosine 5'-phosphate having a sulfo group attached to one the phosphate OH groups.
has related synonym: C10H14N5O10PS
has db xref: CAS:485-84-7
has alternative id: CHEBI:12059
has alternative id: CHEBI:13741
has alternative id: CHEBI:13743
id: CHEBI:17709
has alternative id: CHEBI:22247
has alternative id: CHEBI:2486
has alternative id: CHEBI:40562
has db xref: DrugBank:DB03708
has related synonym: IRLPACMLTUPBCL-KQYNXXCUSA-N
has db xref: KEGG:C00224
has db xref: KNApSAcK:C00007445
has db xref: PDBeChem:ADX
has related synonym: adenosine phosphosulfate
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

ceramide
type: Class
subclass of: sphingolipid
subclass of: carboxamide
has related synonym: 0
has related synonym: 100.040
has related synonym: 100.09590
has related synonym: C4H6NO2R3
has alternative id: CHEBI:12487
has alternative id: CHEBI:13954
id: CHEBI:17761
has alternative id: CHEBI:23074
has alternative id: CHEBI:7242
has related synonym: Cer
has exact synonym: Ceramide
definition: Ceramides (N-acyl-sphingoid bases) are a major subclass of sphingoid base derivatives with an amide-linked fatty acid. The fatty acids are typically saturated or monounsaturated with chain lengths from 14 to 26 carbon atoms; the presence of a hydroxyl group on carbon 2 is fairly common. Ceramides are generally precursors of more complex sphingolipids. In the illustrated generalised structure, R(1) = OH, OX (where X = acyl, glycosyl, phosphate, phosphonate, etc.), or H.
has db xref: KEGG:C00195
has db xref: LIPID_MAPS_class:LMSP02
has related synonym: N-acylated sphingoid
has related synonym: O[C@H]([*])[C@H](C[*])NC([*])=O
has db xref: PMID:7542630
has db xref: Wikipedia:Ceramide
has related synonym: a ceramide
has related synonym: ceramides
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

lipid
type: Class
subclass of: organic molecular entity
definition: 'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids.
has alternative id: CHEBI:14517
id: CHEBI:18059
has alternative id: CHEBI:25054
has alternative id: CHEBI:6486
has db xref: KEGG:C01356
has exact synonym: Lipid
has OBO namespace: chebi_ontology
has exact synonym: lipids
imported from: chebi.owl
in subset: 3 STAR

ribonucleoside
type: Class
subclass of: nucleoside
subclass of: tetrahydrofuranol
has related synonym: 0
has related synonym: 133.050
definition: Any nucleoside where the sugar component is D-ribose.
has related synonym: C5H9O4R
has alternative id: CHEBI:13014
has alternative id: CHEBI:13015
has alternative id: CHEBI:13685
id: CHEBI:18254
has alternative id: CHEBI:21085
has alternative id: CHEBI:26560
has alternative id: CHEBI:4240
has alternative id: CHEBI:8844
has db xref: KEGG:C00911
has related synonym: OC[C@H]1O[C@@H]([*])[C@H](O)[C@@H]1O
has exact synonym: Ribonucleoside
has related synonym: a ribonucleoside
has OBO namespace: chebi_ontology
has related synonym: ribonucleosides
imported from: chebi.owl
in subset: 3 STAR

N-acetyl-beta-D-galactosaminyl-(1->3)-alpha-D-galactosyl-(1->4)-beta-D-galactosyl-(1->4)-beta-D-glucosylceramide
type: Class
subclass of: glycotetraosylceramide
subclass of: globoside
subclass of: N-acetyl-beta-D-galactosaminyl-(1->3)-alpha-D-galactosyl-(1->4)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-ceramide
has related synonym: (Gal)2 (GalNAc)1 (Glc)1 (Cer)1
has related synonym: 0
has related synonym: 1015.507
has related synonym: 1016.10840
definition: A glycotetraosylceramide having N-acetyl-beta-D-galactosaminyl-(1->3)-alpha-D-galactosyl-(1->4)-beta-D-galactosyl-(1->4)-beta-D-glucose as the tetrasaccharide component.
has related synonym: C45H79N2O23R
has db xref: CAS:11034-93-8
has alternative id: CHEBI:12452
has alternative id: CHEBI:12557
id: CHEBI:18259
has alternative id: CHEBI:21508
has alternative id: CHEBI:21513
has alternative id: CHEBI:24252
has alternative id: CHEBI:5388
has related synonym: GalNAc-1->3-Gal-1->4-Gal-1->4-Glc-Cer
has related synonym: GalNAcbeta1-3-Galalpha1-4Galbeta1-4Glcbeta1-1Cer
has related synonym: Gb4 Globoside
has related synonym: Gb4 Globotetraosyl ceramide
has related synonym: Gb4Cer
has related synonym: Gbose4Cer
has related synonym: Globoside GL-4
has related synonym: Globoside I
has related synonym: Globotetraosyl ceramide
has db xref: KEGG:C03272
has db xref: KEGG:G00094
has related synonym: N-Acetyl-D-galactosaminyl-1,3-D-galactosyl-1,4-D-galactosyl-1,4-D-glucosylceramide
has related synonym: N-Acetyl-galactosaminyl-1,3-D-galactosyl-1,4-D-galactosyl-1,4-D-glucosylceramide
has exact synonym: N-[(2S,3R,4E)-1-{[2-acetamido-2-deoxy-beta-D-galactopyranosyl-(1->3)-alpha-D-galactopyranosyl-(1->4)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranosyl]oxy}-3-hydroxyoctadec-4-en-2-yl]alkanamide
has related synonym: N-acetyl-D-galactosaminyl-(1->3)-D-galactosyl-(1->4)-D-galactosyl-(1->4)-D-glucosylceramides
has db xref: PMID:1528196
has db xref: PMID:15495792
has db xref: PMID:15661151
has db xref: PMID:1601891
has db xref: PMID:21252262
has db xref: PMID:21376640
has db xref: PMID:2456994
has db xref: PMID:3220436
has db xref: PMID:4026313
has db xref: PMID:7287743
has db xref: PMID:7690848
has db xref: PMID:8161226
has related synonym: Slt-iiv receptor
has related synonym: VT2vp1 Receptor
has related synonym: an N-acetyl-beta-D-galactosaminyl-(1->3)-alpha-D-galactosyl-(1->4)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-N-acylsphing-4-enine
has related synonym: beta-D-GalNAc-(1->3)-alpha-D-Gal-(1->4)-beta-D-Gal-(1->4)-beta-D-Glc-(1<->1')-Cer
has related synonym: beta-D-GalpNAc-(1->3)-alpha-D-Galp-(1->4)-beta-D-Galp-(1->4)-beta-D-Glcp-(1<->1')-Cer
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: pro.owl
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

2'-deoxyribonucleoside
type: Class
subclass of: deoxyribonucleoside
subclass of: tetrahydrofuranol
has related synonym: 0
has related synonym: 117.055
has related synonym: 2'-Deoxynucleoside
has related synonym: 2'-deoxyribonucleosides
has related synonym: 2-Deoxy-D-ribosyl-base
has related synonym: C5H9O3R
has alternative id: CHEBI:1083
has alternative id: CHEBI:11394
has alternative id: CHEBI:11567
has alternative id: CHEBI:11568
id: CHEBI:18274
has alternative id: CHEBI:19259
has alternative id: CHEBI:19560
has alternative id: CHEBI:4421
has related synonym: Deoxynucleoside
has db xref: KEGG:C02269
has db xref: KEGG:C03216
has related synonym: OC[C@H]1O[C@@H]([*])C[C@@H]1O
has related synonym: a 2'-deoxyribonucleoside
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

jasmonic acid
type: Class
subclass of: oxo monocarboxylic acid
has related synonym: (-)-Jasmonic acid
has related synonym: (-)-jasmonic acid
has related synonym: (1R,2R)-3-oxo-2-(2Z)-2-penten-ylcyclopentanacetic acid
has related synonym: (1R,2R)-3-oxo-2-(pent-2Z-enyl)-cyclopentaneacetic acid
has related synonym: 0
has related synonym: 2-{(1R,2R)-3-oxo-2-[(Z)-pent-2-enyl]cyclopentyl}acetate
has related synonym: 210.126
has related synonym: 210.26950
definition: An oxo monocarboxylic acid that is (3-oxocyclopentyl)acetic acid substituted by a (2Z)-pent-2-en-1-yl group at position 2 of the cyclopentane ring.
has related synonym: C12H18O3
has db xref: CAS:6894-38-8
has related synonym: CC\C=C/C[C@@H]1[C@@H](CC(O)=O)CCC1=O
has alternative id: CHEBI:14486
id: CHEBI:18292
has alternative id: CHEBI:18487
has alternative id: CHEBI:95
has db xref: HMDB:HMDB32797
has related synonym: InChI=1S/C12H18O3/c1-2-3-4-5-10-9(8-12(14)15)6-7-11(10)13/h3-4,9-10H,2,5-8H2,1H3,(H,14,15)/b4-3-/t9-,10-/m1/s1
has related synonym: Jasmonate
has exact synonym: Jasmonic acid
has db xref: KEGG:C08491
has db xref: KNApSAcK:C00000218
has db xref: LIPID_MAPS_instance:LMFA02020001
has db xref: PMID:17470145
has db xref: PMID:19704561
has db xref: Reaxys:2692609
has db xref: Wikipedia:Jasmonic_acid
has related synonym: ZNJFBWYDHIGLCU-HWKXXFMVSA-N
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: pro.owl
has exact synonym: {(1R,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetic acid
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate
type: Class
subclass of: glycerophospholipid
has related synonym: 0
has related synonym: 1,2-Diacyl-sn-glycero-3-phospho-(1'-myo-inositol-4',5'-bisphosphate)
has exact synonym: 1-O-(3-sn-phosphatidyl)-1D-myo-inositol 4,5-bis(dihydrogen phosphate)
has exact synonym: 1-Phosphatidyl-1D-myo-inositol 4,5-bisphosphate
has related synonym: 1-Phosphatidyl-D-myo-inositol 4,5-bisphosphate
has related synonym: 547.973
has related synonym: 548.17840
definition: A phosphatidylinositol bisphosphate in which the two phosphate groups are at C-4 and C-5 of the inositol moiety which has the 1D-myo configuration.
has related synonym: C11H19O19P3R2
has alternative id: CHEBI:11282
has alternative id: CHEBI:11288
has alternative id: CHEBI:14796
id: CHEBI:18348
has alternative id: CHEBI:19087
has alternative id: CHEBI:26028
has alternative id: CHEBI:28910
has alternative id: CHEBI:678
has alternative id: CHEBI:8127
has db xref: KEGG:C04637
has related synonym: PIP2
has related synonym: PIPP
has db xref: PMID:6095072
has related synonym: Phosphatidyl-myo-inositol 4,5-bisphosphate
has related synonym: Phosphatidylinositol-4,5-bisphosphate
has related synonym: PtsIns(4,5)P2
has related synonym: PtsIns-4,5-P2
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: pro.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

pyrimidine 2'-deoxyribonucleoside
type: Class
subclass of: 2'-deoxyribonucleoside
subclass of: pyrimidine deoxyribonucleoside
id: CHEBI:19255
has OBO namespace: chebi_ontology
has related synonym: pyrimidine 2'-deoxyribonucleosides
imported from: chebi.owl
in subset: 3 STAR

N-glycosyl compound
type: Class
subclass of: organonitrogen compound
subclass of: carbohydrate derivative
definition: A glycosyl compound arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to a nitrogen atom, thus creating a C-N bond.
id: CHEBI:21731
has related synonym: N-glycoside
has related synonym: N-glycosides
has related synonym: N-glycosyl compounds
has OBO namespace: chebi_ontology
has exact synonym: glycosylamine
has related synonym: glycosylamines
imported from: chebi.owl
in subset: 3 STAR

adenosine phosphate
type: Class
subclass of: nucleoside phosphate
subclass of: adenyl ribonucleotide
id: CHEBI:22256
has related synonym: adenosine phosphates
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

benzopyrrole
type: Class
subclass of: organic heterobicyclic compound
subclass of: heteroarene
subclass of: organonitrogen heterocyclic compound
id: CHEBI:22728
has related synonym: benzopyrroles
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

glycotetraosylceramide
type: Class
subclass of: oligoglycosylceramide
definition: An oligoglycosylceramide consisting of a glycotetraosyl moiety attached to the ceramide oxygen with an unspecified N-acyl substituent attached to the ceramide nitrogen.
id: CHEBI:23075
has OBO namespace: chebi_ontology
has related synonym: glycotetraosylceramides
imported from: chebi.owl
in subset: 3 STAR

chloride salt
type: Class
subclass of: halogen molecular entity
subclass of: halide salt
id: CHEBI:23114
has OBO namespace: chebi_ontology
has related synonym: chloride salts
has related synonym: chlorides
imported from: chebi.owl
in subset: 3 STAR

molecular entity
type: Class
subclass of: material entity
subclass of: chemical entity
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
id: CHEBI:23367
term from ontology: chebi.owl
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 exact synonym: molecular entity
has related synonym: molekulare Entitaet
term from ontology: obi.owl
term from ontology: pro.owl
imported from: chebi.owl
imported from: pr.owl
in subset: 3 STAR
in_subset: 3 STAR

cytochalasin
type: Class
subclass of: benzopyrrole
id: CHEBI:23528
has db xref: Wikipedia:Cytochalasin
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has related synonym: cytochalasins
term from ontology: obi.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

deoxyribonucleoside
type: Class
subclass of: nucleoside
id: CHEBI:23636
has OBO namespace: chebi_ontology
has related synonym: deoxyribonucleosides
imported from: chebi.owl
in subset: 3 STAR

monoatomic cation
type: Class
subclass of: monoatomic ion
subclass of: cation
id: CHEBI:23906
has OBO namespace: chebi_ontology
has related synonym: monoatomic cations
imported from: chebi.owl
in subset: 3 STAR

N-ethyl-N-nitrosourea
type: Class
subclass of: N-nitrosoureas
has related synonym: 0
has related synonym: 1-(Aminocarbonyl)-1-ethyl-2-oxohydrazine
has related synonym: 1-Ethyl-1-nitrosourea
has exact synonym: 1-ethyl-1-nitrosourea
has related synonym: 117.054
has related synonym: 117.10660
definition: A member of the class of N-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups.
has related synonym: Aethylnitroso-harnstoff
has db xref: Beilstein:1761174
has related synonym: C3H7N3O2
has db xref: CAS:759-73-9
has related synonym: CCN(N=O)C(N)=O
id: CHEBI:23995
has related synonym: ENU
has related synonym: Ethyl nitrosourea
has related synonym: FUSGACRLAFQQRL-UHFFFAOYSA-N
has related synonym: InChI=1S/C3H7N3O2/c1-2-6(5-8)3(4)7/h2H2,1H3,(H2,4,7)
has db xref: KEGG:C19178
has related synonym: N-Ethyl-N-nitroso carbamide
has related synonym: N-Ethyl-N-nitroso-urea
has related synonym: N-Ethylnitrosourea
has related synonym: NEU
has db xref: PMID:11732210
has db xref: PMID:11853764
has db xref: PMID:11880538
has db xref: PMID:16423555
has db xref: PMID:21861612
has db xref: PMID:22012195
has db xref: PMID:22238669
has db xref: PMID:23551873
has db xref: PMID:24175309
has db xref: PMID:8603364
has db xref: Reaxys:1761174
has db xref: Wikipedia:ENU
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

glycosphingolipid
type: Class
subclass of: sphingolipid
subclass of: liposaccharide
definition: A glycosphingolipid is a glycolipid that is a carbohydrate-containing derivative of a sphingoid or ceramide. It is understood that the carbohydrate residue is attached by a glycosidic linkage to O-1 of the sphingoid.
id: CHEBI:24402
has alternative id: CHEBI:5498
has db xref: PMID:18845618
has db xref: PMID:19303901
has db xref: PMID:26954668
has db xref: PMID:26976737
has db xref: PMID:27253729
has db xref: PMID:27325407
has db xref: Wikipedia:Glycosphingolipid
has OBO namespace: chebi_ontology
has related synonym: glycosphingolipids
imported from: chebi.owl
in subset: 3 STAR

chemical entity
type: Class
subclass of: material entity
definition: A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
id: CHEBI:24431
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has exact synonym: chemical entity
term from ontology: pro.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

guanosine phosphate
type: Class
subclass of: nucleoside phosphate
subclass of: purine ribonucleoside
subclass of: guanyl ribonucleotide
id: CHEBI:24455
has OBO namespace: chebi_ontology
has related synonym: guanosine phosphates
imported from: chebi.owl
in subset: 3 STAR

halogen molecular entity
type: Class
subclass of: p-block molecular entity
id: CHEBI:24471
has OBO namespace: chebi_ontology
has related synonym: halogen compounds
has related synonym: halogen molecular entities
has exact synonym: halogen molecular entity
imported from: chebi.owl
in subset: 3 STAR

organic heterocyclic compound
type: Class
subclass of: heteroorganic entity
subclass of: organic cyclic compound
subclass of: heterocyclic compound
definition: A cyclic compound having as ring members atoms of carbon and at least of one other element.
id: CHEBI:24532
has OBO namespace: chebi_ontology
has related synonym: organic heterocycle
has related synonym: organic heterocyclic compounds
imported from: chebi.owl
in subset: 3 STAR

proton
type: Class
subclass of: hydron
subclass of: nucleon
has related synonym: (1)1H(+)
has related synonym: (1)H(+)
has related synonym: +1
has related synonym: 1.00783
has related synonym: 1.008
has db xref: CAS:12408-02-5
id: CHEBI:24636
has related synonym: GPRLSGONYQIRFK-FTGQXOHASA-N
has related synonym: H
has related synonym: InChI=1S/p+1/i/hH
has db xref: KEGG:C00080
definition: Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u.
has related synonym: [1H+]
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
has related synonym: p
has related synonym: p(+)
has exact synonym: protium(1+)
has exact synonym: proton
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

hydroxides
type: Class
subclass of: oxygen molecular entity
subclass of: hydrogen molecular entity
subclass of: heteroatomic molecular entity
id: CHEBI:24651
definition: Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)).
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

indoles
type: Class
subclass of: benzopyrrole
definition: Any compound containing an indole skeleton.
id: CHEBI:24828
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

inorganic molecular entity
type: Class
subclass of: molecular entity
definition: A molecular entity that contains no carbon.
id: CHEBI:24835
has related synonym: anorganische Verbindungen
has OBO namespace: chebi_ontology
has related synonym: inorganic compounds
has related synonym: inorganic entity
has related synonym: inorganic molecular entities
has related synonym: inorganics
imported from: chebi.owl
in subset: 3 STAR

inorganic phosphate
type: Class
subclass of: inorganic molecular entity
subclass of: phosphate
definition: Any phosphate that contains no carbon atom.
id: CHEBI:24838
has OBO namespace: chebi_ontology
has related synonym: inorganic phosphates
imported from: chebi.owl
in subset: 3 STAR

inorganic salt
type: Class
subclass of: inorganic molecular entity
subclass of: salt
id: CHEBI:24839
has related synonym: anorganisches Salz
has OBO namespace: chebi_ontology
has related synonym: inorganic salts
imported from: chebi.owl
in subset: 3 STAR

salt
type: Class
subclass of: heteroatomic molecular entity
definition: A salt is an assembly of cations and anions.
id: CHEBI:24866
has related synonym: Salz
has related synonym: Salze
has OBO namespace: chebi_ontology
has related synonym: ionic compound
has related synonym: ionic compounds
has related synonym: sal
has related synonym: sales
has exact synonym: salt
has related synonym: salts
has related synonym: sel
has related synonym: sels
imported from: chebi.owl
in subset: 3 STAR

monoatomic ion
type: Class
subclass of: ion
subclass of: monoatomic entity
id: CHEBI:24867
has OBO namespace: chebi_ontology
has related synonym: monoatomic ions
imported from: chebi.owl
in subset: 3 STAR

ion
type: Class
subclass of: molecular entity
definition: A molecular entity having a net electric charge.
id: CHEBI:24870
has exact synonym: Ion
has related synonym: Ionen
has OBO namespace: chebi_ontology
has exact synonym: ion
has related synonym: iones
has related synonym: ions
imported from: chebi.owl
in subset: 3 STAR

lactone
type: Class
subclass of: carboxylic ester
subclass of: ester
subclass of: oxacycle
definition: Any cyclic carboxylic ester containing a 1-oxacycloalkan-2-one structure, or an analogue having unsaturation or heteroatoms replacing one or more carbon atoms of the ring.
id: CHEBI:25000
has related synonym: Lacton
has related synonym: Lakton
has related synonym: Laktone
has OBO namespace: chebi_ontology
has related synonym: lactona
has related synonym: lactonas
has exact synonym: lactone
has exact synonym: lactones
imported from: chebi.owl
in subset: 3 STAR

luciferin
type: Class
subclass of: role
definition: A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase.
id: CHEBI:25078
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

molecule
type: Class
subclass of: polyatomic entity
definition: Any polyatomic entity that is an electrically neutral entity consisting of more than one atom.
id: CHEBI:25367
has related synonym: Molekuel
has OBO namespace: chebi_ontology
has related synonym: molecula
has exact synonym: molecule
has related synonym: molecules
has related synonym: neutral molecular compounds
imported from: chebi.owl
in subset: 3 STAR

monocarboxylic acid
type: Class
subclass of: carboxylic acid
definition: An oxoacid containing a single carboxy group.
id: CHEBI:25384
has OBO namespace: chebi_ontology
has exact synonym: monocarboxylic acid
has related synonym: monocarboxylic acids
imported from: chebi.owl
in subset: 3 STAR

nonmetal atom
type: Class
subclass of: atom
id: CHEBI:25585
has related synonym: Nichtmetall
has related synonym: Nichtmetalle
has OBO namespace: chebi_ontology
has related synonym: no metal
has related synonym: no metales
has related synonym: non-metal
has related synonym: non-metaux
has exact synonym: nonmetal
has related synonym: nonmetal
has related synonym: nonmetals
imported from: chebi.owl
in subset: 3 STAR

nucleoside phosphate
type: Class
subclass of: organic phosphate
subclass of: phosphoric ester
subclass of: nucleobase-containing molecular entity
definition: A nucleobase-containing molecular entity that is a nucleoside in which one or more of the sugar hydroxy groups has been converted into a mono- or poly-phosphate. The term includes both nucleotides and non-nucleotide nucleoside phosphates.
id: CHEBI:25608
has db xref: KEGG:C01329
has related synonym: NMP
has related synonym: Nucleoside monophosphate
has OBO namespace: chebi_ontology
has related synonym: nucleoside phosphates
imported from: chebi.owl
in subset: 3 STAR

organic heteromonocyclic compound
type: Class
subclass of: organic heterocyclic compound
subclass of: heteromonocyclic compound
id: CHEBI:25693
has OBO namespace: chebi_ontology
has related synonym: organic heteromonocyclic compounds
imported from: chebi.owl
in subset: 3 STAR

organic phosphate
type: Class
subclass of: organophosphorus compound
subclass of: phosphate
subclass of: phosphoric acid derivative
id: CHEBI:25703
has OBO namespace: chebi_ontology
has exact synonym: organic phosphate
has related synonym: organic phosphate ester
has related synonym: organic phosphate esters
has related synonym: organic phosphates
has related synonym: organophosphate ester
has related synonym: organophosphate esters
imported from: chebi.owl
in subset: 3 STAR

organic sulfate
type: Class
subclass of: organosulfur compound
subclass of: sulfuric acid derivative
id: CHEBI:25704
definition: Compounds of the general formula SO3HOR where R is an organyl group
has OBO namespace: chebi_ontology
has related synonym: organic sulfates
imported from: chebi.owl
in subset: 3 STAR

organophosphorus compound
type: Class
subclass of: phosphorus molecular entity
subclass of: heteroorganic entity
definition: An organophosphorus compound is formally a compound containing at least one carbon-phosphorus bond, but the term is often extended to include esters and thioesters.
id: CHEBI:25710
has OBO namespace: chebi_ontology
has exact synonym: organophosphorus compound
has related synonym: organophosphorus compounds
imported from: chebi.owl
in subset: 3 STAR

oxide
type: Class
subclass of: oxygen molecular entity
subclass of: heteroatomic molecular entity
definition: An oxide is a chemical compound of oxygen with other chemical elements.
id: CHEBI:25741
has OBO namespace: chebi_ontology
has exact synonym: oxide
has related synonym: oxides
imported from: chebi.owl
in subset: 3 STAR

oxygen molecular entity
type: Class
subclass of: chalcogen molecular entity
id: CHEBI:25806
has OBO namespace: chebi_ontology
has related synonym: oxygen molecular entities
has exact synonym: oxygen molecular entity
imported from: chebi.owl
in subset: 3 STAR

aldopentose phosphate
type: Class
subclass of: phospho sugar
subclass of: pentose phosphate
id: CHEBI:25900
has exact synonym: aldopentose phosphate
has related synonym: aldopentose phosphates
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

phosphate
type: Class
subclass of: phosphoric acid derivative
id: CHEBI:26020
definition: Salts and esters of phosphoric and oligophosphoric acids and their chalcogen analogues. In inorganic chemistry, the term is also used to describe anionic coordination entities with phosphorus as central atom.
has OBO namespace: chebi_ontology
has exact synonym: phosphates
has related synonym: phosphates
imported from: chebi.owl
in subset: 3 STAR

phosphoric acid derivative
type: Class
subclass of: phosphorus oxoacid derivative
id: CHEBI:26079
has OBO namespace: chebi_ontology
has related synonym: phosphoric acid derivatives
has related synonym: phosphoric acids
imported from: chebi.owl
in subset: 1 STAR

phosphorus molecular entity
type: Class
subclass of: pnictogen molecular entity
id: CHEBI:26082
has OBO namespace: chebi_ontology
has related synonym: phosphorus molecular entities
imported from: chebi.owl
in subset: 3 STAR

purine nucleoside
type: Class
subclass of: purines
subclass of: nucleoside
id: CHEBI:26394
has OBO namespace: chebi_ontology
has exact synonym: purine nucleoside
has related synonym: purine nucleosides
imported from: chebi.owl
in subset: 3 STAR

purine nucleotide
type: Class
subclass of: purines
subclass of: nucleotide
definition: Any nucleotide that has a purine nucleobase.
id: CHEBI:26395
has OBO namespace: chebi_ontology
has related synonym: purine nucleotides
imported from: chebi.owl
in subset: 3 STAR

purine ribonucleoside monophosphate
type: Class
subclass of: nucleoside 5'-monophosphate
subclass of: ribonucleoside monophosphate
id: CHEBI:26397
has OBO namespace: chebi_ontology
has related synonym: purine ribonucleoside monophosphates
imported from: chebi.owl
in subset: 3 STAR

purine ribonucleoside
type: Class
subclass of: ribonucleoside
subclass of: purine nucleoside
id: CHEBI:26399
has OBO namespace: chebi_ontology
has related synonym: purine ribonucleosides
imported from: chebi.owl
in subset: 3 STAR

purine ribonucleotide
type: Class
subclass of: purine nucleotide
subclass of: ribonucleotide
definition: Any ribonucleotide that has a purine nucleobase.
id: CHEBI:26400
has OBO namespace: chebi_ontology
has related synonym: purine ribonucleotides
imported from: chebi.owl
in subset: 3 STAR

purines
type: Class
subclass of: imidazopyrimidine
definition: A class of imidazopyrimidines that consists of purine and its substituted derivatives.
has alternative id: CHEBI:13678
id: CHEBI:26401
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

pyrimidine nucleoside
type: Class
subclass of: nucleoside
subclass of: diazines
id: CHEBI:26440
has db xref: KEGG:C03169
has related synonym: N-D-Ribosylpyrimidine
has OBO namespace: chebi_ontology
has related synonym: pyrimidine nucleosides
imported from: chebi.owl
in subset: 3 STAR

reactive oxygen species
type: Class
subclass of: oxygen molecular entity
id: CHEBI:26523
definition: Molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers.
has related synonym: ROS
has db xref: Wikipedia:Reactive_oxygen_species
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

ribonucleoside monophosphate
type: Class
subclass of: nucleoside 5'-monophosphate
id: CHEBI:26558
has OBO namespace: chebi_ontology
has related synonym: ribonucleoside monophosphates
imported from: chebi.owl
in subset: 3 STAR

ribonucleotide
type: Class
subclass of: aldopentose phosphate
subclass of: nucleotide
id: CHEBI:26561
has OBO namespace: chebi_ontology
has related synonym: ribonucleotides
imported from: chebi.owl
in subset: 3 STAR

sodium chloride
type: Class
subclass of: inorganic chloride
subclass of: inorganic sodium salt
has related synonym: 0
has related synonym: 57.959
has related synonym: 58.44247
definition: An inorganic chloride salt having sodium(1+) as the counterion.
has db xref: Beilstein:3534976
has db xref: CAS:7647-14-5
id: CHEBI:26710
has related synonym: ClNa
has related synonym: FAPWRFPIFSIZLT-UHFFFAOYSA-M
has db xref: Gmelin:13673
has related synonym: InChI=1S/ClH.Na/h1H;/q;+1/p-1
has db xref: KEGG:C13563
has db xref: KEGG:D02056
has related synonym: Kochsalz
has db xref: MetaCyc:NACL
has related synonym: NaCl
has related synonym: Natriumchlorid
has db xref: Reaxys:3534976
has db xref: Wikipedia:Sodium_Chloride
has related synonym: [Na+].[Cl-]
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has related synonym: chlorure de sodium
has related synonym: cloruro sodico
has related synonym: common salt
has related synonym: halite
has related synonym: natrii chloridum
term from ontology: obi.owl
has related synonym: rock salt
has related synonym: salt
has exact synonym: sodium chloride
has related synonym: table salt
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

sodium salt
type: Class
subclass of: alkali metal molecular entity
subclass of: alkali metal salt
definition: Any alkali metal salt having sodium(1+) as the cation.
id: CHEBI:26714
has related synonym: Natriumsalz
has related synonym: Natriumsalze
has OBO namespace: chebi_ontology
has related synonym: sodium salts
imported from: chebi.owl
in subset: 3 STAR

sphingolipid
type: Class
subclass of: lipid
subclass of: organonitrogen compound
subclass of: organooxygen compound
id: CHEBI:26739
definition: Sphingolipids are a complex family of compounds that share a common structural feature, a sphingoid base backbone.
has OBO namespace: chebi_ontology
has related synonym: sphingolipids
imported from: chebi.owl
in subset: 3 STAR

carbohydrate phosphate
type: Class
subclass of: organic phosphate
subclass of: phosphoric ester
subclass of: carbohydrate derivative
id: CHEBI:26816
has related synonym: carbohydrate phosphates
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

sulfuric ester
type: Class
subclass of: ester
subclass of: sulfuric acid derivative
has related synonym: 0
has related synonym: 95.952
has related synonym: 96.06300
definition: An ester of an alcohol and sulfuric acid.
id: CHEBI:26819
has related synonym: O4SR2
has related synonym: [*]OS(=O)(=O)O[*]
has OBO namespace: chebi_ontology
has related synonym: sulfate ester
has related synonym: sulfuric acid ester
has related synonym: sulfuric acid esters
imported from: chebi.owl
in subset: 3 STAR

sulfur molecular entity
type: Class
subclass of: chalcogen molecular entity
id: CHEBI:26835
has OBO namespace: chebi_ontology
has related synonym: sulfur molecular entities
has exact synonym: sulfur molecular entity
imported from: chebi.owl
in subset: 3 STAR

oxolanes
type: Class
subclass of: organic heteromonocyclic compound
subclass of: oxacycle
definition: Any oxacycle having an oxolane (tetrahydrofuran) skeleton.
id: CHEBI:26912
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

organic heterotricyclic compound
type: Class
subclass of: heteropolycyclic compound
subclass of: organic heteropolycyclic compound
subclass of: organic polycyclic compound
definition: An organic tricyclic compound in which at least one of the rings of the tricyclic skeleton contains one or more heteroatoms.
id: CHEBI:26979
has OBO namespace: chebi_ontology
has related synonym: heterotricyclic compounds
has related synonym: organic heterotricyclic compounds
imported from: chebi.owl
in subset: 3 STAR

transition element atom
type: Class
subclass of: metal atom
definition: An element whose atom has an incomplete d sub-shell, or which can give rise to cations with an incomplete d sub-shell.
id: CHEBI:27081
has related synonym: Uebergangselement
has related synonym: Uebergangsmetalle
has OBO namespace: chebi_ontology
has related synonym: metal de transicion
has related synonym: metal de transition
has related synonym: metales de transicion
has related synonym: metaux de transition
has exact synonym: transition element
has related synonym: transition element
has related synonym: transition elements
has related synonym: transition metal
has related synonym: transition metals
imported from: chebi.owl
in subset: 3 STAR

organic heterobicyclic compound
type: Class
subclass of: heterobicyclic compound
subclass of: organic heteropolycyclic compound
id: CHEBI:27171
has OBO namespace: chebi_ontology
has related synonym: heterobicyclic compounds
has related synonym: organic heterobicyclic compounds
imported from: chebi.owl
in subset: 3 STAR

lead(0)
type: Class
subclass of: carbon group molecular entity
has related synonym: 0
has related synonym: 207.20000
has related synonym: 207.977
has db xref: CAS:7439-92-1
id: CHEBI:27889
has alternative id: CHEBI:6397
has related synonym: InChI=1S/Pb
has db xref: KEGG:C06696
has related synonym: Lead
has related synonym: Pb
has related synonym: Pb(0)
has related synonym: Pbn
has related synonym: WABPQHHGFIMREM-UHFFFAOYSA-N
has related synonym: [Pb]
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has exact synonym: lead
has related synonym: lead metal
has exact synonym: lead(0)
term from ontology: obi.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

chromium atom
type: Class
subclass of: chromium group element atom
subclass of: metal atom
has related synonym: 0
has related synonym: 24Cr
has related synonym: 51.941
has related synonym: 51.99610
definition: A chromium group element atom that has atomic number 24.
has db xref: CAS:7440-47-3
has alternative id: CHEBI:23235
id: CHEBI:28073
has alternative id: CHEBI:3678
has related synonym: Chrom
has related synonym: Chromium
has related synonym: Cr
has related synonym: InChI=1S/Cr
has db xref: KEGG:C06268
has related synonym: VYZAMTAEIAYCRO-UHFFFAOYSA-N
has db xref: WebElements:Cr
has related synonym: [Cr]
has OBO namespace: chebi_ontology
has related synonym: chrome
has exact synonym: chromium
has related synonym: chromium
has related synonym: cromo
imported from: chebi.owl
in subset: 3 STAR

acrylamide
type: Class
subclass of: carboxamide
subclass of: enamide
has related synonym: 0
has related synonym: 2-Propenamide
has related synonym: 71.037
has related synonym: 71.07794
definition: A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia.
has exact synonym: Acrylamide
has related synonym: Akrylamid
has db xref: Beilstein:605349
has related synonym: C3H5NO
has db xref: CAS:79-06-1
has alternative id: CHEBI:22215
has alternative id: CHEBI:2441
id: CHEBI:28619
has db xref: Gmelin:81842
has db xref: HMDB:HMDB04296
has related synonym: HRPVXLWXLXDGHG-UHFFFAOYSA-N
has related synonym: InChI=1S/C3H5NO/c1-2-3(4)5/h2H,1H2,(H2,4,5)
has db xref: KEGG:C01659
has related synonym: NC(=O)C=C
has db xref: PMID:10719038
has db xref: PMID:12166997
has db xref: PMID:15240786
has db xref: PMID:15901921
has db xref: PMID:17032038
has db xref: PMID:17234719
has db xref: PMID:17484107
has db xref: PMID:17558658
has db xref: PMID:17720246
has db xref: PMID:18469268
has db xref: PMID:19022940
has db xref: PMID:19846048
has db xref: PMID:22136129
has db xref: PMID:22784192
has db xref: PMID:7767980
has db xref: Patent:US2535245
has db xref: Reaxys:605349
has db xref: UM-BBD_compID:c0149
has db xref: Wikipedia:Acrylamide
has exact synonym: acrylamide
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has related synonym: ethylenecarboxamide
term from ontology: obi.owl
has exact synonym: prop-2-enamide
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

phosphorus atom
type: Class
subclass of: nonmetal atom
subclass of: atom
has related synonym: 0
has related synonym: 15P
has related synonym: 30.97376
has related synonym: 30.974
has db xref: CAS:7723-14-0
has alternative id: CHEBI:26080
id: CHEBI:28659
has alternative id: CHEBI:8168
has db xref: Gmelin:16235
has related synonym: InChI=1S/P
has db xref: KEGG:C06262
has related synonym: OAICVXFJPJFONN-UHFFFAOYSA-N
has related synonym: P
has related synonym: Phosphor
has related synonym: Phosphorus
has db xref: WebElements:P
has related synonym: [P]
has OBO namespace: chebi_ontology
has related synonym: fosforo
has related synonym: phosphore
has related synonym: phosphorus
has exact synonym: phosphorus
imported from: chebi.owl
in subset: 3 STAR

hydroxyl
type: Class
subclass of: reactive oxygen species
subclass of: oxygen hydride
subclass of: oxygen radical
has related synonym: (OH)(.)
has related synonym: 0
has related synonym: 17.003
has related synonym: 17.00734
has db xref: CAS:3352-57-6
has alternative id: CHEBI:24707
has alternative id: CHEBI:29190
id: CHEBI:29191
has db xref: Gmelin:105
has related synonym: HO
has related synonym: HO(.)
has related synonym: Hydrogen oxide
has related synonym: InChI=1S/HO/h1H
has db xref: KEGG:C16844
has related synonym: TUJKJAMUKRIRHC-UHFFFAOYSA-N
has related synonym: [O][H]
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has exact synonym: hydridooxygen(.)
has exact synonym: hydroxyl
has related synonym: hydroxyl radical
term from ontology: obi.owl
has exact synonym: oxidanyl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

deuterium atom
type: Class
subclass of: hydrogen atom
has related synonym: (2)1H
has related synonym: (2)H
has related synonym: 0
has related synonym: 2.01410
id: CHEBI:29237
has related synonym: D
has related synonym: Deuterium
has related synonym: InChI=1S/H2/h1H/i1+1
definition: The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek deltaepsilonupsilontauepsilonrhoomicronnu, second).
has related synonym: UFHFLCQGNIYNRP-OUBTZVSYSA-N
has related synonym: [2H]
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has related synonym: deuterio
has related synonym: deuterium
has exact synonym: deuterium
has related synonym: heavy hydrogen
has related synonym: hidrogeno pesado
has related synonym: hydrogen-2
term from ontology: obi.owl
has related synonym: schwerer Wasserstoff
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

alkyl sulfate
type: Class
subclass of: organic sulfate
subclass of: sulfuric ester
has alternative id: CHEBI:13810
has alternative id: CHEBI:22325
has alternative id: CHEBI:2583
id: CHEBI:29281
has related synonym: alkyl sulfates
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

ruthenium atom
type: Class
subclass of: transition element atom
subclass of: iron group element atom
has related synonym: 0
has related synonym: 101.07000
has related synonym: 101.904
has related synonym: 44Ru
has db xref: CAS:7440-18-8
id: CHEBI:30682
has related synonym: InChI=1S/Ru
has related synonym: KJTLSVCANCCWHF-UHFFFAOYSA-N
has related synonym: Ru
has related synonym: Ruthenium
has db xref: WebElements:Ru
has related synonym: [Ru]
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
has related synonym: rutenio
has related synonym: ruthenium
has exact synonym: ruthenium
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

alcohol
type: Class
subclass of: organic hydroxy compound
has related synonym: 0
has related synonym: 17.003
definition: A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom.
has exact synonym: Alcohol
has alternative id: CHEBI:13804
has alternative id: CHEBI:22288
has alternative id: CHEBI:2553
id: CHEBI:30879
has related synonym: HOR
has db xref: KEGG:C00069
has related synonym: O[*]
has exact synonym: alcohols
has related synonym: an alcohol
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

fluorescein
type: Class
subclass of: lactone
subclass of: polycyclic compound
subclass of: phenols
subclass of: benzofurans
subclass of: organic heteropentacyclic compound
subclass of: xanthenes
has related synonym: 0
has exact synonym: 3',6'-dihydroxy-3H-spiro[2-benzofuran-1,9'-xanthen]-3-one
has related synonym: 3',6'-dihydroxyfluoran
has related synonym: 3,6-fluorandiol
has related synonym: 332.068
has related synonym: 332.307
has related synonym: 9-(o-carboxyphenyl)-6-hydroxy-3-isoxanthenone
has related synonym: 9-(o-carboxyphenyl)-6-hydroxy-3H-xanthen-3-one
definition: A xanthene dye that is highly fluorescent, detectable even when present in minute quantities. Used forensically to detect traces of blood, in analytical chemistry as an indicator in silver nitrate titrations and in microscopy.
has db xref: Beilstein:94324
has related synonym: C.I. 45350
has related synonym: C.I. Solvent Yellow 94
has related synonym: C20H12O5
has db xref: CAS:2321-07-5
id: CHEBI:31624
has alternative id: CHEBI:606590
has related synonym: D and C Yellow No. 7
has related synonym: D&C Yellow No. 7
has db xref: DrugBank:DB00693
has related synonym: Fluoreszein
has related synonym: GNBHRKFJIUUOQI-UHFFFAOYSA-N
has db xref: Gmelin:248626
has db xref: HMDB:HMDB14831
has related synonym: InChI=1S/C20H12O5/c21-11-5-7-15-17(9-11)24-18-10-12(22)6-8-16(18)20(15)14-4-2-1-3-13(14)19(23)25-20/h1-10,21-22H
has related synonym: Japan Yellow 201
has db xref: KEGG:D01261
has db xref: PDB:4FAB
has db xref: PMID:1517825
has db xref: PMID:15465055
has db xref: PMID:16195545
has db xref: PMID:20371259
has db xref: PMID:2508085
has db xref: PMID:26756394
has db xref: PMID:7868912
has db xref: Reaxys:94324
has related synonym: Solvent Yellow 94
has db xref: Wikipedia:Fluorescein
has related synonym: Yellow fluorescein
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has related synonym: fluoresceine
term from ontology: obi.owl
has related synonym: resorcinolphthalein
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

gadodiamide hydrate
type: Class
subclass of: hydrate
subclass of: gadolinium coordination entity
has related synonym: 0
has related synonym: 591.67000
has related synonym: 592.113
has related synonym: C16H28GdN5O9
has db xref: CAS:122795-43-1
id: CHEBI:31642
has db xref: DrugBank:DB00225
has related synonym: Gadodiamide
has exact synonym: Gadodiamide hydrate
has db xref: Gmelin:898533
has related synonym: InChI=1S/C16H29N5O8.Gd.H2O/c1-17-12(22)7-20(10-15(26)27)5-3-19(9-14(24)25)4-6-21(11-16(28)29)8-13(23)18-2;;/h3-11H2,1-2H3,(H,17,22)(H,18,23)(H,24,25)(H,26,27)(H,28,29);;1H2/q;+3;/p-3
has db xref: KEGG:C13106
has db xref: KEGG:D01645
has related synonym: Omniscan
definition: The hydrate of gadodiamide.
has related synonym: XPCLDSMKWNNKOM-UHFFFAOYSA-K
has related synonym: [H]O[H].CNC1=[O][Gd+3]234567[O-]C(=O)C[N]2(CC[N]3(CC(=O)[O-]4)C1)CC[N]5(CC(=O)[O-]6)CC(NC)=[O]7
has exact synonym: [N,N-bis(2-{[(carboxy-kappaO)methyl][2-(methylamino)-2-(oxo-kappaO)ethyl]amino-kappaN}ethyl)glycinato(3-)-kappa(2)N,O]gadolinium--water (1/1)
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has related synonym: gadodiamida
has related synonym: gadodiamidum
has related synonym: gadolinium 5,8-bis(carboxylatomethyl)-11-[2-(methylamino)-2-oxoethyl]-3-oxo-2,5,8,11-tetraazatridecan-13-oate hydrate
has related synonym: gadolinium [bis(2-{(carboxylatomethyl)[2-(methylamino)-2-oxoethyl]amino}ethyl)amino]acetate--water (1/1)
term from ontology: obi.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

gadoteridol
type: Class
subclass of: gadolinium coordination entity
has related synonym: 0
has related synonym: 558.68000
has related synonym: 559.128
definition: A non-ionic gadolinium chelate having a macrocyclic tetraamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI).
has related synonym: C17H29GdN4O7
has related synonym: C17H29N4O7.Gd
has db xref: CAS:120066-54-8
id: CHEBI:31643
has related synonym: DPNNNPAKRZOSMO-UHFFFAOYSA-K
has db xref: DrugBank:DB00597
has related synonym: GD-HP-DO 3A
has related synonym: Gd-HPDO3A
has db xref: Gmelin:897397
has related synonym: InChI=1S/C17H32N4O7.Gd/c1-14(22)10-18-2-4-19(11-15(23)24)6-8-21(13-17(27)28)9-7-20(5-3-18)12-16(25)26;/h14,22H,2-13H2,1H3,(H,23,24)(H,25,26)(H,27,28);/q;+3/p-3
has db xref: KEGG:D01137
has db xref: Patent:EP292689
has db xref: Patent:US4885363
has db xref: Wikipedia:Gadoteridol
has exact synonym: [2,2',2''-{10-[2-(hydroxy-kappaO)propyl]-1,4,7,10-tetraazacyclododecane-1,4,7-triyl-kappa(4)N(1),N(4),N(7),N(10)}triacetato-kappaO(3-)]gadolinium
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has related synonym: gadolinium 2,2',2''-[10-(2-hydroxypropyl)-1,4,7,10-tetraazacyclododecane-1,4,7-triyl]triacetate
has related synonym: gadolinium-HP-DO3A
has related synonym: gadoteridol
has exact synonym: gadoteridol
has related synonym: gadoteridolum
term from ontology: obi.owl
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

phenol red
type: Class
subclass of: phenols
subclass of: 2,1-benzoxathiole
subclass of: sultone
subclass of: arenesulfonate ester
has related synonym: 0
has related synonym: 3,3-bis(p-hydroxyphenyl)-3H-2,1-benzoxathiole 1,1-dioxide
has related synonym: 354.056
has related synonym: 354.37600
definition: 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 4-hydroxyphenyl groups. A pH indicator changing colour from yellow below pH 6.8 to bright pink above pH 8.2, it is commonly used as an indicator in cell cultures and in home swimming pool test kits. It is also used in the (now infrequently performed) phenolsulfonphthalein (PSP) test for estimation of overall blood flow through the kidney.
has exact synonym: 4,4'-(1,1-dioxido-3H-2,1-benzoxathiole-3,3-diyl)diphenol
has related synonym: 4,4'-(3H-2,1-benzoxathiol-3-ylidene)bisphenol S,S-dioxide
has related synonym: BELBBZDIHDAJOR-UHFFFAOYSA-N
has db xref: Beilstein:326470
has related synonym: C19H14O5S
has db xref: CAS:143-74-8
id: CHEBI:31991
has db xref: Drug_Central:3439
has related synonym: InChI=1S/C19H14O5S/c20-15-9-5-13(6-10-15)19(14-7-11-16(21)12-8-14)17-3-1-2-4-18(17)25(22,23)24-19/h1-12,20-21H
has db xref: KEGG:C12600
has db xref: KEGG:D01200
has related synonym: PSP
has exact synonym: Phenol red
has related synonym: Phenolsulfonphthalein
has related synonym: alpha-hydroxy-alpha,alpha-bis(p-hydroxyphenyl)-o-toluenesulfonic acid gamma-sultone
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

sodium citrate dihydrate
type: Class
subclass of: hydrate
has related synonym: 0
has related synonym: 2-hydroxy-1,2,3-propanetricarboxylic acid trisodium salt dihydrate
has related synonym: 293.994
has related synonym: 294.09960
has db xref: Beilstein:3920956
has related synonym: C6H5O7.3Na.2H2O
has related synonym: C6H9Na3O9
has db xref: CAS:6132-04-3
id: CHEBI:32142
has related synonym: Citronensaeure,Trinatrium-Salz-Dihydrat
has related synonym: InChI=1S/C6H8O7.3Na.2H2O/c7-3(8)1-6(13,5(11)12)2-4(9)10;;;;;/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12);;;;2*1H2/q;3*+1;;/p-3
has db xref: KEGG:D01781
has related synonym: NLJMYIDDQXHKNR-UHFFFAOYSA-K
has related synonym: O.O.[Na+].[Na+].[Na+].OC(CC([O-])=O)(CC([O-])=O)C([O-])=O
has related synonym: Sodium citrate
has related synonym: Sodium citrate hydrate
definition: The dihydrate of trisodium citrate.
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
has exact synonym: trisodium 2-hydroxypropane-1,2,3-tricarboxylate--water (1/2)
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

monoatomic entity
type: Class
subclass of: elemental molecular entity
definition: A monoatomic entity is a molecular entity consisting of a single atom.
id: CHEBI:33238
has related synonym: atomic entity
has OBO namespace: chebi_ontology
has related synonym: monoatomic entities
imported from: chebi.owl
in subset: 3 STAR

oxoacid derivative
type: Class
subclass of: heteroatomic molecular entity
id: CHEBI:33241
has OBO namespace: chebi_ontology
has related synonym: oxoacid derivatives
imported from: chebi.owl
in subset: 3 STAR

inorganic hydride
type: Class
subclass of: inorganic molecular entity
subclass of: hydrides
id: CHEBI:33242
has OBO namespace: chebi_ontology
has related synonym: inorganic hydrides
imported from: chebi.owl
in subset: 3 STAR

organic group
type: Class
subclass of: chemical entity
definition: Any substituent group or skeleton containing carbon.
id: CHEBI:33247
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has related synonym: organic groups
term from ontology: pro.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

atom
type: Class
subclass of: chemical entity
definition: A chemical entity constituting the smallest component of an element having the chemical properties of the element.
has alternative id: CHEBI:22671
has alternative id: CHEBI:23907
id: CHEBI:33250
has exact synonym: atom
has related synonym: atome
has related synonym: atomo
has related synonym: atoms
has related synonym: atomus
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has related synonym: element
has related synonym: elements
term from ontology: obi.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

monoatomic hydrogen
type: Class
subclass of: monoatomic entity
subclass of: elemental hydrogen
has related synonym: 0
has related synonym: 1.00794
has related synonym: 1.008
id: CHEBI:33251
has related synonym: H
has related synonym: InChI=1S/H
has related synonym: YZCKVEUIGOORGS-UHFFFAOYSA-N
has related synonym: [H]
has related synonym: atomic hydrogen
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

nucleon
type: Class
subclass of: baryon
subclass of: nuclear particle
id: CHEBI:33253
definition: Heavy nuclear particle: proton or neutron.
has related synonym: Nukleon
has related synonym: Nukleonen
has OBO namespace: chebi_ontology
has exact synonym: nucleon
has related synonym: nucleons
imported from: chebi.owl
in subset: 3 STAR

primary amide
type: Class
subclass of: nitrogen molecular entity
definition: A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
id: CHEBI:33256
has OBO namespace: chebi_ontology
has exact synonym: primary amide
has exact synonym: primary amides
imported from: chebi.owl
in subset: 3 STAR

elemental molecular entity
type: Class
subclass of: molecular entity
definition: A molecular entity all atoms of which have the same atomic number.
id: CHEBI:33259
has OBO namespace: chebi_ontology
has related synonym: homoatomic entity
has related synonym: homoatomic molecular entities
has related synonym: homoatomic molecular entity
imported from: chebi.owl
in subset: 3 STAR

elemental hydrogen
type: Class
subclass of: inorganic molecular entity
subclass of: elemental molecular entity
subclass of: hydrogen molecular entity
id: CHEBI:33260
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

organosulfur compound
type: Class
subclass of: sulfur molecular entity
subclass of: organochalcogen compound
definition: An organosulfur compound is a compound containing at least one carbon-sulfur bond.
has alternative id: CHEBI:23010
has alternative id: CHEBI:25714
id: CHEBI:33261
has db xref: Wikipedia:Organosulfur_compounds
has OBO namespace: chebi_ontology
has exact synonym: organosulfur compound
has related synonym: organosulfur compounds
imported from: chebi.owl
in subset: 3 STAR

polyatomic anion
type: Class
subclass of: ion
subclass of: polyatomic ion
definition: An anion consisting of more than one atom.
id: CHEBI:33273
has OBO namespace: chebi_ontology
has related synonym: polyatomic anions
imported from: chebi.owl
in subset: 3 STAR

heteroorganic entity
type: Class
subclass of: organic molecular entity
definition: A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms.
id: CHEBI:33285
has OBO namespace: chebi_ontology
has related synonym: heteroorganic entities
has related synonym: organoelement compounds
imported from: chebi.owl
in subset: 3 STAR

alkali metal molecular entity
type: Class
subclass of: s-block molecular entity
definition: A molecular entity containing one or more atoms of an alkali metal.
id: CHEBI:33296
has related synonym: alkali metal molecular entities
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

pnictogen molecular entity
type: Class
subclass of: p-block molecular entity
definition: A p-block molecular entity containing any pnictogen.
id: CHEBI:33302
has OBO namespace: chebi_ontology
has related synonym: pnictogen molecular entities
has exact synonym: pnictogen molecular entity
imported from: chebi.owl
in subset: 3 STAR

chalcogen molecular entity
type: Class
subclass of: p-block molecular entity
definition: Any p-block molecular entity containing a chalcogen.
id: CHEBI:33304
has related synonym: chalcogen compounds
has related synonym: chalcogen molecular entities
has exact synonym: chalcogen molecular entity
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

carboxylic ester
type: Class
subclass of: ester
subclass of: carbonyl compound
has related synonym: 0
has related synonym: 43.990
definition: An ester of a carboxylic acid, R(1)C(=O)OR(2), where R(1) = H or organyl and R(2) = organyl.
has alternative id: CHEBI:13204
has alternative id: CHEBI:23028
id: CHEBI:33308
has alternative id: CHEBI:3408
has related synonym: CO2R2
has exact synonym: Carboxylic ester
has db xref: KEGG:C02391
has db xref: Wikipedia:Ester
has related synonym: [*]C(=O)O[*]
has related synonym: a carboxylic ester
has related synonym: carboxylic acid esters
has exact synonym: carboxylic esters
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

lanthanoid atom
type: Class
subclass of: rare earth metal atom
id: CHEBI:33319
has related synonym: Lanthanoid
has related synonym: Lanthanoide
has related synonym: Lanthanoidengruppe
has related synonym: Lanthanoidenreiche
has related synonym: Ln
has OBO namespace: chebi_ontology
has related synonym: lanthanide
has related synonym: lanthanides
has related synonym: lanthanoid
has exact synonym: lanthanoids
imported from: chebi.owl
in subset: 3 STAR

rare earth metal atom
type: Class
subclass of: transition element atom
id: CHEBI:33321
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
has related synonym: rare earth metal
has exact synonym: rare earth metals
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

chromium group element atom
type: Class
subclass of: transition element atom
subclass of: d-block element atom
id: CHEBI:33350
has OBO namespace: chebi_ontology
has related synonym: chromium group element
has related synonym: chromium group elements
has exact synonym: group 6 elements
imported from: chebi.owl
in subset: 3 STAR

iron group element atom
type: Class
subclass of: transition element atom
subclass of: d-block element atom
id: CHEBI:33356
has OBO namespace: chebi_ontology
has exact synonym: group 8 elements
has related synonym: iron group element
has related synonym: iron group elements
imported from: chebi.owl
in subset: 3 STAR

cobalt group element atom
type: Class
subclass of: transition element atom
subclass of: d-block element atom
id: CHEBI:33358
has OBO namespace: chebi_ontology
has related synonym: cobalt group element
has related synonym: cobalt group elements
has exact synonym: group 9 elements
imported from: chebi.owl
in subset: 3 STAR

rhodium atom
type: Class
subclass of: cobalt group element atom
has related synonym: 0
has related synonym: 102.90550
has related synonym: 102.906
has related synonym: 45Rh
definition: A cobalt group element atom of atomic number 45.
has db xref: CAS:7440-16-6
id: CHEBI:33359
has related synonym: InChI=1S/Rh
has related synonym: MHOVAHRLVXNVSD-UHFFFAOYSA-N
has db xref: PMID:2936374
has related synonym: Rh
has db xref: WebElements:Rh
has db xref: Wikipedia:Rhodium
has related synonym: [Rh]
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
has exact synonym: rhodium
has related synonym: rhodium
has related synonym: rodio
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

gadolinium atom
type: Class
subclass of: lanthanoid atom
subclass of: f-block element atom
has related synonym: 0
has related synonym: 157.25000
has related synonym: 157.924
has related synonym: 64Gd
has db xref: CAS:7440-54-2
id: CHEBI:33375
has related synonym: Gd
has db xref: Gmelin:16286
has related synonym: InChI=1S/Gd
has related synonym: UIWYJDYFSGRHKR-UHFFFAOYSA-N
has db xref: WebElements:Gd
has related synonym: [Gd]
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has related synonym: gadolinio
has related synonym: gadolinium
has exact synonym: gadolinium
term from ontology: obi.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

terbium atom
type: Class
subclass of: lanthanoid atom
subclass of: f-block element atom
has related synonym: 0
has related synonym: 158.925
has related synonym: 158.92534
has related synonym: 65Tb
has db xref: CAS:7440-27-9
id: CHEBI:33376
has related synonym: GZCRRIHWUXGPOV-UHFFFAOYSA-N
has db xref: Gmelin:16311
has related synonym: InChI=1S/Tb
has related synonym: Tb
has db xref: WebElements:Tb
has related synonym: [Tb]
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
has related synonym: terbio
has exact synonym: terbium
has related synonym: terbium
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

sulfur oxoacid derivative
type: Class
subclass of: sulfur molecular entity
subclass of: oxoacid derivative
id: CHEBI:33424
has OBO namespace: chebi_ontology
has exact synonym: sulfur oxoacid derivative
has related synonym: sulfur oxoacid derivatives
imported from: chebi.owl
in subset: 3 STAR

phospho sugar
type: Class
subclass of: carbohydrate phosphate
subclass of: monosaccharide derivative
definition: Any monosaccharide containing an alcoholic hydroxy group esterified with phosphoric acid.
has alternative id: CHEBI:15132
has alternative id: CHEBI:25406
has alternative id: CHEBI:26086
id: CHEBI:33447
has alternative id: CHEBI:9320
has db xref: KEGG:C00934
has db xref: PMID:18186488
has OBO namespace: chebi_ontology
has related synonym: monosaccharide phosphates
has exact synonym: phospho sugar
has related synonym: phospho sugars
has related synonym: phosphorylated sugar
has related synonym: phosphorylated sugars
has related synonym: phosphosugar
has related synonym: phosphosugars
imported from: chebi.owl
in subset: 3 STAR

sulfur oxoanion
type: Class
subclass of: sulfur molecular entity
subclass of: chalcogen oxoanion
id: CHEBI:33482
has OBO namespace: chebi_ontology
has related synonym: oxoanions of sulfur
has exact synonym: sulfur oxoanion
has related synonym: sulfur oxoanions
imported from: chebi.owl
in subset: 3 STAR

chalcogen oxoanion
type: Class
subclass of: chalcogen molecular entity
subclass of: oxoanion
id: CHEBI:33485
has exact synonym: chalcogen oxoanion
has related synonym: chalcogen oxoanions
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

metal atom
type: Class
subclass of: atom
definition: An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity.
has alternative id: CHEBI:25217
id: CHEBI:33521
has alternative id: CHEBI:6788
has db xref: KEGG:C00050
has db xref: PMID:21784043
has db xref: Wikipedia:Metal
has OBO namespace: chebi_ontology
has related synonym: elemental metal
has related synonym: elemental metals
has related synonym: metal element
has related synonym: metal elements
has related synonym: metals
imported from: chebi.owl
in subset: 3 STAR

organosulfonic acid
type: Class
subclass of: organosulfur compound
subclass of: sulfonic acid derivative
has related synonym: 0
has related synonym: 80.965
has related synonym: 81.07100
definition: An organic derivative of sulfonic acid in which the sulfo group is linked directly to carbon.
id: CHEBI:33551
has related synonym: HO3SR
has related synonym: OS([*])(=O)=O
has OBO namespace: chebi_ontology
has related synonym: organosulfonic acids
has related synonym: sulfonic acids
imported from: chebi.owl
in subset: 3 STAR

sulfonic acid derivative
type: Class
subclass of: sulfur oxoacid derivative
id: CHEBI:33552
has OBO namespace: chebi_ontology
has related synonym: derivatives of sulfonic acid
has exact synonym: sulfonic acid derivative
has related synonym: sulfonic acid derivatives
imported from: chebi.owl
in subset: 3 STAR

d-block element atom
type: Class
subclass of: transition element atom
subclass of: metal atom
id: CHEBI:33561
has OBO namespace: chebi_ontology
has related synonym: d-block element
has related synonym: d-block elements
imported from: chebi.owl
in subset: 3 STAR

f-block element atom
type: Class
subclass of: transition element atom
id: CHEBI:33562
has OBO namespace: chebi_ontology
has related synonym: f-block element
has related synonym: f-block elements
imported from: chebi.owl
in subset: 3 STAR

carboxylic acid
type: Class
subclass of: carbon oxoacid
subclass of: carbonyl compound
subclass of: organic molecular entity
has related synonym: 0
has related synonym: 44.998
has related synonym: 45.01740
definition: A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid.
has alternative id: CHEBI:13428
has alternative id: CHEBI:13627
has alternative id: CHEBI:23027
id: CHEBI:33575
has related synonym: CHO2R
has related synonym: Carbonsaeure
has related synonym: Carbonsaeuren
has related synonym: Karbonsaeure
has related synonym: OC([*])=O
has db xref: PMID:17147560
has db xref: PMID:18433345
has related synonym: RC(=O)OH
has db xref: Wikipedia:Carboxylic_acid
has related synonym: acide carboxylique
has related synonym: acides carboxyliques
has related synonym: acido carboxilico
has related synonym: acidos carboxilicos
has exact synonym: carboxylic acid
has exact synonym: carboxylic acids
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

main group molecular entity
type: Class
subclass of: molecular entity
definition: A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table.
id: CHEBI:33579
has OBO namespace: chebi_ontology
has related synonym: main group compounds
has related synonym: main group molecular entities
imported from: chebi.owl
in subset: 3 STAR

carbon group molecular entity
type: Class
subclass of: p-block molecular entity
id: CHEBI:33582
has related synonym: carbon group molecular entities
has exact synonym: carbon group molecular entity
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

cyclic compound
type: Class
subclass of: molecule
definition: Any molecule that consists of a series of atoms joined together to form a ring.
id: CHEBI:33595
has db xref: Wikipedia:Cyclic_compound
has OBO namespace: chebi_ontology
has related synonym: cyclic compounds
imported from: chebi.owl
in subset: 3 STAR

hydrogen molecular entity
type: Class
subclass of: s-block molecular entity
id: CHEBI:33608
has OBO namespace: chebi_ontology
has related synonym: hydrogen compounds
has related synonym: hydrogen molecular entities
imported from: chebi.owl
in subset: 3 STAR

polycyclic compound
type: Class
subclass of: cyclic compound
id: CHEBI:33635
has OBO namespace: chebi_ontology
has related synonym: polycyclic compounds
imported from: chebi.owl
in subset: 3 STAR

organic aromatic compound
type: Class
subclass of: cyclic compound
subclass of: organic cyclic compound
id: CHEBI:33659
has OBO namespace: chebi_ontology
has related synonym: organic aromatic compounds
imported from: chebi.owl
in subset: 3 STAR

heteromonocyclic compound
type: Class
subclass of: cyclic compound
subclass of: heterocyclic compound
id: CHEBI:33670
has OBO namespace: chebi_ontology
has exact synonym: heteromonocyclic compound
has exact synonym: heteromonocyclic compounds
imported from: chebi.owl
in subset: 3 STAR

heteropolycyclic compound
type: Class
subclass of: polycyclic compound
subclass of: heterocyclic compound
id: CHEBI:33671
has OBO namespace: chebi_ontology
has exact synonym: heteropolycyclic compounds
has related synonym: polyheterocyclic compounds
imported from: chebi.owl
in subset: 3 STAR

heterobicyclic compound
type: Class
subclass of: cyclic compound
subclass of: heterocyclic compound
definition: A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom.
id: CHEBI:33672
has OBO namespace: chebi_ontology
has exact synonym: heterobicyclic compounds
imported from: chebi.owl
in subset: 3 STAR

s-block molecular entity
type: Class
subclass of: main group molecular entity
definition: An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element.
id: CHEBI:33674
has OBO namespace: chebi_ontology
has related synonym: s-block compounds
has related synonym: s-block molecular entities
has exact synonym: s-block molecular entity
imported from: chebi.owl
in subset: 3 STAR

p-block molecular entity
type: Class
subclass of: main group molecular entity
definition: A main group molecular entity that contains one or more atoms of a p-block element.
id: CHEBI:33675
has OBO namespace: chebi_ontology
has related synonym: p-block compounds
has related synonym: p-block molecular entities
has related synonym: p-block molecular entitiy
imported from: chebi.owl
in subset: 3 STAR

hydrides
type: Class
subclass of: hydrogen molecular entity
subclass of: heteroatomic molecular entity
id: CHEBI:33692
definition: Hydrides are chemical compounds of hydrogen with other chemical elements.
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

oxygen hydride
type: Class
subclass of: chalcogen hydride
id: CHEBI:33693
has OBO namespace: chebi_ontology
has related synonym: hydrides of oxygen
has exact synonym: oxygen hydride
has related synonym: oxygen hydrides
imported from: chebi.owl
in subset: 3 STAR

biomacromolecule
type: Class
subclass of: macromolecule
subclass of: organic molecular entity
definition: A macromolecule formed by a living organism.
has related synonym: Biopolymere
id: CHEBI:33694
has related synonym: biomacromolecules
has exact synonym: biopolymer
has related synonym: biopolymers
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

nucleic acid
type: Class
subclass of: polynucleotide
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.
id: CHEBI:33696
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
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has exact synonym: nucleic acids
term from ontology: obi.owl
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

ribonucleic acid
type: Class
subclass of: nucleic acid
has db xref: CAS:63231-63-0
id: CHEBI:33697
definition: High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
has related synonym: RNA
has related synonym: RNS
has related synonym: Ribonukleinsaeure
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
has related synonym: pentosenucleic acids
has exact synonym: ribonucleic acid
has related synonym: ribonucleic acids
has exact synonym: ribonucleic acids
has related synonym: ribose nucleic acid
has related synonym: yeast nucleic acid
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

amino-acid residue
type: Class
subclass of: organic group
id: CHEBI:33708
definition: When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue.
has related synonym: amino acid residue
has exact synonym: amino-acid residue
has related synonym: amino-acid residues
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: pro.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

amino acid
type: Class
subclass of: carboxylic acid
subclass of: organic amino compound
definition: A carboxylic acid containing one or more amino groups.
has related synonym: Aminocarbonsaeure
has related synonym: Aminokarbonsaeure
has related synonym: Aminosaeure
has alternative id: CHEBI:13815
has alternative id: CHEBI:22477
id: CHEBI:33709
has db xref: Wikipedia:Amino_acid
has related synonym: amino acids
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

lanthanoid molecular entity
type: Class
subclass of: molecular entity
id: CHEBI:33775
has OBO namespace: chebi_ontology
has related synonym: lanthanoid compounds
has related synonym: lanthanoid molecular entities
imported from: chebi.owl
in subset: 3 STAR

organic hydroxy compound
type: Class
subclass of: hydroxides
subclass of: organic molecular entity
definition: An organic compound having at least one hydroxy group attached to a carbon atom.
id: CHEBI:33822
has alternative id: CHEBI:64710
has OBO namespace: chebi_ontology
has exact synonym: hydroxy compounds
has related synonym: organic alcohol
has related synonym: organic hydroxy compounds
imported from: chebi.owl
in subset: 3 STAR

organic cyclic compound
type: Class
subclass of: cyclic compound
subclass of: organic molecule
definition: Any organic molecule that consists of atoms connected in the form of a ring.
id: CHEBI:33832
has OBO namespace: chebi_ontology
has related synonym: organic cyclic compounds
imported from: chebi.owl
in subset: 3 STAR

heteroarene
type: Class
subclass of: organic heterocyclic compound
subclass of: organic aromatic compound
definition: A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2).
id: CHEBI:33833
has OBO namespace: chebi_ontology
has related synonym: hetarenes
has exact synonym: heteroarenes
imported from: chebi.owl
in subset: 3 STAR

nucleoside
type: Class
subclass of: N-glycosyl compound
subclass of: oxolanes
subclass of: nucleobase-containing molecular entity
has related synonym: 0
has related synonym: 116.047
has related synonym: 116.115
definition: An N-glycosyl compound that has both a nucleobase, normally adenine, guanine, xanthine, thymine, cytosine or uracil, and either a ribose or deoxyribose as functional parents.
has related synonym: C5H8O3R2
has alternative id: CHEBI:13661
has alternative id: CHEBI:25611
id: CHEBI:33838
has alternative id: CHEBI:7647
has db xref: KEGG:C00801
has exact synonym: Nucleoside
has related synonym: [C@H]1([C@H]([C@@H](*)[C@@H](O1)*)O)CO
has related synonym: a nucleoside
has OBO namespace: chebi_ontology
has related synonym: nucleosides
has exact synonym: nucleosides
imported from: chebi.owl
in subset: 3 STAR

macromolecule
type: Class
subclass of: polyatomic entity
definition: A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
id: CHEBI:33839
has db xref: Wikipedia:Macromolecule
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has exact synonym: macromolecule
has related synonym: macromolecules
term from ontology: obi.owl
has related synonym: polymer
has related synonym: polymer molecule
has related synonym: polymers
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

phenols
type: Class
subclass of: organic aromatic compound
subclass of: organic hydroxy compound
has related synonym: Aryl alcohol
has alternative id: CHEBI:13664
has alternative id: CHEBI:13825
has alternative id: CHEBI:25969
has alternative id: CHEBI:2857
id: CHEBI:33853
has db xref: KEGG:C15584
has db xref: MetaCyc:Aryl-Alcohol
definition: Organic aromatic compounds having one or more hydroxy groups attached to a benzene or other arene ring.
has db xref: Wikipedia:Phenols
has related synonym: arenols
has related synonym: aryl alcohol
has OBO namespace: chebi_ontology
has exact synonym: phenols
imported from: chebi.owl
in subset: 3 STAR

halide salt
type: Class
subclass of: salt
subclass of: halide
id: CHEBI:33958
has OBO namespace: chebi_ontology
has related synonym: halide salts
has related synonym: halides
imported from: chebi.owl
in subset: 3 STAR

benzofurans
type: Class
subclass of: oxacycle
subclass of: organic heteropolycyclic compound
has alternative id: CHEBI:22721
id: CHEBI:35259
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

steroid
type: Class
subclass of: lipid
subclass of: organic polycyclic compound
has related synonym: 0
has related synonym: 259.243
has related synonym: 259.450
definition: Any of naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. Natural steroids are derived biogenetically from squalene, so may be considered as triterpenoids.
has related synonym: C12C(C3C(C(CC3)*)(C)CC1)CCC4C2(CCCC4)C
has related synonym: C19H31R
has alternative id: CHEBI:13687
has alternative id: CHEBI:26768
id: CHEBI:35341
has alternative id: CHEBI:9263
has db xref: KEGG:C00377
has db xref: MetaCyc:Steroids
has exact synonym: Steroid
has related synonym: a steroid
has OBO namespace: chebi_ontology
has exact synonym: steroids
imported from: chebi.owl
in subset: 3 STAR

3beta-sterol
type: Class
subclass of: 3-hydroxy steroid
subclass of: 3beta-hydroxy steroid
has related synonym: 0
has related synonym: 275.237
has related synonym: 275.450
has related synonym: 3beta-Hydroxysteroid
has related synonym: 3beta-hydroxysteroids
has related synonym: 3beta-sterols
definition: A sterol that has a hydroxy group at position 3 with beta- configuration.
has related synonym: C19H31OR
has alternative id: CHEBI:13609
has alternative id: CHEBI:1725
has alternative id: CHEBI:20248
id: CHEBI:35348
has db xref: KEGG:C02945
has related synonym: a 3beta-hydroxysterol
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

hydroxy steroid
type: Class
subclass of: organic hydroxy compound
subclass of: steroid
has alternative id: CHEBI:24748
id: CHEBI:35350
has alternative id: CHEBI:5814
has related synonym: Hydroxysteroid
has db xref: KEGG:C02159
has OBO namespace: chebi_ontology
has related synonym: hydroxy steroids
has related synonym: hydroxysteroids
imported from: chebi.owl
in subset: 3 STAR

organonitrogen compound
type: Class
subclass of: heteroorganic entity
subclass of: nitrogen molecular entity
definition: Any heteroorganic entity containing at least one carbon-nitrogen bond.
id: CHEBI:35352
has OBO namespace: chebi_ontology
has exact synonym: organonitrogen compounds
has related synonym: organonitrogens
imported from: chebi.owl
in subset: 3 STAR

oxoanion
type: Class
subclass of: oxide
subclass of: polyatomic anion
definition: An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen.
has alternative id: CHEBI:33274
has alternative id: CHEBI:33436
id: CHEBI:35406
has OBO namespace: chebi_ontology
has related synonym: oxoacid anions
has exact synonym: oxoanion
has related synonym: oxoanions
imported from: chebi.owl
in subset: 3 STAR

alkali metal salt
type: Class
subclass of: salt
subclass of: alkali metal molecular entity
id: CHEBI:35479
has related synonym: alkali metal salts
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

hydrate
type: Class
subclass of: heteroatomic molecular entity
definition: An addition compound that contains water in weak chemical combination with another compound.
id: CHEBI:35505
has related synonym: Hydrat
has OBO namespace: chebi_ontology
has related synonym: hidrato
has related synonym: hidratos
has related synonym: hydrates
imported from: chebi.owl
in subset: 3 STAR

carbon oxoacid
type: Class
subclass of: hydroxides
subclass of: organooxygen compound
id: CHEBI:35605
has related synonym: carbon oxoacids
has OBO namespace: chebi_ontology
has related synonym: oxoacids of carbon
imported from: chebi.owl
in subset: 3 STAR

ester
type: Class
subclass of: organooxygen compound
definition: A compound formally derived from an oxoacid RkE(=O)l(OH)m (l > 0) and an alcohol, phenol, heteroarenol, or enol by linking with formal loss of water from an acidic hydroxy group of the former and a hydroxy group of the latter.
has alternative id: CHEBI:23960
id: CHEBI:35701
has alternative id: CHEBI:4859
has exact synonym: Ester
has db xref: KEGG:C00287
has db xref: Wikipedia:Ester
has OBO namespace: chebi_ontology
has related synonym: esters
imported from: chebi.owl
in subset: 3 STAR

gadolinium molecular entity
type: Class
subclass of: lanthanoid molecular entity
id: CHEBI:35729
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has related synonym: gadolinium compounds
has related synonym: gadolinium molecular entities
has exact synonym: gadolinium molecular entity
term from ontology: obi.owl
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

gadolinium coordination entity
type: Class
subclass of: lanthanoid molecular entity
subclass of: gadolinium molecular entity
id: CHEBI:35730
has OBO namespace: chebi_ontology
has related synonym: gadolinium coordination compounds
has related synonym: gadolinium coordination entities
has exact synonym: gadolinium coordination entity
imported from: chebi.owl
in subset: 3 STAR

liposaccharide
type: Class
subclass of: lipid
subclass of: carbohydrate derivative
id: CHEBI:35740
has OBO namespace: chebi_ontology
has related synonym: liposaccharides
imported from: chebi.owl
in subset: 3 STAR

tetracarboxylic acid
type: Class
subclass of: carboxylic acid
definition: An oxoacid containing four carboxy groups.
has related synonym: C4H4O8R
id: CHEBI:35742
has OBO namespace: chebi_ontology
has related synonym: tetracarboxylic acids
imported from: chebi.owl
in subset: 3 STAR

oxo monocarboxylic acid
type: Class
subclass of: monocarboxylic acid
subclass of: carboxylic acid
definition: Any monocarboxylic acid having at least one additional oxo functional group.
id: CHEBI:35871
has OBO namespace: chebi_ontology
has related synonym: oxo monocarboxylic acids
imported from: chebi.owl
in subset: 3 STAR

carboxylic anhydride
type: Class
subclass of: carbonyl compound
subclass of: acid anhydride
definition: Anhydrides derived from carboxylic acids.
id: CHEBI:35873
has exact synonym: carboxylic anhydride
has exact synonym: carboxylic anhydrides
has related synonym: carboxylic anhydrides
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

imidazopyrimidine
type: Class
subclass of: organic heterobicyclic compound
subclass of: heteroarene
subclass of: organonitrogen heterocyclic compound
id: CHEBI:35875
has OBO namespace: chebi_ontology
has related synonym: imidazopyrimidines
imported from: chebi.owl
in subset: 3 STAR

inorganic chloride
type: Class
subclass of: chloride salt
subclass of: inorganic salt
id: CHEBI:36093
has OBO namespace: chebi_ontology
has related synonym: inorganic chloride salt
has related synonym: inorganic chloride salts
has related synonym: inorganic chlorides
imported from: chebi.owl
in subset: 3 STAR

baryon
type: Class
subclass of: subatomic particle
subclass of: composite particle
definition: Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy).
id: CHEBI:36339
has related synonym: baryons
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

subatomic particle
type: Class
subclass of: material entity
definition: A particle smaller than an atom.
id: CHEBI:36342
has OBO namespace: chebi_ontology
has related synonym: subatomic particles
imported from: chebi.owl
in subset: 3 STAR

composite particle
type: Class
subclass of: subatomic particle
definition: A subatomic particle known to have substructure (i.e. consisting of smaller particles).
id: CHEBI:36343
has OBO namespace: chebi_ontology
has related synonym: composite particles
imported from: chebi.owl
in subset: 3 STAR

nuclear particle
type: Class
subclass of: subatomic particle
definition: A nucleus or any of its constituents in any of their energy states.
id: CHEBI:36347
has OBO namespace: chebi_ontology
has exact synonym: nuclear particle
imported from: chebi.owl
in subset: 3 STAR

polyatomic entity
type: Class
subclass of: molecular entity
definition: Any molecular entity consisting of more than one atom.
id: CHEBI:36357
has OBO namespace: chebi_ontology
has related synonym: polyatomic entities
imported from: chebi.owl
in subset: 3 STAR

polyatomic ion
type: Class
subclass of: ion
subclass of: polyatomic entity
definition: An ion consisting of more than one atom.
id: CHEBI:36358
has OBO namespace: chebi_ontology
has related synonym: polyatomic ions
imported from: chebi.owl
in subset: 3 STAR

phosphorus oxoacid derivative
type: Class
subclass of: phosphorus molecular entity
subclass of: oxoacid derivative
id: CHEBI:36359
has OBO namespace: chebi_ontology
has exact synonym: phosphorus oxoacid derivative
imported from: chebi.owl
in subset: 3 STAR

oligoglycosylceramide
type: Class
subclass of: ceramide
subclass of: glycosphingolipid
has alternative id: CHEBI:24253
has alternative id: CHEBI:25672
id: CHEBI:36520
has db xref: KEGG:C03956
has OBO namespace: chebi_ontology
has related synonym: globosides
has related synonym: oligoglycosylceramides
has related synonym: oligoglycosylglucosylceramides
imported from: chebi.owl
in subset: 1 STAR

carbonyl compound
type: Class
subclass of: organooxygen compound
subclass of: organic molecule
definition: Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives.
id: CHEBI:36586
has exact synonym: carbonyl compounds
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

acid anhydride
type: Class
subclass of: organic molecular entity
id: CHEBI:36606
definition: Compounds consisting of two acyl groups bonded to the same oxygen atom acyl-O-acyl.
has exact synonym: acid anhydride
has exact synonym: acid anhydrides
has related synonym: acid anhydrides
has related synonym: anhydride d'acide
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

acyclic acid anhydride
type: Class
subclass of: acid anhydride
id: CHEBI:36608
has exact synonym: acyclic acid anhydride
has exact synonym: acyclic acid anhydrides
has related synonym: acyclic acid anhydrides
has related synonym: acyclic anhydrides
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

acyclic carboxylic anhydride
type: Class
subclass of: carboxylic anhydride
subclass of: acyclic acid anhydride
id: CHEBI:36631
has exact synonym: acyclic carboxylic acid anhydrides
has exact synonym: acyclic carboxylic anhydride
has related synonym: acyclic carboxylic anhydrides
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

organohalogen compound
type: Class
subclass of: heteroorganic entity
subclass of: halide
definition: A compound containing at least one carbon-halogen bond.
id: CHEBI:36684
has OBO namespace: chebi_ontology
has related synonym: organohalogen compounds
imported from: chebi.owl
in subset: 3 STAR

3-hydroxy steroid
type: Class
subclass of: hydroxy steroid
has related synonym: 3-hydroxy steroids
definition: Any hydroxy steroid carrying a hydroxy group at position 3.
id: CHEBI:36834
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

3beta-hydroxy steroid
type: Class
subclass of: alcohol
subclass of: 3-hydroxy steroid
has related synonym: 0
has related synonym: 275.237
has related synonym: 275.450
has related synonym: 3beta-hydroxy steroids
definition: A 3-hydroxy steroid in which the 3-hydroxy substituent is in the beta-position.
has related synonym: C19H31OR
id: CHEBI:36836
has alternative id: CHEBI:71195
has db xref: MetaCyc:3-Beta-Hydroxysterols
has db xref: PMID:10535978
has db xref: PMID:12829805
has related synonym: a 3beta-hydroxysteroid
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

inorganic radical
type: Class
subclass of: molecular entity
subclass of: inorganic molecular entity
id: CHEBI:36871
has OBO namespace: chebi_ontology
has related synonym: inorganic radicals
imported from: chebi.owl
in subset: 3 STAR

chalcogen hydride
type: Class
subclass of: inorganic hydride
subclass of: chalcogen molecular entity
id: CHEBI:36902
has exact synonym: chalcogen hydride
has related synonym: chalcogen hydrides
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

inorganic ion
type: Class
subclass of: inorganic molecular entity
subclass of: ion
id: CHEBI:36914
has OBO namespace: chebi_ontology
has related synonym: inorganic ions
imported from: chebi.owl
in subset: 3 STAR

inorganic cation
type: Class
subclass of: inorganic ion
subclass of: cation
id: CHEBI:36915
has OBO namespace: chebi_ontology
has related synonym: inorganic cations
imported from: chebi.owl
in subset: 3 STAR

cation
type: Class
subclass of: ion
definition: A monoatomic or polyatomic species having one or more elementary charges of the proton.
has alternative id: CHEBI:23058
has alternative id: CHEBI:3473
id: CHEBI:36916
has exact synonym: Cation
has db xref: KEGG:C01373
has related synonym: Kation
has related synonym: Kationen
has exact synonym: cation
has related synonym: cationes
has related synonym: cations
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

organochalcogen compound
type: Class
subclass of: heteroorganic entity
subclass of: chalcogen molecular entity
definition: An organochalcogen compound is a compound containing at least one carbon-chalcogen bond.
id: CHEBI:36962
has OBO namespace: chebi_ontology
has exact synonym: organochalcogen compound
has related synonym: organochalcogen compounds
imported from: chebi.owl
in subset: 3 STAR

organooxygen compound
type: Class
subclass of: oxygen molecular entity
subclass of: organochalcogen compound
definition: An organochalcogen compound containing at least one carbon-oxygen bond.
id: CHEBI:36963
has db xref: PMID:17586126
has OBO namespace: chebi_ontology
has exact synonym: organooxygen compound
has related synonym: organooxygen compounds
imported from: chebi.owl
in subset: 3 STAR

nucleotide
type: Class
subclass of: nucleoside phosphate
definition: A nucleotide is a nucleoside phosphate resulting from the condensation of the 3 or 5 hydroxy group of a nucleoside with phosphoric acid.
has alternative id: CHEBI:13215
has alternative id: CHEBI:13663
id: CHEBI:36976
has alternative id: CHEBI:7656
has db xref: KEGG:C00215
has exact synonym: Nucleotide
has related synonym: a nucleotide
has OBO namespace: chebi_ontology
has related synonym: nucleotides
imported from: chebi.owl
in subset: 3 STAR

ribonucleoside 5'-monophosphate
type: Class
subclass of: ribonucleoside monophosphate
subclass of: ribonucleoside 5'-phosphate
has alternative id: CHEBI:1976
has alternative id: CHEBI:1977
has alternative id: CHEBI:20500
has alternative id: CHEBI:36996
id: CHEBI:37010
has OBO namespace: chebi_ontology
has related synonym: ribonucleoside 5'-monophosphates
imported from: chebi.owl
in subset: 3 STAR

ribonucleoside 5'-phosphate
type: Class
subclass of: ribonucleotide
subclass of: nucleotide
id: CHEBI:37015
has OBO namespace: chebi_ontology
has related synonym: ribonucleoside 5'-phosphates
imported from: chebi.owl
in subset: 3 STAR

purine ribonucleoside 5'-monophosphate
type: Class
subclass of: purine ribonucleoside monophosphate
subclass of: purine ribonucleotide
subclass of: ribonucleoside 5'-monophosphate
id: CHEBI:37021
has OBO namespace: chebi_ontology
has related synonym: purine ribonucleoside 5'-monophosphates
imported from: chebi.owl
in subset: 3 STAR

purine ribonucleoside 5'-diphosphate
type: Class
subclass of: nucleoside phosphate
subclass of: purine ribonucleotide
subclass of: ribonucleoside 5'-phosphate
id: CHEBI:37038
has OBO namespace: chebi_ontology
has related synonym: purine ribonucleoside 5'-diphosphates
imported from: chebi.owl
in subset: 3 STAR

purine ribonucleoside 5'-triphosphate
type: Class
subclass of: nucleoside phosphate
subclass of: purine ribonucleotide
subclass of: ribonucleoside 5'-phosphate
id: CHEBI:37045
has OBO namespace: chebi_ontology
has related synonym: purine ribonucleoside 5'-triphosphates
imported from: chebi.owl
in subset: 3 STAR

adenosine 5'-phosphate
type: Class
subclass of: adenosine phosphate
subclass of: purine ribonucleoside 5'-monophosphate
id: CHEBI:37096
has related synonym: adenosine 5'-phosphates
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

guanosine 5'-phosphate
type: Class
subclass of: guanosine phosphate
id: CHEBI:37121
has OBO namespace: chebi_ontology
has related synonym: guanosine 5'-phosphates
imported from: chebi.owl
in subset: 3 STAR

organobromine compound
type: Class
subclass of: halogen molecular entity
subclass of: organohalogen compound
definition: A compound containing at least one carbon-bromine bond.
id: CHEBI:37141
has related synonym: bromoorganic compound
has OBO namespace: chebi_ontology
has related synonym: organobromine compounds
imported from: chebi.owl
in subset: 3 STAR

gadodiamide
type: Class
subclass of: gadolinium coordination entity
has related synonym: 0
has related synonym: 573.66000
has related synonym: 574.102
definition: A non-ionic gadolinium chelate having a macrocyclic triamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI).
has related synonym: C16H26GdN5O8
has db xref: CAS:131410-48-5
id: CHEBI:37333
has related synonym: CNC1=[O][Gd+3]234567[O-]C(=O)C[N]2(CC[N]3(CC(=O)[O-]4)C1)CC[N]5(CC(=O)[O-]6)CC(NC)=[O]7
has db xref: DrugBank:DB00225
has related synonym: HZHFFEYYPYZMNU-UHFFFAOYSA-K
has related synonym: InChI=1S/C16H29N5O8.Gd/c1-17-12(22)7-20(10-15(26)27)5-3-19(9-14(24)25)4-6-21(11-16(28)29)8-13(23)18-2;/h3-11H2,1-2H3,(H,17,22)(H,18,23)(H,24,25)(H,26,27)(H,28,29);/q;+3/p-3
has db xref: Wikipedia:Gadodiamide
has exact synonym: [N,N-bis(2-{[(carboxy-kappaO)methyl][2-(methylamino)-2-(oxo-kappaO)ethyl]amino-kappaN}ethyl)glycinato(3-)-kappa(2)N,O]gadolinium
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has related synonym: gadolinium 5,8-bis(carboxylatomethyl)-11-[2-(methylamino)-2-oxoethyl]-3-oxo-2,5,8,11-tetraazatridecan-13-oate
has related synonym: gadolinium [bis(2-{(carboxylatomethyl)[2-(methylamino)-2-oxoethyl]amino}ethyl)amino]acetate
term from ontology: obi.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

heteroatomic molecular entity
type: Class
subclass of: polyatomic entity
definition: A molecular entity consisting of two or more chemical elements.
id: CHEBI:37577
has OBO namespace: chebi_ontology
has related synonym: chemical compound
has related synonym: heteroatomic molecular entities
imported from: chebi.owl
in subset: 3 STAR

halide
type: Class
subclass of: halogen molecular entity
subclass of: heteroatomic molecular entity
definition: Any heteroatomic molecular entity that is a chemical compound of halogen with other chemical elements.
id: CHEBI:37578
has db xref: Wikipedia:Halide
has OBO namespace: chebi_ontology
has related synonym: halides
imported from: chebi.owl
in subset: 3 STAR

sodium phosphate
type: Class
subclass of: inorganic phosphate
subclass of: sodium salt
has db xref: CAS:7632-05-5
id: CHEBI:37586
has db xref: Wikipedia:Sodium_phosphates
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
has related synonym: phosphoric acid, sodium salt
has related synonym: sodium orthophosphate
has exact synonym: sodium phosphate
has related synonym: sodium phosphates
has related synonym: sodium salt of phosphoric acid
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

carboxamide
type: Class
subclass of: primary amide
subclass of: organonitrogen compound
subclass of: organooxygen compound
has related synonym: 0
has related synonym: 41.998
has related synonym: 42.01680
definition: An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom.
has alternative id: CHEBI:35354
has alternative id: CHEBI:35355
id: CHEBI:37622
has related synonym: CNOR3
has related synonym: [*]C(=O)N([*])[*]
has exact synonym: carboxamides
has related synonym: carboxamides
has OBO namespace: chebi_ontology
has related synonym: primary carboxamide
imported from: chebi.owl
in subset: 3 STAR

phosphoric ester
type: Class
subclass of: phosphoric acid derivative
subclass of: ester
has alternative id: CHEBI:26019
id: CHEBI:37734
has OBO namespace: chebi_ontology
has related synonym: phosphate esters
has related synonym: phosphoric esters
imported from: chebi.owl
in subset: 1 STAR

glycerophospholipid
type: Class
subclass of: phospholipid
subclass of: lipid
definition: Any glycerolipid having a phosphate group ester-linked to a terminal carbon of the glycerol backbone.
has alternative id: CHEBI:24362
id: CHEBI:37739
has alternative id: CHEBI:5456
has exact synonym: Glycerophospholipid
has db xref: PMID:17393491
has OBO namespace: chebi_ontology
has related synonym: glycerophospholipids
has related synonym: phosphatide
has related synonym: phosphatides
has related synonym: phosphoglyceride
has related synonym: phosphoglycerides
imported from: chebi.owl
in subset: 3 STAR

acyclic mixed acid anhydride
type: Class
subclass of: acyclic acid anhydride
id: CHEBI:37787
has related synonym: acyclic mixed acid anhydrides
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

sulfuric acid derivative
type: Class
subclass of: sulfur oxoacid derivative
id: CHEBI:37826
has OBO namespace: chebi_ontology
has exact synonym: sulfuric acid derivative
has related synonym: sulfuric acid derivatives
imported from: chebi.owl
in subset: 3 STAR

acyl sulfate
type: Class
subclass of: organic sulfate
subclass of: acyclic mixed acid anhydride
id: CHEBI:37875
has related synonym: acyl sulfates
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

cyanine dye
type: Class
subclass of: organonitrogen compound
id: CHEBI:37960
definition: Cyanine dyes are synthetic dyes with the general formula R2N[CH=CH]nCH=N(+)R2 <-> R2N(+)=CH[CH=CH]nNR2 (n is a small number) in which the nitrogen and part of the conjugated chain usually form part of a heterocyclic system, such as imidazole, pyridine, pyrrole, quinoline and thiazole.
has related synonym: Cyaninfarbstoff
has related synonym: Zyaninfarbstoff
has OBO namespace: chebi_ontology
has exact synonym: cyanine dyes
imported from: chebi.owl
in subset: 3 STAR

phosphorus-32 atom
type: Class
subclass of: phosphorus atom
has related synonym: (32)15P
has related synonym: (32)P
has related synonym: 0
has related synonym: 30.974
has related synonym: 31.97391
has db xref: CAS:14596-37-3
id: CHEBI:37972
has related synonym: InChI=1S/P/i1+1
has db xref: KEGG:C19162
has related synonym: OAICVXFJPJFONN-OUBTZVSYSA-N
has related synonym: P
has related synonym: Phosphorus, isotope of mass 32
definition: The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days.
has related synonym: [32P]
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
has related synonym: phosphorus, isotope of mass 32
has exact synonym: phosphorus-32
has related synonym: phosphorus-32
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

phosphorus-33 atom
type: Class
subclass of: phosphorus atom
has related synonym: (33)15P
has related synonym: (33)P
has related synonym: 0
has related synonym: 30.974
has related synonym: 32.97173
has db xref: CAS:15749-66-3
id: CHEBI:37973
has related synonym: InChI=1S/P/i1+2
has related synonym: OAICVXFJPJFONN-NJFSPNSNSA-N
has related synonym: P
definition: The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2.
has related synonym: [33P]
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
has related synonym: phosphorus, isotope of mass 33
has exact synonym: phosphorus-33
has related synonym: phosphorus-33
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

Cy3 dye
type: Class
subclass of: indoles
subclass of: cyanine dye
has related synonym: +1
has related synonym: 271.124
has related synonym: 271.33580
has related synonym: C19H15N2R2
id: CHEBI:37987
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

Cy5 dye
type: Class
subclass of: indoles
subclass of: cyanine dye
has related synonym: +1
has related synonym: 297.139
has related synonym: 297.37310
has related synonym: C21H17N2R2
id: CHEBI:37989
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

benzoxathiole
type: Class
subclass of: organic heterobicyclic compound
subclass of: oxacycle
subclass of: organosulfur heterocyclic compound
id: CHEBI:38086
has related synonym: benzoxathioles
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

2,1-benzoxathiole
type: Class
subclass of: benzoxathiole
has related synonym: 2,1-benzoxathioles
id: CHEBI:38087
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

sultone
type: Class
subclass of: ester
definition: An intramolecular cyclic ester of a hydroxy sulfonic acid, analogous to lactone.
id: CHEBI:38088
has OBO namespace: chebi_ontology
has exact synonym: sultones
imported from: chebi.owl
in subset: 3 STAR

arenesulfonate ester
type: Class
subclass of: sulfonic acid derivative
subclass of: organosulfonic ester
definition: An organosulfonic ester resulting from the formal condensation of an arenesulfonic acid with the hydroxy group of an alcohol, enol, phenol or heteroarenol.
id: CHEBI:38094
has related synonym: arenesulfonate esters
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

organonitrogen heterocyclic compound
type: Class
subclass of: organic heterocyclic compound
subclass of: organonitrogen compound
definition: Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms.
id: CHEBI:38101
has OBO namespace: chebi_ontology
has related synonym: heterocyclic organonitrogen compounds
has related synonym: organonitrogen heterocyclic compounds
imported from: chebi.owl
in subset: 3 STAR

oxacycle
type: Class
subclass of: organic heterocyclic compound
subclass of: organooxygen compound
definition: Any organic heterocyclic compound containing at least one ring oxygen atom.
id: CHEBI:38104
has db xref: PMID:17134300
has OBO namespace: chebi_ontology
has related synonym: heterocyclic organooxygen compounds
has related synonym: organooxygen heterocyclic compounds
has related synonym: oxacycles
imported from: chebi.owl
in subset: 3 STAR

organosulfur heterocyclic compound
type: Class
subclass of: organic heterocyclic compound
subclass of: organosulfur compound
id: CHEBI:38106
has OBO namespace: chebi_ontology
has related synonym: heterocyclic organosulfur compounds
has related synonym: organosulfur heterocyclic compounds
imported from: chebi.owl
in subset: 3 STAR

organic heteropentacyclic compound
type: Class
subclass of: organic heteropolycyclic compound
id: CHEBI:38164
has OBO namespace: chebi_ontology
has related synonym: organic heteropentacyclic compounds
imported from: chebi.owl
in subset: 3 STAR

organic heteropolycyclic compound
type: Class
subclass of: organic heterocyclic compound
subclass of: heteropolycyclic compound
has alternative id: CHEBI:25429
has alternative id: CHEBI:38075
id: CHEBI:38166
has OBO namespace: chebi_ontology
has related synonym: organic heteropolycyclic compounds
imported from: chebi.owl
in subset: 3 STAR

azabicycloalkane
type: Class
subclass of: organic heterobicyclic compound
subclass of: organonitrogen heterocyclic compound
id: CHEBI:38295
has related synonym: azabicycloalkanes
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

thiabicycloalkane
type: Class
subclass of: organic heterobicyclic compound
subclass of: organosulfur heterocyclic compound
id: CHEBI:38297
has OBO namespace: chebi_ontology
has related synonym: thiabicycloalkanes
imported from: chebi.owl
in subset: 3 STAR

diazines
type: Class
subclass of: organic heteromonocyclic compound
subclass of: organonitrogen heterocyclic compound
definition: Any organic heterocyclic compound containing a benzene ring in which two of the C-H fragments have been replaced by isolobal nitrogens (the diazine parent structure).
id: CHEBI:38313
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

inorganic sodium salt
type: Class
subclass of: inorganic salt
subclass of: sodium salt
id: CHEBI:38702
has OBO namespace: chebi_ontology
has related synonym: inorganic sodium salts
imported from: chebi.owl
in subset: 3 STAR

xanthenes
type: Class
subclass of: dibenzopyran
id: CHEBI:38835
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

dibenzopyran
type: Class
subclass of: oxacycle
subclass of: organic heteropolycyclic compound
definition: Any organic heteropolycyclic compound based on a skeleton consisting of a pyran ring fused with two benzene rings.
id: CHEBI:39203
has OBO namespace: chebi_ontology
has related synonym: dibenzopyrans
imported from: chebi.owl
in subset: 3 STAR

dibenzopyridine
type: Class
subclass of: organic heterotricyclic compound
subclass of: organonitrogen heterocyclic compound
id: CHEBI:39206
has OBO namespace: chebi_ontology
has related synonym: dibenzopyridines
imported from: chebi.owl
in subset: 3 STAR

digoxigenin
type: Class
subclass of: 3beta-sterol
subclass of: hydroxy steroid
subclass of: 3beta-hydroxy steroid
has related synonym: 0
has related synonym: 390.241
has related synonym: 390.51306
has exact synonym: 3beta,12beta,14-trihydroxy-5beta-card-20(22)-enolide
definition: A hydroxy steroid that consists of 5beta-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3beta-, 12beta- and 14beta-positions. It has been isolated from the plant species of the genus Digitalis.
has related synonym: C23H34O5
has db xref: CAS:1672-46-4
has alternative id: CHEBI:38020
has alternative id: CHEBI:42096
id: CHEBI:42098
has db xref: HMDB:HMDB60731
has related synonym: InChI=1S/C23H34O5/c1-21-7-5-15(24)10-14(21)3-4-17-18(21)11-19(25)22(2)16(6-8-23(17,22)27)13-9-20(26)28-12-13/h9,14-19,24-25,27H,3-8,10-12H2,1-2H3/t14-,15+,16-,17-,18+,19-,21+,22+,23+/m1/s1
has db xref: LIPID_MAPS_instance:LMST01120008
has db xref: PDBeChem:DOG
has db xref: PMID:10438974
has db xref: PMID:23344238
has db xref: PMID:23383657
has db xref: PMID:8080093
has db xref: PMID:9470094
has related synonym: SHIBSTMRCDJXLN-KCZCNTNESA-N
has db xref: Wikipedia:Digoxigenin
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

ethylenediaminetetraacetic acid
type: Class
subclass of: amino acid
subclass of: tetracarboxylic acid
subclass of: organic amino compound
has exact synonym: (ethane-1,2-diyldinitrilo)tetraacetate
has exact synonym: (ethane-1,2-diyldinitrilo)tetraacetic acid
has related synonym: (ethylenedinitrilo)tetraacetic acid, ion(4-)
has related synonym: 0
has related synonym: 2,2',2'',2'''-(ethane-1,2-diyldinitrilo)tetraacetate
has related synonym: 292.091
has related synonym: 292.24272
has related synonym: Acide ethylenediaminetetracetique
has db xref: Beilstein:1716295
has db xref: Beilstein:3914756
has related synonym: C10H16N2O8
has db xref: CAS:150-43-6
has db xref: CAS:60-00-4
has alternative id: CHEBI:30378
has alternative id: CHEBI:42189
id: CHEBI:42191
has alternative id: CHEBI:4735
has db xref: DrugBank:DB00974
has db xref: Drug_Central:987
has related synonym: EDTA
has related synonym: EDTA, ion(4-)
has related synonym: Edetic acid
has exact synonym: Ethylenediaminetetraacetic acid
has db xref: Gmelin:144943
has related synonym: H4edta
has related synonym: InChI=1S/C10H16N2O8/c13-7(14)3-11(4-8(15)16)1-2-12(5-9(17)18)6-10(19)20/h1-6H2,(H,13,14)(H,15,16)(H,17,18)(H,19,20)
has related synonym: KCXVZYZYPLLWCC-UHFFFAOYSA-N
has db xref: KEGG:C00284
has db xref: KEGG:D00052
has related synonym: N,N'-1,2-Ethane diylbis-(N-(carboxymethyl)glycine)
has related synonym: OC(=O)CN(CCN(CC(O)=O)CC(O)=O)CC(O)=O
has db xref: PDBeChem:EDT
has db xref: Wikipedia:Edetate
has related synonym: acide edetique
has related synonym: acido edetico
has related synonym: acidum edeticum
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has related synonym: edetic acid
has related synonym: edta
has related synonym: ethylenediaminetetraacetate
has exact synonym: ethylenediaminetetraacetic acid
term from ontology: obi.owl
has related synonym: {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

indolyl carboxylic acid
type: Class
subclass of: indoles
subclass of: carboxylic acid
id: CHEBI:46867
has OBO namespace: chebi_ontology
has related synonym: indolyl carboxylic acids
imported from: chebi.owl
in subset: 3 STAR

oxazinane
type: Class
subclass of: organic heteromonocyclic compound
subclass of: organonitrogen heterocyclic compound
subclass of: oxacycle
id: CHEBI:46952
has OBO namespace: chebi_ontology
has related synonym: oxazinanes
imported from: chebi.owl
in subset: 3 STAR

benzoxazine
type: Class
subclass of: organic heterobicyclic compound
subclass of: organonitrogen heterocyclic compound
subclass of: oxacycle
id: CHEBI:46969
has related synonym: benzoxazines
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

tetrahydrofuranol
type: Class
subclass of: oxolanes
id: CHEBI:47017
has OBO namespace: chebi_ontology
has related synonym: tetrahydrofuranols
imported from: chebi.owl
in subset: 3 STAR

double-stranded DNA
type: Class
subclass of: deoxyribonucleic acid
has related synonym: C10H17O8PR2(C5H8O5PR)n.C10H17O7PR2(C5H8O6PR)n
id: CHEBI:4705
has exact synonym: Double-stranded DNA
has db xref: KEGG:C00434
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
term from ontology: pro.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

5-bromo-2'-deoxyuridine
type: Class
subclass of: pyrimidine 2'-deoxyribonucleoside
has related synonym: 0
has related synonym: 305.985
has related synonym: 307.09800
has related synonym: 5-Bdu
has related synonym: 5-Bromodeoxyuridine
has related synonym: 5-Bromodesoxyuridine
has related synonym: 5-Bromouracil deoxyriboside
has related synonym: 5-Bromouracil-2-deoxyriboside
has exact synonym: 5-bromo-2'-deoxyuridine
definition: A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase.
has db xref: Beilstein:4236087
has related synonym: BrdU
has related synonym: Bromodeoxyuridine
has related synonym: Bromouracil deoxyriboside
has related synonym: C9H11BrN2O5
has db xref: CAS:59-14-3
has alternative id: CHEBI:31310
id: CHEBI:472552
has alternative id: CHEBI:47713
has db xref: Drug_Central:3042
has related synonym: InChI=1S/C9H11BrN2O5/c10-4-2-12(9(16)11-8(4)15)7-1-5(14)6(3-13)17-7/h2,5-7,13-14H,1,3H2,(H,11,15,16)/t5-,6+,7+/m0/s1
has db xref: PDBeChem:U33
has db xref: PMID:17325220
has db xref: PMID:17341060
has db xref: PMID:3950402
has related synonym: WOVKYSAHUYNSMH-RRKCRQDMSA-N
has db xref: Wikipedia:Bromodeoxyuridine
has related synonym: broxuridina
has related synonym: broxuridine
has related synonym: broxuridinum
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

ureas
type: Class
subclass of: primary amide
has alternative id: CHEBI:27220
has alternative id: CHEBI:36947
id: CHEBI:47857
has OBO namespace: chebi_ontology
has related synonym: urea derivatives
imported from: chebi.owl
in subset: 3 STAR

hydrogen atom
type: Class
subclass of: inorganic molecular entity
subclass of: nonmetal atom
subclass of: atom
has related synonym: 0
has related synonym: 1.00794
has related synonym: 1.008
has related synonym: 1H
has alternative id: CHEBI:24634
has alternative id: CHEBI:49636
id: CHEBI:49637
has related synonym: H
has related synonym: InChI=1S/H
has related synonym: Wasserstoff
has db xref: WebElements:H
has related synonym: YZCKVEUIGOORGS-UHFFFAOYSA-N
has related synonym: [H]
has OBO namespace: chebi_ontology
has related synonym: hidrogeno
has related synonym: hydrogen
has exact synonym: hydrogen
has related synonym: hydrogene
imported from: chebi.owl
in subset: 3 STAR

organic amino compound
type: Class
subclass of: organonitrogen compound
subclass of: organic molecular entity
definition: A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups.
id: CHEBI:50047
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has related synonym: organic amino compounds
term from ontology: pro.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

chromium-51
type: Class
subclass of: chromium atom
has related synonym: (51)24Cr
has related synonym: (51)Cr
has related synonym: 0
has related synonym: 50.94477
has related synonym: 51.941
has related synonym: 51Cr
definition: A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival.
has db xref: CAS:14392-02-0
id: CHEBI:50076
has related synonym: Chromium, isotope of mass 51
has related synonym: Cr
has related synonym: InChI=1S/Cr/i1-1
has related synonym: VYZAMTAEIAYCRO-BJUDXGSMSA-N
has related synonym: [51Cr]
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has exact synonym: chromium-51
term from ontology: obi.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

organic molecular entity
type: Class
subclass of: carbon group molecular entity
definition: Any molecular entity that contains carbon.
has alternative id: CHEBI:25700
has alternative id: CHEBI:33244
id: CHEBI:50860
has OBO namespace: chebi_ontology
has related synonym: organic compounds
has related synonym: organic entity
has related synonym: organic molecular entities
imported from: chebi.owl
in subset: 3 STAR

nitrogen molecular entity
type: Class
subclass of: pnictogen molecular entity
has alternative id: CHEBI:25556
id: CHEBI:51143
has alternative id: CHEBI:7594
has db xref: KEGG:C06061
has related synonym: Nitrogenous compounds
has OBO namespace: chebi_ontology
has related synonym: nitrogen compounds
has related synonym: nitrogen molecular entities
imported from: chebi.owl
in subset: 3 STAR

biotins
type: Class
subclass of: monocarboxylic acid
subclass of: azabicycloalkane
subclass of: thiabicycloalkane
subclass of: ureas
id: CHEBI:51570
definition: Compounds containing a biotin (5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid) skeleton.
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

enamide
type: Class
subclass of: carboxamide
subclass of: organic molecular entity
has related synonym: 0
has related synonym: 65.998
has related synonym: 66.03820
definition: An alpha,beta-unsaturated carboxylic acid amide of general formula R(1)R(2)C=CR(3)-C(=O)NR(4)R(5) in which the amide C=O function is conjugated to a C=C double bond at the alpha,beta position.
has related synonym: C3NOR5
id: CHEBI:51751
has related synonym: [*]\C([*])=C(\[*])C(=O)N([*])[*]
has OBO namespace: chebi_ontology
has related synonym: enamides
imported from: chebi.owl
in subset: 3 STAR

Alexa Fluor 532
type: Class
subclass of: organosulfonic acid
subclass of: organic heteropentacyclic compound
has related synonym: 0
has exact synonym: 5-(4-{[(2,5-dioxopyrrolidin-1-yl)oxy]carbonyl}phenyl)-2,3,3,7,7,8-hexamethyl-2,3,7,8-tetrahydro-1H-pyrano[3,2-f:5,6-f']diindole-10,12-disulfonic acid
has related synonym: 723.156
has related synonym: 723.77144
has related synonym: Alexa Fluor 532 carboxylic acid, succinimidyl ester
has related synonym: C34H33N3O11S2
id: CHEBI:51756
has related synonym: WHVNXSBKJGAXKU-UHFFFAOYSA-N
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

Alexa Fluor 546
type: Class
subclass of: organic heteropentacyclic compound
has related synonym: 0
has related synonym: 1078.114
has related synonym: 1080.39800
has related synonym: Alexa Fluor 546 carboxylic acid, succinimidyl ester
has related synonym: C44H46Cl3N4NaO14S3
id: CHEBI:51760
has related synonym: ZAINTDRBUHCDPZ-UHFFFAOYSA-M
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
has exact synonym: sodium 6-(2-carboxy-3,4,6-trichloro-5-{[2-({6-[(2,5-dioxopyrrolidin-1-yl)oxy]-6-oxohexyl}amino)-2-oxoethyl]thio}phenyl)-2,2,4,8,10,10-hexamethyl-3,4,5a,8,9,10,11,12a-octahydro-2H-pyrano[3,2-g:5,6-g']diquinolin-1-ium-12,14-disulfonate
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

organic polycyclic compound
type: Class
subclass of: polycyclic compound
subclass of: organic cyclic compound
id: CHEBI:51958
has OBO namespace: chebi_ontology
has related synonym: organic polycyclic compounds
imported from: chebi.owl
in subset: 3 STAR

inorganic hydroxy compound
type: Class
subclass of: hydroxides
subclass of: inorganic molecular entity
id: CHEBI:52625
has OBO namespace: chebi_ontology
has related synonym: inorganic hydroxides
imported from: chebi.owl
in subset: 3 STAR

Alexa Fluor 555
type: Class
subclass of: xanthenes
has related synonym: 0
has exact synonym: 4-(6-amino-3-imino-4,5-disulfo-3H-xanthen-9-yl)benzene-1,3-dicarboxylic acid
has related synonym: 534.004
has related synonym: 534.47300
definition: A fluorescent dye of absorption wavelength 555 nm and emission wavelength 565 nm, derived from a 3,6-diaminoxanthene-4,5-disulfate.
has related synonym: C21H14N2O11S2
id: CHEBI:52673
has related synonym: IGAZHQIYONOHQN-UHFFFAOYSA-N
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

tritiated thymidine
type: Class
subclass of: pyrimidine 2'-deoxyribonucleoside
has related synonym: (3)HTdR
has related synonym: (3H)Thymidine
has db xref: CAS:50-88-4
id: CHEBI:53526
definition: Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis.
has related synonym: Thymidine-(H-3)
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
has related synonym: tritiated thymidines
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

heterocyclic compound
type: Class
subclass of: cyclic compound
definition: A cyclic compound having as ring members atoms of at least two different elements.
id: CHEBI:5686
has exact synonym: Heterocyclic compound
has OBO namespace: chebi_ontology
has related synonym: compuesto heterociclico
has related synonym: compuestos heterociclicos
has related synonym: heterocycle
has related synonym: heterocyclic compounds
imported from: chebi.owl
in subset: 3 STAR

dimethyl sulfate
type: Class
subclass of: alkyl sulfate
has related synonym: 0
has related synonym: 125.999
has related synonym: 126.13200
has db xref: Beilstein:635994
has related synonym: C2H6O4S
has db xref: CAS:77-78-1
has alternative id: CHEBI:371544
id: CHEBI:59050
has related synonym: COS(=O)(=O)OC
has related synonym: DMS
has related synonym: Dimethoxysulfone
has related synonym: Dimethyl monosulfate
has related synonym: Dimethyl sulphate
has related synonym: InChI=1S/C2H6O4S/c1-5-7(3,4)6-2/h1-2H3
has db xref: KEGG:C19177
has db xref: PMID:2299638
has related synonym: Sulfate dimethylique
has related synonym: Sulfato de dimetilo
has related synonym: Sulfuric acid dimethyl ester
definition: The dimethyl ester of sulfuric acid.
has related synonym: VAYGXNSJCAHWJZ-UHFFFAOYSA-N
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has exact synonym: dimethyl sulfate
term from ontology: obi.owl
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

diethyl pyrocarbonate
type: Class
subclass of: acyclic carboxylic anhydride
has related synonym: 0
has related synonym: 162.053
has related synonym: 162.14060
has db xref: Beilstein:637031
has related synonym: C6H10O5
has db xref: CAS:1609-47-8
has related synonym: CCOC(=O)OC(=O)OCC
has alternative id: CHEBI:4525
id: CHEBI:59051
has related synonym: Dicarbonic acid diethyl ester
has related synonym: Diethyl oxydiformate
has exact synonym: Diethyl pyrocarbonate
has related synonym: Diethyl pyrocarbonic acid
has related synonym: Ethyl pyrocarbonate
has related synonym: FFYPMLJYZAEMQB-UHFFFAOYSA-N
has db xref: Gmelin:602268
has related synonym: InChI=1S/C6H10O5/c1-3-9-5(7)11-6(8)10-4-2/h3-4H2,1-2H3
has db xref: KEGG:C11592
has related synonym: Oxydiformic acid diethyl ester
has related synonym: Pyrocarbonate d'ethyle
has related synonym: Pyrocarbonic acid diethyl ester
has related synonym: Pyrokohlensaeure diaethyl ester
definition: The diethyl ester of dicarbonic acid.
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has exact synonym: diethyl dicarbonate
term from ontology: obi.owl
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

1,1-dihydroxy-3-ethoxy-2-butanone
type: Class
subclass of: alcohol
subclass of: carbonyl compound
has related synonym: 0
has related synonym: 148.074
has related synonym: 148.15710
has related synonym: 3-Ethoxy-1,1-dihydroxy-2-butanone
has exact synonym: 3-ethoxy-1,1-dihydroxybutan-2-one
definition: A butanone derivative having two hydroxy substituents at the 1-position and an ethoxy substituent at the 3-position.
has db xref: Beilstein:8677948
has related synonym: C6H12O4
has db xref: CAS:27762-78-3
has related synonym: CCOC(C)C(=O)C(O)O
id: CHEBI:59052
has related synonym: Chetossale
has db xref: Drug_Central:3202
has related synonym: InChI=1S/C6H12O4/c1-3-10-4(2)5(7)6(8)9/h4,6,8-9H,3H2,1-2H3
has db xref: KEGG:D04651
has related synonym: YRCRRHNVYVFNTM-UHFFFAOYSA-N
has related synonym: beta-Ethoxy-alpha-ketobutyraldehyde
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has related synonym: kethoxal
has related synonym: ketoxalum
term from ontology: obi.owl
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide
type: Class
subclass of: organonitrogen compound
subclass of: oxazinane
has related synonym: 0
has related synonym: 1-Cmec
has related synonym: 1-Cyclohexyl-3-(2-(4-morpholinyl)ethyl)carbodiimide
has related synonym: 237.184
has related synonym: 237.34120
definition: A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two N-substituents.
has db xref: Beilstein:196522
has related synonym: C13H23N3O
has related synonym: C1CCC(CC1)N=C=NCCN1CCOCC1
has db xref: CAS:15580-20-8
id: CHEBI:59053
has related synonym: CMCT
has related synonym: InChI=1S/C13H23N3O/c1-2-4-13(5-3-1)15-12-14-6-7-16-8-10-17-11-9-16/h13H,1-11H2
has related synonym: N-cyclohexyl-N'-(2-morpholin-4-ylethyl)methanediimine
has exact synonym: N-cyclohexyl-N'-[2-(morpholin-4-yl)ethyl]carbodiimide
has related synonym: XNPOFXIBHOVFFH-UHFFFAOYSA-N
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

N-methylisatoic anhydride
type: Class
subclass of: benzoxazine
has related synonym: 0
has exact synonym: 1-methyl-2H-3,1-benzoxazine-2,4(1H)-dione
has related synonym: 1-methyl-3,1-benzoxazine-2,4-dione
has related synonym: 177.043
has related synonym: 177.15680
definition: A 3,1-benzoxazin-1,4-dione having an N-methyl substituent.
has db xref: Beilstein:383957
has related synonym: C9H7NO3
has db xref: CAS:10328-92-4
id: CHEBI:59054
has related synonym: Cn1c2ccccc2c(=O)oc1=O
has related synonym: InChI=1S/C9H7NO3/c1-10-7-5-3-2-4-6(7)8(11)13-9(10)12/h2-5H,1H3
has related synonym: KJMRWDHBVCNLTQ-UHFFFAOYSA-N
has related synonym: Methyl-N-carboxyanthranilic anhydride
has related synonym: N-Methyl IA
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

(S)-1-(4-bromoacetamidobenzyl)EDTA
type: Class
subclass of: tetracarboxylic acid
has related synonym: 0
has related synonym: 1-(para-Bromoacetamidobenzyl)edta
has exact synonym: 2,2',2'',2'''-{[(2S)-3-{4-[(bromoacetyl)amino]phenyl}propane-1,2-diyl]dinitrilo}tetraacetic acid
has related synonym: 2-[[(2S)-1-[bis(carboxymethyl)amino]-3-[4-[(2-bromoacetyl)amino]phenyl] propan-2-yl]-(carboxymethyl)amino]acetic acid
has related synonym: 517.070
has related synonym: 518.31300
definition: A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (S)-configuration.
has db xref: Beilstein:7236603
has related synonym: C19H24BrN3O9
has db xref: CAS:81677-64-7
id: CHEBI:59055
has related synonym: InChI=1S/C19H24BrN3O9/c20-6-15(24)21-13-3-1-12(2-4-13)5-14(23(10-18(29)30)11-19(31)32)7-22(8-16(25)26)9-17(27)28/h1-4,14H,5-11H2,(H,21,24)(H,25,26)(H,27,28)(H,29,30)(H,31,32)/t14-/m0/s1
has related synonym: N-4-(2,3-Bis(bis(carboxymethyl)amino)propyl)phenyl bromoacetamide
has related synonym: VOQPQBGCWBEYEV-AWEZNQCLSA-N
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

EDTA methidiumpropylamide
type: Class
subclass of: dibenzopyridine
has related synonym: 0
has related synonym: 645.291
has related synonym: 645.70550
definition: A combined intercalating and chelating reagent. The iron chelate, prepared by adding Fe(NH4)2(SO4)2, effects random oxidative cleavage of DNA in the presence of O2 and a reducing agent. This activity is useful as a footprinting probe.
has related synonym: C33H39N7O7
id: CHEBI:59056
has related synonym: InChI=1S/C33H39N7O7/c1-38-28-16-23(35)6-10-26(28)25-9-5-22(34)15-27(25)33(38)21-3-7-24(8-4-21)36-11-2-12-37-29(41)17-39(18-30(42)43)13-14-40(19-31(44)45)20-32(46)47/h3-10,15-16H,2,11-14,17-20,34H2,1H3,(H6,35,36,37,41,42,43,44,45,46,47)
has related synonym: PFGGLNMBUNROLG-UHFFFAOYSA-N
has exact synonym: [(carboxymethyl){2-[(carboxymethyl){2-[(3-{[4-(3,8-diamino-5-methylphenanthridinium-6-yl)phenyl]amino}propyl)amino]-2-oxoethyl}amino]ethyl}amino]acetate
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

bromophenol blue
type: Class
subclass of: phenols
subclass of: organobromine compound
subclass of: 2,1-benzoxathiole
subclass of: sultone
subclass of: arenesulfonate ester
has related synonym: 0
has related synonym: 3',3'',5',5''-tetrabromophenolsulfonephthalein
has related synonym: 3',3'',5',5''-tetrabromophenolsulfophthalein
definition: 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye.
has exact synonym: 4,4'-(1,1-dioxido-3H-2,1-benzoxathiole-3,3-diyl)bis(2,6-dibromophenol)
has related synonym: 665.698
has related synonym: 669.96100
has db xref: Beilstein:61698
has related synonym: C19H10Br4O5S
has db xref: CAS:115-39-9
id: CHEBI:59424
has related synonym: InChI=1S/C19H10Br4O5S/c20-12-5-9(6-13(21)17(12)24)19(10-7-14(22)18(25)15(23)8-10)11-3-1-2-4-16(11)29(26,27)28-19/h1-8,24-25H
has related synonym: UDSAIICHUKSCKT-UHFFFAOYSA-N
has related synonym: bromophenol blue, sultone form
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
imported from: chebi.owl
in subset: 3 STAR
in_subset: 3 STAR

oxygen radical
type: Class
subclass of: reactive oxygen species
subclass of: inorganic radical
definition: An inorganic radical in which a free electron resides on one or more oxygen atoms of an oxygen species.
id: CHEBI:61073
has OBO namespace: chebi_ontology
has related synonym: oxygen radicals
imported from: chebi.owl
in subset: 3 STAR

nucleobase-containing molecular entity
type: Class
subclass of: heteroarene
subclass of: nitrogen molecular entity
definition: Any compound that has a nucleobase as a part.
id: CHEBI:61120
has OBO namespace: chebi_ontology
has related synonym: nucleobase-containing compound
has related synonym: nucleobase-containing compounds
has related synonym: nucleobase-containing molecular entities
imported from: chebi.owl
in subset: 3 STAR

guanyl ribonucleotide
type: Class
subclass of: purine nucleotide
subclass of: purine ribonucleotide
definition: A purine ribonucleotide where the purine is guanine.
id: CHEBI:61295
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

adenyl ribonucleotide
type: Class
subclass of: purine nucleotide
subclass of: purine ribonucleotide
definition: A purine riboncleotide where adenine is the purine.
id: CHEBI:61296
has related synonym: adenine ribonucleotide
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

globoside
type: Class
subclass of: glycosphingolipid
definition: Any glycosphingolipid where the oligosaccharide component has an N-acetylgalactosaminyl residue at the non-reducing end.
id: CHEBI:61360
has db xref: Wikipedia:Globoside
has OBO namespace: chebi_ontology
has related synonym: globosides
imported from: chebi.owl
in subset: 3 STAR

carbohydrate derivative
type: Class
subclass of: carbohydrates and carbohydrate derivatives
definition: Any organooxygen compound derived from a carbohydrate by replacement of one or more hydroxy group(s) by an amino group, a thiol group or similar heteroatomic groups. The term also includes derivatives of these compounds.
id: CHEBI:63299
has related synonym: carbohydrate derivatives
has OBO namespace: chebi_ontology
has related synonym: derivatised carbohydrate
has related synonym: derivatised carbohydrates
has related synonym: derivatized carbohydrate
has related synonym: derivatized carbohydrates
imported from: chebi.owl
in subset: 3 STAR

monosaccharide derivative
type: Class
subclass of: carbohydrate derivative
definition: A carbohydrate derivative that is formally obtained from a monosaccharide.
id: CHEBI:63367
has OBO namespace: chebi_ontology
has related synonym: monosaccharide derivatives
imported from: chebi.owl
in subset: 3 STAR

polysaccharide derivative
type: Class
subclass of: biomacromolecule
subclass of: carbohydrate derivative
definition: A carbohydrate derivative that is any derivative of a polysaccharide.
id: CHEBI:65212
has OBO namespace: chebi_ontology
has related synonym: polysaccharide derivatives
imported from: chebi.owl
in subset: 3 STAR

double-stranded RNA
type: Class
subclass of: ribonucleic acid
definition: A ribonucleic acid with two complementary strands, similar to the DNA found in all cells.
id: CHEBI:67208
has db xref: Wikipedia:RNA#Double-stranded_RNA
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
has related synonym: double stranded ribonucleic acid
has related synonym: dsRNA
term from ontology: pro.owl
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

pyrimidine deoxyribonucleoside
type: Class
subclass of: deoxyribonucleoside
subclass of: pyrimidine nucleoside
definition: A deoxyribonucleoside containing a pyrimidine base.
id: CHEBI:68472
has db xref: MetaCyc:Pyrimidine-Deoxyribonucleosides
has OBO namespace: chebi_ontology
has related synonym: pyrimidine deoxyribonucleosides
imported from: chebi.owl
in subset: 3 STAR

organic molecule
type: Class
subclass of: molecule
subclass of: organic molecular entity
definition: Any molecule that consists of at least one carbon atom as part of the electrically neutral entity.
id: CHEBI:72695
has OBO namespace: chebi_ontology
has related synonym: organic compound
has related synonym: organic compounds
has related synonym: organic molecules
imported from: chebi.owl
in subset: 3 STAR

N-nitrosoureas
type: Class
subclass of: ureas
subclass of: nitrogen molecular entity
definition: A nitroso compound that is any urea in which one of the nitrogens is substituted by a nitroso group
id: CHEBI:76551
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

carbohydrates and carbohydrate derivatives
type: Class
subclass of: organooxygen compound
definition: Any organooxygen compound that is a polyhydroxy-aldehyde or -ketone, or a compound derived from one. Carbohydrates contain only carbon, hydrogen and oxygen and usually have an empirical formula Cm(H2O)n; carbohydrate derivatives may contain other elements by substitution or condensation.
id: CHEBI:78616
has related synonym: carbohydrates and derivatives
has related synonym: carbohydrates and their derivatives
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

organosulfonic ester
type: Class
subclass of: sulfur oxoacid derivative
subclass of: ester
has related synonym: 0
has related synonym: 79.957
has related synonym: 80.06300
definition: An ester resulting from the formal condensation of the hydroxy group of an alcohol, phenol, heteroarenol, or enol with an organosulfonic acid.
id: CHEBI:83347
has related synonym: O3SR2
has related synonym: [*]S(=O)(=O)O[*]
has OBO namespace: chebi_ontology
has related synonym: organosulfonate ester
has related synonym: organosulfonate esters
has related synonym: organosulfonic esters
imported from: chebi.owl
in subset: 3 STAR

pentose phosphate
type: Class
subclass of: phospho sugar
subclass of: monosaccharide derivative
definition: Any phospho sugar that is the phosphate derivative of pentose.
id: CHEBI:84055
has OBO namespace: chebi_ontology
has related synonym: pentose phosphates
imported from: chebi.owl
in subset: 3 STAR

N-acetyl-beta-D-galactosaminyl-(1->3)-alpha-D-galactosyl-(1->4)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-ceramide
type: Class
subclass of: glycotetraosylceramide
subclass of: globoside
has related synonym: 0
has related synonym: 806.280
has related synonym: 806.719
definition: A glycotetraosylceramide having N-acetyl-beta-D-galactosaminyl-(1->3)-alpha-D-galactosyl-(1->4)-beta-D-galactosyl-(1->4)-beta-D-glucosyl component attached to the primary hydroxy function of a ceramide with undefined sphingoid base.
has related synonym: C30H50N2O23R2
id: CHEBI:88167
has exact synonym: N-acetyl-beta-D-galactosaminyl-(1->3)-alpha-D-galactosyl-(1->4)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1')-ceramide
has related synonym: beta-D-GalNAc-(1->3)-alpha-D-Gal-(1->4)-beta-D-Gal-(1->4)-beta-D-Glc-(1<->1')-Cer
has related synonym: beta-D-GalpNAc-(1->3)-alpha-D-Galp-(1->4)-beta-D-Galp-(1->4)-beta-D-Glcp-(1<->1')-Cer
has OBO namespace: chebi_ontology
imported from: chebi.owl
in subset: 3 STAR

tris
type: Class
subclass of: organic hydroxy compound
subclass of: organic amino compound
has related synonym: 0
has related synonym: 1,1,1-tris(hydroxymethyl)methanamine
has related synonym: 121.074
has related synonym: 121.13500
has related synonym: 2-Amino-2-(hydroxymethyl)-1,3-propanediol
has exact synonym: 2-amino-2-(hydroxymethyl)propane-1,3-diol
definition: A primary amino compound that is tert-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC.
has db xref: Beilstein:741883
has related synonym: C4H11NO3
has db xref: CAS:77-86-1
id: CHEBI:9754
has db xref: DrugBank:DB03754
has db xref: Drug_Central:2771
has db xref: Gmelin:217857
has related synonym: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2
has db xref: KEGG:C07182
has db xref: KEGG:D00396
has related synonym: LENZDBCJOHFCAS-UHFFFAOYSA-N
has related synonym: NC(CO)(CO)CO
has db xref: PDBeChem:TRS
has db xref: PMID:22553829
has db xref: Reaxys:741883
has related synonym: THAM
has exact synonym: Tris
has related synonym: Tris amino
has related synonym: Tris base
has related synonym: Tris buffer
has related synonym: Tris-base
has related synonym: Trizma
has related synonym: Trometamol
has related synonym: Tromethamine
has db xref: Wikipedia:Tris
has related synonym: aminotris(hydroxymethyl)methane
term from ontology: chebi.owl
has OBO namespace: chebi_ontology
term from ontology: obi.owl
has related synonym: tris(hydroxymethyl)aminomethane
imported from: chebi.owl
in_subset: 3 STAR
in subset: 3 STAR

disease
type: Class
subclass of: disposition
definition: A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
id: DOID:4
has db xref: MESH:D004194
has db xref: NCI:C2991
has db xref: SNOMEDCT_US_2016_03_01:64572001
has db xref: UMLS_CUI:C0012634
has OBO namespace: disease_ontology
imported from: doid.owl

phosphopyruvate hydratase complex
type: Class
subclass of: cytosolic part
subclass of: catalytic complex
definition: A multimeric enzyme complex, usually a dimer or an octamer, that catalyzes the conversion of 2-phospho-D-glycerate to phosphoenolpyruvate and water.
id: GO:0000015
has OBO namespace: cellular_component
has exact synonym: enolase complex
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl
in subset: goslim metagenomics
in_subset: goslim metagenomics
in_subset: gosubset prok
in subset: gosubset prok

transcription factor TFIIIC complex
type: Class
subclass of: RNA polymerase III transcription factor complex
definition: A heterotrimeric transcription factor complex that is involved in regulating transcription from RNA polymerase III (Pol III) promoters. TFIIIC contains three conserved subunits that associate with the proximal Pol III promoter element, and additional subunits that associate with sequence elements downstream of the promoter and are more diverged among species. It also functions as a boundary element to partition genome content into distinct domains outside Pol III promoter regions.
id: GO:0000127
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

ubiquitin ligase complex
type: Class
subclass of: intracellular part
subclass of: transferase complex
definition: A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex.
id: GO:0000151
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl
in subset: goslim pir
in_subset: goslim pir

nuclear ubiquitin ligase complex
type: Class
subclass of: ubiquitin ligase complex
subclass of: nuclear part
definition: A ubiquitin ligase complex found in the nucleus.
id: GO:0000152
has OBO namespace: cellular_component
imported from: go.owl

cyclin-dependent protein kinase holoenzyme complex
type: Class
subclass of: protein complex
subclass of: intracellular part
subclass of: serine/threonine protein kinase complex
has exact synonym: CDK holoenzyme
definition: Cyclin-dependent protein kinases (CDKs) are enzyme complexes that contain a kinase catalytic subunit associated with a regulatory cyclin partner.
id: GO:0000307
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl
in_subset: goslim pir
in subset: goslim pir

DNA-directed RNA polymerase complex
type: Class
subclass of: RNA polymerase complex
definition: A protein complex that possesses DNA-directed RNA polymerase activity.
id: GO:0000428
has OBO namespace: cellular_component
imported from: go.owl

proteasome complex
type: Class
subclass of: protein complex
subclass of: intracellular part
subclass of: endopeptidase complex
has narrow synonym: 26S proteasome
definition: A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.
id: GO:0000502
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
has exact synonym: proteasome
imported from: go.owl
in subset: goslim pir
in_subset: goslim pir

glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex
type: Class
subclass of: membrane part
subclass of: endoplasmic reticulum part
subclass of: transferase complex
definition: An enzyme complex that catalyzes the transfer of GlcNAc from UDP-GlcNAc to an acceptor phosphatidylinositol, the first step in the production of GPI anchors for cell surface proteins. The complex contains PIG-A, PIG-C, PIG-H, PIG-Q, PIG-P, and DPM2 in human, and Eri1p, Gpi1p, Gpi2p, Gpi15p, Gpi19p, and Spt14p in budding yeast.
id: GO:0000506
has exact synonym: GPI-GlcNAc transferase complex
has exact synonym: GPI-GnT complex
has exact synonym: GPI-N-acetylglucosaminyltransferase complex
comment: Note that this term should not be confused with 'GPI-anchor transamidase complex ; GO:0042765', which represents a distinct complex with a different catalytic activity.
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

telomere cap complex
type: Class
subclass of: protein-DNA complex
subclass of: chromosomal part
definition: A complex of DNA and protein located at the end of a linear chromosome that protects and stabilizes a linear chromosome.
id: GO:0000782
comment: Note that this term can be used in place of the obsolete cellular component term 'telomere ; GO:0005696'. Use with caution because this term refers to a specific protein complex and not a region of the chromosome.
has OBO namespace: cellular_component
imported from: go.owl
in subset: goslim pir
in subset: gosubset prok

nuclear telomere cap complex
type: Class
subclass of: telomere cap complex
subclass of: nuclear chromosome part
definition: A complex of DNA and protein located at the end of a linear chromosome in the nucleus that protects and stabilizes a linear chromosome.
id: GO:0000783
comment: Note that this term can be used in place of the obsolete cellular component term 'telomere ; GO:0005696'. Use with caution because this term refers to a specific protein complex and not a region of the chromosome.
has OBO namespace: cellular_component
imported from: go.owl

regulatory region DNA binding
type: Class
subclass of: regulatory region nucleic acid binding
subclass of: DNA binding
creation date: 2010-08-10T10:56:24Z
id: GO:0000975
definition: Interacting selectively and non-covalently with a DNA region that regulates a DNA-based process. Such processes include transcription, DNA replication, and DNA repair.
created by: kchris
has OBO namespace: molecular_function
imported from: go.owl

core promoter binding
type: Class
subclass of: transcription regulatory region DNA binding
creation date: 2010-08-27T03:00:52Z
id: GO:0001047
definition: Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
term from ontology: go.owl
created by: kchris
has OBO namespace: molecular_function
term from ontology: obi.owl
imported from: go.owl

regulatory region nucleic acid binding
type: Class
subclass of: nucleic acid binding
creation date: 2010-10-21T04:08:56Z
id: GO:0001067
definition: Interacting selectively and non-covalently with a nucleic acid region that regulates a nucleic acid-based process. Such processes include transcription, DNA replication, and DNA repair.
created by: kchris
has OBO namespace: molecular_function
imported from: go.owl

cell activation
type: Class
subclass of: single-organism cellular process
definition: A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand.
id: GO:0001775
has OBO namespace: biological_process
imported from: go.owl
in subset: goslim pir

antibody-dependent cellular cytotoxicity
type: Class
subclass of: type IIa hypersensitivity
subclass of: leukocyte mediated cytotoxicity
subclass of: single-organism process
has exact synonym: ADCC
definition: Cytolysis of target cells by natural killer cells, eosinophils, neutrophils, monocytes, or macrophages following engagement of antibodies bound to the target cells by Fc receptors on the effector cells.
id: GO:0001788
has db xref: Wikipedia:Antibody-dependent_cell-mediated_cytotoxicity
has db xref: Wikipedia:Antibody-dependent_cellular_cytotoxicity
has exact synonym: antibody dependent cell death
has exact synonym: antibody dependent cell killing
has exact synonym: antibody-dependent cell death
has exact synonym: antibody-dependent cell killing
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
has exact synonym: type VI hypersensitivity
imported from: go.owl

type IIa hypersensitivity
type: Class
subclass of: type II hypersensitivity
definition: An inflammatory response resulting in cell death mediated by activation of the classical complement pathway or induction of effector cell phagocytosis or cytolysis mechanisms via complement or Fc receptors following the binding of antibodies to cell surface antigens on a target cell.
id: GO:0001794
comment: Note that some type IIb hypersensitivity responses (GO:0001795) are referred to simply as type II hypersensitivity in the earlier literature, but are mechanistically distinct from type IIa hypersensitivity.
has OBO namespace: biological_process
imported from: go.owl

type IV hypersensitivity
type: Class
subclass of: T cell mediated immunity
subclass of: hypersensitivity
definition: An inflammatory response driven by T cell recognition of processed soluble or cell-associated antigens leading to cytokine release and leukocyte activation.
id: GO:0001806
has alternative id: GO:0016069
has db xref: Wikipedia:Type_IV_hypersensitivity
has OBO namespace: biological_process
has exact synonym: delayed hypersensitivity response
has exact synonym: delayed-type hypersensitivity
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

cytokine production
type: Class
subclass of: single-multicellular organism process
id: GO:0001816
comment: Note that this term is intended for use when a gene product is seen to cause apparent increases in intracellular or extracellular cytokine levels, without specific regard as to whether the increase is due to increased biosynthesis, increased secretion of preexisting cytokine molecules, or increased conversion from precursor molecules.
definition: The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
has narrow synonym: interferon production
has narrow synonym: interleukin production
term from ontology: obi.owl
imported from: go.owl
in_subset: goslim pir
in subset: goslim pir

histamine secretion
type: Class
subclass of: secretion
subclass of: histamine transport
id: GO:0001821
definition: The regulated release of histamine by a cell or tissue. It is formed by decarboxylation of histidine and it acts through receptors in smooth muscle and in secretory systems.
has OBO namespace: biological_process
imported from: go.owl

cell killing
type: Class
subclass of: biological_process
definition: Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
id: GO:0001906
has OBO namespace: biological_process
term from ontology: go.owl
has related synonym: necrosis
term from ontology: obi.owl
imported from: go.owl
in_subset: goslim pir
in subset: goslim pir
in subset: gosubset prok
in_subset: gosubset prok

leukocyte mediated cytotoxicity
type: Class
subclass of: cell killing
id: GO:0001909
definition: The directed killing of a target cell by a leukocyte.
comment: This term was improved by GO_REF:0000022. It was moved. Note that this term and its children describe contact-dependent killing of target cells by lymphocytes and myeloid cells of the immune system.
has OBO namespace: biological_process
has exact synonym: immune cell mediated cell death
has exact synonym: immune cell mediated cell killing
has exact synonym: immune cell mediated cytotoxicity
has exact synonym: leucocyte mediated cytotoxicity
imported from: go.owl

T cell mediated cytotoxicity
type: Class
subclass of: leukocyte mediated cytotoxicity
subclass of: T cell mediated immunity
subclass of: single-organism process
id: GO:0001913
comment: Note that either or both mechanisms mentioned in the definition may be used in this process. Note that both granule release and the engagement of death receptors on target cells result in the induction of apoptosis in the target cell. Note that both CD4 and CD8 positive T cells can mediate apoptosis of target cells, independently of their definition as 'helper' T cells or not.
has exact synonym: T cell mediated apoptosis
has exact synonym: T cell mediated cell death
has exact synonym: T cell mediated cell killing
has related synonym: T cell mediated cytolysis
has exact synonym: T lymphocyte mediated cytotoxicity
has exact synonym: T-cell mediated apoptosis
has exact synonym: T-cell mediated cell death
has exact synonym: T-cell mediated cell killing
has exact synonym: T-cell mediated cytotoxicity
has exact synonym: T-lymphocyte mediated cytotoxicity
definition: The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

3-methylcrotonyl-CoA carboxylase complex, mitochondrial
type: Class
subclass of: mitochondrial part
subclass of: methylcrotonoyl-CoA carboxylase complex
creation date: 2010-03-15T04:58:08Z
has exact synonym: 3-methylcrotonyl-CoA carboxylase holoenzyme
definition: A mitochondrial protein complex which is capable of 3-methylcrotonyl-CoA carboxylase activity. In mammals, at least, consists as a dodecamer of 6 alpha and 6 beta subunits. MCCC-alpha has a covalently bound biotin essential for the ATP-dependent carboxylation. MCCC-beta possesses carboxyltransferase activity which presumably is essential for binding to 3-methylcrotonyl-CoA.
id: GO:0002169
has exact synonym: MCCC complex
has OBO namespace: cellular_component
term from ontology: go.owl
created by: hjd
has exact synonym: methylcrotonoyl-CoA carboxylase complex
term from ontology: pro.owl
imported from: go.owl

palmitoyltransferase complex
type: Class
subclass of: transferase complex
creation date: 2010-12-03T10:49:17Z
definition: A protein complex with palmitoyltransferase activity.
id: GO:0002178
has OBO namespace: cellular_component
term from ontology: go.owl
created by: hjd
term from ontology: pro.owl
imported from: go.owl

homodimeric serine palmitoyltransferase complex
type: Class
subclass of: serine C-palmitoyltransferase complex
creation date: 2010-12-03T10:50:59Z
definition: A homodimeric complex which transfers a palmitoyl group onto serine, forming 3-dehydro-D-sphinganine.
id: GO:0002179
comment: This complex occurs primarily in bacteria.
has OBO namespace: cellular_component
term from ontology: go.owl
created by: hjd
term from ontology: pro.owl
imported from: go.owl

5-lipoxygenase complex
type: Class
subclass of: nuclear membrane part
subclass of: oxidoreductase complex
creation date: 2011-06-09T01:05:53Z
definition: An nuclear membrane protein complex having arachidonate 5-lipoxygenase activity.
id: GO:0002180
has OBO namespace: cellular_component
term from ontology: go.owl
created by: hjd
term from ontology: pro.owl
imported from: go.owl

creatine kinase complex
type: Class
subclass of: transferase complex, transferring phosphorus-containing groups
creation date: 2011-06-14T02:12:19Z
definition: A protein complex having creatine kinase activity.
id: GO:0002185
has OBO namespace: cellular_component
term from ontology: go.owl
created by: hjd
term from ontology: pro.owl
imported from: go.owl

cytosolic creatine kinase complex
type: Class
subclass of: creatine kinase complex
subclass of: cytosolic part
creation date: 2011-06-14T02:14:16Z
definition: A dimeric protein complex having creatine kinase activity.
id: GO:0002186
has OBO namespace: cellular_component
term from ontology: go.owl
created by: hjd
term from ontology: pro.owl
imported from: go.owl

xanthine dehydrogenase complex
type: Class
subclass of: oxidoreductase complex
creation date: 2011-10-03T03:55:57Z
definition: A homodimeric protein complex having xanthine dehydrogenase activity.
id: GO:0002197
has OBO namespace: cellular_component
term from ontology: go.owl
created by: hjd
term from ontology: pro.owl
imported from: go.owl

zona pellucida receptor complex
type: Class
subclass of: protein complex
creation date: 2011-12-23T01:33:23Z
definition: A multisubunit complex comprising the chaperonin-containing T-complex and several other components involved in mediating sperm-oocyte Interaction.
id: GO:0002199
has OBO namespace: cellular_component
term from ontology: go.owl
created by: hjd
term from ontology: pro.owl
has related synonym: sperm protein complex I
imported from: go.owl

adaptive immune response
type: Class
subclass of: immune response
definition: An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
id: GO:0002250
comment: This term was added by GO_REF:0000022.
has db xref: Wikipedia:Adaptive_immune_system
has exact synonym: acquired immune response
has OBO namespace: biological_process
term from ontology: go.owl
has exact synonym: immune memory response
term from ontology: obi.owl
imported from: go.owl

immune effector process
type: Class
subclass of: immune system process
definition: Any process of the immune system that can potentially contribute to an immune response.
id: GO:0002252
comment: This term was added by GO_REF:0000022.
has OBO namespace: biological_process
imported from: go.owl

cell activation involved in immune response
type: Class
subclass of: cell activation
subclass of: immune effector process
definition: A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand, leading to the initiation or perpetuation of an immune response.
id: GO:0002263
comment: This term was added by GO_REF:0000022.
has OBO namespace: biological_process
has related synonym: cell activation during immune response
imported from: go.owl

lymphocyte activation involved in immune response
type: Class
subclass of: leukocyte activation involved in immune response
subclass of: lymphocyte activation
definition: A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response.
id: GO:0002285
has OBO namespace: biological_process
has related synonym: lymphocyte activation during immune response
imported from: go.owl

T cell activation involved in immune response
type: Class
subclass of: lymphocyte activation involved in immune response
subclass of: T cell activation
id: GO:0002286
has related synonym: T cell activation during immune response
has related synonym: T lymphocyte activation during immune response
has related synonym: T-cell activation during immune response
has related synonym: T-lymphocyte activation during immune response
definition: The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response.
has OBO namespace: biological_process
imported from: go.owl

leukocyte activation involved in immune response
type: Class
subclass of: cell activation involved in immune response
subclass of: leukocyte activation
definition: A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response.
id: GO:0002366
has OBO namespace: biological_process
has related synonym: immune cell activation during immune response
has related synonym: leucocyte activation during immune response
has related synonym: leukocyte activation during immune response
imported from: go.owl

cytokine production involved in immune response
type: Class
equivalent class: Class
  intersection of: cytokine production
  intersection of: Restriction
    on property: part of
    some values from: immune response
subclass of: cytokine production
subclass of: production of molecular mediator of immune response
id: GO:0002367
definition: The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus contributing to an immune response, resulting in an increase in its intracellular or extracellular levels.
comment: This term was added by GO_REF:0000022. Note that this term is intended for use when a gene product is seen to cause apparent increases in intracellular or extracellular cytokine levels, without specific regard as to whether the increase is due to increased biosynthesis, increased secretion of preexisting cytokine molecules, or increased conversion from precursor molecules.
has OBO namespace: biological_process
has related synonym: cytokine production during immune response
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

immune system process
type: Class
subclass of: biological_process
definition: Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
id: GO:0002376
comment: Note that this term is a direct child of 'biological_process ; GO:0008150' because some immune system processes are types of cellular process (GO:0009987), whereas others are types of multicellular organism process (GO:0032501). This term was added by GO_REF:0000022.
has db xref: Wikipedia:Immune_system
has OBO namespace: biological_process
imported from: go.owl
in subset: goslim agr
in subset: goslim chembl
in subset: goslim generic
in subset: goslim mouse
in subset: goslim pir

platelet activating factor production
type: Class
subclass of: cytokine production
id: GO:0002390
definition: The synthesis or release of platelet activating factor following a stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

inflammatory response to antigenic stimulus
type: Class
subclass of: inflammatory response
subclass of: immune response
definition: An inflammatory response to an antigenic stimulus, which can be include any number of T cell or B cell epitopes.
id: GO:0002437
has OBO namespace: biological_process
imported from: go.owl

acute inflammatory response to antigenic stimulus
type: Class
subclass of: inflammatory response to antigenic stimulus
subclass of: acute inflammatory response
definition: An acute inflammatory response to an antigenic stimulus. An acute inflammatory response occurs within a matter of minutes or hours, and either resolves within a few days or becomes a chronic inflammatory response.
id: GO:0002438
comment: This term was added by GO_REF:0000022.
has OBO namespace: biological_process
imported from: go.owl

production of molecular mediator of immune response
type: Class
subclass of: immune system process
id: GO:0002440
definition: The synthesis or release of any molecular mediator of the immune response, resulting in an increase in its intracellular or extracellular levels.
comment: This term was added by GO_REF:0000022.
has OBO namespace: biological_process
has related synonym: production of cellular mediator of immune response
imported from: go.owl

histamine secretion involved in inflammatory response
type: Class
subclass of: histamine secretion
subclass of: hormone secretion
id: GO:0002441
definition: The regulated release of histamine by a cell as part of an inflammatory response.
has OBO namespace: biological_process
has broad synonym: histamine secretion involved in acute inflammatory response
imported from: go.owl

leukocyte mediated immunity
type: Class
subclass of: immune effector process
definition: Any process involved in the carrying out of an immune response by a leukocyte.
id: GO:0002443
has alternative id: GO:0019723
has alternative id: GO:0042087
comment: This term was added by GO_REF:0000022.
has OBO namespace: biological_process
has related synonym: cell-mediated immune response
has related synonym: cellular immune response
has exact synonym: immune cell effector process
has exact synonym: immune cell mediated immunity
has exact synonym: leucocyte immune effector process
has exact synonym: leucocyte mediated immunity
has exact synonym: leukocyte immune effector process
imported from: go.owl

myeloid leukocyte mediated immunity
type: Class
subclass of: leukocyte mediated immunity
definition: Any process involved in the carrying out of an immune response by a myeloid leukocyte.
id: GO:0002444
comment: This term was added by GO_REF:0000022.
has OBO namespace: biological_process
has exact synonym: myeloid leucocyte immune effector process
has exact synonym: myeloid leucocyte mediated immunity
has exact synonym: myeloid leukocyte immune effector process
imported from: go.owl

type II hypersensitivity
type: Class
subclass of: myeloid leukocyte mediated immunity
subclass of: hypersensitivity
subclass of: immunoglobulin mediated immune response
definition: An inflammatory response resulting in cell death or dysfunction mediated by activation of the classical complement pathway or induction of effector cell phagocytosis, cytolysis mechanisms via complement or Fc receptors following the binding of antibodies to cell surface antigens on a target cell, or mediated by the direct binding of antibody to cellular receptors.
id: GO:0002445
has db xref: Wikipedia:Type_II_hypersensitivity
has OBO namespace: biological_process
imported from: go.owl

lymphocyte mediated immunity
type: Class
subclass of: leukocyte mediated immunity
definition: Any process involved in the carrying out of an immune response by a lymphocyte.
id: GO:0002449
comment: This term was added by GO_REF:0000022.
has OBO namespace: biological_process
has broad synonym: cell-mediated immunity
has broad synonym: cellular immune response
imported from: go.owl

T cell mediated immunity
type: Class
subclass of: lymphocyte mediated immunity
subclass of: adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
definition: Any process involved in the carrying out of an immune response by a T cell.
id: GO:0002456
has exact synonym: T lymphocyte mediated immunity
has exact synonym: T-cell mediated immunity
has exact synonym: T-lymphocyte mediated immunity
comment: This term was added by GO_REF:0000022.
has OBO namespace: biological_process
has broad synonym: cell-mediated immunity
has broad synonym: cellular immune response
imported from: go.owl

adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
type: Class
subclass of: adaptive immune response
definition: An immune response mediated by lymphocytes expressing specific receptors for antigen produced through a somatic diversification process that includes somatic recombination of germline gene segments encoding immunoglobulin superfamily domains. Recombined receptors for antigen encoded by immunoglobulin superfamily domains include T cell receptors and immunoglobulins (antibodies) produced by B cells. The first encounter with antigen elicits a primary immune response that is slow and not of great magnitude. T and B cells selected by antigen become activated and undergo clonal expansion. A fraction of antigen-reactive T and B cells become memory cells, whereas others differentiate into effector cells. The memory cells generated during the primary response enable a much faster and stronger secondary immune response upon subsequent exposures to the same antigen (immunological memory). An example of this is the adaptive immune response found in Mus musculus.
id: GO:0002460
has OBO namespace: biological_process
imported from: go.owl

tolerance induction
type: Class
subclass of: immune system process
definition: A process that directly activates any of the steps required for tolerance, a physiologic state in which the immune system does not react destructively against the components of an organism that harbors it or against antigens that are introduced to it.
id: GO:0002507
comment: This term was added by GO_REF:0000022.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

B cell tolerance induction
type: Class
subclass of: tolerance induction
definition: A process involving any mechanism for tolerance induction in B cells.
has exact synonym: B lymphocyte tolerance induction
has exact synonym: B-cell tolerance induction
has exact synonym: B-lymphocyte tolerance induction
id: GO:0002514
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

T cell tolerance induction
type: Class
subclass of: tolerance induction
definition: A process involving any mechanism for tolerance induction in T cells.
id: GO:0002517
has exact synonym: T lymphocyte tolerance induction
has exact synonym: T-cell tolerance induction
has exact synonym: T-lymphocyte tolerance induction
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

hypersensitivity
type: Class
subclass of: acute inflammatory response to antigenic stimulus
definition: An inflammatory response to an exogenous environmental antigen or an endogenous antigen initiated by the adaptive immune system.
id: GO:0002524
has db xref: Wikipedia:Hypersensitivity
has OBO namespace: biological_process
term from ontology: go.owl
has related synonym: hypersensitivity response
term from ontology: obi.owl
imported from: go.owl

acute inflammatory response
type: Class
subclass of: inflammatory response
id: GO:0002526
definition: Inflammation which comprises a rapid, short-lived, relatively uniform response to acute injury or antigenic challenge and is characterized by accumulations of fluid, plasma proteins, and granulocytic leukocytes. An acute inflammatory response occurs within a matter of minutes or hours, and either resolves within a few days or becomes a chronic inflammatory response.
comment: This term was added by GO_REF:0000022.
has OBO namespace: biological_process
imported from: go.owl

production of molecular mediator involved in inflammatory response
type: Class
subclass of: single-multicellular organism process
id: GO:0002532
definition: The synthesis or release of any molecular mediator of the inflammatory response following an inflammatory stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
has related synonym: production of cellular mediator of acute inflammation
has broad synonym: production of molecular mediator involved in acute inflammatory response
imported from: go.owl

cytokine production involved in inflammatory response
type: Class
subclass of: cytokine production
subclass of: production of molecular mediator involved in inflammatory response
id: GO:0002534
definition: The synthesis or release of a cytokine following a inflammatory stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
has broad synonym: cytokine production involved in acute inflammatory response
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

regulation of immune system process
type: Class
subclass of: regulation of biological process
definition: Any process that modulates the frequency, rate, or extent of an immune system process.
id: GO:0002682
has OBO namespace: biological_process
imported from: go.owl

positive regulation of immune system process
type: Class
subclass of: regulation of immune system process
subclass of: positive regulation of biological process
definition: Any process that activates or increases the frequency, rate, or extent of an immune system process.
id: GO:0002684
has narrow synonym: activation of immune system process
has OBO namespace: biological_process
has narrow synonym: stimulation of immune system process
has exact synonym: up regulation of immune system process
has exact synonym: up-regulation of immune system process
has exact synonym: upregulation of immune system process
imported from: go.owl

regulation of immune effector process
type: Class
subclass of: regulation of immune system process
definition: Any process that modulates the frequency, rate, or extent of an immune effector process.
id: GO:0002697
has OBO namespace: biological_process
imported from: go.owl

positive regulation of immune effector process
type: Class
subclass of: positive regulation of immune system process
subclass of: regulation of immune effector process
definition: Any process that activates or increases the frequency, rate, or extent of an immune effector process.
id: GO:0002699
has narrow synonym: activation of immune effector process
has OBO namespace: biological_process
has narrow synonym: stimulation of immune effector process
has exact synonym: up regulation of immune effector process
has exact synonym: up-regulation of immune effector process
has exact synonym: upregulation of immune effector process
imported from: go.owl

regulation of leukocyte mediated immunity
type: Class
subclass of: regulation of immune effector process
definition: Any process that modulates the frequency, rate, or extent of leukocyte mediated immunity.
id: GO:0002703
has OBO namespace: biological_process
has exact synonym: regulation of immune cell mediated immunity
has exact synonym: regulation of leucocyte mediated immunity
imported from: go.owl

positive regulation of leukocyte mediated immunity
type: Class
subclass of: positive regulation of immune effector process
subclass of: regulation of leukocyte mediated immunity
definition: Any process that activates or increases the frequency, rate, or extent of leukocyte mediated immunity.
id: GO:0002705
has narrow synonym: activation of leukocyte mediated immunity
has OBO namespace: biological_process
has exact synonym: positive regulation of immune cell mediated immunity
has exact synonym: positive regulation of leucocyte mediated immunity
has narrow synonym: stimulation of leukocyte mediated immunity
has exact synonym: up regulation of leukocyte mediated immunity
has exact synonym: up-regulation of leukocyte mediated immunity
has exact synonym: upregulation of leukocyte mediated immunity
imported from: go.owl

regulation of lymphocyte mediated immunity
type: Class
subclass of: regulation of leukocyte mediated immunity
definition: Any process that modulates the frequency, rate, or extent of lymphocyte mediated immunity.
id: GO:0002706
has OBO namespace: biological_process
imported from: go.owl

positive regulation of lymphocyte mediated immunity
type: Class
subclass of: positive regulation of leukocyte mediated immunity
subclass of: regulation of lymphocyte mediated immunity
definition: Any process that activates or increases the frequency, rate, or extent of lymphocyte mediated immunity.
id: GO:0002708
has narrow synonym: activation of lymphocyte mediated immunity
has OBO namespace: biological_process
has narrow synonym: stimulation of lymphocyte mediated immunity
has exact synonym: up regulation of lymphocyte mediated immunity
has exact synonym: up-regulation of lymphocyte mediated immunity
has exact synonym: upregulation of lymphocyte mediated immunity
imported from: go.owl

regulation of T cell mediated immunity
type: Class
subclass of: regulation of lymphocyte mediated immunity
subclass of: regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
definition: Any process that modulates the frequency, rate, or extent of T cell mediated immunity.
id: GO:0002709
has OBO namespace: biological_process
has exact synonym: regulation of T lymphocyte mediated immunity
has exact synonym: regulation of T-cell mediated immunity
has exact synonym: regulation of T-lymphocyte mediated immunity
imported from: go.owl

positive regulation of T cell mediated immunity
type: Class
subclass of: positive regulation of lymphocyte mediated immunity
subclass of: regulation of T cell mediated immunity
subclass of: positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
definition: Any process that activates or increases the frequency, rate, or extent of T cell mediated immunity.
id: GO:0002711
has narrow synonym: activation of T cell mediated immunity
has OBO namespace: biological_process
has exact synonym: positive regulation of T lymphocyte mediated immunity
has exact synonym: positive regulation of T-cell mediated immunity
has exact synonym: positive regulation of T-lymphocyte mediated immunity
has narrow synonym: stimulation of T cell mediated immunity
has exact synonym: up regulation of T cell mediated immunity
has exact synonym: up-regulation of T cell mediated immunity
has exact synonym: upregulation of T cell mediated immunity
imported from: go.owl

regulation of B cell mediated immunity
type: Class
subclass of: regulation of lymphocyte mediated immunity
subclass of: regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
definition: Any process that modulates the frequency, rate, or extent of B cell mediated immunity.
id: GO:0002712
has OBO namespace: biological_process
has exact synonym: regulation of B lymphocyte mediated immunity
has exact synonym: regulation of B-cell mediated immunity
has exact synonym: regulation of B-lymphocyte mediated immunity
imported from: go.owl

positive regulation of B cell mediated immunity
type: Class
subclass of: positive regulation of lymphocyte mediated immunity
subclass of: regulation of B cell mediated immunity
subclass of: positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
definition: Any process that activates or increases the frequency, rate, or extent of B cell mediated immunity.
id: GO:0002714
has narrow synonym: activation of B cell mediated immunity
has OBO namespace: biological_process
has exact synonym: positive regulation of B lymphocyte mediated immunity
has exact synonym: positive regulation of B-cell mediated immunity
has exact synonym: positive regulation of B-lymphocyte mediated immunity
has narrow synonym: stimulation of B cell mediated immunity
has exact synonym: up regulation of B cell mediated immunity
has exact synonym: up-regulation of B cell mediated immunity
has exact synonym: upregulation of B cell mediated immunity
imported from: go.owl

regulation of adaptive immune response
type: Class
subclass of: regulation of immune response
definition: Any process that modulates the frequency, rate, or extent of an adaptive immune response.
id: GO:0002819
has OBO namespace: biological_process
imported from: go.owl

positive regulation of adaptive immune response
type: Class
subclass of: regulation of adaptive immune response
subclass of: positive regulation of immune response
definition: Any process that activates or increases the frequency, rate, or extent of an adaptive immune response.
id: GO:0002821
has narrow synonym: activation of adaptive immune response
has OBO namespace: biological_process
has narrow synonym: stimulation of adaptive immune response
has exact synonym: up regulation of adaptive immune response
has exact synonym: up-regulation of adaptive immune response
has exact synonym: upregulation of adaptive immune response
imported from: go.owl

regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
type: Class
subclass of: regulation of adaptive immune response
definition: Any process that modulates the frequency, rate, or extent of an adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. An example of this process is found in the Gnathostomata.
id: GO:0002822
has OBO namespace: biological_process
imported from: go.owl

positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
type: Class
subclass of: positive regulation of adaptive immune response
subclass of: regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
definition: Any process that activates or increases the frequency, rate, or extent of an adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. An example of this process is found in the Gnathostomata.
id: GO:0002824
has OBO namespace: biological_process
imported from: go.owl

tumor necrosis factor receptor superfamily complex
type: Class
subclass of: receptor complex
creation date: 2012-12-20T13:26:39Z
definition: A receptor complex that contains one or more members of the tumor necrosis factor (TNF) receptor superfamily.
id: GO:0002947
has related synonym: TNF receptor superfamily complex
has OBO namespace: cellular_component
term from ontology: go.owl
created by: hjd
term from ontology: pro.owl
imported from: go.owl

molecular_function
type: Class
subclass of: function
definition: Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
id: GO:0003674
has alternative id: GO:0005554
comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. Note that when this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
term from ontology: go.owl
has exact synonym: molecular function
has OBO namespace: molecular_function
term from ontology: obi.owl
imported from: go.owl
in subset: goslim aspergillus
in_subset: goslim aspergillus
in_subset: goslim candida
in subset: goslim candida
in subset: goslim chembl
in_subset: goslim chembl
in subset: goslim generic
in_subset: goslim generic
in subset: goslim metagenomics
in_subset: goslim metagenomics
in subset: goslim pir
in_subset: goslim pir
in subset: goslim plant
in_subset: goslim plant
in_subset: goslim yeast
in subset: goslim yeast
in subset: gosubset prok
in_subset: gosubset prok

nucleic acid binding
type: Class
subclass of: organic cyclic compound binding
subclass of: heterocyclic compound binding
id: GO:0003676
definition: Interacting selectively and non-covalently with any nucleic acid.
has OBO namespace: molecular_function
imported from: go.owl
in subset: goslim chembl
in subset: goslim metagenomics
in subset: goslim pir
in subset: goslim plant
in subset: gosubset prok

DNA binding
type: Class
subclass of: nucleic acid binding
definition: Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
id: GO:0003677
has alternative id: GO:0043566
has related synonym: microtubule/chromatin interaction
has OBO namespace: molecular_function
has narrow synonym: plasmid binding
has related synonym: structure specific DNA binding
has related synonym: structure-specific DNA binding
imported from: go.owl
in subset: goslim agr
in subset: goslim aspergillus
in subset: goslim candida
in subset: goslim chembl
in subset: goslim generic
in subset: goslim mouse
in subset: goslim plant
in subset: goslim yeast
in subset: gosubset prok

antigen binding
type: Class
subclass of: binding
has related synonym: B cell receptor activity
id: GO:0003823
definition: Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
has related synonym: antibody
term from ontology: go.owl
has related synonym: immunoglobulin
has OBO namespace: molecular_function
term from ontology: obi.owl
has related synonym: opsonin activity
imported from: go.owl
in_subset: goslim chembl
in subset: goslim chembl
in subset: goslim pir
in_subset: goslim pir

catalytic activity
type: Class
subclass of: molecular_function
definition: Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
id: GO:0003824
has db xref: Wikipedia:Enzyme
has exact synonym: enzyme activity
term from ontology: go.owl
has OBO namespace: molecular_function
term from ontology: obi.owl
imported from: go.owl
in subset: goslim agr
in_subset: goslim agr
in_subset: goslim chembl
in subset: goslim chembl
in_subset: goslim metagenomics
in subset: goslim metagenomics
in subset: goslim pir
in_subset: goslim pir
in subset: goslim plant
in_subset: goslim plant
in subset: gosubset prok
in_subset: gosubset prok

RNA-directed DNA polymerase activity
type: Class
subclass of: DNA polymerase activity
definition: Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
has exact synonym: DNA nucleotidyltransferase (RNA-directed) activity
has db xref: EC:2.7.7.49
id: GO:0003964
has db xref: MetaCyc:RNA-DIRECTED-DNA-POLYMERASE-RXN
has exact synonym: RNA revertase activity
has exact synonym: RNA-dependent DNA polymerase activity
has exact synonym: RNA-dependent deoxyribonucleate nucleotidyltransferase activity
has narrow synonym: RNA-directed DNA polymerase, group II intron encoded
has narrow synonym: RNA-directed DNA polymerase, transposon encoded
has exact synonym: RNA-instructed DNA polymerase activity
has related synonym: RT
has db xref: Reactome:REACT_9039
has db xref: Reactome:REACT_9049
has exact synonym: deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (RNA-directed) activity
term from ontology: go.owl
has OBO namespace: molecular_function
term from ontology: obi.owl
has exact synonym: reverse transcriptase activity
has related synonym: revertase activity
imported from: go.owl
in subset: gosubset prok
in_subset: gosubset prok

transporter activity
type: Class
subclass of: molecular_function
definition: Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
id: GO:0005215
has alternative id: GO:0005478
has db xref: Reactome:REACT_6315
has OBO namespace: molecular_function
has related synonym: small-molecule carrier or transporter
imported from: go.owl
in subset: goslim agr
in subset: goslim aspergillus
in subset: goslim candida
in subset: goslim chembl
in subset: goslim metagenomics
in subset: goslim mouse
in subset: goslim pir
in subset: goslim plant
in subset: gosubset prok

ion channel activity
type: Class
subclass of: ion transmembrane transporter activity
subclass of: substrate-specific channel activity
definition: Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
id: GO:0005216
term from ontology: go.owl
has OBO namespace: molecular_function
term from ontology: obi.owl
imported from: go.owl
in_subset: gosubset prok
in subset: gosubset prok

binding
type: Class
subclass of: molecular_function
id: GO:0005488
comment: Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children.
definition: The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.
has db xref: Wikipedia:Binding_(molecular)
has narrow synonym: ligand
has OBO namespace: molecular_function
imported from: go.owl
in subset: gocheck do not manually annotate
in subset: goslim pir
in subset: goslim plant
in subset: gosubset prok

protein binding
type: Class
subclass of: binding
id: GO:0005515
has alternative id: GO:0045308
definition: Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
has db xref: Reactome:REACT_100287
has db xref: Reactome:REACT_101129
has db xref: Reactome:REACT_102084
has db xref: Reactome:REACT_102457
has db xref: Reactome:REACT_103972
has db xref: Reactome:REACT_104029
has db xref: Reactome:REACT_104599
has db xref: Reactome:REACT_105776
has db xref: Reactome:REACT_105895
has db xref: Reactome:REACT_106168
has db xref: Reactome:REACT_106189
has db xref: Reactome:REACT_107402
has db xref: Reactome:REACT_108283
has db xref: Reactome:REACT_109392
has db xref: Reactome:REACT_110419
has db xref: Reactome:REACT_110570
has db xref: Reactome:REACT_15321
has db xref: Reactome:REACT_15325
has db xref: Reactome:REACT_15355
has db xref: Reactome:REACT_15417
has db xref: Reactome:REACT_15419
has db xref: Reactome:REACT_15506
has db xref: Reactome:REACT_15541
has db xref: Reactome:REACT_20509
has db xref: Reactome:REACT_20539
has db xref: Reactome:REACT_28794
has db xref: Reactome:REACT_30571
has db xref: Reactome:REACT_30672
has db xref: Reactome:REACT_31305
has db xref: Reactome:REACT_31537
has db xref: Reactome:REACT_31641
has db xref: Reactome:REACT_31648
has db xref: Reactome:REACT_32973
has db xref: Reactome:REACT_33135
has db xref: Reactome:REACT_34719
has db xref: Reactome:REACT_6923
has db xref: Reactome:REACT_6945
has db xref: Reactome:REACT_78382
has db xref: Reactome:REACT_78466
has db xref: Reactome:REACT_79634
has db xref: Reactome:REACT_80470
has db xref: Reactome:REACT_80778
has db xref: Reactome:REACT_83147
has db xref: Reactome:REACT_83165
has db xref: Reactome:REACT_83532
has db xref: Reactome:REACT_85250
has db xref: Reactome:REACT_85858
has db xref: Reactome:REACT_85975
has db xref: Reactome:REACT_87187
has db xref: Reactome:REACT_87374
has db xref: Reactome:REACT_87652
has db xref: Reactome:REACT_88068
has db xref: Reactome:REACT_88138
has db xref: Reactome:REACT_88223
has db xref: Reactome:REACT_89261
has db xref: Reactome:REACT_90027
has db xref: Reactome:REACT_90105
has db xref: Reactome:REACT_90666
has db xref: Reactome:REACT_91560
has db xref: Reactome:REACT_92029
has db xref: Reactome:REACT_93175
has db xref: Reactome:REACT_93938
has db xref: Reactome:REACT_94522
has db xref: Reactome:REACT_94808
has db xref: Reactome:REACT_95241
has db xref: Reactome:REACT_95561
has db xref: Reactome:REACT_95647
has db xref: Reactome:REACT_96236
has db xref: Reactome:REACT_96264
has db xref: Reactome:REACT_98028
has db xref: Reactome:REACT_98807
has related synonym: alpha-2 macroglobulin receptor-associated protein activity
has OBO namespace: molecular_function
has exact synonym: protein amino acid binding

cellular_component
type: Class
subclass of: material entity
id: GO:0005575
has alternative id: GO:0008372
has db xref: NIF_Subcellular:sao-1337158144
has db xref: NIF_Subcellular:sao1337158144
comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
definition: The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
has exact synonym: cell or subcellular entity
has exact synonym: cellular component
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: obi.owl
term from ontology: pro.owl
has related synonym: subcellular entity
imported from: go.owl
in_subset: goslim aspergillus
in subset: goslim aspergillus
in_subset: goslim candida
in subset: goslim candida
in_subset: goslim chembl
in subset: goslim chembl
in_subset: goslim generic
in subset: goslim generic
in subset: goslim metagenomics
in_subset: goslim metagenomics
in_subset: goslim pir
in subset: goslim pir
in_subset: goslim plant
in subset: goslim plant
in_subset: goslim yeast
in subset: goslim yeast
in subset: gosubset prok
in_subset: gosubset prok

laminin-5 complex
type: Class
subclass of: laminin complex
definition: A laminin complex composed of alpha3, beta3 and gamma2 polypeptide chains.
id: GO:0005610
has OBO namespace: cellular_component
term from ontology: go.owl
has narrow synonym: laminin-332 complex
has exact synonym: laminin-3A32 complex
has exact synonym: laminin-5A complex
term from ontology: pro.owl
imported from: go.owl

alpha DNA polymerase:primase complex
type: Class
subclass of: nuclear chromosome part
subclass of: nuclear DNA-directed RNA polymerase complex
definition: A complex of four polypeptides, comprising large and small DNA polymerase alpha subunits and two primase subunits, which catalyzes the synthesis of an RNA primer on the lagging strand of replicating DNA; the smaller of the two primase subunits alone can catalyze oligoribonucleotide synthesis.
has exact synonym: DNA polymerase alpha:primase complex
id: GO:0005658
has OBO namespace: cellular_component
term from ontology: go.owl
has exact synonym: heterotetrameric polymerase alpha holoenzyme
has related synonym: pol-prim
has broad synonym: primosome
term from ontology: pro.owl
imported from: go.owl

DNA replication factor A complex
type: Class
subclass of: protein complex
subclass of: nuclear chromosome part
definition: A conserved heterotrimeric complex that binds nonspecifically to single-stranded DNA and is required for multiple processes in eukaryotic DNA metabolism, including DNA replication, DNA repair, and recombination. In all eukaryotic organisms examined the complex is composed of subunits of approximately 70, 30, and 14 kDa.
id: GO:0005662
has exact synonym: RPA
has db xref: Wikipedia:Replication_protein_A
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
has exact synonym: replication protein A
imported from: go.owl

DNA replication factor C complex
type: Class
subclass of: protein complex
subclass of: chromosomal part
definition: A complex that loads the DNA polymerase processivity factor proliferating cell nuclear antigen (PCNA) onto DNA, thereby permitting processive DNA synthesis catalyzed by DNA polymerase. In eukaryotes the complex consists of five polypeptides.
id: GO:0005663
has exact synonym: RFC complex
has exact synonym: activator 1 complex
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl
in subset: goslim pir
in_subset: goslim pir
in_subset: gosubset prok
in subset: gosubset prok

transcription factor complex
type: Class
subclass of: protein complex
subclass of: intracellular part
definition: A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.
id: GO:0005667
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl
in_subset: goslim pir
in subset: goslim pir

transcription factor TFIID complex
type: Class
subclass of: nucleoplasm part
subclass of: RNA polymerase II transcription factor complex
definition: A complex composed of TATA binding protein (TBP) and TBP associated factors (TAFs); the total mass is typically about 800 kDa. Most of the TAFs are conserved across species. In TATA-containing promoters for RNA polymerase II (Pol II), TFIID is believed to recognize at least two distinct elements, the TATA element and a downstream promoter element. TFIID is also involved in recognition of TATA-less Pol II promoters. Binding of TFIID to DNA is necessary but not sufficient for transcription initiation from most RNA polymerase II promoters.
id: GO:0005669
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

transcription factor TFIIF complex
type: Class
subclass of: nucleoplasm part
subclass of: RNA polymerase II transcription factor complex
definition: A general transcription initiation factor which in humans consists of a heterodimer of an alpha and a beta subunit. Helps recruit RNA polymerase II to the initiation complex and promotes translation elongation.
id: GO:0005674
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

anaphase-promoting complex
type: Class
subclass of: nuclear ubiquitin ligase complex
subclass of: cullin-RING ubiquitin ligase complex
definition: A ubiquitin ligase complex that degrades mitotic cyclins and anaphase inhibitory protein, thereby triggering sister chromatid separation and exit from mitosis. Substrate recognition by APC occurs through degradation signals, the most common of which is termed the Dbox degradation motif, originally discovered in cyclin B.
has broad synonym: APC
id: GO:0005680
comment: Note that the synonym 'APC' should not be confused with the abbreviation for the adenomatous polyposis coli gene and protein.
has db xref: Wikipedia:Anaphase-promoting_complex
has exact synonym: anaphase promoting complex
has OBO namespace: cellular_component
has exact synonym: cyclosome
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

chromosome
type: Class
subclass of: intracellular non-membrane-bounded organelle
definition: A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
comment: Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore.
id: GO:0005694
has db xref: Wikipedia:Chromosome
has OBO namespace: cellular_component
has related synonym: chromatid
term from ontology: go.owl
has narrow synonym: interphase chromosome
term from ontology: obi.owl
has narrow synonym: prophase chromosome
imported from: go.owl
in subset: goslim agr
in_subset: goslim agr
in_subset: goslim aspergillus
in subset: goslim aspergillus
in_subset: goslim candida
in subset: goslim candida
in subset: goslim chembl
in_subset: goslim chembl
in subset: goslim generic
in_subset: goslim generic
in_subset: goslim metagenomics
in subset: goslim metagenomics
in subset: goslim pir
in_subset: goslim pir
in_subset: goslim yeast
in subset: goslim yeast
in subset: gosubset prok
in_subset: gosubset prok

DNA-directed RNA polymerase I complex
type: Class
subclass of: nucleolar part
subclass of: nuclear DNA-directed RNA polymerase complex
has related synonym: DNA-directed RNA polymerase I activity
id: GO:0005736
definition: RNA polymerase I, one of three nuclear DNA-directed RNA polymerases found in all eukaryotes, is a multisubunit complex; typically it produces rRNAs. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The remainder of the complex is composed of smaller subunits (generally ten or more), some of which are also found in RNA polymerase III and others of which are also found in RNA polymerases II and III. Although the core is competent to mediate ribonucleic acid synthesis, it requires additional factors to select the appropriate template.
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

mitochondrion
type: Class
subclass of: intracellular membrane-bounded organelle
subclass of: cytoplasmic part
definition: A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
id: GO:0005739
has db xref: NIF_Subcellular:sao1860313010
comment: Some anaerobic or microaerophilic organisms (e.g. Entamoeba histolytica, Giardia intestinalis and several Microsporidia species) do not have mitochondria, and contain mitochondrion-related organelles (MROs) instead, called mitosomes or hydrogenosomes, very likely derived from mitochondria. To annotate gene products located in these mitochondrial relics in species such as Entamoeba histolytica, Giardia intestinalis or others, please use GO:0032047 'mitosome' or GO:0042566 'hydrogenosome'. (See PMID:24316280 for a list of species currently known to contain mitochondrion-related organelles.)
has db xref: Wikipedia:Mitochondrion
has OBO namespace: cellular_component
term from ontology: go.owl
has exact synonym: mitochondria
term from ontology: obi.owl
imported from: go.owl
in_subset: goslim agr
in subset: goslim agr
in subset: goslim aspergillus
in_subset: goslim aspergillus
in subset: goslim candida
in_subset: goslim candida
in subset: goslim chembl
in_subset: goslim chembl
in subset: goslim generic
in_subset: goslim generic
in_subset: goslim mouse
in subset: goslim mouse
in_subset: goslim pir
in subset: goslim pir
in subset: goslim plant
in_subset: goslim plant
in subset: goslim yeast
in_subset: goslim yeast

mitochondrial respiratory chain complex IV
type: Class
equivalent class: Class
  intersection of: respiratory chain complex IV
  intersection of: Restriction
    on property: part of
    some values from: mitochondrion
subclass of: respiratory chain complex IV
subclass of: inner mitochondrial membrane protein complex
definition: A protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. Contains the 13 polypeptide subunits of cytochrome c oxidase, including cytochrome a and cytochrome a3. Catalyzes the oxidation of reduced cytochrome c by dioxygen (O2).
id: GO:0005751
has alternative id: GO:0005752
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

signal peptidase complex
type: Class
subclass of: endoplasmic reticulum part
subclass of: membrane protein complex
subclass of: peptidase complex
definition: A protein complex that is located in the endoplasmic reticulum membrane and cleaves the signal sequence from precursor proteins following their transport out of the cytoplasmic space.
id: GO:0005787
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

chaperonin-containing T-complex
type: Class
subclass of: cytosolic part
subclass of: chaperone complex
definition: A multisubunit ring-shaped complex that mediates protein folding in the cytosol without a cofactor.
has exact synonym: CCT particle
id: GO:0005832
has exact synonym: TriC
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

heterotrimeric G-protein complex
type: Class
subclass of: intracellular part
subclass of: plasma membrane protein complex
subclass of: GTPase complex
definition: Any of a family of heterotrimeric GTP-binding and hydrolyzing proteins; they belong to a superfamily of GTPases that includes monomeric proteins such as EF-Tu and RAS. Heterotrimeric G-proteins consist of three subunits; the alpha subunit contains the guanine nucleotide binding site and possesses GTPase activity; the beta and gamma subunits are tightly associated and function as a beta-gamma heterodimer; extrinsic plasma membrane proteins (cytoplasmic face) that function as a complex to transduce signals from G-protein coupled receptors to an effector protein.
id: GO:0005834
comment: See also the molecular function term 'G-protein coupled receptor activity ; GO:0004930'.
has OBO namespace: cellular_component
term from ontology: go.owl
has related synonym: heterotrimeric G-protein GTPase activity
has narrow synonym: heterotrimeric G-protein GTPase, alpha-subunit
has narrow synonym: heterotrimeric G-protein GTPase, beta-subunit
has narrow synonym: heterotrimeric G-protein GTPase, gamma-subunit
term from ontology: pro.owl
imported from: go.owl
in subset: gosubset prok
in_subset: gosubset prok

mRNA cap binding complex
type: Class
subclass of: RNA cap binding complex
subclass of: intracellular part
definition: Any protein complex that binds to an mRNA cap at any time in the lifetime of the mRNA.
id: GO:0005845
has OBO namespace: cellular_component
term from ontology: go.owl
has related synonym: mRNA cap complex
term from ontology: pro.owl
imported from: go.owl

mRNA cleavage stimulating factor complex
type: Class
subclass of: mRNA cleavage factor complex
definition: A protein complex required for mRNA cleavage but not for poly(A) addition.
has narrow synonym: CstF complex
id: GO:0005848
has OBO namespace: cellular_component
has related synonym: cleavage stimulation factor activity
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

mRNA cleavage factor complex
type: Class
subclass of: protein complex
subclass of: nucleoplasm part
definition: Any macromolecular complex involved in cleavage or polyadenylation of mRNA molecules.
id: GO:0005849
has OBO namespace: cellular_component
imported from: go.owl
in subset: goslim pir

eukaryotic translation initiation factor 2 complex
type: Class
subclass of: protein complex
subclass of: cytoplasmic part
definition: Complex of three heterogeneous polypeptide chains, that form a ternary complex with initiator methionyl-tRNA and GTP. This ternary complex binds to free 40S subunit, which subsequently binds the 5' end of mRNA.
id: GO:0005850
has db xref: Wikipedia:EIF-2
has OBO namespace: cellular_component
has exact synonym: eIF-2
has exact synonym: eIF2
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

kinesin complex
type: Class
subclass of: microtubule associated complex
definition: Any complex that includes a dimer of molecules from the kinesin superfamily, a group of related proteins that contain an extended region of predicted alpha-helical coiled coil in the main chain that likely produces dimerization. The native complexes of several kinesin family members have also been shown to contain additional peptides, often designated light chains as all of the noncatalytic subunits that are currently known are smaller than the chain that contains the motor unit. Kinesin complexes generally possess a force-generating enzymatic activity, or motor, which converts the free energy of the gamma phosphate bond of ATP into mechanical work.
id: GO:0005871
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

minus-end kinesin complex
type: Class
subclass of: kinesin complex
definition: Any complex that includes a dimer of molecules from the kinesin superfamily and any associated proteins, and moves towards the minus end of a microtubule.
id: GO:0005872
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

plus-end kinesin complex
type: Class
subclass of: kinesin complex
definition: Any complex that includes a dimer of molecules from the kinesin superfamily and any associated proteins, and moves towards the plus end of a microtubule.
id: GO:0005873
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

microtubule associated complex
type: Class
subclass of: protein complex
subclass of: cytoskeletal part
definition: Any multimeric complex connected to a microtubule.
id: GO:0005875
has OBO namespace: cellular_component
imported from: go.owl

plasma membrane
type: Class
subclass of: membrane
subclass of: cell part
id: GO:0005886
has alternative id: GO:0005904
has db xref: NIF_Subcellular:sao1663586795
definition: The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
has db xref: Wikipedia:Cell_membrane
has narrow synonym: bacterial inner membrane
has exact synonym: cell membrane
has exact synonym: cellular membrane
has OBO namespace: cellular_component
has exact synonym: cytoplasmic membrane
term from ontology: go.owl
has narrow synonym: inner endospore membrane
has broad synonym: juxtamembrane
has narrow synonym: plasma membrane lipid bilayer
has exact synonym: plasmalemma
term from ontology: pro.owl
imported from: go.owl
in subset: goslim aspergillus
in_subset: goslim aspergillus
in subset: goslim candida
in_subset: goslim candida
in subset: goslim chembl
in_subset: goslim chembl
in subset: goslim generic
in_subset: goslim generic
in_subset: goslim metagenomics
in subset: goslim metagenomics
in_subset: goslim mouse
in subset: goslim mouse
in_subset: goslim plant
in subset: goslim plant
in_subset: goslim yeast
in subset: goslim yeast
in_subset: gosubset prok
in subset: gosubset prok

acetylcholine-gated channel complex
type: Class
subclass of: ion channel complex
subclass of: plasma membrane receptor complex
definition: A homo- or hetero-pentameric protein complex that forms a transmembrane channel through which ions may pass in response to acetylcholine binding.
id: GO:0005892
has OBO namespace: cellular_component
term from ontology: go.owl
has broad synonym: nicotinic acetylcholine receptor
has exact synonym: nicotinic acetylcholine-gated receptor-channel complex
term from ontology: pro.owl
imported from: go.owl

connexin complex
type: Class
subclass of: plasma membrane protein complex
definition: An assembly of six molecules of connexin, made in the Golgi apparatus and subsequently transported to the plasma membrane, where docking of two connexons on apposed plasma membranes across the extracellular space forms a gap junction.
id: GO:0005922
has db xref: NIF_Subcellular:sao445019788
has OBO namespace: cellular_component
has exact synonym: connexon
has related synonym: connexon complex
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

phosphatidylinositol 3-kinase complex
type: Class
subclass of: membrane part
subclass of: transferase complex, transferring phosphorus-containing groups
has exact synonym: 1-phosphatidylinositol 3-kinase complex
definition: A protein complex capable of phosphatidylinositol 3-kinase activity and containing subunits of any phosphatidylinositol 3-kinase (PI3K) enzyme. These complexes are divided in three classes (called I, II and III) that differ for their presence across taxonomic groups and for the type of their constituents. Catalytic subunits of phosphatidylinositol 3-kinase enzymes are present in all 3 classes; regulatory subunits of phosphatidylinositol 3-kinase enzymes are present in classes I and III; adaptor proteins have been observed in class II complexes and may be present in other classes too.
comment: For discussion of membrane association, please see https://sourceforge.net/p/geneontology/ontology-requests/11559/
id: GO:0005942
has narrow synonym: PI3-kinase p85-subunit alpha- PI3-kinase p110 complex
has exact synonym: PI3K complex
has narrow synonym: PIK3C3-PIK3R4 complex
has narrow synonym: PIK3CA-PIK3R1 complex
has OBO namespace: cellular_component
term from ontology: go.owl
has exact synonym: phosphoinositide 3-kinase complex
term from ontology: pro.owl
imported from: go.owl
in subset: goslim pir
in_subset: goslim pir

6-phosphofructokinase complex
type: Class
subclass of: cytosolic part
subclass of: transferase complex, transferring phosphorus-containing groups
definition: A protein complex that possesses 6-phosphofructokinase activity; homodimeric, homooctameric, and allosteric homotetrameric forms are known.
id: GO:0005945
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl
in subset: gosubset prok
in_subset: gosubset prok

CAAX-protein geranylgeranyltransferase complex
type: Class
subclass of: intracellular part
subclass of: transferase complex
definition: A heterodimeric enzyme, composed of an alpha and a beta subunit. Participates in the post-translational C-terminal modification of several small GTPases, allowing their targeting to the membrane.
id: GO:0005953
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

protein kinase CK2 complex
type: Class
subclass of: protein complex
subclass of: intracellular part
definition: A protein complex that possesses protein serine/threonine kinase activity, and contains two catalytic alpha subunits and two regulatory beta subunits. Protein kinase CK2 complexes are found in nearly every subcellular compartment, and can phosphorylate many protein substrates in addition to casein.
id: GO:0005956
comment: Note that this term represents a location and not a function; the activity possessed by this complex is mentioned in the definition for the purpose of describing and distinguishing the complex.
has exact synonym: casein kinase II complex
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

mitochondrial isocitrate dehydrogenase complex (NAD+)
type: Class
subclass of: mitochondrial tricarboxylic acid cycle enzyme complex
subclass of: isocitrate dehydrogenase complex (NAD+)
id: GO:0005962
definition: Mitochondrial complex that possesses isocitrate dehydrogenase (NAD+) activity.
comment: Note that this term represents a location and not a function; the activity possessed by this complex is mentioned in the definition for the purpose of describing and distinguishing the complex. The function of this complex is represented by the molecular function term 'isocitrate dehydrogenase (NAD+) activity ; GO:0004449'.
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

phosphorylase kinase complex
type: Class
subclass of: cytoplasmic part
subclass of: serine/threonine protein kinase complex
definition: An enzyme complex that catalyzes the phosphorylation of phosphorylase b to form phosphorylase a.
id: GO:0005964
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

protein farnesyltransferase complex
type: Class
subclass of: cytoplasmic part
subclass of: transferase complex
definition: A protein complex that possesses protein farnesyltransferase activity.
id: GO:0005965
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

ribonucleoside-diphosphate reductase complex
type: Class
subclass of: cytosolic part
subclass of: oxidoreductase complex
definition: An enzyme complex composed of 2-4 or more subunits, which usually contains nonheme iron and requires ATP for catalysis. Catalyzes the formation of 2'-deoxyribonucleoside diphosphate from ribonucleoside diphosphate, using either thioredoxin disulfide or glutaredoxin disulfide as an acceptor.
id: GO:0005971
has exact synonym: RNR complex
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
has exact synonym: ribonucleotide reductase complex
imported from: go.owl
in_subset: gosubset prok
in subset: gosubset prok

carbohydrate metabolic process
type: Class
subclass of: primary metabolic process
subclass of: organic substance metabolic process
id: GO:0005975
has db xref: Reactome:REACT_102834
has db xref: Reactome:REACT_103806
has db xref: Reactome:REACT_104502
has db xref: Reactome:REACT_105321
has db xref: Reactome:REACT_106046
has db xref: Reactome:REACT_107409
has db xref: Reactome:REACT_115733
has db xref: Reactome:REACT_28218
has db xref: Reactome:REACT_32291
has db xref: Reactome:REACT_33141
has db xref: Reactome:REACT_33953
has db xref: Reactome:REACT_34800
has db xref: Reactome:REACT_474
has db xref: Reactome:REACT_77669
has db xref: Reactome:REACT_81945
has db xref: Reactome:REACT_83038
has db xref: Reactome:REACT_83329
has db xref: Reactome:REACT_88330
has db xref: Reactome:REACT_88558
has db xref: Reactome:REACT_90099
has db xref: Reactome:REACT_96375
has db xref: Reactome:REACT_98394
definition: The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
has db xref: Wikipedia:Carbohydrate_metabolism
has OBO namespace: biological_process
has exact synonym: carbohydrate metabolism
imported from: go.owl
in subset: goslim aspergillus
in subset: goslim candida
in subset: goslim chembl
in subset: goslim generic
in subset: goslim metagenomics
in subset: goslim pir
in subset: goslim plant
in subset: goslim pombe
in subset: goslim yeast
in subset: gosubset prok

monosaccharide metabolic process
type: Class
subclass of: small molecule metabolic process
subclass of: single-organism carbohydrate metabolic process
id: GO:0005996
definition: The chemical reactions and pathways involving monosaccharides, the simplest carbohydrates. They are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
has OBO namespace: biological_process
has exact synonym: monosaccharide metabolism
imported from: go.owl
in subset: gosubset prok

glucose metabolic process
type: Class
subclass of: hexose metabolic process
id: GO:0006006
has db xref: Reactome:REACT_101127
has db xref: Reactome:REACT_101310
has db xref: Reactome:REACT_102479
has db xref: Reactome:REACT_102806
has db xref: Reactome:REACT_104683
has db xref: Reactome:REACT_105053
has db xref: Reactome:REACT_106618
has db xref: Reactome:REACT_29390
has db xref: Reactome:REACT_30713
has db xref: Reactome:REACT_30754
has db xref: Reactome:REACT_32548
has db xref: Reactome:REACT_723
has db xref: Reactome:REACT_80637
has db xref: Reactome:REACT_81545
has db xref: Reactome:REACT_85067
has db xref: Reactome:REACT_85844
has db xref: Reactome:REACT_94241
has db xref: Reactome:REACT_97466
has db xref: Reactome:REACT_98401
has db xref: Reactome:REACT_98764
has db xref: Reactome:REACT_99558
definition: The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
has OBO namespace: biological_process
has exact synonym: cellular glucose metabolic process
has exact synonym: glucose metabolism
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl
in_subset: gosubset prok
in subset: gosubset prok

nucleobase-containing compound metabolic process
type: Class
subclass of: cellular aromatic compound metabolic process
subclass of: cellular nitrogen compound metabolic process
subclass of: primary metabolic process
subclass of: heterocycle metabolic process
subclass of: organic cyclic compound metabolic process
definition: Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
id: GO:0006139
has alternative id: GO:0055134
has OBO namespace: biological_process
has exact synonym: cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
has exact synonym: cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism
has related synonym: nucleobase, nucleoside and nucleotide metabolic process
has related synonym: nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
has exact synonym: nucleobase, nucleoside, nucleotide and nucleic acid metabolism
imported from: go.owl
in subset: goslim pir
in subset: goslim plant
in subset: gosubset prok

DNA metabolic process
type: Class
subclass of: cellular macromolecule metabolic process
subclass of: nucleic acid metabolic process
definition: Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
has exact synonym: DNA metabolism
id: GO:0006259
has alternative id: GO:0055132
has OBO namespace: biological_process
has exact synonym: cellular DNA metabolism
imported from: go.owl
in subset: goslim agr
in subset: goslim aspergillus
in subset: goslim candida
in subset: goslim chembl
in subset: goslim generic
in subset: goslim metagenomics
in subset: goslim pir
in subset: goslim plant
in subset: gosubset prok

DNA replication
type: Class
subclass of: DNA metabolic process
subclass of: cellular macromolecule biosynthetic process
comment: DNA biosynthesis is only part of this process. See also the biological process terms 'DNA-dependent DNA replication ; GO:0006261' and 'RNA-dependent DNA replication ; GO:0006278'.
id: GO:0006260
has alternative id: GO:0055133
has db xref: Reactome:REACT_100559
has db xref: Reactome:REACT_101280
has db xref: Reactome:REACT_101497
has db xref: Reactome:REACT_102679
has db xref: Reactome:REACT_103614
has db xref: Reactome:REACT_104547
has db xref: Reactome:REACT_105292
has db xref: Reactome:REACT_105467
has db xref: Reactome:REACT_105835
has db xref: Reactome:REACT_106018
has db xref: Reactome:REACT_106104
has db xref: Reactome:REACT_106382
has db xref: Reactome:REACT_106434
has db xref: Reactome:REACT_106732
has db xref: Reactome:REACT_107075
has db xref: Reactome:REACT_107423
has db xref: Reactome:REACT_108461
has db xref: Reactome:REACT_108634
has db xref: Reactome:REACT_108739
has db xref: Reactome:REACT_108768
has db xref: Reactome:REACT_108929
has db xref: Reactome:REACT_109137
has db xref: Reactome:REACT_112472
has db xref: Reactome:REACT_113703
has db xref: Reactome:REACT_29423
has db xref: Reactome:REACT_29444
has db xref: Reactome:REACT_29691
has db xref: Reactome:REACT_29764
has db xref: Reactome:REACT_30149
has db xref: Reactome:REACT_31024
has db xref: Reactome:REACT_31919
has db xref: Reactome:REACT_32546
has db xref: Reactome:REACT_32932
has db xref: Reactome:REACT_33572
has db xref: Reactome:REACT_33874
has db xref: Reactome:REACT_50018
has db xref: Reactome:REACT_53588
has db xref: Reactome:REACT_6729
has db xref: Reactome:REACT_6738
has db xref: Reactome:REACT_6750
has db xref: Reactome:REACT_6769
has db xref: Reactome:REACT_6798
has db xref: Reactome:REACT_6869
has db xref: Reactome:REACT_6936
has db xref: Reactome:REACT_6939
has db xref: Reactome:REACT_77532
has db xref: Reactome:REACT_79188
has db xref: Reactome:REACT_79450
has db xref: Reactome:REACT_80432
has db xref: Reactome:REACT_80571
has db xref: Reactome:REACT_80896
has db xref: Reactome:REACT_80988
has db xref: Reactome:REACT_81803
has db xref: Reactome:REACT_83095
has db xref: Reactome:REACT_84829
has db xref: Reactome:REACT_85561
has db xref: Reactome:REACT_86410
has db xref: Reactome:REACT_86739
has db xref: Reactome:REACT_87233
has db xref: Reactome:REACT_87449
has db xref: Reactome:REACT_87590
has db xref: Reactome:REACT_88085
has db xref: Reactome:REACT_88384
has db xref: Reactome:REACT_88529
has db xref: Reactome:REACT_89355
has db xref: Reactome:REACT_89439
has db xref: Reactome:REACT_89725
has db xref: Reactome:REACT_90512
has db xref: Reactome:REACT_90809
has db xref: Reactome:REACT_90838
has db xref: Reactome:REACT_91184
has db xref: Reactome:REACT_91302
has db xref: Reactome:REACT_92527

DNA modification
type: Class
subclass of: DNA metabolic process
subclass of: macromolecule modification
id: GO:0006304
definition: The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties.
has OBO namespace: biological_process
imported from: go.owl
in subset: goslim pir
in subset: gosubset prok

DNA alkylation
type: Class
subclass of: DNA modification
id: GO:0006305
definition: The addition of alkyl groups to many positions on all four bases of DNA. Alkylating agents can also modify the bases of incoming nucleotides in the course of DNA synthesis.
has OBO namespace: biological_process
imported from: go.owl
in subset: gosubset prok

DNA methylation
type: Class
subclass of: DNA alkylation
subclass of: macromolecule methylation
subclass of: DNA methylation or demethylation
id: GO:0006306
definition: The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
has db xref: Wikipedia:DNA_methylation
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl
in subset: gosubset prok
in_subset: gosubset prok

chromatin organization
type: Class
subclass of: cellular component organization
definition: Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.
id: GO:0006325
has alternative id: GO:0016568
has OBO namespace: biological_process
has related synonym: chromatin modification
has exact synonym: chromatin organisation
has exact synonym: establishment or maintenance of chromatin architecture
imported from: go.owl
in subset: goslim pombe
in subset: goslim yeast

chromatin remodeling
type: Class
subclass of: chromatin organization
definition: Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
id: GO:0006338
has OBO namespace: biological_process
has exact synonym: chromatin modeling
has exact synonym: chromatin modelling
has exact synonym: chromatin remodelling
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

protein complex assembly
type: Class
subclass of: macromolecular complex assembly
subclass of: protein complex subunit organization
id: GO:0006461
definition: The aggregation, arrangement and bonding together of a set of components to form a protein complex.
has OBO namespace: biological_process
has related synonym: chaperone activity
has exact synonym: protein complex formation
imported from: go.owl
in subset: goslim chembl
in subset: goslim generic
in subset: goslim pombe
in subset: gosubset prok

cellular protein modification process
type: Class
subclass of: protein modification process
subclass of: cellular protein metabolic process
id: GO:0006464
definition: The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
has OBO namespace: biological_process
has related synonym: process resulting in protein modification
has broad synonym: protein modification process
has related synonym: protein tagging activity
imported from: go.owl
in subset: goslim aspergillus
in subset: goslim candida
in subset: goslim chembl
in subset: goslim generic
in subset: goslim pir
in subset: goslim plant
in subset: gosubset prok

cellular aromatic compound metabolic process
type: Class
subclass of: cellular metabolic process
id: GO:0006725
definition: The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
has exact synonym: aromatic compound metabolism
has narrow synonym: aromatic hydrocarbon metabolic process
has narrow synonym: aromatic hydrocarbon metabolism
has OBO namespace: biological_process
imported from: go.owl
in subset: goslim pir
in subset: gosubset prok

nitrogen compound metabolic process
type: Class
subclass of: metabolic process
id: GO:0006807
comment: Note that amino acid and derivative metabolism should not be annotated here. Instead use the 'amino acid and derivative metabolism' node.
definition: The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen, including (but not limited to) nitrogen fixation, nitrification, denitrification, assimilatory/dissimilatory nitrate reduction and the interconversion of nitrogenous organic matter and ammonium.
has OBO namespace: biological_process
has exact synonym: nitrogen compound metabolism
imported from: go.owl
in subset: goslim metagenomics
in subset: goslim pir
in subset: gosubset prok

transport
type: Class
subclass of: establishment of localization
id: GO:0006810
has alternative id: GO:0015457
has alternative id: GO:0015460
definition: The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
has related synonym: auxiliary transport protein activity
has OBO namespace: biological_process
has narrow synonym: small molecule transport
has narrow synonym: solute:solute exchange
has related synonym: transport accessory protein activity
imported from: go.owl
in subset: goslim aspergillus
in subset: goslim candida
in subset: goslim chembl
in subset: goslim generic
in subset: goslim metagenomics
in subset: goslim pir
in subset: goslim plant
in subset: gosubset prok

ion transport
type: Class
subclass of: transport
id: GO:0006811
has db xref: Reactome:REACT_102356
has db xref: Reactome:REACT_102895
has db xref: Reactome:REACT_106972
has db xref: Reactome:REACT_109067
has db xref: Reactome:REACT_110862
has db xref: Reactome:REACT_19397
has db xref: Reactome:REACT_29110
has db xref: Reactome:REACT_31978
has db xref: Reactome:REACT_33992
has db xref: Reactome:REACT_34201
has db xref: Reactome:REACT_79109
has db xref: Reactome:REACT_82618
has db xref: Reactome:REACT_87822
has db xref: Reactome:REACT_91472
has db xref: Reactome:REACT_91958
has db xref: Reactome:REACT_92903
has db xref: Reactome:REACT_93485
has db xref: Reactome:REACT_94357
has db xref: Reactome:REACT_96078
has db xref: Reactome:REACT_96919
has db xref: Reactome:REACT_98077
definition: The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
has OBO namespace: biological_process
imported from: go.owl
in subset: goslim pir
in subset: goslim yeast
in subset: gosubset prok

cation transport
type: Class
subclass of: ion transport
id: GO:0006812
has alternative id: GO:0006819
has alternative id: GO:0015674
definition: The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
has OBO namespace: biological_process
has narrow synonym: di-, tri-valent inorganic cation transport
imported from: go.owl
in subset: gosubset prok

exocytosis
type: Class
subclass of: vesicle-mediated transport
subclass of: secretion by cell
definition: A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
id: GO:0006887
has alternative id: GO:0016194
has alternative id: GO:0016195
has db xref: Wikipedia:Exocytosis
has OBO namespace: biological_process
has related synonym: nonselective vesicle exocytosis
has exact synonym: vesicle exocytosis
imported from: go.owl
in subset: goslim yeast
in subset: gosubset prok

endocytosis
type: Class
subclass of: vesicle-mediated transport
definition: A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
id: GO:0006897
has alternative id: GO:0016193
has alternative id: GO:0016196
has db xref: Wikipedia:Endocytosis
has OBO namespace: biological_process
has related synonym: nonselective vesicle endocytosis
has exact synonym: plasma membrane invagination
has exact synonym: vesicle endocytosis
imported from: go.owl
in subset: goslim yeast
in subset: gosubset prok

phagocytosis
type: Class
subclass of: endocytosis
subclass of: single-organism transport
definition: An endocytosis process that results in the engulfment of external particulate material by phagocytes. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles.
id: GO:0006909
has db xref: Wikipedia:Phagocytosis
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

movement of cell or subcellular component
type: Class
subclass of: single-organism cellular process
id: GO:0006928
comment: Note that in GO cellular components include whole cells (cell is_a cellular component).
definition: The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
has OBO namespace: biological_process
has related synonym: cell movement
has exact synonym: cellular component motion
has exact synonym: cellular component movement
imported from: go.owl
in subset: goantislim grouping
in subset: gocheck do not annotate
in subset: goslim pir
in subset: gosubset prok

response to stress
type: Class
subclass of: response to stimulus
definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
id: GO:0006950
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: biological_process
has related synonym: response to abiotic stress
has related synonym: response to biotic stress
imported from: go.owl
in subset: gocheck do not manually annotate
in subset: goslim aspergillus
in subset: goslim candida
in subset: goslim chembl
in subset: goslim generic
in subset: goslim metagenomics
in subset: goslim plant
in subset: gosubset prok

defense response
type: Class
subclass of: response to stress
has alternative id: GO:0002217
id: GO:0006952
has alternative id: GO:0042829
definition: Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
has related synonym: antimicrobial peptide activity
has OBO namespace: biological_process
has exact synonym: defence response
has related synonym: defense/immunity protein activity
has exact synonym: physiological defense response
imported from: go.owl
in subset: gosubset prok

inflammatory response
type: Class
subclass of: defense response
id: GO:0006954
has broad synonym: Inflammation
definition: The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
comment: This term was improved by GO_REF:0000022. It was moved.
has db xref: Wikipedia:Inflammation
has OBO namespace: biological_process
imported from: go.owl

immune response
type: Class
subclass of: immune system process
subclass of: response to stimulus
definition: Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
id: GO:0006955
comment: This term was improved by GO_REF:0000022. It was redefined and moved.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

cellular response to DNA damage stimulus
type: Class
subclass of: cellular response to stress
definition: Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
has exact synonym: DNA damage response
id: GO:0006974
has alternative id: GO:0034984
has OBO namespace: biological_process
has exact synonym: cellular DNA damage response
term from ontology: go.owl
term from ontology: obi.owl
has broad synonym: response to DNA damage stimulus
has exact synonym: response to genotoxic stress
imported from: go.owl
in_subset: goslim yeast
in subset: goslim yeast
in_subset: gosubset prok
in subset: gosubset prok

organelle organization
type: Class
subclass of: cellular component organization
definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
id: GO:0006996
has OBO namespace: biological_process
has exact synonym: organelle organisation
has related synonym: organelle organization and biogenesis
imported from: go.owl
in subset: goslim aspergillus
in subset: goslim candida
in subset: goslim pir
in subset: gosubset prok

actin filament organization
type: Class
subclass of: supramolecular fiber organization
definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking.
id: GO:0007015
has exact synonym: actin filament organisation
has OBO namespace: biological_process
has narrow synonym: regulation of actin filament localization
imported from: go.owl

cell cycle
type: Class
subclass of: single-organism cellular process
id: GO:0007049
definition: The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
has db xref: Wikipedia:Cell_cycle
has OBO namespace: biological_process
has exact synonym: cell-division cycle
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl
in subset: gocheck do not manually annotate
in_subset: gocheck do not manually annotate
in subset: goslim aspergillus
in_subset: goslim aspergillus
in subset: goslim candida
in_subset: goslim candida
in subset: goslim chembl
in_subset: goslim chembl
in_subset: goslim generic
in subset: goslim generic
in subset: goslim pir
in_subset: goslim pir
in subset: goslim plant
in_subset: goslim plant
in_subset: gosubset prok
in subset: gosubset prok

blood coagulation
type: Class
subclass of: hemostasis
subclass of: coagulation
id: GO:0007596
has db xref: Reactome:REACT_101311
has db xref: Reactome:REACT_101372
has db xref: Reactome:REACT_102544
has db xref: Reactome:REACT_102650
has db xref: Reactome:REACT_105166
has db xref: Reactome:REACT_105212
has db xref: Reactome:REACT_107268
has db xref: Reactome:REACT_108583
has db xref: Reactome:REACT_113650
has db xref: Reactome:REACT_114152
has db xref: Reactome:REACT_118351
has db xref: Reactome:REACT_1439
has db xref: Reactome:REACT_2051
has db xref: Reactome:REACT_32530
has db xref: Reactome:REACT_32765
has db xref: Reactome:REACT_33270
has db xref: Reactome:REACT_34525
has db xref: Reactome:REACT_604
has db xref: Reactome:REACT_76944
has db xref: Reactome:REACT_78290
has db xref: Reactome:REACT_81054
has db xref: Reactome:REACT_81972
has db xref: Reactome:REACT_82283
has db xref: Reactome:REACT_82383
has db xref: Reactome:REACT_82403
has db xref: Reactome:REACT_82445
has db xref: Reactome:REACT_82812
has db xref: Reactome:REACT_82940
has db xref: Reactome:REACT_83271
has db xref: Reactome:REACT_84055
has db xref: Reactome:REACT_84833
has db xref: Reactome:REACT_85674
has db xref: Reactome:REACT_86354
has db xref: Reactome:REACT_89750
has db xref: Reactome:REACT_89805
has db xref: Reactome:REACT_90236
has db xref: Reactome:REACT_90805
has db xref: Reactome:REACT_92318
has db xref: Reactome:REACT_94085
has db xref: Reactome:REACT_94213
has db xref: Reactome:REACT_94315
has db xref: Reactome:REACT_94798
has db xref: Reactome:REACT_96458
definition: The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
has db xref: Wikipedia:Coagulation
has OBO namespace: biological_process
has exact synonym: blood clotting
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

hemostasis
type: Class
subclass of: regulation of body fluid levels
id: GO:0007599
definition: The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
has db xref: Wikipedia:Hemostasis
has OBO namespace: biological_process
imported from: go.owl

transcription elongation factor complex
type: Class
subclass of: protein complex
subclass of: nucleoplasm part
definition: Any protein complex that interacts with RNA polymerase II to increase (positive transcription elongation factor) or reduce (negative transcription elongation factor) the rate of transcription elongation.
id: GO:0008023
has OBO namespace: cellular_component
imported from: go.owl
in subset: goslim pir

cyclin/CDK positive transcription elongation factor complex
type: Class
subclass of: transcription elongation factor complex
subclass of: nuclear cyclin-dependent protein kinase holoenzyme complex
subclass of: carboxy-terminal domain protein kinase complex
definition: A transcription elongation factor complex that facilitates the transition from abortive to productive elongation by phosphorylating the CTD domain of the large subunit of DNA-directed RNA polymerase II, holoenzyme. Contains a cyclin and a cyclin-dependent protein kinase catalytic subunit.
id: GO:0008024
comment: See also the cellular component terms 'cyclin-dependent protein kinase activating kinase holoenzyme complex ; GO:0019907' and 'DNA-directed RNA polymerase II, holoenzyme ; GO:0016591'.
has OBO namespace: cellular_component
term from ontology: go.owl
has related synonym: positive transcription elongation factor complex b
term from ontology: pro.owl
imported from: go.owl

biological_process
type: Class
subclass of: process
definition: Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
has alternative id: GO:0000004
has alternative id: GO:0007582
id: GO:0008150
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
has db xref: Wikipedia:Biological_process
has exact synonym: biological process
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
has exact synonym: physiological process
imported from: go.owl
in subset: goslim aspergillus
in_subset: goslim aspergillus
in subset: goslim candida
in_subset: goslim candida
in subset: goslim chembl
in_subset: goslim chembl
in_subset: goslim generic
in subset: goslim generic
in_subset: goslim metagenomics
in subset: goslim metagenomics
in subset: goslim pir
in_subset: goslim pir
in subset: goslim plant
in_subset: goslim plant
in_subset: goslim pombe
in subset: goslim pombe
in subset: goslim yeast
in_subset: goslim yeast
in_subset: gosubset prok
in subset: gosubset prok

metabolic process
type: Class
subclass of: biological_process
id: GO:0008152
comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
definition: The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
has db xref: Wikipedia:Metabolism
has OBO namespace: biological_process
has narrow synonym: metabolic process resulting in cell growth
has exact synonym: metabolism
has narrow synonym: metabolism resulting in cell growth
imported from: go.owl
in subset: gocheck do not manually annotate
in subset: goslim chembl
in subset: goslim metagenomics
in subset: goslim pir
in subset: goslim plant
in subset: gosubset prok

actin polymerization or depolymerization
type: Class
subclass of: actin filament organization
definition: Assembly or disassembly of actin filaments by the addition or removal of actin monomers from a filament.
id: GO:0008154
has OBO namespace: biological_process
imported from: go.owl

opsonization
type: Class
subclass of: immune effector process
id: GO:0008228
definition: The process in which a microorganism (or other particulate material) is rendered more susceptible to phagocytosis by coating with an opsonin, a blood serum protein such as a complement component or antibody.
has db xref: Wikipedia:Opsonin
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

cohesin complex
type: Class
subclass of: protein complex
subclass of: chromosomal part
has narrow synonym: 14S cohesin
has narrow synonym: 9S cohesin
definition: A protein complex that is required for sister chromatid cohesion in eukaryotes. The cohesin complex forms a molecular ring complex, and is composed of structural maintenance of chromosomes (SMC) and kleisin proteins. For example, in yeast, the complex is composed of the SMC proteins Smc1p and Smc3p, and the kleisin protein Scc1p. In vertebrates, the complex is composed of the SMC1 (SMC1A or SMC1B) and SMC3 heterodimer attached via their hinge domains to a kleisin (RAD21, REC8 or RAD21L) which links them, and one STAG protein (STAG1, STAG2 or STAG3).
id: GO:0008278
has alternative id: GO:0008279
has alternative id: GO:0008280
has alternative id: GO:0043222
has related synonym: SMC complex
has exact synonym: SMC/kleisin ring complex
has narrow synonym: Smc1-Smc3 complex
has OBO namespace: cellular_component
has related synonym: cohesin core heterodimer
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl
in_subset: goslim pir
in subset: goslim pir

cell proliferation
type: Class
subclass of: single-organism process
id: GO:0008283
definition: The multiplication or reproduction of cells, resulting in the expansion of a cell population.
comment: This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. Also note that this term is intended to be used for the proliferation of cells within a multicellular organism, not for the expansion of a population of single-celled organisms.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl
in_subset: goslim agr
in subset: goslim agr
in subset: goslim chembl
in_subset: goslim chembl
in subset: goslim generic
in_subset: goslim generic
in subset: goslim mouse
in_subset: goslim mouse
in subset: goslim pir
in_subset: goslim pir
in_subset: gosubset prok
in subset: gosubset prok

F-actin capping protein complex
type: Class
subclass of: protein complex
subclass of: cytoskeletal part
definition: A heterodimer consisting of alpha and beta subunits that binds to and caps the barbed ends of actin filaments, thereby regulating the polymerization of actin monomers but not severing actin filaments.
id: GO:0008290
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl
in_subset: goslim pir
in subset: goslim pir

caspase complex
type: Class
subclass of: cytosolic part
subclass of: endopeptidase complex
definition: A protein complex that is located in the cytosol and contains one or more cysteine-type endopeptidases (also called caspases), which give the complex a peptidase activity with specificity for the hydrolysis of aspartyl bonds. These complexes may be involved e.g. in apoptotic or inflammation processes.
id: GO:0008303
comment: Note that this term was reinstated from obsolete.
has OBO namespace: cellular_component
has exact synonym: cysteine-type endopeptidase complex
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

integrin complex
type: Class
subclass of: protein complex involved in cell adhesion
subclass of: plasma membrane protein complex
subclass of: plasma membrane receptor complex
definition: A protein complex that is composed of one alpha subunit and one beta subunit, both of which are members of the integrin superfamily of cell adhesion receptors; the complex spans the plasma membrane and binds to extracellular matrix ligands, cell-surface ligands, and soluble ligands.
id: GO:0008305
has OBO namespace: cellular_component
term from ontology: go.owl
has related synonym: laminin receptor protein
term from ontology: pro.owl
imported from: go.owl
in_subset: gosubset prok
in subset: gosubset prok

IkappaB kinase complex
type: Class
subclass of: cytosolic part
subclass of: serine/threonine protein kinase complex
definition: A trimeric protein complex that phosphorylates inhibitory-kappaB (I-kappaB) proteins. The complex is composed of two kinase subunits (alpha and beta) and a regulatory gamma subunit (also called NEMO). In a resting state, NF-kappaB dimers are bound to inhibitory IKB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription.
id: GO:0008385
has exact synonym: IKK complex
has OBO namespace: cellular_component
term from ontology: go.owl
has exact synonym: heterotrimeric IKK complex
term from ontology: pro.owl
has exact synonym: trimeric IKK complex
imported from: go.owl

biosynthetic process
type: Class
subclass of: metabolic process
id: GO:0009058
definition: The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
has db xref: Wikipedia:Anabolism
has exact synonym: anabolism
has OBO namespace: biological_process
has exact synonym: biosynthesis
has exact synonym: formation
has exact synonym: synthesis
imported from: go.owl
in subset: goslim chembl
in subset: goslim generic
in subset: goslim metagenomics
in subset: goslim plant
in subset: gosubset prok

macromolecule biosynthetic process
type: Class
subclass of: macromolecule metabolic process
subclass of: organic substance biosynthetic process
id: GO:0009059
has alternative id: GO:0043284
definition: The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
has OBO namespace: biological_process
has exact synonym: biopolymer biosynthetic process
has exact synonym: macromolecule anabolism
has exact synonym: macromolecule biosynthesis
has exact synonym: macromolecule formation
has exact synonym: macromolecule synthesis
imported from: go.owl
in subset: gosubset prok

ornithine carbamoyltransferase complex
type: Class
subclass of: cytoplasmic part
subclass of: transferase complex
definition: A homotrimeric protein complex that catalyzes the transfer of a carbamoyl group to ornithine, forming citrulline.
id: GO:0009348
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl
in_subset: gosubset prok
in subset: gosubset prok

riboflavin synthase complex
type: Class
subclass of: cell part
subclass of: transferase complex
definition: An flavoprotein that catalyzes the reaction the breakdown of dimethyl(ribityl)lumazine to form riboflavin and ribitylamino-amino-dihydroxypyrimidine.
id: GO:0009349
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl
in subset: goslim metagenomics
in_subset: goslim metagenomics
in_subset: gosubset prok
in subset: gosubset prok

fertilization
type: Class
subclass of: single organism reproductive process
id: GO:0009566
definition: The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy).
has db xref: Wikipedia:Fertilisation
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
has exact synonym: syngamy
imported from: go.owl

hormone transport
type: Class
subclass of: regulation of hormone levels
subclass of: single-organism transport
id: GO:0009914
definition: The directed movement of hormones into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
has OBO namespace: biological_process
imported from: go.owl
in subset: goslim pir

cellular process
type: Class
subclass of: biological_process
definition: Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
has alternative id: GO:0008151
id: GO:0009987
has alternative id: GO:0050875
has OBO namespace: biological_process
has narrow synonym: cell growth and/or maintenance
has exact synonym: cell physiology
has exact synonym: cellular physiological process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl
in subset: goslim pir
in_subset: goslim pir
in_subset: goslim plant
in subset: goslim plant
in_subset: gosubset prok
in subset: gosubset prok

endosome membrane
type: Class
subclass of: endosomal part
subclass of: bounding membrane of organelle
subclass of: whole membrane
id: GO:0010008
has db xref: NIF_Subcellular:sao978443756
definition: The lipid bilayer surrounding an endosome.
has OBO namespace: cellular_component
has exact synonym: endosomal membrane
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

gene expression
type: Class
subclass of: macromolecule metabolic process
id: GO:0010467
has db xref: Reactome:REACT_100537
has db xref: Reactome:REACT_101147
has db xref: Reactome:REACT_101952
has db xref: Reactome:REACT_105649
has db xref: Reactome:REACT_108313
has db xref: Reactome:REACT_29068
has db xref: Reactome:REACT_34240
has db xref: Reactome:REACT_71
has db xref: Reactome:REACT_78136
has db xref: Reactome:REACT_78959
has db xref: Reactome:REACT_79662
has db xref: Reactome:REACT_85241
has db xref: Reactome:REACT_85359
has db xref: Reactome:REACT_86357
has db xref: Reactome:REACT_89816
has db xref: Reactome:REACT_91657
has db xref: Reactome:REACT_91965
has db xref: Reactome:REACT_93586
has db xref: Reactome:REACT_93968
has db xref: Reactome:REACT_94814
has db xref: Reactome:REACT_98256
definition: The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
has db xref: Wikipedia:Gene_expression
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl
in_subset: goslim agr
in subset: goslim agr
in_subset: gosubset prok
in subset: gosubset prok

regulation of gene expression
type: Class
subclass of: regulation of macromolecule metabolic process
definition: Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
id: GO:0010468
comment: This class covers any process that regulates the rate of production of a mature gene product, and so includes processes that regulate that rate by regulating the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that regulates the level, stability or availability of mRNA or circRNA for translation and thereby regulates the rate of production of the encoded protein via translation.
has db xref: Wikipedia:Regulation_of_gene_expression
has OBO namespace: biological_process
has related synonym: regulation of gene product expression
has narrow synonym: regulation of protein expression
imported from: go.owl
in subset: gosubset prok

vascular endothelial growth factor production
type: Class
subclass of: cytokine production
id: GO:0010573
definition: The appearance of vascular endothelial growth factor production due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has exact synonym: VEGF production
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

regulation of hormone levels
type: Class
subclass of: regulation of biological quality
definition: Any process that modulates the levels of hormone within an organism or a tissue. A hormone is any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action.
id: GO:0010817
has OBO namespace: biological_process
imported from: go.owl

ion transmembrane transporter activity
type: Class
subclass of: substrate-specific transmembrane transporter activity
definition: Enables the transfer of an ion from one side of a membrane to the other.
id: GO:0015075
has exact synonym: ion transporter activity
has OBO namespace: molecular_function
imported from: go.owl
in subset: gosubset prok

channel activity
type: Class
subclass of: passive transmembrane transporter activity
definition: Enables the energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules.
has alternative id: GO:0015249
id: GO:0015267
has alternative id: GO:0015268
has db xref: TC:1
has related synonym: alpha-type channel activity
has related synonym: channel-forming toxin activity
has exact synonym: channel/pore class transporter activity
has OBO namespace: molecular_function
has exact synonym: nonselective channel activity
has broad synonym: pore activity
has related synonym: pore class transporter activity
imported from: go.owl
in subset: gosubset prok

ammonium transport
type: Class
subclass of: cation transport
subclass of: nitrogen compound transport
id: GO:0015696
definition: The directed movement of ammonium into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Ammonium is the cation NH4+ which is formed from N2 by root-nodule bacteria in leguminous plants and is an excretory product in ammonotelic animals.
has related synonym: ammonia transport
has OBO namespace: biological_process
imported from: go.owl
in subset: gosubset prok

membrane
type: Class
subclass of: cellular_component
definition: A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
id: GO:0016020
has db xref: Wikipedia:Biological_membrane
has OBO namespace: cellular_component
imported from: go.owl
in subset: goslim agr
in subset: goslim aspergillus
in subset: goslim candida
in subset: goslim chembl
in subset: goslim metagenomics
in subset: goslim pir
in subset: goslim plant
in subset: goslim yeast
in subset: gosubset prok

cellular component organization
type: Class
subclass of: cellular process
subclass of: cellular component organization or biogenesis
definition: A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
id: GO:0016043
has alternative id: GO:0044235
has alternative id: GO:0071842
has OBO namespace: biological_process
has exact synonym: cell organisation
has related synonym: cell organization and biogenesis
has exact synonym: cellular component organisation at cellular level
has exact synonym: cellular component organisation in other organism
has exact synonym: cellular component organization at cellular level
has exact synonym: cellular component organization in other organism
imported from: go.owl
in subset: goslim mouse
in subset: goslim pir
in subset: goslim plant
in subset: gosubset prok

immunoglobulin mediated immune response
type: Class
subclass of: B cell mediated immunity
definition: An immune response mediated by immunoglobulins, whether cell-bound or in solution.
id: GO:0016064
comment: This term was improved by GO_REF:0000022. It was renamed and redefined.
has exact synonym: antibody-mediated immune response
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

vesicle-mediated transport
type: Class
subclass of: transport
definition: A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
has alternative id: GO:0006899
id: GO:0016192
has OBO namespace: biological_process
has narrow synonym: nonselective vesicle transport
has related synonym: protein sorting along secretory pathway
has related synonym: vesicle trafficking
has exact synonym: vesicle transport
has exact synonym: vesicular transport
imported from: go.owl
in subset: goslim aspergillus
in subset: goslim candida
in subset: goslim chembl
in subset: goslim generic
in subset: goslim pir
in subset: goslim pombe
in subset: gosubset prok

prefoldin complex
type: Class
subclass of: protein complex
definition: A multisubunit chaperone that is capable of delivering unfolded proteins to cytosolic chaperonin, which it acts as a cofactor for. In humans, the complex is a heterohexamer of two PFD-alpha and four PFD-beta type subunits. In Saccharomyces cerevisiae, it also acts in the nucleus to regulate the rate of elongation by RNA polymerase II via a direct effect on histone dynamics.
has narrow synonym: GIM complex
id: GO:0016272
has db xref: Wikipedia:Prefoldin
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl
in subset: gosubset prok
in_subset: gosubset prok

mitochondrial fatty acid beta-oxidation multienzyme complex
type: Class
subclass of: fatty acid beta-oxidation multienzyme complex
subclass of: mitochondrial part
definition: A complex that includes the long-chain 3-hydroxyacyl-CoA dehydrogenase and long-chain enoyl-CoA hydratase activities in two subunits (alpha and beta), catalyzing two steps of the fatty acid beta-oxidation cycle within the mitochondrial matrix.
id: GO:0016507
has OBO namespace: cellular_component
has broad synonym: fatty acid beta-oxidation multienzyme complex
term from ontology: go.owl
term from ontology: pro.owl
has related synonym: trifunctional enzyme
imported from: go.owl

cyclin-dependent protein kinase 5 holoenzyme complex
type: Class
subclass of: macromolecular complex
definition: A protein complex that activates cyclin-dependent kinase 5; composed of regulatory and catalytic subunits.
id: GO:0016533
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

covalent chromatin modification
type: Class
subclass of: chromatin organization
subclass of: macromolecule modification
id: GO:0016569
definition: The alteration of DNA or protein in chromatin by the covalent addition or removal of chemical groups.
has OBO namespace: biological_process
has exact synonym: chromatin modification
imported from: go.owl

histone modification
type: Class
subclass of: cellular protein modification process
subclass of: covalent chromatin modification
id: GO:0016570
definition: The covalent alteration of one or more amino acid residues within a histone protein.
has db xref: Wikipedia:Histone#Histone_modifications_in_chromatin_regulation
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl
in_subset: goslim yeast
in subset: goslim yeast

mediator complex
type: Class
subclass of: protein complex
subclass of: nucleoplasm part
definition: A protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The mediator complex is required for activation of transcription of most protein-coding genes, but can also act as a transcriptional corepressor. The Saccharomyces complex contains several identifiable subcomplexes: a head domain comprising Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p; and a regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins.
has related synonym: CDK8-containing TRAP/mediator complex
has alternative id: GO:0000119
id: GO:0016592
has exact synonym: L mediator complex
has exact synonym: Srb-mediator complex
has narrow synonym: TRAP complex
has db xref: Wikipedia:Mediator_(coactivator)
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

transferase activity
type: Class
subclass of: catalytic activity
definition: Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
has db xref: EC:2
id: GO:0016740
has db xref: Reactome:REACT_25050
has OBO namespace: molecular_function
imported from: go.owl
in subset: goslim aspergillus
in subset: goslim candida
in subset: goslim chembl
in subset: goslim metagenomics
in subset: goslim mouse
in subset: goslim pir
in subset: goslim plant
in subset: goslim yeast
in subset: gosubset prok

transferase activity, transferring phosphorus-containing groups
type: Class
subclass of: transferase activity
definition: Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
has db xref: EC:2.7
id: GO:0016772
comment: Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides.
has OBO namespace: molecular_function
imported from: go.owl
in subset: goslim chembl
in subset: gosubset prok

nucleotidyltransferase activity
type: Class
subclass of: transferase activity, transferring phosphorus-containing groups
definition: Catalysis of the transfer of a nucleotidyl group to a reactant.
has db xref: EC:2.7.7
id: GO:0016779
has OBO namespace: molecular_function
imported from: go.owl
in subset: goslim aspergillus
in subset: goslim candida
in subset: goslim chembl
in subset: goslim generic
in subset: goslim metagenomics
in subset: goslim yeast
in subset: gosubset prok

transcriptional repressor complex
type: Class
subclass of: macromolecular complex
definition: A protein complex that possesses activity that prevents or downregulates transcription.
id: GO:0017053
has OBO namespace: cellular_component
has exact synonym: transcription factor inhibitor complex
imported from: go.owl
in subset: goslim pir

serine C-palmitoyltransferase complex
type: Class
subclass of: endoplasmic reticulum palmitoyltransferase complex
definition: An enzyme complex that catalyzes the transfer of a palmitoyl on to serine, forming 3-dehydro-D-sphinganine.
id: GO:0017059
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

aminoacyl-tRNA synthetase multienzyme complex
type: Class
subclass of: protein complex
subclass of: intracellular part
definition: A multienzyme complex found in all multicellular eukaryotes composed of eight proteins with aminoacyl-tRNA synthetase activities (abbreviated as: ArgRS, AspRS, GluProRS, GlnRS, IleRS, LeuRS, LysRS, MetRS where RS is the enzyme, preceded by the amino acid it uses as a substrate) as well as three non-synthetase proteins (p43, p38, and p18) with diverse functions. Several of these subunits are known dimers, so the total polypeptide count in the multisynthetase complex is at least fifteen. All of the enzymes in this assembly catalyze the same reaction, the covalent attachment of an amino acid to either the 2'- or 3'-hydroxyl of the 3'-terminal adenosine of tRNA, but using different substrates.
id: GO:0017101
has exact synonym: aminoacyl-tRNA synthetase complex
has OBO namespace: cellular_component
term from ontology: go.owl
has exact synonym: multisynthetase complex
term from ontology: pro.owl
imported from: go.owl

glutamate-cysteine ligase complex
type: Class
subclass of: cytoplasmic part
subclass of: catalytic complex
definition: An enzyme complex that catalyzes the ligation of glutamate to cysteine, forming glutamylcysteine.
id: GO:0017109
has OBO namespace: cellular_component
has exact synonym: gamma-glutamylcysteine synthetase complex
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

SCF ubiquitin ligase complex
type: Class
subclass of: cullin-RING ubiquitin ligase complex
definition: A ubiquitin ligase complex in which a cullin from the Cul1 subfamily and a RING domain protein form the catalytic core; substrate specificity is conferred by a Skp1 adaptor and an F-box protein. SCF complexes are involved in targeting proteins for degradation by the proteasome. The best characterized complexes are those from yeast and mammals (with core subunits named Cdc53/Cul1, Rbx1/Hrt1/Roc1).
has exact synonym: CDL1 complex
has exact synonym: CRL1 complex
has exact synonym: Cul1-RING ubiquitin ligase complex
id: GO:0019005
has exact synonym: SCF complex
has narrow synonym: SCF complex substrate recognition subunit
has exact synonym: Skp1/Cul1/F-box protein complex
has db xref: Wikipedia:SCF_complex
has OBO namespace: cellular_component
has exact synonym: cullin-RING ligase 1
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

snRNA-activating protein complex
type: Class
subclass of: nuclear transcription factor complex
definition: A protein complex that recognizes the proximal sequence element of RNA polymerase II and III snRNA promoters.
id: GO:0019185
has exact synonym: SNAPc
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

regulation of nucleobase-containing compound metabolic process
type: Class
subclass of: regulation of cellular metabolic process
subclass of: regulation of nitrogen compound metabolic process
subclass of: regulation of primary metabolic process
definition: Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids.
id: GO:0019219
has OBO namespace: biological_process
has related synonym: regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
has exact synonym: regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism
imported from: go.owl
in subset: gosubset prok

regulation of metabolic process
type: Class
subclass of: regulation of biological process
definition: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
id: GO:0019222
has OBO namespace: biological_process
has exact synonym: regulation of metabolism
imported from: go.owl
in subset: goslim metagenomics
in subset: gosubset prok

hexose metabolic process
type: Class
subclass of: monosaccharide metabolic process
id: GO:0019318
definition: The chemical reactions and pathways involving a hexose, any monosaccharide with a chain of six carbon atoms in the molecule.
has OBO namespace: biological_process
has exact synonym: hexose metabolism
imported from: go.owl
in subset: gosubset prok

protein metabolic process
type: Class
subclass of: macromolecule metabolic process
subclass of: primary metabolic process
subclass of: organonitrogen compound metabolic process
has alternative id: GO:0006411
id: GO:0019538
definition: The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification.
has db xref: Wikipedia:Protein_metabolism
has OBO namespace: biological_process
has exact synonym: protein metabolic process and modification
has exact synonym: protein metabolism
has exact synonym: protein metabolism and modification
imported from: go.owl
in subset: goslim agr
in subset: goslim mouse
in subset: goslim pir
in subset: goslim plant
in subset: gosubset prok

B cell mediated immunity
type: Class
subclass of: lymphocyte mediated immunity
subclass of: adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
definition: Any process involved with the carrying out of an immune response by a B cell, through, for instance, the production of antibodies or cytokines, or antigen presentation to T cells.
has exact synonym: B lymphocyte mediated immune effector process
has exact synonym: B lymphocyte mediated immunity
has exact synonym: B-cell mediated immune effector process
has exact synonym: B-cell mediated immunity
has exact synonym: B-lymphocyte mediated immune effector process
has exact synonym: B-lymphocyte mediated immunity
id: GO:0019724
comment: This term was improved by GO_REF:0000022. It was moved.
has OBO namespace: biological_process
imported from: go.owl

immunoglobulin complex
type: Class
subclass of: protein complex
definition: A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
id: GO:0019814
comment: Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available.
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl
in subset: goslim pir
in_subset: goslim pir

B cell receptor complex
type: Class
subclass of: immunoglobulin complex
subclass of: plasma membrane protein complex
subclass of: plasma membrane receptor complex
definition: An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins.
has related synonym: B cell receptor accessory molecule complex
has exact synonym: B lymphocyte receptor complex
has exact synonym: B-cell receptor complex
has exact synonym: B-lymphocyte receptor complex
has exact synonym: BCR complex
id: GO:0019815
has alternative id: GO:0042570
comment: Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available.
has related synonym: antibody
has OBO namespace: cellular_component
term from ontology: go.owl
has exact synonym: immunoglobulin complex, membrane bound
term from ontology: obi.owl
imported from: go.owl

antigen processing and presentation
type: Class
subclass of: immune system process
id: GO:0019882
has alternative id: GO:0030333
definition: The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
comment: This term was improved by GO_REF:0000022. It was renamed and redefined.
has db xref: Wikipedia:Antigen_presentation
has exact synonym: antigen presentation
has exact synonym: antigen processing
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

protein domain specific binding
type: Class
subclass of: protein binding
id: GO:0019904
definition: Interacting selectively and non-covalently with a specific domain of a protein.
term from ontology: go.owl
has OBO namespace: molecular_function
term from ontology: obi.owl
has exact synonym: protein domain-specific binding
imported from: go.owl
in subset: goslim chembl
in_subset: goslim chembl
in_subset: gosubset prok
in subset: gosubset prok

cyclin-dependent protein kinase activating kinase holoenzyme complex
type: Class
subclass of: nuclear cyclin-dependent protein kinase holoenzyme complex
subclass of: carboxy-terminal domain protein kinase complex
definition: A cyclin-dependent kinase activating kinase complex capable of activating cyclin-dependent kinases by threonine phosphorylation, thus regulating cell cycle progression. consists of a kinase, cyclin and optional assembly factors, in human CDK7, CCNH and MNAT1. CAK activity is itself regulated throughout the cell cycle by T-loop phosphorylation of its kinase component (CDK7 in human). Phosphorylation of serine residues during mitosis inactivates the enzyme. Also capable of CAK phosphorylating the carboxyl-terminal domain (CTD) of RNA polymerase II and other transcription activating proteins, as part of the general transcription factor TFIIH.
has exact synonym: CAK complex
has exact synonym: CDK-activating kinase complex
id: GO:0019907
has db xref: IntAct:EBI-1246076
has db xref: IntAct:EBI-9868598
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

nuclear cyclin-dependent protein kinase holoenzyme complex
type: Class
subclass of: cyclin-dependent protein kinase holoenzyme complex
subclass of: nuclear part
has broad synonym: CDK holoenzyme
definition: Cyclin-dependent protein kinase (CDK) complex found in the nucleus.
id: GO:0019908
has OBO namespace: cellular_component
imported from: go.owl

reproductive process
type: Class
subclass of: biological_process
definition: A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
id: GO:0022414
has OBO namespace: biological_process
imported from: go.owl
in subset: gosubset prok

cellular component assembly
type: Class
subclass of: cellular component organization
id: GO:0022607
has alternative id: GO:0071844
definition: The aggregation, arrangement and bonding together of a cellular component.
has OBO namespace: biological_process
has exact synonym: cell structure assembly
has exact synonym: cellular component assembly at cellular level
imported from: go.owl
in subset: goslim chembl
in subset: goslim generic
in subset: goslim pir
in subset: gosubset prok

passive transmembrane transporter activity
type: Class
subclass of: transmembrane transporter activity
definition: Enables the transfer of a solute from one side of the membrane to the other, down the solute's concentration gradient.
id: GO:0022803
has db xref: Reactome:REACT_118066
has db xref: Reactome:REACT_118091
has db xref: Reactome:REACT_118204
has db xref: Reactome:REACT_118231
has db xref: Reactome:REACT_118327
has db xref: Reactome:REACT_118347
has db xref: Reactome:REACT_118350
has db xref: Reactome:REACT_118478
has db xref: Reactome:REACT_118490
has db xref: Reactome:REACT_118544
has db xref: Reactome:REACT_19251
has OBO namespace: molecular_function
imported from: go.owl
in subset: gosubset prok

substrate-specific channel activity
type: Class
subclass of: channel activity
subclass of: substrate-specific transmembrane transporter activity
definition: Enables the energy-independent facilitated diffusion, mediated by passage of a specific solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules.
id: GO:0022838
has OBO namespace: molecular_function
imported from: go.owl

transmembrane transporter activity
type: Class
subclass of: transporter activity
definition: Enables the transfer of a substance from one side of a membrane to the other.
has alternative id: GO:0005386
has alternative id: GO:0015646
id: GO:0022857
has db xref: Reactome:REACT_100033
has db xref: Reactome:REACT_106735
has db xref: Reactome:REACT_111088
has db xref: Reactome:REACT_111933
has db xref: Reactome:REACT_113047
has db xref: Reactome:REACT_113116
has db xref: Reactome:REACT_113829
has db xref: Reactome:REACT_114161
has db xref: Reactome:REACT_19288
has db xref: Reactome:REACT_77235
has db xref: Reactome:REACT_81225
has db xref: Reactome:REACT_88503
has db xref: Reactome:REACT_91849
has db xref: Reactome:REACT_94185
has OBO namespace: molecular_function
imported from: go.owl
in subset: goslim chembl
in subset: goslim generic
in subset: goslim yeast
in subset: gosubset prok

substrate-specific transmembrane transporter activity
type: Class
subclass of: transmembrane transporter activity
subclass of: substrate-specific transporter activity
definition: Enables the transfer of a specific substance or group of related substances from one side of a membrane to the other.
id: GO:0022891
has OBO namespace: molecular_function
imported from: go.owl
in subset: gosubset prok

substrate-specific transporter activity
type: Class
subclass of: transporter activity
definition: Enables the directed movement of a specific substance or group of related substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
id: GO:0022892
has OBO namespace: molecular_function
imported from: go.owl
in subset: gosubset prok

signal release
type: Class
subclass of: secretion by cell
creation date: 2010-02-16T09:30:50Z
id: GO:0023061
definition: The process in which a signal is secreted or discharged into the extracellular medium from a cellular source.
has OBO namespace: biological_process
has exact synonym: signal secretion
imported from: go.owl

actin filament polymerization
type: Class
subclass of: actin polymerization or depolymerization
subclass of: protein polymerization
definition: Assembly of actin filaments by the addition of actin monomers to a filament.
id: GO:0030041
has exact synonym: actin polymerization
has related synonym: actin polymerizing activity
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

mitochondrial tricarboxylic acid cycle enzyme complex
type: Class
subclass of: tricarboxylic acid cycle enzyme complex
subclass of: mitochondrial protein complex
definition: Any of the heteromeric enzymes, located in the mitochondrion, that act in the tricarboxylic acid (TCA) cycle.
id: GO:0030062
has broad synonym: TCA cycle enzyme complex
has OBO namespace: cellular_component
imported from: go.owl

hemopoiesis
type: Class
subclass of: hematopoietic or lymphoid organ development
id: GO:0030097
definition: The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
has db xref: Wikipedia:Haematopoiesis
has OBO namespace: biological_process
has exact synonym: blood cell biosynthesis
has exact synonym: blood cell formation
term from ontology: go.owl
has exact synonym: haemopoiesis
has exact synonym: hematopoiesis
term from ontology: obi.owl
imported from: go.owl

membrane coat
type: Class
subclass of: cytoplasmic part
subclass of: membrane protein complex
definition: Any of several different proteinaceous coats that can associate with membranes. Membrane coats include those formed by clathrin plus an adaptor complex, the COPI and COPII complexes, and possibly others. They are found associated with membranes on many vesicles as well as other membrane features such as pits and perhaps tubules.
id: GO:0030117
has OBO namespace: cellular_component
imported from: go.owl

vesicle coat
type: Class
subclass of: membrane coat
subclass of: cytoplasmic vesicle part
definition: A membrane coat found on a coated vesicle.
id: GO:0030120
has db xref: NIF_Subcellular:sao1177708494
has OBO namespace: cellular_component
imported from: go.owl

COPI vesicle coat
type: Class
subclass of: vesicle coat
subclass of: Golgi apparatus part
has alternative id: GO:0017167
id: GO:0030126
definition: One of two multimeric complexes that forms a membrane vesicle coat. The mammalian COPI subunits are called alpha-, beta-, beta'-, gamma-, delta-, epsilon- and zeta-COP. Vesicles with COPI coats are found associated with Golgi membranes at steady state.
has OBO namespace: cellular_component
has exact synonym: coatomer
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

RNA polymerase complex
type: Class
subclass of: intracellular part
subclass of: transferase complex, transferring phosphorus-containing groups
definition: Any complex that possesses RNA polymerase activity; generally comprises a catalytic subunit and one or more additional subunits.
id: GO:0030880
has OBO namespace: cellular_component
term from ontology: go.owl
has exact synonym: multisubunit RNA polymerase
term from ontology: pro.owl
imported from: go.owl
in_subset: goslim pir
in subset: goslim pir
in subset: gosubset prok
in_subset: gosubset prok

ISWI-type complex
type: Class
subclass of: SWI/SNF superfamily-type complex
definition: Any nuclear protein complex that contains an ATPase subunit of the imitation switch (ISWI) family. ISWI ATPases are involved in assembling chromatin and in sliding and spacing nucleosomes to regulate transcription of nuclear RNA polymerases I, II, and III and also DNA replication, recombination and repair.
id: GO:0031010
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

organelle membrane
type: Class
subclass of: membrane
subclass of: organelle part
definition: A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.
id: GO:0031090
has db xref: NIF_Subcellular:sao830981606
has OBO namespace: cellular_component
has related synonym: intracellular membrane
imported from: go.owl
in subset: gosubset prok

endoplasmic reticulum palmitoyltransferase complex
type: Class
subclass of: palmitoyltransferase complex
subclass of: membrane part
subclass of: endoplasmic reticulum part
definition: A complex of the endoplasmic reticulum that catalyzes S-palmitoylation, the addition of palmitate (C16:0) or other long-chain fatty acids to proteins at a cysteine residue.
id: GO:0031211
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

death-inducing signaling complex
type: Class
subclass of: plasma membrane protein complex
definition: A protein complex formed by the association of signaling proteins with a death receptor upon ligand binding. The complex includes procaspases and death domain-containing proteins in addition to the ligand-bound receptor, and may control the activation of caspases 8 and 10.
has exact synonym: DISC
has exact synonym: DISC protein complex
id: GO:0031264
comment: Gene products that may be annotated to this term include: 1) ligand-bound receptors such as FAS/CD95 (though care should be taken because FAS can also act as a non-apoptotic signal transducer); 2) signaling molecules such as FADD (FAS-associated protein with a death domain), cIAPs (cellular inhibitor of apoptosis proteins), c-FLIPs and caspases 8 and 10.
has db xref: Wikipedia:Death-inducing_signaling_complex
has OBO namespace: cellular_component
has exact synonym: death receptor-induced signaling complex
has exact synonym: death receptor-induced signalling complex
has exact synonym: death-inducing signalling complex
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl
in subset: goslim pir
in_subset: goslim pir

regulation of cellular metabolic process
type: Class
subclass of: regulation of metabolic process
subclass of: regulation of cellular process
definition: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
id: GO:0031323
has OBO namespace: biological_process
has exact synonym: regulation of cellular metabolism
imported from: go.owl
in subset: gosubset prok

cullin-RING ubiquitin ligase complex
type: Class
subclass of: ubiquitin ligase complex
definition: Any ubiquitin ligase complex in which the catalytic core consists of a member of the cullin family and a RING domain protein; the core is associated with one or more additional proteins that confer substrate specificity.
has exact synonym: CRL complex
id: GO:0031461
has OBO namespace: cellular_component
has exact synonym: cullin complex
has related synonym: cullin-RING ligase
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

mannosyltransferase complex
type: Class
subclass of: intracellular part
subclass of: transferase complex
definition: A complex that posseses mannosyltransferase activity.
id: GO:0031501
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl
in subset: goslim pir
in_subset: goslim pir

TORC2 complex
type: Class
subclass of: TOR complex
subclass of: protein complex
definition: A protein complex that contains at least TOR (target of rapamycin) and Rictor (rapamycin-insensitive companion of TOR), or orthologs of, in complex with other signaling components. Mediates the phosphorylation and activation of PKB (also called AKT). In Saccharomyces, the complex contains Avo1p, Avo2p, Tsc11p, Lst8p, Bit61p, Slm1p, Slm2p, and Tor2p.
id: GO:0031932
has exact synonym: TOR complex 2
has exact synonym: TORC 2 complex
has exact synonym: TORC2
has db xref: Wikipedia:MTORC1
has OBO namespace: cellular_component
term from ontology: go.owl
has narrow synonym: mTORC2
term from ontology: pro.owl
has exact synonym: rapamycin and nutrient-insensitive TOR complex
imported from: go.owl

4-aminobutyrate transaminase complex
type: Class
subclass of: intracellular part
subclass of: transferase complex
definition: A homodimeric protein complex that possesses 4-aminobutyrate transaminase activity.
has exact synonym: ABAT complex
has exact synonym: GABA transaminase complex
has exact synonym: GABA-T complex
id: GO:0032144
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

methylation
type: Class
subclass of: metabolic process
id: GO:0032259
has db xref: Reactome:REACT_100463
has db xref: Reactome:REACT_104378
has db xref: Reactome:REACT_106986
has db xref: Reactome:REACT_107353
has db xref: Reactome:REACT_107808
has db xref: Reactome:REACT_110691
has db xref: Reactome:REACT_34638
has db xref: Reactome:REACT_6946
has db xref: Reactome:REACT_77304
has db xref: Reactome:REACT_78116
has db xref: Reactome:REACT_87183
has db xref: Reactome:REACT_88148
has db xref: Reactome:REACT_90436
has db xref: Reactome:REACT_92149
has db xref: Reactome:REACT_92596
has db xref: Reactome:REACT_93357
has db xref: Reactome:REACT_95391
has db xref: Reactome:REACT_98332
has db xref: Reactome:REACT_99471
has db xref: Reactome:REACT_99529
definition: The process in which a methyl group is covalently attached to a molecule.
has db xref: Wikipedia:Methylation
has OBO namespace: biological_process
imported from: go.owl
in subset: goslim chembl

ribonuclease H2 complex
type: Class
subclass of: protein complex
subclass of: intracellular part
definition: A protein complex that possesses ribonuclease H activity, in which the catalytic subunit is a member of the RNase H2 (or HII) class. For example, in Saccharomyces the complex contains Rnh201p, Rnh202p and Rnh203p.
id: GO:0032299
has exact synonym: RNase H2 complex
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

multicellular organismal process
type: Class
subclass of: biological_process
definition: Any biological process, occurring at the level of a multicellular organism, pertinent to its function.
id: GO:0032501
has alternative id: GO:0050874
has OBO namespace: biological_process
has exact synonym: organismal physiological process
imported from: go.owl
in subset: goslim pir

developmental process
type: Class
subclass of: biological_process
definition: A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
id: GO:0032502
has OBO namespace: biological_process
has narrow synonym: development
imported from: go.owl
in subset: goslim agr
in subset: goslim aspergillus
in subset: goslim pir
in subset: gosubset prok

connective tissue growth factor production
type: Class
subclass of: cytokine production
has exact synonym: CCN2 production
has exact synonym: CTGF production
has exact synonym: Fisp12 production
id: GO:0032601
has exact synonym: Hcs24 production
has exact synonym: IGFBP8 production
definition: The appearance of connective tissue growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
has exact synonym: hypertrophic chondrocyte-specific gene product 24 production
term from ontology: obi.owl
imported from: go.owl

chemokine production
type: Class
subclass of: cytokine production
id: GO:0032602
definition: The appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

granulocyte macrophage colony-stimulating factor production
type: Class
subclass of: cytokine production
has exact synonym: GM-CSF production
id: GO:0032604
definition: The appearance of granulocyte macrophage colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
has exact synonym: granulocyte macrophage colony stimulating factor production
term from ontology: obi.owl
imported from: go.owl

hepatocyte growth factor production
type: Class
subclass of: cytokine production
id: GO:0032605
definition: The appearance of hepatocyte growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

type I interferon production
type: Class
subclass of: cytokine production
id: GO:0032606
definition: The appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
has OBO namespace: biological_process
term from ontology: go.owl
has exact synonym: interferon type I production
term from ontology: obi.owl
has exact synonym: type I IFN production
imported from: go.owl

interferon-beta production
type: Class
subclass of: type I interferon production
id: GO:0032608
has exact synonym: IFN-beta production
has exact synonym: IFNB production
definition: The appearance of interferon-beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interferon-gamma production
type: Class
subclass of: cytokine production
id: GO:0032609
has exact synonym: IFNG production
definition: The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
has broad synonym: type II IFN production
has broad synonym: type II interferon production
imported from: go.owl

interleukin-1 alpha production
type: Class
subclass of: interleukin-1 production
id: GO:0032610
has exact synonym: IL-1 alpha production
definition: The appearance of interleukin-1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-1 beta production
type: Class
subclass of: interleukin-1 production
id: GO:0032611
has exact synonym: IL-1 beta production
definition: The appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-1 production
type: Class
subclass of: cytokine production
id: GO:0032612
has exact synonym: IL-1 production
definition: The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-10 production
type: Class
subclass of: cytokine production
id: GO:0032613
has exact synonym: IL-10 production
definition: The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-11 production
type: Class
subclass of: cytokine production
id: GO:0032614
has exact synonym: IL-11 production
definition: The appearance of interleukin-11 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-12 production
type: Class
subclass of: cytokine production
id: GO:0032615
has exact synonym: IL-12 production
definition: The appearance of interleukin-12 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-13 production
type: Class
subclass of: cytokine production
id: GO:0032616
has exact synonym: IL-13 production
definition: The appearance of interleukin-13 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-14 production
type: Class
subclass of: cytokine production
id: GO:0032617
has exact synonym: IL-14 production
definition: The appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-15 production
type: Class
subclass of: cytokine production
id: GO:0032618
has exact synonym: IL-15 production
definition: The appearance of interleukin-15 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-16 production
type: Class
subclass of: cytokine production
id: GO:0032619
has exact synonym: IL-16 production
definition: The appearance of interleukin-16 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-17 production
type: Class
subclass of: cytokine production
id: GO:0032620
has exact synonym: IL-17 production
definition: The appearance of any member of the interleukin-17 family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-18 production
type: Class
subclass of: cytokine production
id: GO:0032621
has exact synonym: IL-18 production
definition: The appearance of interleukin-18 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-19 production
type: Class
subclass of: cytokine production
id: GO:0032622
has exact synonym: IL-19 production
definition: The appearance of interleukin-19 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-2 production
type: Class
subclass of: cytokine production
id: GO:0032623
has exact synonym: IL-2 production
definition: The appearance of interleukin-2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-20 production
type: Class
subclass of: cytokine production
id: GO:0032624
has exact synonym: IL-20 production
definition: The appearance of interleukin-20 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-21 production
type: Class
subclass of: cytokine production
id: GO:0032625
has exact synonym: IL-21 production
definition: The appearance of interleukin-21 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-22 production
type: Class
subclass of: cytokine production
id: GO:0032626
has exact synonym: IL-22 production
definition: The appearance of interleukin-22 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-23 production
type: Class
subclass of: cytokine production
id: GO:0032627
has exact synonym: IL-23 production
definition: The appearance of interleukin-23 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-24 production
type: Class
subclass of: cytokine production
id: GO:0032628
has exact synonym: IL-24 production
definition: The appearance of interleukin-24 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-25 production
type: Class
subclass of: cytokine production
id: GO:0032629
has exact synonym: IL-25 production
definition: The appearance of interleukin-25 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-26 production
type: Class
subclass of: cytokine production
id: GO:0032630
has exact synonym: IL-26 production
definition: The appearance of interleukin-26 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-27 production
type: Class
subclass of: cytokine production
id: GO:0032631
has exact synonym: IL-27 production
definition: The appearance of interleukin-27 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-3 production
type: Class
subclass of: cytokine production
id: GO:0032632
has exact synonym: IL-3 production
definition: The appearance of interleukin-3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-4 production
type: Class
subclass of: cytokine production
id: GO:0032633
has exact synonym: IL-4 production
definition: The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-5 production
type: Class
subclass of: cytokine production
id: GO:0032634
has exact synonym: IL-5 production
definition: The appearance of interleukin-5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-6 production
type: Class
subclass of: cytokine production
id: GO:0032635
has exact synonym: IL-6 production
definition: The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-7 production
type: Class
subclass of: cytokine production
id: GO:0032636
has exact synonym: IL-7 production
definition: The appearance of interleukin-7 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-8 production
type: Class
subclass of: cytokine production
id: GO:0032637
has exact synonym: IL-8 production
definition: The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

interleukin-9 production
type: Class
subclass of: cytokine production
id: GO:0032638
has exact synonym: IL-9 production
definition: The appearance of interleukin-9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

TRAIL production
type: Class
subclass of: tumor necrosis factor superfamily cytokine production
id: GO:0032639
definition: The appearance of TRAIL due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

tumor necrosis factor production
type: Class
subclass of: tumor necrosis factor superfamily cytokine production
id: GO:0032640
comment: Note that this term refers only to the specific, original 'tumor necrosis factor' protein (TNF) and not other members of the tumor necrosis factor superfamily (those with the gene symbol root 'TNFSF').
has exact synonym: TNF production
has exact synonym: TNF-alpha production
definition: The appearance of tumor necrosis factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
has exact synonym: tumor necrosis factor-alpha production
imported from: go.owl

lymphotoxin A production
type: Class
subclass of: tumor necrosis factor superfamily cytokine production
id: GO:0032641
has exact synonym: LTA production
has exact synonym: TNF-beta production
definition: The appearance of lymphotoxin A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
has exact synonym: lymphotoxin-alpha production
term from ontology: obi.owl
has exact synonym: tumor necrosis factor-beta production
imported from: go.owl

carboxy-terminal domain protein kinase complex
type: Class
subclass of: protein complex
subclass of: nuclear part
subclass of: serine/threonine protein kinase complex
definition: A protein complex that phosphorylates amino acid residues of RNA polymerase II C-terminal domain repeats; phosphorylation occurs mainly on Ser2 and Ser5.
has exact synonym: CTDK complex
id: GO:0032806
has OBO namespace: cellular_component
imported from: go.owl

transforming growth factor beta1 production
type: Class
subclass of: transforming growth factor beta production
id: GO:0032905
has exact synonym: TGF-B1 production
has exact synonym: TGFB1 production
definition: The appearance of transforming growth factor-beta1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
has exact synonym: transforming growth factor-beta1 production
imported from: go.owl

transforming growth factor beta2 production
type: Class
subclass of: transforming growth factor beta production
id: GO:0032906
has exact synonym: TGF-B2 production
has exact synonym: TGFB2 production
definition: The appearance of transforming growth factor-beta2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
has exact synonym: transforming growth factor-beta2 production
imported from: go.owl

transforming growth factor beta3 production
type: Class
subclass of: transforming growth factor beta production
id: GO:0032907
has exact synonym: TGF-B3 production
has exact synonym: TGFB3 production
definition: The appearance of transforming growth factor-beta3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
has exact synonym: transforming growth factor-beta3 production
imported from: go.owl

secretion by cell
type: Class
subclass of: single-organism cellular process
subclass of: secretion
id: GO:0032940
definition: The controlled release of a substance by a cell.
has db xref: Wikipedia:Secretion
has OBO namespace: biological_process
has exact synonym: cellular secretion
imported from: go.owl

mononuclear cell proliferation
type: Class
subclass of: leukocyte proliferation
id: GO:0032943
has narrow synonym: PBMC proliferation
definition: The expansion of a mononuclear cell population by cell division. A mononuclear cell is a leukocyte with a single non-segmented nucleus in the mature form.
has OBO namespace: biological_process
has narrow synonym: peripheral blood mononuclear cell proliferation
imported from: go.owl

macromolecular complex
type: Class
subclass of: cellular_component
definition: A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
id: GO:0032991
has OBO namespace: cellular_component
term from ontology: go.owl
has exact synonym: macromolecule complex
term from ontology: pro.owl
has exact synonym: protein containing complex
imported from: go.owl
in subset: goslim agr
in_subset: goslim agr
in subset: goslim pir
in_subset: goslim pir
in_subset: gosubset prok
in subset: gosubset prok

protein-DNA complex
type: Class
subclass of: macromolecular complex
definition: A macromolecular complex containing both protein and DNA molecules.
has exact synonym: DNA-protein complex
id: GO:0032993
comment: Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here.
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl
in subset: gosubset prok
in_subset: gosubset prok

Bcl3-Bcl10 complex
type: Class
subclass of: protein complex
subclass of: intracellular part
definition: A protein complex containing Bcl3 and Bcl10, which forms when Akt1 is activated by TNF-alpha to phosphorylate Bcl10; the Bcl3-Bcl10 complex is translocated to the nucleus.
id: GO:0032996
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

macromolecule localization
type: Class
subclass of: localization
definition: Any process in which a macromolecule is transported to, or maintained in, a specific location.
id: GO:0033036
has OBO namespace: biological_process
term from ontology: go.owl
has exact synonym: macromolecule localisation
term from ontology: obi.owl
imported from: go.owl
in subset: gosubset prok
in_subset: gosubset prok

dolichol-phosphate-mannose synthase complex
type: Class
subclass of: mannosyltransferase complex
definition: A protein complex that possesses dolichyl-phosphate beta-D-mannosyltransferase activity; contains a catalytic subunit, a regulatory subunit, and a third subunit that stabilizes the complex. In human and several other metazoa, the subunits are named DPM1, DPM2 and DPM3, respectively.
has exact synonym: DPM synthase complex
id: GO:0033185
has OBO namespace: cellular_component
has exact synonym: dolichyl-phosphate beta-D-mannosyltransferase complex
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

amide binding
type: Class
subclass of: binding
id: GO:0033218
definition: Interacting selectively and non-covalently with an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
has OBO namespace: molecular_function
imported from: go.owl
in subset: goslim pir

cellular response to stress
type: Class
subclass of: response to stress
subclass of: cellular response to stimulus
definition: Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
id: GO:0033554
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: biological_process
imported from: go.owl
in subset: gocheck do not manually annotate

mitotic checkpoint complex
type: Class
subclass of: protein complex
subclass of: nuclear part
definition: A multiprotein complex that functions as a mitotic checkpoint inhibitor of the anaphase-promoting complex/cyclosome (APC/C). In budding yeast this complex consists of Mad2p, Mad3p, Bub3p and Cdc20p, and in mammalian cells it consists of MAD2, BUBR1, BUB3, and CDC20.
id: GO:0033597
has exact synonym: MCC
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

DNA polymerase activity
type: Class
subclass of: nucleotidyltransferase activity
definition: Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group.
has exact synonym: DNA nucleotidyltransferase activity
id: GO:0034061
has db xref: Reactome:REACT_115680
has db xref: Reactome:REACT_115778
has db xref: Reactome:REACT_115899
has db xref: Reactome:REACT_115932
has db xref: Reactome:REACT_116106
has db xref: Reactome:REACT_116167
has exact synonym: deoxynucleate polymerase activity
has exact synonym: deoxyribonucleate nucleotidyltransferase activity
has exact synonym: deoxyribonucleic acid polymerase activity
has exact synonym: deoxyribonucleic polymerase activity
term from ontology: go.owl
has OBO namespace: molecular_function
term from ontology: obi.owl
imported from: go.owl
in subset: gosubset prok
in_subset: gosubset prok

type III interferon production
type: Class
subclass of: cytokine production
id: GO:0034343
comment: Note that IL-28A, IL-28B, and IL-29 are types of interferon-lambda.
definition: The appearance of type III interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon lambda is the only member of the type III interferon found so far.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
has exact synonym: type III IFN production
imported from: go.owl

RNA cap binding complex
type: Class
subclass of: macromolecular complex
definition: Any protein complex that binds to a specialized RNA cap structure at any time in the lifetime of the RNA.
id: GO:0034518
has OBO namespace: cellular_component
imported from: go.owl

cellular macromolecular complex assembly
type: Class
subclass of: macromolecular complex assembly
id: GO:0034622
definition: The aggregation, arrangement and bonding together of a set of macromolecules to form a complex, carried out at the cellular level.
has OBO namespace: biological_process
has exact synonym: cellular macromolecule complex assembly
imported from: go.owl
in subset: goslim pir
in subset: gosubset prok

cellular nitrogen compound metabolic process
type: Class
subclass of: nitrogen compound metabolic process
subclass of: cellular metabolic process
id: GO:0034641
has db xref: Reactome:REACT_102000
has db xref: Reactome:REACT_103710
has db xref: Reactome:REACT_107293
has db xref: Reactome:REACT_108179
has db xref: Reactome:REACT_109042
has db xref: Reactome:REACT_13
has db xref: Reactome:REACT_28699
has db xref: Reactome:REACT_29108
has db xref: Reactome:REACT_32429
has db xref: Reactome:REACT_33347
has db xref: Reactome:REACT_34326
has db xref: Reactome:REACT_55564
has db xref: Reactome:REACT_77741
has db xref: Reactome:REACT_82379
has db xref: Reactome:REACT_86268
has db xref: Reactome:REACT_90299
has db xref: Reactome:REACT_91959
has db xref: Reactome:REACT_93580
has db xref: Reactome:REACT_95666
has db xref: Reactome:REACT_98086
has db xref: Reactome:REACT_99241
definition: The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.
has OBO namespace: biological_process
has exact synonym: cellular nitrogen compound metabolism
imported from: go.owl
in subset: goslim chembl
in subset: goslim generic
in subset: gosubset prok

cellular macromolecule biosynthetic process
type: Class
subclass of: macromolecule biosynthetic process
subclass of: cellular biosynthetic process
subclass of: cellular macromolecule metabolic process
id: GO:0034645
has alternative id: GO:0034961
definition: The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, carried out by individual cells.
has OBO namespace: biological_process
has exact synonym: cellular biopolymer biosynthetic process
has exact synonym: cellular macromolecule anabolism
has exact synonym: cellular macromolecule biosynthesis
has exact synonym: cellular macromolecule formation
has exact synonym: cellular macromolecule synthesis
imported from: go.owl

integrin alphaM-beta2 complex
type: Class
subclass of: integrin complex
definition: An integrin complex that comprises one alphaM subunit and one beta2 subunit.
id: GO:0034688
has narrow synonym: Itgam-Itgb2 complex
has exact synonym: alphaM-beta2 integrin complex
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

ion channel complex
type: Class
subclass of: transmembrane transporter complex
definition: A protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
id: GO:0034702
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

methyltransferase complex
type: Class
subclass of: intracellular part
subclass of: transferase complex
definition: A protein complex that possesses methyltransferase activity.
id: GO:0034708
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl
in_subset: gosubset prok
in subset: gosubset prok

Toll-like receptor 1-Toll-like receptor 2 protein complex
type: Class
subclass of: plasma membrane receptor complex
creation date: 2010-03-04T04:35:44Z
definition: A heterodimeric protein complex containing Toll-like receptor 1 (TLR1) and Toll-like receptor 2 (TLR2).
id: GO:0035354
has alternative id: GO:0038125
has db xref: Reactome:REACT_8486.1
has exact synonym: TLR1-TLR2 protein complex
has exact synonym: TLR1:TLR2 complex
has exact synonym: TLR2:TLR1 heterodimer
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
created by: rfoulger
has exact synonym: toll-like receptor TLR1:TLR2 heterodimeric complex
imported from: go.owl

Toll-like receptor 2-Toll-like receptor 6 protein complex
type: Class
subclass of: plasma membrane receptor complex
creation date: 2010-03-04T04:37:00Z
definition: A heterodimeric protein complex containing Toll-like receptor 2 (TLR2) and Toll-like receptor 6 (TLR6).
id: GO:0035355
has alternative id: GO:0038126
has db xref: Reactome:REACT_8554.1
has exact synonym: TLR2-TLR6 protein complex
has exact synonym: TLR2:TLR6 heterodimer
has exact synonym: TLR6:TLR2 complex
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
created by: rfoulger
has exact synonym: toll-like receptor TLR6:TLR2 heterodimeric complex
imported from: go.owl

chemokine (C-X-C motif) ligand 9 production
type: Class
subclass of: chemokine production
creation date: 2010-03-23T10:03:20Z
has exact synonym: CXCL9 production
id: GO:0035393
has exact synonym: MIG production
has exact synonym: Monokine induced by gamma interferon production
definition: The appearance of chemokine (C-X-C motif) ligand 9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
created by: rfoulger
imported from: go.owl

helper T cell enhancement of adaptive immune response
type: Class
subclass of: positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
creation date: 2010-03-23T10:38:31Z
id: GO:0035397
definition: Positive regulation of an adaptive immune response mediated via cytokine production by helper T cell.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
has exact synonym: provision of T cell help
created by: rfoulger
imported from: go.owl

helper T cell enhancement of T cell mediated immune response
type: Class
subclass of: positive regulation of T cell mediated immunity
subclass of: helper T cell enhancement of adaptive immune response
creation date: 2010-03-23T10:40:00Z
id: GO:0035398
definition: Positive regulation of a T cell mediated immune response mediated via cytokine production by a helper T cell.
has OBO namespace: biological_process
term from ontology: go.owl
has exact synonym: helper T cell enhancement of T cell mediated immunity
term from ontology: obi.owl
has exact synonym: provision of T cell help to T cell
created by: rfoulger
imported from: go.owl

helper T cell enhancement of B cell mediated immune response
type: Class
subclass of: positive regulation of B cell mediated immunity
subclass of: helper T cell enhancement of adaptive immune response
creation date: 2010-03-23T10:41:46Z
id: GO:0035399
definition: Positive regulation of a B cell mediated immune response mediated via cytokine production by a helper T cell.
has OBO namespace: biological_process
term from ontology: go.owl
has exact synonym: helper T cell enhancement of B cell mediated immunity
term from ontology: obi.owl
has exact synonym: provision of T cell help to B cell
created by: rfoulger
imported from: go.owl

NF-kappaB p50/p65 complex
type: Class
subclass of: NF-kappaB complex
creation date: 2010-05-05T10:45:13Z
definition: A heterodimer of NF-kappa B p50 and p65 subunits.
id: GO:0035525
has exact synonym: NF-kappa B1/RelA complex
has exact synonym: NF-kappa B1/p65 complex
has related synonym: NF-kappa p105/RelA complex
has related synonym: NF-kappa p105/p65 complex
has exact synonym: NF-kappa p50/RelA complex
comment: Note that the p50 subunit is encoded by NFKB1 gene in human and the p65 subunit is encoded by the RELA gene in human. Similar nomenclature is used in other vertebrate species. The p50 subunit has a precursor form p105 in some publications.
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
created by: rfoulger
imported from: go.owl

granzyme A production
type: Class
subclass of: production of molecular mediator of immune response
creation date: 2011-03-17T02:39:11Z
id: GO:0035746
definition: The appearance of granzyme A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
created by: rfoulger
imported from: go.owl

perforin production
type: Class
subclass of: production of molecular mediator of immune response
creation date: 2011-07-27T11:44:21Z
id: GO:0035944
definition: The appearance of a perforin protein due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
created by: rfoulger
imported from: go.owl

fatty acid beta-oxidation multienzyme complex
type: Class
subclass of: macromolecular complex
creation date: 2012-02-28T02:10:39Z
definition: A multienzyme complex possessing three kinds of enzymes that catalyze the chain reactions in the fatty acid beta-oxidation cycle, enoyl-CoA hydratase (ECH), 3-hydroxyacyl-CoA dehydrogenase (HACD), and acetyl-CoA C-acyltransferase (KACT).
comment: For fatty acid beta-oxidation multienzyme complexes located in the mitochondrial matrix, consider instead the term 'mitochondrial fatty acid beta-oxidation multienzyme complex ; GO:0016507'.
id: GO:0036125
has OBO namespace: cellular_component
created by: rfoulger
imported from: go.owl

protein modification process
type: Class
subclass of: protein metabolic process
subclass of: macromolecule modification
creation date: 2012-04-26T01:47:12Z
id: GO:0036211
definition: The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
has OBO namespace: biological_process
has exact synonym: protein modification
created by: rfoulger
imported from: go.owl

granulysin production
type: Class
subclass of: production of molecular mediator of immune response
creation date: 2012-06-18T02:11:15Z
id: GO:0036262
definition: The appearance of granulysin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
created by: rfoulger
imported from: go.owl

growth factor complex
type: Class
subclass of: protein complex
creation date: 2013-11-07T11:27:16Z
definition: A protein complex that has growth factor activity.
id: GO:0036454
has OBO namespace: cellular_component
created by: rfoulger
imported from: go.owl

TOR complex
type: Class
subclass of: intracellular part
creation date: 2013-12-09T14:38:09Z
definition: A protein complex that contains at least TOR (target of rapamycin) in complex with other signaling components. Mediates the phosphorylation and activation of downstream signaling components including PKB (AKT) or S6K.
id: GO:0038201
has exact synonym: TOR signaling complex
has OBO namespace: cellular_component
has narrow synonym: mTOR complex
created by: rfoulger
has exact synonym: target of rapamycin complex
imported from: go.owl

locomotion
type: Class
subclass of: biological_process
id: GO:0040011
definition: Self-propelled movement of a cell or organism from one location to another.
has OBO namespace: biological_process
imported from: go.owl
in subset: goslim chembl
in subset: goslim generic
in subset: goslim pir
in subset: gosubset prok

regulation of gene expression, epigenetic
type: Class
subclass of: regulation of gene expression
definition: Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence.
id: GO:0040029
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl
in_subset: goslim plant
in subset: goslim plant
in_subset: gosubset prok
in subset: gosubset prok

regulation of molecular function, epigenetic
type: Class
subclass of: regulation of molecular function
definition: Any heritable epigenetic process that modulates the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya.
id: GO:0040030
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
has exact synonym: regulation of protein activity, epigenetic
imported from: go.owl

T cell proliferation
type: Class
subclass of: T cell activation
subclass of: lymphocyte proliferation
id: GO:0042098
has alternative id: GO:0042111
has exact synonym: T lymphocyte proliferation
has exact synonym: T-cell proliferation
has exact synonym: T-lymphocyte proliferation
definition: The expansion of a T cell population by cell division. Follows T cell activation.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

T cell receptor complex
type: Class
subclass of: plasma membrane receptor complex
definition: A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains.
id: GO:0042101
has exact synonym: T lymphocyte receptor complex
has exact synonym: T-cell receptor complex
has exact synonym: T-lymphocyte receptor complex
has related synonym: TCR
has exact synonym: TCR complex
has db xref: Wikipedia:T_cell_receptor
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

T cell activation
type: Class
subclass of: lymphocyte activation
id: GO:0042110
has exact synonym: T lymphocyte activation
has exact synonym: T-cell activation
has exact synonym: T-lymphocyte activation
definition: The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

peptide binding
type: Class
subclass of: amide binding
id: GO:0042277
definition: Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
has OBO namespace: molecular_function
imported from: go.owl
in subset: goslim chembl
in subset: goslim pir
in subset: gosubset prok

MCM complex
type: Class
subclass of: protein complex
definition: A hexameric protein complex required for the initiation and regulation of DNA replication.
id: GO:0042555
has OBO namespace: cellular_component
term from ontology: go.owl
has exact synonym: mini-chromosome maintenance complex
term from ontology: pro.owl
imported from: go.owl

immunoglobulin complex, circulating
type: Class
subclass of: immunoglobulin complex
subclass of: extracellular region part
definition: An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
id: GO:0042571
comment: Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available.
has db xref: Wikipedia:Antibody
has exact synonym: antibody
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

DNA polymerase complex
type: Class
subclass of: intracellular part
subclass of: transferase complex, transferring phosphorus-containing groups
definition: A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA.
id: GO:0042575
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl
in subset: goslim metagenomics
in_subset: goslim metagenomics
in subset: goslim pir
in_subset: goslim pir
in_subset: gosubset prok
in subset: gosubset prok

peptide antigen binding
type: Class
subclass of: antigen binding
subclass of: peptide binding
id: GO:0042605
has alternative id: GO:0042606
has alternative id: GO:0042607
definition: Interacting selectively and non-covalently with an antigen peptide.
comment: Note that this term can be used to describe the binding of a peptide to an MHC molecule.
has narrow synonym: endogenous peptide antigen binding
has narrow synonym: exogenous peptide antigen binding
term from ontology: go.owl
has OBO namespace: molecular_function
term from ontology: obi.owl
imported from: go.owl
in subset: goslim chembl
in_subset: goslim chembl

MHC protein complex
type: Class
subclass of: plasma membrane protein complex
definition: A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen.
id: GO:0042611
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl
in subset: goslim pir
in_subset: goslim pir

succinate-CoA ligase complex
type: Class
subclass of: tricarboxylic acid cycle enzyme complex
subclass of: catalytic complex
definition: A heterodimeric enzyme complex, usually composed of an alpha and beta chain. Functions in the TCA cycle, hydrolyzing succinyl-CoA into succinate and CoA, thereby forming ATP or GTP.
id: GO:0042709
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl
in subset: gosubset prok
in_subset: gosubset prok

GPI-anchor transamidase complex
type: Class
subclass of: membrane part
subclass of: endoplasmic reticulum part
subclass of: catalytic complex
definition: An enzyme complex which in humans and yeast consists of at least five proteins; for example, the complex contains GAA1, GPI8, PIG-S, PIG-U, and PIG-T in human, and Gaa1p, Gab1p, Gpi8p, Gpi16p, and Gpi17p in yeast. Catalyzes the posttranslational attachment of the carboxyl-terminus of a precursor protein to a GPI-anchor.
id: GO:0042765
has exact synonym: GPIT complex
comment: Note that this term should not be confused with 'glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex ; GO:0000506', which represents a distinct complex with a different catalytic activity.
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

macromolecule metabolic process
type: Class
subclass of: organic substance metabolic process
id: GO:0043170
has alternative id: GO:0043283
definition: The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
has OBO namespace: biological_process
has exact synonym: biopolymer metabolic process
has exact synonym: macromolecule metabolism
imported from: go.owl
in subset: goslim pir
in subset: gosubset prok

organelle
type: Class
subclass of: cellular_component
id: GO:0043226
has db xref: NIF_Subcellular:sao1539965131
definition: Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
has db xref: Wikipedia:Organelle
has OBO namespace: cellular_component
imported from: go.owl
in subset: goslim chembl
in subset: goslim generic
in subset: goslim pir
in subset: gosubset prok

membrane-bounded organelle
type: Class
subclass of: organelle
id: GO:0043227
has db xref: NIF_Subcellular:sao414196390
definition: Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
has OBO namespace: cellular_component
term from ontology: go.owl
has exact synonym: membrane-enclosed organelle
term from ontology: obi.owl
imported from: go.owl
in_subset: gosubset prok
in subset: gosubset prok

non-membrane-bounded organelle
type: Class
subclass of: organelle
id: GO:0043228
has db xref: NIF_Subcellular:sao1456184038
definition: Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes.
has OBO namespace: cellular_component
has exact synonym: non-membrane-enclosed organelle
imported from: go.owl
in subset: gosubset prok

intracellular organelle
type: Class
subclass of: organelle
subclass of: intracellular part
id: GO:0043229
definition: Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
has OBO namespace: cellular_component
imported from: go.owl
in subset: goslim pir
in subset: gosubset prok

intracellular membrane-bounded organelle
type: Class
subclass of: membrane-bounded organelle
subclass of: intracellular organelle
id: GO:0043231
definition: Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
has OBO namespace: cellular_component
has exact synonym: intracellular membrane-enclosed organelle
imported from: go.owl
in subset: goslim pir
in subset: gosubset prok

intracellular non-membrane-bounded organelle
type: Class
subclass of: non-membrane-bounded organelle
subclass of: intracellular organelle
id: GO:0043232
definition: Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes.
has OBO namespace: cellular_component
has exact synonym: intracellular non-membrane-enclosed organelle
imported from: go.owl
in subset: goslim mouse
in subset: goslim pir
in subset: gosubset prok

protein complex
type: Class
subclass of: macromolecular complex
comment: A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole.
definition: A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
id: GO:0043234
has db xref: Wikipedia:Protein_complex
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: obi.owl
term from ontology: pro.owl
has exact synonym: protein-protein complex
imported from: go.owl
in subset: goslim chembl
in_subset: goslim chembl
in_subset: goslim generic
in subset: goslim generic
in_subset: goslim pir
in subset: goslim pir
in subset: gosubset prok
in_subset: gosubset prok

receptor complex
type: Class
subclass of: macromolecular complex
definition: Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
id: GO:0043235
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl
in_subset: goslim pir
in subset: goslim pir
in subset: gosubset prok
in_subset: gosubset prok

Fanconi anaemia nuclear complex
type: Class
subclass of: protein complex
subclass of: nucleoplasm part
definition: A protein complex composed of the Fanconi anaemia (FA) proteins including A, C, E, G and F (FANCA-F). Functions in the activation of the downstream protein FANCD2 by monoubiquitylation, and is essential for protection against chromosome breakage.
has exact synonym: FA complex
has exact synonym: FA core complex
has exact synonym: FA nuclear complex
has exact synonym: Fanconi anaemia complex
id: GO:0043240
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

laminin complex
type: Class
subclass of: protein complex
subclass of: extracellular matrix component
definition: A large, extracellular glycoprotein complex composed of three different polypeptide chains, alpha, beta and gamma. Provides an integral part of the structural scaffolding of basement membranes.
id: GO:0043256
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl
in_subset: goslim pir
in subset: goslim pir

leukocyte degranulation
type: Class
subclass of: immune effector process
subclass of: regulated exocytosis
id: GO:0043299
definition: The regulated exocytosis of secretory granules by a leukocyte.
comment: This term was improved by GO_REF:0000022. It was moved.
has OBO namespace: biological_process
has exact synonym: immune cell degranulation
has exact synonym: immune cell granule exocytosis
has exact synonym: leucocyte degranulation
has exact synonym: leukocyte granule exocytosis
imported from: go.owl

cytotoxic T cell degranulation
type: Class
subclass of: T cell activation involved in immune response
subclass of: leukocyte degranulation
id: GO:0043316
definition: The regulated exocytosis of secretory granules containing preformed mediators such as perforin and granzymes by a cytotoxic T cell.
has OBO namespace: biological_process
has exact synonym: cytotoxic T cell granule exocytosis
has exact synonym: cytotoxic T lymphocyte degranulation
has exact synonym: cytotoxic T lymphocyte granule exocytosis
has exact synonym: cytotoxic T-cell degranulation
has exact synonym: cytotoxic T-cell granule exocytosis
has exact synonym: cytotoxic T-lymphocyte degranulation
has exact synonym: cytotoxic T-lymphocyte granule exocytosis
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

macromolecule modification
type: Class
subclass of: macromolecule metabolic process
id: GO:0043412
definition: The covalent alteration of one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule, resulting in a change in its properties.
has OBO namespace: biological_process
imported from: go.owl
in subset: goslim pir
in subset: gosubset prok

macromolecule methylation
type: Class
subclass of: methylation
subclass of: macromolecule modification
subclass of: cellular macromolecule metabolic process
id: GO:0043414
definition: The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule.
has OBO namespace: biological_process
imported from: go.owl
in subset: gosubset prok

interleukin-12 complex
type: Class
subclass of: protein complex
subclass of: extracellular region part
definition: A protein complex that is composed of an interleukin-12 alpha (p35, product of the IL12A gene) and an interleukin-12 beta subunit (p40, product of the IL12B gene) and is secreted into the extracellular space.
id: GO:0043514
has exact synonym: IL-12 complex
has narrow synonym: IL12A
has narrow synonym: IL12B
comment: Note that this heterodimeric cytokine utilizes the IL-12p35 subunit as its alpha chain, which is also used by IL-35 as its alpha chain, and utilizes the IL-12p40 subunit as its beta chain, which is also used by IL-23 as its beta chain.
has OBO namespace: cellular_component
term from ontology: go.owl
has narrow synonym: p35
has narrow synonym: p40
term from ontology: pro.owl
imported from: go.owl

6-phosphofructo-2-kinase/fructose-2,6-biphosphatase complex
type: Class
subclass of: cytosolic part
subclass of: transferase complex, transferring phosphorus-containing groups
has narrow synonym: 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 complex
has narrow synonym: 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 complex
has narrow synonym: 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 complex
has narrow synonym: 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 complex
definition: A homodimeric, bifunctional enzyme complex which catalyzes the synthesis and degradation of fructose 2,6-bisphosphate, and is required for both glycolysis and gluconeogenesis.
id: GO:0043540
comment: Note that we use this single class to represent all 4 isoforms of this complex. We decided to do this because the isoforms do not differ in function, rather in expression and regulation. We may want to revisit this in future.
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

sequence-specific DNA binding
type: Class
subclass of: DNA binding
id: GO:0043565
definition: Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
term from ontology: go.owl
has OBO namespace: molecular_function
term from ontology: obi.owl
has exact synonym: sequence specific DNA binding
imported from: go.owl
in subset: gosubset prok
in_subset: gosubset prok

cellular protein complex assembly
type: Class
subclass of: protein complex assembly
subclass of: cellular macromolecular complex assembly
id: GO:0043623
definition: The aggregation, arrangement and bonding together of a set of components to form a protein complex, occurring at the level of an individual cell.
has OBO namespace: biological_process
imported from: go.owl
in subset: gosubset prok

PCNA complex
type: Class
subclass of: DNA polymerase processivity factor complex
definition: A protein complex composed of three identical PCNA monomers, each comprising two similar domains, which are joined in a head-to-tail arrangement to form a homotrimer. Forms a ring-like structure in solution, with a central hole sufficiently large to accommodate the double helix of DNA. Originally characterized as a DNA sliding clamp for replicative DNA polymerases and as an essential component of the replisome, and has also been shown to be involved in other processes including Okazaki fragment processing, DNA repair, translesion DNA synthesis, DNA methylation, chromatin remodeling and cell cycle regulation.
id: GO:0043626
has exact synonym: PCNA homotrimer
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
has exact synonym: proliferating cell nuclear antigen complex
has broad synonym: sliding clamp
imported from: go.owl
in subset: gosubset prok
in_subset: gosubset prok

macromolecular complex subunit organization
type: Class
subclass of: cellular component organization
definition: Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a macromolecular complex.
has alternative id: GO:0034600
has alternative id: GO:0034621
id: GO:0043933
has OBO namespace: biological_process
has exact synonym: cellular macromolecular complex organization
has exact synonym: cellular macromolecular complex subunit organisation
has exact synonym: cellular macromolecular complex subunit organization
has exact synonym: macromolecular complex organization
has exact synonym: macromolecular complex subunit organisation
imported from: go.owl
in subset: gosubset prok

regulation of DNA methylation
type: Class
subclass of: regulation of DNA metabolic process
definition: Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
id: GO:0044030
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl

transcription regulatory region DNA binding
type: Class
subclass of: regulatory region DNA binding
creation date: 2009-11-04T12:58:25Z
id: GO:0044212
definition: Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
comment: The word "promoter" is used variously in the literature to describe the core promoter specifically or the entire proximal regulatory region (excluding any distal enhancers) including both the core promoter and the upstream region where activating transcription factors such as Gal4 in S. cerevisiae or catabolite activator protein (CAP) in E. coli bind. To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" in order to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind, and "enhancer" regions which are typically more distal from the core promoter. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription. ANNOTATION NOTE: Regarding annotation to "transcription regulatory region DNA binding" (GO:0044212) and any of its is_a children, note that annotation to these terms specifies DNA binding only without any statement about transcription factor activity. To make an annotation about a function of transcription factor activity, consider "sequence-specific DNA binding transcription factor activity" (GO:0003700) or its is_a children which have has_part relationships to the appropriate kind of "transcription regulatory region DNA binding".
created by: jane
has OBO namespace: molecular_function
imported from: go.owl

cellular metabolic process
type: Class
subclass of: metabolic process
subclass of: cellular process
id: GO:0044237
definition: The chemical reactions and pathways by which individual cells transform chemical substances.
has OBO namespace: biological_process
has exact synonym: cellular metabolism
has related synonym: intermediary metabolism
imported from: go.owl
in subset: goslim pir
in subset: gosubset prok

primary metabolic process
type: Class
subclass of: metabolic process
id: GO:0044238
definition: The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
has OBO namespace: biological_process
has exact synonym: primary metabolism
imported from: go.owl
in subset: goslim pir
in subset: gosubset prok

cellular biosynthetic process
type: Class
subclass of: biosynthetic process
subclass of: cellular metabolic process
id: GO:0044249
definition: The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
has OBO namespace: biological_process
has exact synonym: cellular anabolism
has exact synonym: cellular biosynthesis
has exact synonym: cellular formation
has exact synonym: cellular synthesis
imported from: go.owl
in subset: gosubset prok

cellular macromolecule metabolic process
type: Class
subclass of: macromolecule metabolic process
subclass of: cellular metabolic process
has alternative id: GO:0034960
id: GO:0044260
definition: The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells.
has OBO namespace: biological_process
has exact synonym: cellular biopolymer metabolic process
has exact synonym: cellular macromolecule metabolism
imported from: go.owl
in subset: gosubset prok

cellular protein metabolic process
type: Class
subclass of: protein metabolic process
subclass of: cellular macromolecule metabolic process
id: GO:0044267
has db xref: Reactome:REACT_101554
has db xref: Reactome:REACT_102155
has db xref: Reactome:REACT_105825
has db xref: Reactome:REACT_106151
has db xref: Reactome:REACT_108005
has db xref: Reactome:REACT_109022
has db xref: Reactome:REACT_17015
has db xref: Reactome:REACT_32904
has db xref: Reactome:REACT_34473
has db xref: Reactome:REACT_80561
has db xref: Reactome:REACT_81994
has db xref: Reactome:REACT_82523
has db xref: Reactome:REACT_85873
has db xref: Reactome:REACT_86658
has db xref: Reactome:REACT_89852
has db xref: Reactome:REACT_91052
has db xref: Reactome:REACT_93132
has db xref: Reactome:REACT_96466
has db xref: Reactome:REACT_99179
definition: The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
has OBO namespace: biological_process
has exact synonym: cellular protein metabolism
imported from: go.owl
in subset: gosubset prok

small molecule metabolic process
type: Class
subclass of: single-organism metabolic process
creation date: 2010-01-26T12:05:20Z
id: GO:0044281
has db xref: Reactome:REACT_111217
has db xref: Reactome:REACT_112077
has db xref: Reactome:REACT_112140
has db xref: Reactome:REACT_112621
has db xref: Reactome:REACT_112912
has db xref: Reactome:REACT_113131
has db xref: Reactome:REACT_113305
has db xref: Reactome:REACT_113457
has db xref: Reactome:REACT_113568
has db xref: Reactome:REACT_113610
has db xref: Reactome:REACT_113934
has db xref: Reactome:REACT_114081
has db xref: Reactome:REACT_114137
has db xref: Reactome:REACT_114421
has db xref: Reactome:REACT_114473
has db xref: Reactome:REACT_114495
has db xref: Reactome:REACT_114668
has db xref: Reactome:REACT_114983
has db xref: Reactome:REACT_115063
has db xref: Reactome:REACT_115388
has db xref: Reactome:REACT_115420
has db xref: Reactome:REACT_115655
comment: Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.
definition: The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule.
has OBO namespace: biological_process
created by: jane
has exact synonym: small molecule metabolism
imported from: go.owl
in subset: goslim agr
in subset: goslim chembl
in subset: goslim generic
in subset: goslim metagenomics

extracellular matrix component
type: Class
subclass of: extracellular region part
definition: Any constituent part of the extracellular matrix, the structure lying external to one or more cells, which provides structural support for cells or tissues; may be completely external to the cell (as in animals) or be part of the cell (as often seen in plants).
id: GO:0044420
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: cellular_component
has exact synonym: extracellular matrix part
imported from: go.owl
in subset: goantislim grouping
in subset: gocheck do not annotate
in subset: gosubset prok

extracellular region part
type: Class
subclass of: cellular_component
definition: Any constituent part of the extracellular region, the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers constituent parts of the host cell environment outside an intracellular parasite.
id: GO:0044421
has db xref: NIF_Subcellular:sao9117790637
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: cellular_component
has related synonym: extracellular structure
imported from: go.owl
in subset: goantislim grouping
in subset: gocheck do not annotate
in subset: gosubset prok

organelle part
type: Class
subclass of: cellular_component
definition: Any constituent part of an organelle, an organized structure of distinctive morphology and function. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, but excludes the plasma membrane.
id: GO:0044422
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: cellular_component
imported from: go.owl
in subset: goantislim grouping
in subset: gocheck do not annotate
in subset: gosubset prok

intracellular part
type: Class
subclass of: cell part
definition: Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
id: GO:0044424
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: cellular_component
imported from: go.owl
in subset: goantislim grouping
in subset: gocheck do not annotate
in subset: gosubset prok

membrane part
type: Class
subclass of: cellular_component
definition: Any constituent part of a membrane, a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
id: GO:0044425
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: cellular_component
imported from: go.owl
in subset: goantislim grouping
in subset: gocheck do not annotate
in subset: gosubset prok

chromosomal part
type: Class
subclass of: intracellular organelle part
definition: Any constituent part of a chromosome, a structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
id: GO:0044427
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: cellular_component
has exact synonym: chromosomal component
has exact synonym: chromosome component
has exact synonym: chromosome part
imported from: go.owl
in subset: goantislim grouping
in subset: gocheck do not annotate
in subset: gosubset prok

nuclear part
type: Class
subclass of: intracellular organelle part
definition: Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated.
id: GO:0044428
has db xref: NIF_Subcellular:sao1499850686
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: cellular_component
has exact synonym: nuclear subcomponent
has exact synonym: nucleus component
imported from: go.owl
in subset: goantislim grouping
in subset: gocheck do not annotate

mitochondrial part
type: Class
subclass of: cytoplasmic part
subclass of: intracellular organelle part
definition: Any constituent part of a mitochondrion, a semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
id: GO:0044429
has db xref: NIF_Subcellular:sao666410040
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: cellular_component
has exact synonym: mitochondrial subcomponent
has exact synonym: mitochondrion component
imported from: go.owl
in subset: goantislim grouping
in subset: gocheck do not annotate

cytoskeletal part
type: Class
subclass of: intracellular organelle part
definition: Any constituent part of the cytoskeleton, a cellular scaffolding or skeleton that maintains cell shape, enables some cell motion (using structures such as flagella and cilia), and plays important roles in both intra-cellular transport (e.g. the movement of vesicles and organelles) and cellular division. Includes constituent parts of intermediate filaments, microfilaments, microtubules, and the microtrabecular lattice.
id: GO:0044430
has db xref: NIF_Subcellular:sao1635329413
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: cellular_component
has exact synonym: cytoskeletal element
has exact synonym: cytoskeleton component
imported from: go.owl
in subset: goantislim grouping
in subset: gocheck do not annotate

Golgi apparatus part
type: Class
subclass of: cytoplasmic part
subclass of: intracellular organelle part
definition: Any constituent part of the Golgi apparatus, a compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack.
id: GO:0044431
has exact synonym: Golgi component
has exact synonym: Golgi subcomponent
has db xref: NIF_Subcellular:sao624292949
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: cellular_component
imported from: go.owl
in subset: goantislim grouping
in subset: gocheck do not annotate

endoplasmic reticulum part
type: Class
subclass of: cytoplasmic part
subclass of: intracellular organelle part
definition: Any constituent part of the endoplasmic reticulum, the irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae.
has exact synonym: ER component
id: GO:0044432
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: cellular_component
imported from: go.owl
in subset: goantislim grouping
in subset: gocheck do not annotate

cytoplasmic vesicle part
type: Class
subclass of: cytoplasmic part
subclass of: intracellular organelle part
definition: Any constituent part of cytoplasmic vesicle, a vesicle formed of membrane or protein, found in the cytoplasm of a cell.
id: GO:0044433
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: cellular_component
imported from: go.owl
in subset: goantislim grouping
in subset: gocheck do not annotate
in subset: gosubset prok

endosomal part
type: Class
subclass of: cytoplasmic vesicle part
definition: Any constituent part of an endosome, a membrane-bounded organelle to which materials ingested by endocytosis are delivered.
id: GO:0044440
has db xref: NIF_Subcellular:sao1683772610
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: cellular_component
has exact synonym: endosomal subcomponent
has exact synonym: endosome component
imported from: go.owl
in subset: goantislim grouping
in subset: gocheck do not annotate

cytoplasmic part
type: Class
subclass of: intracellular part
definition: Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
id: GO:0044444
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: cellular_component
has exact synonym: cytoplasm component
imported from: go.owl
in subset: goantislim grouping
in subset: gocheck do not annotate
in subset: gosubset prok

cytosolic part
type: Class
subclass of: cytoplasmic part
definition: Any constituent part of cytosol, that part of the cytoplasm that does not contain membranous or particulate subcellular components.
id: GO:0044445
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: cellular_component
has exact synonym: cytosol component
imported from: go.owl
in subset: goantislim grouping
in subset: gocheck do not annotate
in subset: gosubset prok

intracellular organelle part
type: Class
subclass of: organelle part
subclass of: intracellular part
definition: A constituent part of an intracellular organelle, an organized structure of distinctive morphology and function, occurring within the cell. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton but excludes the plasma membrane.
id: GO:0044446
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: cellular_component
imported from: go.owl
in subset: gocheck do not annotate
in subset: gosubset prok

nucleoplasm part
type: Class
subclass of: nuclear part
definition: Any constituent part of the nucleoplasm, that part of the nuclear content other than the chromosomes or the nucleolus.
id: GO:0044451
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: cellular_component
imported from: go.owl
in subset: goantislim grouping
in subset: gocheck do not annotate

nucleolar part
type: Class
subclass of: nuclear part
definition: Any constituent part of a nucleolus, a small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis.
id: GO:0044452
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: cellular_component
has exact synonym: nucleolus component
imported from: go.owl
in subset: goantislim grouping
in subset: gocheck do not annotate

nuclear membrane part
type: Class
subclass of: membrane part
subclass of: nuclear part
definition: Any constituent part of the nuclear membrane, the envelope that surrounds the nucleus of eukaryotic cells.
id: GO:0044453
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: cellular_component
imported from: go.owl
in subset: goantislim grouping
in subset: gocheck do not annotate

nuclear chromosome part
type: Class
subclass of: chromosomal part
subclass of: nuclear part
definition: Any constituent part of a nuclear chromosome, a chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
id: GO:0044454
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: cellular_component
imported from: go.owl
in subset: goantislim grouping
in subset: gocheck do not annotate

mitochondrial membrane part
type: Class
subclass of: membrane part
subclass of: mitochondrial part
definition: Any constituent part of a mitochondrial membrane, either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.
id: GO:0044455
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: cellular_component
imported from: go.owl
in subset: goantislim grouping
in subset: gocheck do not annotate

plasma membrane part
type: Class
subclass of: membrane part
subclass of: cell part
definition: Any constituent part of the plasma membrane, the membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
id: GO:0044459
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: cellular_component
imported from: go.owl
in subset: goantislim grouping
in subset: gocheck do not annotate
in subset: gosubset prok

cell part
type: Class
subclass of: cellular_component
definition: Any constituent part of a cell, the basic structural and functional unit of all organisms.
id: GO:0044464
has db xref: NIF_Subcellular:sao628508602
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has exact synonym: cellular subcomponent
has OBO namespace: cellular_component
has related synonym: protoplast
imported from: go.owl
in subset: goantislim grouping
in subset: gocheck do not annotate
in subset: goslim pir
in subset: gosubset prok

single-organism process
type: Class
subclass of: biological_process
creation date: 2012-09-19T15:05:24Z
definition: A biological process that involves only one organism.
id: GO:0044699
has OBO namespace: biological_process
created by: janelomax
has exact synonym: single organism process
imported from: go.owl

single organism reproductive process
type: Class
subclass of: reproductive process
subclass of: single-organism process
creation date: 2012-09-19T15:56:06Z
definition: A biological process that directly contributes to the process of producing new individuals, involving a single organism.
id: GO:0044702
has OBO namespace: biological_process
created by: janelomax
imported from: go.owl

single-multicellular organism process
type: Class
subclass of: multicellular organismal process
subclass of: single-organism process
creation date: 2012-09-19T16:07:47Z
definition: A biological process occurring within a single, multicellular organism.
id: GO:0044707
has OBO namespace: biological_process
created by: janelomax
imported from: go.owl

single-organism metabolic process
type: Class
subclass of: metabolic process
subclass of: single-organism process
creation date: 2012-10-17T15:46:40Z
definition: A metabolic process - chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances - which involves a single organism.
id: GO:0044710
has OBO namespace: biological_process
created by: janelomax
imported from: go.owl

single-organism carbohydrate metabolic process
type: Class
subclass of: carbohydrate metabolic process
subclass of: single-organism metabolic process
creation date: 2012-10-23T15:40:34Z
id: GO:0044723
definition: The chemical reactions and pathways involving carbohydrates, occurring within a single organism.
has OBO namespace: biological_process
created by: janelomax
imported from: go.owl

DNA methylation or demethylation
type: Class
subclass of: DNA modification
creation date: 2012-10-24T14:49:41Z
id: GO:0044728
definition: The process of adding or removing a methyl group from one or more nucleotides within an DNA molecule.
has OBO namespace: biological_process
has related synonym: changes in DNA methylation
created by: janelomax
imported from: go.owl

single-organism cellular process
type: Class
subclass of: cellular process
subclass of: single-organism process
creation date: 2012-12-11T16:56:55Z
definition: Any process that is carried out at the cellular level, occurring within a single organism.
id: GO:0044763
has OBO namespace: biological_process
created by: janelomax
imported from: go.owl

single-organism transport
type: Class
subclass of: transport
subclass of: single-organism localization
creation date: 2012-12-13T16:25:32Z
id: GO:0044765
definition: The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore, involving a single organism.
has OBO namespace: biological_process
created by: janelomax
imported from: go.owl

single-organism developmental process
type: Class
subclass of: developmental process
subclass of: single-organism process
creation date: 2012-12-19T12:21:31Z
definition: A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition, involving only one organism.
id: GO:0044767
has OBO namespace: biological_process
created by: janelomax
imported from: go.owl

DNA polymerase processivity factor complex
type: Class
subclass of: protein complex
subclass of: intracellular part
creation date: 2013-08-28T11:16:14Z
definition: A protein complex which is capable of increasing the processivity of nucleotide polymerization by DNA polymerase as a part of DNA replication.
id: GO:0044796
has OBO namespace: cellular_component
created by: janelomax
imported from: go.owl

nuclear transcription factor complex
type: Class
subclass of: transcription factor complex
subclass of: nuclear part
creation date: 2013-08-28T12:12:27Z
definition: A protein complex, located in the nucleus, that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.
id: GO:0044798
has OBO namespace: cellular_component
created by: janelomax
imported from: go.owl

macrophage migration inhibitory factor production
type: Class
subclass of: cytokine production
creation date: 2013-09-11T12:04:09Z
id: GO:0044807
has exact synonym: MIF production
definition: The appearance of macrophage migration inhibitory factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
created by: janelomax
term from ontology: obi.owl
imported from: go.owl

Oncostatin M production
type: Class
subclass of: cytokine production
creation date: 2013-09-11T12:18:00Z
id: GO:0044808
has exact synonym: OSM production
definition: The appearance of Oncostatin M due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
created by: janelomax
term from ontology: obi.owl
imported from: go.owl

chemokine (C-C motif) ligand 17 production
type: Class
subclass of: chemokine production
creation date: 2013-09-11T12:21:31Z
has exact synonym: CCL17 production
id: GO:0044809
has exact synonym: TARC production
definition: The appearance of chemokine (C-C motif) ligand 17 (CCL17) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
created by: janelomax
term from ontology: obi.owl
has exact synonym: thymus and activation regulated chemokine production
imported from: go.owl

regulated exocytosis
type: Class
subclass of: exocytosis
definition: A process of exocytosis in which soluble proteins and other substances are initially stored in secretory vesicles for later release. It is found mainly in cells that are specialized for secreting products such as hormones, neurotransmitters, or digestive enzymes rapidly on demand.
id: GO:0045055
has OBO namespace: biological_process
has exact synonym: regulated secretory pathway
imported from: go.owl

azole transport
type: Class
subclass of: organic substance transport
subclass of: nitrogen compound transport
id: GO:0045117
definition: The directed movement of azoles, heterocyclic compounds found in many biologically important substances, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
has OBO namespace: biological_process
imported from: go.owl

tricarboxylic acid cycle enzyme complex
type: Class
subclass of: protein complex
subclass of: cytoplasmic part
definition: Any of the heteromeric enzymes that act in the TCA cycle.
id: GO:0045239
has exact synonym: TCA cycle enzyme complex
has OBO namespace: cellular_component
imported from: go.owl
in subset: goslim pir
in subset: gosubset prok

isocitrate dehydrogenase complex (NAD+)
type: Class
subclass of: tricarboxylic acid cycle enzyme complex
subclass of: oxidoreductase complex
definition: Complex that possesses isocitrate dehydrogenase (NAD+) activity.
id: GO:0045242
has OBO namespace: cellular_component
imported from: go.owl
in subset: gosubset prok

succinate-CoA ligase complex (GDP-forming)
type: Class
subclass of: mitochondrial tricarboxylic acid cycle enzyme complex
subclass of: succinate-CoA ligase complex
definition: A heterodimeric enzyme complex, usually composed of an alpha and beta chain. Functions in the TCA cycle, hydrolyzing succinyl-CoA into succinate and CoA, thereby forming GTP.
has alternative id: GO:0008325
id: GO:0045244
has alternative id: GO:0045245
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
has exact synonym: succinyl-CoA synthetase, GDP-forming
imported from: go.owl

respiratory chain complex IV
type: Class
subclass of: intracellular part
subclass of: cytochrome complex
subclass of: respiratory chain complex
definition: A part of the respiratory chain, containing the 13 polypeptide subunits of cytochrome c oxidase, including cytochrome a and cytochrome a3. Catalyzes the oxidation of reduced cytochrome c by dioxygen (O2).
id: GO:0045277
has alternative id: GO:0045287
has OBO namespace: cellular_component
has exact synonym: cytochrome c oxidase complex
has related synonym: electron transport complex IV
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl
in subset: goslim pir
in_subset: goslim pir
in subset: gosubset prok
in_subset: gosubset prok

leukocyte activation
type: Class
subclass of: cell activation
subclass of: immune system process
definition: A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor.
id: GO:0045321
has db xref: Wikipedia:Immunologic_activation
has OBO namespace: biological_process
has exact synonym: immune cell activation
has exact synonym: leucocyte activation
imported from: go.owl

heterocycle metabolic process
type: Class
subclass of: cellular metabolic process
id: GO:0046483
definition: The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
has OBO namespace: biological_process
has exact synonym: heterocycle metabolism
imported from: go.owl
in subset: goslim pir
in subset: gosubset prok

lymphocyte activation
type: Class
subclass of: leukocyte activation
definition: A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor.
id: GO:0046649
has OBO namespace: biological_process
imported from: go.owl

lymphocyte proliferation
type: Class
subclass of: mononuclear cell proliferation
subclass of: lymphocyte activation
id: GO:0046651
definition: The expansion of a lymphocyte population by cell division.
has OBO namespace: biological_process
imported from: go.owl

lipopolysaccharide receptor complex
type: Class
subclass of: receptor complex
subclass of: membrane part
definition: A multiprotein complex that consists of at least three proteins, CD14, TLR4, and MD-2, each of which is glycosylated and which functions as a lipopolysaccharide (LPS) receptor that primes the innate immune response against bacterial pathogens.
id: GO:0046696
has exact synonym: LPS receptor complex
comment: Note that this term should not be used to refer to CD14 alone, but the multiprotein receptor complex that it is part of.
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

hormone secretion
type: Class
subclass of: hormone transport
subclass of: signal release
id: GO:0046879
definition: The regulated release of hormones, substances with a specific regulatory effect on a particular organ or group of cells.
has OBO namespace: biological_process
imported from: go.owl

secretion
type: Class
subclass of: single-organism transport
id: GO:0046903
definition: The controlled release of a substance by a cell or a tissue.
has OBO namespace: biological_process
imported from: go.owl
in subset: goslim pir
in subset: gosubset prok

animal organ development
type: Class
subclass of: anatomical structure development
definition: Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
id: GO:0048513
has db xref: Wikipedia:Organogenesis
has OBO namespace: biological_process
has exact synonym: development of an organ
has exact synonym: organogenesis
imported from: go.owl

positive regulation of biological process
type: Class
subclass of: regulation of biological process
definition: Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
has alternative id: GO:0043119
id: GO:0048518
has narrow synonym: activation of biological process
has OBO namespace: biological_process
has exact synonym: positive regulation of physiological process
has narrow synonym: stimulation of biological process
has exact synonym: up regulation of biological process
has exact synonym: up-regulation of biological process
has exact synonym: upregulation of biological process
imported from: go.owl
in subset: gosubset prok

hematopoietic or lymphoid organ development
type: Class
subclass of: single-organism developmental process
subclass of: animal organ development
id: GO:0048534
definition: The process whose specific outcome is the progression of any organ involved in hematopoiesis (also known as hemopoiesis) or lymphoid cell activation over time, from its formation to the mature structure. Such development includes differentiation of resident cell types (stromal cells) and of migratory cell types dependent on the unique microenvironment afforded by the organ for their proper differentiation.
has OBO namespace: biological_process
has exact synonym: haematopoietic or lymphoid organ development
has exact synonym: haemopoietic or lymphoid organ development
has exact synonym: hemopoietic or lymphoid organ development
imported from: go.owl

regulation of response to stimulus
type: Class
subclass of: regulation of biological process
definition: Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
id: GO:0048583
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: biological_process
imported from: go.owl
in subset: gocheck do not manually annotate
in subset: gosubset prok

positive regulation of response to stimulus
type: Class
subclass of: positive regulation of biological process
subclass of: regulation of response to stimulus
definition: Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
id: GO:0048584
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has narrow synonym: activation of response to stimulus
has OBO namespace: biological_process
has narrow synonym: stimulation of response to stimulus
has exact synonym: up regulation of response to stimulus
has exact synonym: up-regulation of response to stimulus
has exact synonym: upregulation of response to stimulus
imported from: go.owl
in subset: gocheck do not manually annotate

anatomical structure development
type: Class
subclass of: developmental process
id: GO:0048856
definition: The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
comment: This term was added by GO_REF:0000021.
has OBO namespace: biological_process
has exact synonym: development of an anatomical structure
imported from: go.owl
in subset: goslim chembl
in subset: goslim generic

cellular developmental process
type: Class
subclass of: single-organism cellular process
subclass of: single-organism developmental process
definition: A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition.
id: GO:0048869
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl
in subset: gosubset prok
in_subset: gosubset prok

cell motility
type: Class
subclass of: movement of cell or subcellular component
subclass of: locomotion
definition: Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.
id: GO:0048870
has OBO namespace: biological_process
has exact synonym: cell locomotion
has related synonym: cell movement
has exact synonym: movement of a cell
imported from: go.owl
in subset: goslim chembl
in subset: goslim generic
in subset: gosubset prok

regulation of immune response
type: Class
subclass of: regulation of immune system process
subclass of: regulation of response to stimulus
definition: Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
id: GO:0050776
has db xref: Reactome:REACT_101484
has db xref: Reactome:REACT_106667
has db xref: Reactome:REACT_107426
has db xref: Reactome:REACT_11152
has db xref: Reactome:REACT_81657
has db xref: Reactome:REACT_82803
has db xref: Reactome:REACT_87475
has db xref: Reactome:REACT_94152
has db xref: Reactome:REACT_95389
has db xref: Reactome:REACT_97860
has OBO namespace: biological_process
imported from: go.owl

positive regulation of immune response
type: Class
subclass of: positive regulation of immune system process
subclass of: positive regulation of response to stimulus
subclass of: regulation of immune response
definition: Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
id: GO:0050778
has OBO namespace: biological_process
has narrow synonym: stimulation of immune response
has exact synonym: up regulation of immune response
has exact synonym: up-regulation of immune response
has exact synonym: upregulation of immune response
imported from: go.owl

regulation of biological process
type: Class
subclass of: biological regulation
definition: Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
id: GO:0050789
has alternative id: GO:0050791
has OBO namespace: biological_process
has exact synonym: regulation of physiological process
imported from: go.owl
in subset: goslim agr
in subset: goslim aspergillus
in subset: goslim candida
in subset: gosubset prok

regulation of cellular process
type: Class
subclass of: regulation of biological process
definition: Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
id: GO:0050794
has alternative id: GO:0051244
has OBO namespace: biological_process
has exact synonym: regulation of cellular physiological process
imported from: go.owl
in subset: gosubset prok

coagulation
type: Class
subclass of: single-multicellular organism process
id: GO:0050817
definition: The process in which a fluid solution, or part of it, changes into a solid or semisolid mass.
has OBO namespace: biological_process
has exact synonym: clotting
imported from: go.owl
in subset: goslim pir

regulation of body fluid levels
type: Class
subclass of: regulation of biological quality
definition: Any process that modulates the levels of body fluids.
id: GO:0050878
has OBO namespace: biological_process
imported from: go.owl
in subset: goslim pir

response to stimulus
type: Class
subclass of: biological_process
definition: Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
id: GO:0050896
has alternative id: GO:0051869
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
has exact synonym: physiological response to stimulus
imported from: go.owl
in subset: gocheck do not manually annotate
in_subset: gocheck do not manually annotate
in_subset: goslim agr
in subset: goslim agr
in subset: goslim mouse
in_subset: goslim mouse
in subset: goslim pir
in_subset: goslim pir
in_subset: gosubset prok
in subset: gosubset prok

regulation of DNA metabolic process
type: Class
subclass of: regulation of nucleobase-containing compound metabolic process
subclass of: regulation of macromolecule metabolic process
definition: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA.
id: GO:0051052
has OBO namespace: biological_process
has exact synonym: regulation of DNA metabolism
imported from: go.owl
in subset: goslim yeast
in subset: gosubset prok

regulation of nitrogen compound metabolic process
type: Class
subclass of: regulation of metabolic process
definition: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
id: GO:0051171
has OBO namespace: biological_process
has exact synonym: regulation of nitrogen metabolic process
has exact synonym: regulation of nitrogen metabolism
imported from: go.owl
in subset: gosubset prok

localization
type: Class
subclass of: biological_process
definition: Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation.
id: GO:0051179
has OBO namespace: biological_process
has narrow synonym: establishment and maintenance of cellular component location
has exact synonym: establishment and maintenance of localization
has exact synonym: establishment and maintenance of position
has narrow synonym: establishment and maintenance of substance location
has narrow synonym: establishment and maintenance of substrate location
has exact synonym: localisation
imported from: go.owl
in subset: goslim agr
in subset: goslim pir
in subset: gosubset prok

establishment of localization
type: Class
subclass of: localization
definition: Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.
id: GO:0051234
has OBO namespace: biological_process
has exact synonym: establishment of localisation
imported from: go.owl
in subset: goslim mouse
in subset: goslim pir
in subset: gosubset prok

protein polymerization
type: Class
subclass of: cellular protein complex assembly
id: GO:0051258
definition: The process of creating protein polymers, compounds composed of a large number of component monomers; polymeric proteins may be made up of different or identical monomers. Polymerization occurs by the addition of extra monomers to an existing poly- or oligomeric protein.
has OBO namespace: biological_process
has exact synonym: protein polymer biosynthesis
has exact synonym: protein polymer biosynthetic process
has exact synonym: protein polymer formation
imported from: go.owl
in subset: goslim pir
in subset: gosubset prok

chromosome organization
type: Class
subclass of: organelle organization
definition: A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.
has alternative id: GO:0007001
id: GO:0051276
has alternative id: GO:0051277
has OBO namespace: biological_process
has exact synonym: chromosome organisation
has related synonym: chromosome organization and biogenesis
term from ontology: go.owl
has related synonym: maintenance of genome integrity
has related synonym: nuclear genome maintenance
term from ontology: obi.owl
imported from: go.owl
in_subset: goslim chembl
in subset: goslim chembl
in_subset: goslim generic
in subset: goslim generic
in_subset: goslim pir
in subset: goslim pir
in subset: gosubset prok
in_subset: gosubset prok

histamine transport
type: Class
subclass of: ammonium transport
subclass of: azole transport
id: GO:0051608
definition: The directed movement of histamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Histamine is a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans.
has OBO namespace: biological_process
imported from: go.owl

cellular response to stimulus
type: Class
subclass of: cellular process
subclass of: response to stimulus
definition: Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell.
id: GO:0051716
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: biological_process
imported from: go.owl
in subset: gocheck do not manually annotate
in subset: gosubset prok

nuclear DNA-directed RNA polymerase complex
type: Class
subclass of: DNA-directed RNA polymerase complex
subclass of: nuclear part
definition: A protein complex, located in the nucleus, that possesses DNA-directed RNA polymerase activity.
id: GO:0055029
has OBO namespace: cellular_component
imported from: go.owl

regulation of macromolecule metabolic process
type: Class
subclass of: regulation of metabolic process
definition: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
id: GO:0060255
has OBO namespace: biological_process
imported from: go.owl
in subset: gosubset prok

transferase complex, transferring phosphorus-containing groups
type: Class
subclass of: transferase complex
creation date: 2015-05-06T11:22:38Z
definition: A transferase complex capable of catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
id: GO:0061695
has OBO namespace: cellular_component
created by: dph
imported from: go.owl

macromolecular complex assembly
type: Class
subclass of: cellular component assembly
subclass of: macromolecular complex subunit organization
id: GO:0065003
definition: The aggregation, arrangement and bonding together of a set of macromolecules to form a complex.
has OBO namespace: biological_process
has exact synonym: macromolecule complex assembly
imported from: go.owl
in subset: goslim chembl
in subset: goslim generic
in subset: goslim metagenomics
in subset: goslim pir
in subset: gosubset prok

biological regulation
type: Class
subclass of: biological_process
definition: Any process that modulates a measurable attribute of any biological process, quality or function.
id: GO:0065007
has OBO namespace: biological_process
has broad synonym: regulation
imported from: go.owl
in subset: goslim pir
in subset: gosubset prok

regulation of biological quality
type: Class
subclass of: biological regulation
definition: Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc.
id: GO:0065008
has OBO namespace: biological_process
has exact synonym: regulation of biological attribute
has exact synonym: regulation of biological characteristic
imported from: go.owl
in subset: gosubset prok

regulation of molecular function
type: Class
subclass of: biological regulation
definition: Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
id: GO:0065009
has OBO namespace: biological_process
has exact synonym: regulation of a molecular function
imported from: go.owl
in subset: gosubset prok

transforming growth factor beta type I receptor homodimeric complex
type: Class
subclass of: transforming growth factor beta receptor complex
definition: A receptor complex that consists of two transforming growth factor beta (TGF-beta) type I receptor monomers. TGF-beta type I receptor dimers form in the presence or absence of ligand, and can associate with ligand-bound TGF-beta type II receptor dimers.
id: GO:0070018
has exact synonym: TGF-beta type I receptor complex
has exact synonym: TGF-beta type I receptor dimer
has exact synonym: TGFBR1 homodimer
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
has exact synonym: transforming growth factor beta type I receptor complex
imported from: go.owl

transforming growth factor beta type II receptor homodimeric complex
type: Class
subclass of: transforming growth factor beta receptor complex
definition: A receptor complex that consists of two transforming growth factor beta (TGF-beta) type II receptor monomers. TGF-beta type II receptor dimers form in the presence or absence of ligand, and upon ligand binding can associate with TGF-beta type I receptor dimers.
id: GO:0070019
has exact synonym: TGF-beta type II receptor complex
has exact synonym: TGF-beta type II receptor dimer
has exact synonym: TGFBR2 homodimer
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
has exact synonym: transforming growth factor beta type II receptor complex
imported from: go.owl

transforming growth factor beta receptor complex
type: Class
subclass of: plasma membrane receptor complex
subclass of: serine/threonine protein kinase complex
definition: A homodimeric receptor complex that consists of two TGF-beta receptor monomers.
id: GO:0070022
has broad synonym: TGF-beta receptor complex
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
has exact synonym: transforming growth factor beta receptor complex
imported from: go.owl

cytochrome complex
type: Class
subclass of: protein complex
definition: A protein complex in which at least one of the proteins is a cytochrome, i.e. a heme-containing protein involved in catalysis of redox reactions.
id: GO:0070069
has OBO namespace: cellular_component
imported from: go.owl

shelterin complex
type: Class
subclass of: nuclear telomere cap complex
definition: A nuclear telomere cap complex that is formed by the association of telomeric ssDNA- and dsDNA-binding proteins with telomeric DNA, and is involved in telomere protection and recruitment of telomerase. The complex is known to contain TERF1, TERF2, POT1, RAP1, TINF2 and ACD in mammalian cells, and Pot1, Tpz1, Rap1, Rif1, Rif2 and Taz1 in Schizosaccharomyces. Taz1 and Rap1 (or their mammalian equivalents) form a dsDNA-binding subcomplex, Pot1 and Tpz1 form an ssDNA-binding subcomplex, and the two subcomplexes are bridged by Poz1, which acts as an effector molecule along with Ccq1.
id: GO:0070187
has exact synonym: Pot1 complex
has exact synonym: Pot1-Tpz1 complex
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
has exact synonym: telosome
imported from: go.owl

actin polymerization-dependent cell motility
type: Class
subclass of: cell motility
definition: A process involved in the controlled movement of a bacterial cell powered by the continuous polymerization of actin at one pole of the cell.
id: GO:0070358
has OBO namespace: biological_process
has exact synonym: cell motility by actin tail formation
term from ontology: go.owl
term from ontology: obi.owl
imported from: go.owl
in_subset: gosubset prok
in subset: gosubset prok

Mad-Max complex
type: Class
subclass of: RNA polymerase II transcription repressor complex
definition: A transcriptional repressor complex that consists of a heterodimer of the bHLH-ZIP proteins Mad and Max.
id: GO:0070443
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

SWI/SNF superfamily-type complex
type: Class
subclass of: protein complex
subclass of: nuclear part
creation date: 2009-04-29T12:55:46Z
definition: A protein complex that contains an ortholog of the Saccharomyces ATPase Swi2/Snf2 as one of the core components and mediates assembly of nucleosomes, changes to the spacing or structure of nucleosomes, or some combination of those activities in a manner that requires ATP.
id: GO:0070603
has related synonym: SWI-SNF global transcription activator complex
has exact synonym: SWI-SNF-type complex
has related synonym: SWI/SNF-type complex
has related synonym: SWI2/SNF2 superfamily ATP-dependent chromatin remodeling complex
has OBO namespace: cellular_component
term from ontology: go.owl
created by: midori
term from ontology: pro.owl
imported from: go.owl

leukocyte proliferation
type: Class
subclass of: cell proliferation
creation date: 2009-05-28T05:25:28Z
id: GO:0070661
definition: The expansion of a leukocyte population by cell division.
has OBO namespace: biological_process
created by: midori
imported from: go.owl

P-TEFb complex
type: Class
subclass of: cyclin/CDK positive transcription elongation factor complex
creation date: 2009-06-03T03:12:56Z
definition: A dimeric positive transcription elongation factor complex b that comprises a cyclin-dependent kinase containing the catalytic subunit, Cdk9, and a regulatory subunit, cyclin T.
has narrow synonym: Bur1/Bur2 complex
id: GO:0070691
has narrow synonym: Sgv1/Bur2 complex
has OBO namespace: cellular_component
has related synonym: dimeric positive transcription elongation factor complex b
term from ontology: go.owl
created by: midori
term from ontology: pro.owl
imported from: go.owl

interleukin-23 complex
type: Class
subclass of: protein complex
subclass of: extracellular region part
creation date: 2009-06-23T01:06:02Z
definition: A protein complex that is composed of an interleukin-23 alpha (p19, product of the IL23A gene) and an interleukin-12 beta (p40, product of the IL12B gene) subunit and is secreted into the extracellular space.
id: GO:0070743
has exact synonym: IL-23 complex
has narrow synonym: IL12B
has narrow synonym: IL23A
comment: Note that this heterodimeric cytokine utilizes the same beta subunit as IL-12.
has OBO namespace: cellular_component
term from ontology: go.owl
created by: midori
has narrow synonym: p19
has narrow synonym: p40
term from ontology: pro.owl
imported from: go.owl

SMAD protein complex
type: Class
subclass of: protein complex
subclass of: intracellular part
creation date: 2009-11-16T02:28:59Z
definition: A protein complex that consists of only SMAD proteins; may be homomeric or heteromeric.
id: GO:0071141
has exact synonym: SMAD complex
has OBO namespace: cellular_component
term from ontology: go.owl
created by: midori
term from ontology: pro.owl
imported from: go.owl

SMAD2-SMAD4 protein complex
type: Class
subclass of: transcription factor complex
subclass of: SMAD protein complex
creation date: 2009-11-16T02:47:15Z
definition: A heteromeric SMAD protein complex that contains SMAD2 and SMAD4.
id: GO:0071145
has exact synonym: SMAD2-SMAD4 heteromer complex
has OBO namespace: cellular_component
term from ontology: go.owl
created by: midori
term from ontology: pro.owl
imported from: go.owl

NF-kappaB complex
type: Class
subclass of: protein complex
subclass of: intracellular part
creation date: 2009-11-17T02:03:34Z
definition: A protein complex that consists of a homo- or heterodimer of members of a family of structurally related proteins that contain a conserved N-terminal region called the Rel homology domain (RHD). In the nucleus, NF-kappaB complexes act as transcription factors. In unstimulated cells, NF-kappaB dimers are sequestered in the cytoplasm by IkappaB monomers; signals that induce NF-kappaB activity cause degradation of IkappaB, allowing NF-kappaB dimers to translocate to the nucleus and induce gene expression.
id: GO:0071159
has OBO namespace: cellular_component
term from ontology: go.owl
created by: midori
term from ontology: pro.owl
imported from: go.owl

transforming growth factor beta production
type: Class
subclass of: cytokine production
creation date: 2010-02-05T03:56:57Z
id: GO:0071604
has exact synonym: TGF-B production
has exact synonym: TGF-beta production
has exact synonym: TGFB production
has exact synonym: TGFb production
definition: The appearance of any member of the transforming growth factor-beta family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Transforming growth factor-beta family members include TGF-B1, TGF-B2, and TGF-B3.
has OBO namespace: biological_process
term from ontology: go.owl
created by: midori
term from ontology: obi.owl
has exact synonym: transforming growth factor-beta production
imported from: go.owl

monocyte chemotactic protein-1 production
type: Class
subclass of: chemokine production
creation date: 2010-02-05T04:09:53Z
has exact synonym: CCL2 production
id: GO:0071605
has exact synonym: MCP-1 production
definition: The appearance of monocyte chemotactic protein-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
created by: midori
term from ontology: obi.owl
imported from: go.owl

chemokine (C-C motif) ligand 4 production
type: Class
subclass of: chemokine production
creation date: 2010-02-05T04:16:42Z
has exact synonym: CCL4 production
id: GO:0071606
has exact synonym: MIP-1b production
definition: The appearance of chemokine (C-C motif) ligand 4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
has broad synonym: macrophage inflammatory protein production
created by: midori
term from ontology: obi.owl
imported from: go.owl

macrophage inflammatory protein-1 gamma production
type: Class
subclass of: chemokine production
creation date: 2010-02-05T04:19:52Z
has exact synonym: CCL9 production
id: GO:0071607
has exact synonym: MIP-1g production
definition: The appearance of macrophage inflammatory protein-1 gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
has exact synonym: chemokine (C-C motif) ligand 9 production
term from ontology: go.owl
created by: midori
term from ontology: obi.owl
imported from: go.owl

macrophage inflammatory protein-1 alpha production
type: Class
subclass of: chemokine production
creation date: 2010-02-05T04:24:17Z
has exact synonym: CCL3 production
id: GO:0071608
has exact synonym: MIP-1a production
definition: The appearance of macrophage inflammatory protein 1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
has exact synonym: chemokine (C-C motif) ligand 3 production
term from ontology: go.owl
has broad synonym: macrophage inflammatory protein production
created by: midori
term from ontology: obi.owl
imported from: go.owl

chemokine (C-C motif) ligand 5 production
type: Class
subclass of: chemokine production
creation date: 2010-02-05T04:32:35Z
has exact synonym: CCL5 production
id: GO:0071609
has exact synonym: RANTES production
has exact synonym: Regulated upon Activation, Normal T-cell Expressed, and Secreted production
definition: The appearance of chemokine (C-C motif) ligand 5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
created by: midori
term from ontology: obi.owl
imported from: go.owl

chemokine (C-C motif) ligand 1 production
type: Class
subclass of: chemokine production
creation date: 2010-02-05T04:35:00Z
has exact synonym: CCL1 production
id: GO:0071610
has exact synonym: T cell activation 3 production
has exact synonym: TCA-3 production
definition: The appearance of chemokine (C-C motif) ligand 1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
created by: midori
term from ontology: obi.owl
imported from: go.owl

granulocyte colony-stimulating factor production
type: Class
subclass of: cytokine production
creation date: 2010-02-05T04:38:11Z
has exact synonym: CSF3 production
has exact synonym: G-CSF production
id: GO:0071611
definition: The appearance of granulocyte colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
has exact synonym: colony stimulating factor 3 (granulocyte) production
has exact synonym: filgrastim production
term from ontology: go.owl
has exact synonym: granulocyte colony stimulating factor production
has exact synonym: lenograstim production
created by: midori
term from ontology: obi.owl
has exact synonym: pluripoietin production
imported from: go.owl

IP-10 production
type: Class
subclass of: chemokine production
creation date: 2010-02-05T04:43:56Z
has exact synonym: CXCL10 production
id: GO:0071612
definition: The appearance of IP-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
has exact synonym: chemokine (C-C motif) ligand 10 production
term from ontology: go.owl
created by: midori
term from ontology: obi.owl
imported from: go.owl

granzyme B production
type: Class
subclass of: production of molecular mediator of immune response
creation date: 2010-02-05T04:47:15Z
id: GO:0071613
definition: The appearance of granzyme B due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
created by: midori
term from ontology: obi.owl
imported from: go.owl

organic substance transport
type: Class
subclass of: transport
creation date: 2010-03-08T02:15:14Z
id: GO:0071702
definition: The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon.
has OBO namespace: biological_process
created by: midori
imported from: go.owl

organic substance metabolic process
type: Class
subclass of: metabolic process
creation date: 2010-03-08T03:32:18Z
id: GO:0071704
definition: The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.
has OBO namespace: biological_process
created by: midori
has exact synonym: organic molecular entity metabolic process
has exact synonym: organic molecular entity metabolism
has exact synonym: organic substance metabolism
imported from: go.owl

nitrogen compound transport
type: Class
subclass of: transport
creation date: 2010-03-08T03:56:28Z
id: GO:0071705
definition: The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
has OBO namespace: biological_process
created by: midori
imported from: go.owl

tumor necrosis factor superfamily cytokine production
type: Class
subclass of: cytokine production
creation date: 2010-03-09T02:40:35Z
id: GO:0071706
has related synonym: TNF superfamily production
has exact synonym: TNFSF cytokine production
definition: The appearance of any member of the TNF superfamily due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
created by: midori
term from ontology: obi.owl
imported from: go.owl

protein complex subunit organization
type: Class
subclass of: macromolecular complex subunit organization
creation date: 2010-09-08T10:01:42Z
definition: Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex.
id: GO:0071822
has OBO namespace: biological_process
created by: midori
has exact synonym: protein complex subunit organisation
imported from: go.owl

cellular component organization or biogenesis
type: Class
subclass of: biological_process
creation date: 2010-09-10T01:39:16Z
definition: A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.
id: GO:0071840
has alternative id: GO:0071841
has OBO namespace: biological_process
has exact synonym: cellular component organisation or biogenesis
has exact synonym: cellular component organisation or biogenesis at cellular level
has exact synonym: cellular component organization or biogenesis at cellular level
created by: midori
imported from: go.owl
in subset: goslim agr
in subset: goslim metagenomics

chemokine (C-C motif) ligand 22 production
type: Class
subclass of: chemokine production
creation date: 2010-09-28T11:33:13Z
has exact synonym: C-C motif chemokine 22 production
has exact synonym: CCL-22 production
has exact synonym: CCL22 production
id: GO:0071924
definition: The appearance of chemokine (C-C motif) ligand 22 (CCL22) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
created by: midori
term from ontology: obi.owl
imported from: go.owl

Myc-Max complex
type: Class
subclass of: RNA polymerase II transcription factor complex
creation date: 2010-10-01T11:56:17Z
definition: A transcription factor complex that consists of a heterodimer of the bHLH-ZIP proteins Myc and Max.
id: GO:0071943
has OBO namespace: cellular_component
term from ontology: go.owl
created by: midori
term from ontology: pro.owl
imported from: go.owl

tumor necrosis factor (ligand) superfamily member 11 production
type: Class
subclass of: tumor necrosis factor superfamily cytokine production
creation date: 2011-01-14T01:42:23Z
id: GO:0072535
has exact synonym: RANKL production
has exact synonym: TNFSF11 production
definition: The appearance of tumor necrosis factor superfamily member 11 (TNFSF11; RANKL) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
created by: midori
term from ontology: obi.owl
has exact synonym: tumor necrosis factor ligand superfamily member 11 production
imported from: go.owl

Cul4-RING E3 ubiquitin ligase complex
type: Class
subclass of: cullin-RING ubiquitin ligase complex
definition: A ubiquitin ligase complex in which a cullin from the Cul4 family and a RING domain protein form the catalytic core; substrate specificity is conferred by an adaptor protein.
id: GO:0080008
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

regulation of primary metabolic process
type: Class
subclass of: regulation of metabolic process
creation date: 2009-04-22T04:30:52Z
definition: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
id: GO:0080090
has OBO namespace: biological_process
created by: donghui
imported from: go.owl

nucleic acid metabolic process
type: Class
subclass of: nucleobase-containing compound metabolic process
subclass of: macromolecule metabolic process
creation date: 2010-04-07T10:18:47Z
definition: Any cellular metabolic process involving nucleic acids.
id: GO:0090304
has OBO namespace: biological_process
created by: tanyaberardini
imported from: go.owl

nuclear transcriptional repressor complex
type: Class
subclass of: transcriptional repressor complex
subclass of: nucleoplasm part
creation date: 2014-05-09T13:23:51Z
definition: A protein complex, located in the nucleus, that possesses activity that prevents or downregulates transcription.
id: GO:0090568
has OBO namespace: cellular_component
created by: tanyaberardini
imported from: go.owl

RNA polymerase II transcription repressor complex
type: Class
subclass of: nuclear transcriptional repressor complex
creation date: 2014-05-09T13:26:16Z
definition: A protein complex, located in the nucleus, that possesses activity that prevents or downregulates transcription from a RNA polymerase II promoter.
id: GO:0090571
has OBO namespace: cellular_component
created by: tanyaberardini
imported from: go.owl

RNA polymerase II transcription factor complex
type: Class
subclass of: nuclear transcription factor complex
creation date: 2014-05-09T14:04:37Z
definition: A transcription factor complex that acts at promoters of genes transcribed by RNA polymerase II.
id: GO:0090575
has OBO namespace: cellular_component
created by: tanyaberardini
imported from: go.owl

RNA polymerase III transcription factor complex
type: Class
subclass of: nuclear transcription factor complex
creation date: 2014-05-09T14:04:37Z
definition: A transcription factor complex that acts at promoters of genes transcribed by RNA polymerase III.
id: GO:0090576
has OBO namespace: cellular_component
created by: tanyaberardini
imported from: go.owl

interferon regulatory factor complex
type: Class
subclass of: protein complex
creation date: 2011-06-15T04:22:30Z
definition: A protein complex that consists of two interferon regulatory proteins (IRFs); may be homodimeric or heterodimeric. The activation of a latent closed conformation of IRF in the cytoplasm is triggered by phosphorylation of Ser/Thr residues in a C-terminal region. Phosphorylation stimulates the C-terminal autoinhibitory domain to attain a highly extended conformation triggering dimerization through extensive contacts to a second subunit.
id: GO:0097071
has exact synonym: IRF complex
has OBO namespace: cellular_component
term from ontology: go.owl
created by: paola
term from ontology: pro.owl
imported from: go.owl

interferon regulatory factor 5 complex
type: Class
subclass of: interferon regulatory factor complex
creation date: 2011-06-15T04:28:57Z
definition: An interferon regulatory factor complex that consists of a homodimer of interferon regulatory factor 5.
id: GO:0097073
has exact synonym: IRF5:IRF5 complex
has OBO namespace: cellular_component
term from ontology: go.owl
created by: paola
term from ontology: pro.owl
imported from: go.owl

interleukin-17A production
type: Class
subclass of: interleukin-17 production
creation date: 2011-06-23T11:31:10Z
id: GO:0097087
has exact synonym: IL-17A production
definition: The appearance of interleukin-17A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
created by: paola
imported from: go.owl

interleukin-17F production
type: Class
subclass of: interleukin-17 production
creation date: 2011-06-23T11:32:59Z
id: GO:0097088
has exact synonym: IL-17F production
definition: The appearance of interleukin-17F due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
created by: paola
imported from: go.owl

organic cyclic compound binding
type: Class
subclass of: binding
creation date: 2011-09-23T02:31:01Z
id: GO:0097159
definition: Interacting selectively and non-covalently with an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure.
has OBO namespace: molecular_function
created by: paola
imported from: go.owl

complement-dependent cytotoxicity
type: Class
subclass of: cell killing
subclass of: single-organism process
creation date: 2012-03-22T05:04:04Z
id: GO:0097278
definition: Lysis of a cell resulting from triggering of the complement cascade. An example can be seen with complement activation and subsequent lysis of a bacterial cell as a result of the binding of IgM to the cell surface followed by the binding of complement proteins to that antibody.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
created by: paola
imported from: go.owl

histamine secretion mediated by immunoglobulin
type: Class
subclass of: inflammatory response to antigenic stimulus
subclass of: histamine secretion involved in inflammatory response
creation date: 2012-03-26T01:30:25Z
id: GO:0097280
definition: Histamine release triggered by the binding of an antigen to an immunoglobulin bound to the cell surface.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
created by: paola
imported from: go.owl

immune complex formation
type: Class
subclass of: immunoglobulin mediated immune response
creation date: 2012-03-26T01:35:21Z
id: GO:0097281
definition: The process that gives rise to an immune complex. Immune complexes are clusters of antibodies bound to antigen, to which complement may also be fixed, and which may precipitate or remain in solution. Examples are the clumping of cells such as bacteria or red blood cells in the presence of an antibody, precipitation of a toxin after an antibody binds to it, and clumping of viral particles as a result of antibody binding to the virus.
has exact synonym: antibody-mediated agglutination
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
created by: paola
imported from: go.owl

immunoglobulin-mediated neutralization
type: Class
subclass of: immunoglobulin mediated immune response
creation date: 2012-03-26T01:55:24Z
id: GO:0097282
definition: The inhibition of an antigen's biological effects by antibody binding to it. An example is neutralization of diphtheria toxin by preventing its entry into human cells via the binding of antibody specific for diphtheria toxin.
has exact synonym: antibody-mediated neutralization
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
created by: paola
imported from: go.owl

chemokine (C-C motif) ligand 19 production
type: Class
subclass of: chemokine production
creation date: 2012-10-23T07:54:10Z
has exact synonym: CCL19 production
has exact synonym: EBI1 ligand chemokine production
has exact synonym: ELC production
id: GO:0097388
has exact synonym: MIP-3-beta production
definition: The appearance of chemokine (C-C motif) ligand 19 (CCL19) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
has exact synonym: macrophage inflammatory protein-3-beta production
term from ontology: obi.owl
created by: paola
imported from: go.owl

chemokine (C-C motif) ligand 21 production
type: Class
subclass of: chemokine production
creation date: 2012-10-23T07:56:26Z
has exact synonym: CCL21 production
id: GO:0097389
definition: The appearance of chemokine (C-C motif) ligand 21 (CCL21) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
created by: paola
imported from: go.owl

chemokine (C-X-C motif) ligand 12 production
type: Class
subclass of: chemokine production
creation date: 2012-10-23T07:57:28Z
has exact synonym: CXCL12 production
id: GO:0097390
definition: The appearance of chemokine (C-X-C motif) ligand 12 (CXCL12) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
created by: paola
imported from: go.owl

chemokine (C-X-C motif) ligand 13 production
type: Class
subclass of: chemokine production
creation date: 2012-10-23T07:58:28Z
has exact synonym: CXCL13 production
id: GO:0097391
definition: The appearance of chemokine (C-X-C motif) ligand 13 (CXCL13) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
created by: paola
imported from: go.owl

chemokine (C-X-C motif) ligand 16 production
type: Class
subclass of: chemokine production
creation date: 2012-10-23T07:59:43Z
has exact synonym: CXCL16 production
id: GO:0097392
definition: The appearance of chemokine (C-X-C motif) ligand 16 (CXCL16) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
has OBO namespace: biological_process
term from ontology: go.owl
term from ontology: obi.owl
created by: paola
imported from: go.owl

supramolecular fiber organization
type: Class
subclass of: cellular component organization
subclass of: single-organism cellular process
creation date: 2012-11-27T15:46:25Z
definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a supramolecular fiber, a polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure.
has alternative id: GO:0043206
id: GO:0097435
has OBO namespace: biological_process
has narrow synonym: extracellular fibril organisation
has narrow synonym: extracellular fibril organization
has narrow synonym: extracellular fibril organization and biogenesis
has related synonym: fibril organisation
has related synonym: fibril organization
created by: paola
imported from: go.owl

GAIT complex
type: Class
subclass of: protein complex
creation date: 2012-12-19T09:32:25Z
definition: A protein complex which mediates interferon-gamma-induced transcript-selective translation inhibition in inflammation processes. The complex binds to stem loop-containing GAIT elements in the 3'-UTR of diverse inflammatory mRNAs and suppresses their translation by blocking the recruitment of the 43S ribosomal complex to m7G cap-bound eIF4G. In humans it includes RPL13A, EPRS, SYNCRIP and GAPDH; mouse complexes lack SYNCRIP.
id: GO:0097452
has exact synonym: IFN-gamma-activated inhibitor of translation complex
has OBO namespace: cellular_component
has exact synonym: gamma interferon-activated inhibitor of translation complex
term from ontology: go.owl
created by: paola
term from ontology: pro.owl
imported from: go.owl

bounding membrane of organelle
type: Class
subclass of: organelle membrane
creation date: 2014-02-26T13:41:31Z
comment: Examples include the outer membranes of double membrane bound organelles such as mitochondria as well as the bounding membranes of single-membrane bound organelles such as lysosomes.
id: GO:0098588
definition: The lipid bilayer that forms the outer-most layer of an organelle.
has OBO namespace: cellular_component
created by: davidos
imported from: go.owl

protein complex involved in cell adhesion
type: Class
subclass of: macromolecular complex
definition: Any protein complex that is capable of carrying out some part of the process of cell adhesion to the cell matrix or to another cell.
id: GO:0098636
has alternative id: GO:1990307
has related synonym: cell adhesion complex
has OBO namespace: cellular_component
imported from: go.owl

membrane protein complex
type: Class
subclass of: protein complex
subclass of: membrane part
definition: Any protein complex that is part of a membrane.
id: GO:0098796
has OBO namespace: cellular_component
imported from: go.owl
in subset: goslim metagenomics

plasma membrane protein complex
type: Class
subclass of: plasma membrane part
subclass of: membrane protein complex
definition: Any protein complex that is part of the plasma membrane.
id: GO:0098797
has OBO namespace: cellular_component
imported from: go.owl

mitochondrial protein complex
type: Class
subclass of: protein complex
subclass of: mitochondrial part
definition: A protein complex that is part of a mitochondrion.
id: GO:0098798
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: cellular_component
imported from: go.owl
in subset: gocheck do not manually annotate

inner mitochondrial membrane protein complex
type: Class
subclass of: mitochondrial membrane part
subclass of: membrane protein complex
subclass of: mitochondrial protein complex
definition: Any protein complex that is part of the inner mitochondrial membrane.
id: GO:0098800
has OBO namespace: cellular_component
imported from: go.owl

plasma membrane receptor complex
type: Class
subclass of: receptor complex
subclass of: plasma membrane part
definition: Any protein complex that is part of the plasma membrane and which functions as a receptor.
id: GO:0098802
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: cellular_component
imported from: go.owl
in subset: gocheck do not manually annotate

respiratory chain complex
type: Class
subclass of: membrane protein complex
definition: Any protein complex that is part of a respiratory chain
id: GO:0098803
has OBO namespace: cellular_component
imported from: go.owl

whole membrane
type: Class
subclass of: membrane
definition: Any lipid bilayer that completely encloses some structure, and all the proteins embedded in it or attached to it. Examples include the plasma membrane and most organelle membranes.
id: GO:0098805
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
has OBO namespace: cellular_component
imported from: go.owl
in subset: gocheck do not annotate

chaperone complex
type: Class
subclass of: protein complex
definition: A protein complex required for the non-covalent folding or unfolding, maturation, stabilization or assembly or disassembly of macromolecular structures. Usually active during or immediately after completion of translation. Many chaperone complexes contain heat shock proteins.
comment: An example of this is HSP90AB1 in human (P08238) in PMID:21855797 (inferred from direct assay).
id: GO:0101031
has OBO namespace: cellular_component
imported from: go.owl

organic cyclic compound metabolic process
type: Class
subclass of: organic substance metabolic process
creation date: 2012-09-14T09:03:51Z
id: GO:1901360
definition: The chemical reactions and pathways involving organic cyclic compound.
created by: bf
has OBO namespace: biological_process
has exact synonym: organic cyclic compound metabolism
imported from: go.owl

heterocyclic compound binding
type: Class
subclass of: binding
creation date: 2012-09-14T13:53:50Z
id: GO:1901363
definition: Interacting selectively and non-covalently with heterocyclic compound.
created by: bf
has OBO namespace: molecular_function
imported from: go.owl

organonitrogen compound metabolic process
type: Class
subclass of: nitrogen compound metabolic process
subclass of: organic substance metabolic process
creation date: 2012-11-04T15:17:52Z
id: GO:1901564
definition: The chemical reactions and pathways involving organonitrogen compound.
has OBO namespace: biological_process
has exact synonym: organonitrogen compound metabolism
created by: pr
imported from: go.owl

organic substance biosynthetic process
type: Class
subclass of: biosynthetic process
subclass of: organic substance metabolic process
creation date: 2012-11-05T11:04:40Z
id: GO:1901576
definition: The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.
has OBO namespace: biological_process
has exact synonym: organic molecular entity anabolism
has exact synonym: organic molecular entity biosynthesis
has exact synonym: organic molecular entity biosynthetic process
has exact synonym: organic molecular entity formation
has exact synonym: organic molecular entity synthesis
has exact synonym: organic substance anabolism
has exact synonym: organic substance biosynthesis
has exact synonym: organic substance formation
has exact synonym: organic substance synthesis
created by: pr
imported from: go.owl

catalytic complex
type: Class
subclass of: macromolecular complex
creation date: 2013-11-13T16:18:47Z
definition: A protein complex which is capable of catalytic activity.
id: GO:1902494
created by: bhm
has OBO namespace: cellular_component
has exact synonym: enzyme complex
imported from: go.owl
in subset: goslim metagenomics

transmembrane transporter complex
type: Class
subclass of: membrane part
subclass of: transporter complex
creation date: 2013-11-13T16:23:04Z
definition: A transmembrane protein complex which enables the transfer of a substance from one side of a membrane to the other.
id: GO:1902495
created by: bhm
has OBO namespace: cellular_component
imported from: go.owl

serine/threonine protein kinase complex
type: Class
subclass of: protein kinase complex
creation date: 2013-12-06T16:06:12Z
definition: A protein complex which is capable of protein serine/threonine kinase activity.
comment: An example is IRE1 in S. cerevisiae (UniProt ID P32361) in PMID:18191223 (inferred from direct assay).
id: GO:1902554
has related synonym: PDR16 complex dimer
has related synonym: PDR16 complex homodimer
created by: bhm
has OBO namespace: cellular_component
imported from: go.owl

single-organism localization
type: Class
subclass of: single-organism process
subclass of: localization
creation date: 2013-12-18T13:51:04Z
definition: A localization which involves only one organism.
id: GO:1902578
has OBO namespace: biological_process
created by: jl
has exact synonym: single organism localization
imported from: go.owl

protein kinase complex
type: Class
subclass of: transferase complex, transferring phosphorus-containing groups
creation date: 2014-04-17T13:52:40Z
definition: A protein complex which is capable of protein kinase activity.
comment: An example of this is PKM2 in human (P14618) in PMID:24606918 (inferred from direct assay).
id: GO:1902911
created by: bhm
has OBO namespace: cellular_component
imported from: go.owl

methylcrotonoyl-CoA carboxylase complex
type: Class
subclass of: catalytic complex
creation date: 2016-05-16T11:03:20Z
definition: A protein complex which is capable of methylcrotonoyl-CoA carboxylase activity.
id: GO:1905202
created by: bf
has OBO namespace: cellular_component
imported from: go.owl

GTPase complex
type: Class
subclass of: catalytic complex
creation date: 2016-08-11T15:34:44Z
definition: A protein complex which is capable of GTPase activity.
comment: An example of this is HRAS in human (P01112) in PMID:9178006 (inferred from direct assay).
id: GO:1905360
has narrow synonym: HRAS-SOS1 complex
has narrow synonym: RASH-SOS1 complex
created by: bhm
has OBO namespace: cellular_component
imported from: go.owl

peptidase complex
type: Class
subclass of: catalytic complex
creation date: 2016-08-16T12:49:36Z
definition: A protein complex which is capable of peptidase activity.
comment: An example of this is PLAU in human (UniProt symbol P00749) in PMID:1689240 (inferred from direct assay).
id: GO:1905368
created by: bhm
has OBO namespace: cellular_component
imported from: go.owl

endopeptidase complex
type: Class
subclass of: peptidase complex
creation date: 2016-08-16T12:52:16Z
definition: A protein complex which is capable of endopeptidase activity.
comment: An example of this is PLAU in human (UniProt symbol P00749) in PMID:1689240 (inferred from direct assay).
id: GO:1905369
created by: bhm
has OBO namespace: cellular_component
imported from: go.owl

oxidoreductase complex
type: Class
subclass of: cell part
subclass of: catalytic complex
creation date: 2013-10-07T08:24:47Z
definition: Any protein complex that possesses oxidoreductase activity.
id: GO:1990204
created by: bhm
has OBO namespace: cellular_component
has exact synonym: oxidation-reduction complex
has exact synonym: redox complex
imported from: go.owl
in subset: goslim metagenomics

transferase complex
type: Class
subclass of: catalytic complex
creation date: 2013-11-12T13:20:12Z
definition: A protein complex capable of catalyzing the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor).
id: GO:1990234
created by: bhm
has OBO namespace: cellular_component
imported from: go.owl

platelet-derived growth factor complex
type: Class
subclass of: growth factor complex
creation date: 2014-01-09T16:09:11Z
definition: A protein complex consisting of two chains of platelet-derived growth factor (PDGF) subunits. PDGF dimers bind to PDGF receptors in the plasma membrane and induce receptor dimerisation and activation. PDGFs are involved in a wide variety of signalling processes. PDGFs are found in all vertebrates where at least 2 different chains (A and B) exist. In human (and other mammals), four types of PDGF chains (A, B, C, and D) are known which form five different dimers (AA, AB, BB, CC and DD).
comment: An example of this is PDGFA in human (P04085) in PMID:20534510 (inferred from direct assay).
id: GO:1990265
has db xref: IntAct:EBI-2881436
has db xref: IntAct:EBI-2881443
has db xref: IntAct:EBI-2881451
has related synonym: PDGF complex
has narrow synonym: PDGF-AA dimer
has narrow synonym: PDGF-AB dimer
has narrow synonym: PDGF-BB dimer
has narrow synonym: PDGF-CC dimer
has narrow synonym: PDGF-DD dimer
created by: bhm
has OBO namespace: cellular_component
term from ontology: go.owl
term from ontology: pro.owl
imported from: go.owl

transporter complex
type: Class
subclass of: macromolecular complex
creation date: 2014-03-26T14:23:27Z
definition: A protein complex facilitating transport of molecules (proteins, small molecules, nucleic acids) into, out of or within a cell, or between cells.
comment: An example of this is GTR1 in human (UniProt symbol P11166) in PMID:15449578 (inferred from direct assay).
id: GO:1990351
created by: bhm
has OBO namespace: cellular_component
imported from: go.owl

Mus musculus
type: Class
subclass of: Murinae
has db xref: GC_ID:1
has related synonym: Mus muscaris
has alternative id: NCBITaxon:85055
has exact synonym: house mouse
has related synonym: mice C57BL/6xCBA/CaJ hybrid
has exact synonym: mouse
has OBO namespace: ncbi_taxonomy
term from ontology: obi.owl
term from ontology: pro.owl
has_rank: NCBITaxon species
imported from: ncbitaxon.owl

Rattus norvegicus
type: Class
subclass of: Murinae
has db xref: GC_ID:1
has related synonym: Gunn rats
has alternative id: NCBITaxon:36465
has exact synonym: Norway rat
has related synonym: Rattus norvegicus8
has related synonym: Rattus norwegicus
has related synonym: Rattus rattiscus
has exact synonym: Rattus sp. strain Wistar
has exact synonym: brown rat
has OBO namespace: ncbi_taxonomy
term from ontology: obi.owl
term from ontology: pro.owl
has exact synonym: rat
has exact synonym: rats
has_rank: NCBITaxon species
imported from: ncbitaxon.owl

Viruses
type: Class
subclass of: organism
has db xref: GC_ID:1
has related synonym: Vira
has related synonym: Viridae
has OBO namespace: ncbi_taxonomy
term from ontology: obi.owl
term from ontology: pro.owl
has related synonym: viruses
has_rank: NCBITaxon superkingdom
imported from: ncbitaxon.owl

Euteleostomi
type: Class
subclass of: Bilateria
has db xref: GC_ID:1
has alternative id: NCBITaxon:40673
has exact synonym: bony vertebrates
has OBO namespace: ncbi_taxonomy
imported from: ncbitaxon.owl

Ecdysozoa
type: Class
subclass of: Bilateria
has db xref: GC_ID:1
has OBO namespace: ncbi_taxonomy
imported from: ncbitaxon.owl

Clupeocephala
type: Class
subclass of: Euteleostomi
has db xref: GC_ID:1
has OBO namespace: ncbi_taxonomy
imported from: ncbitaxon.owl

Bacteria
type: Class
subclass of: organism
has db xref: GC_ID:11
has related synonym: Monera
has db xref: PMID:10425795
has db xref: PMID:10425796
has db xref: PMID:10425797
has db xref: PMID:10490293
has db xref: PMID:10843050
has db xref: PMID:10939651
has db xref: PMID:10939673
has db xref: PMID:10939677
has db xref: PMID:11211268
has db xref: PMID:11321083
has db xref: PMID:11321113
has db xref: PMID:11411719
has db xref: PMID:11540071
has db xref: PMID:11542017
has db xref: PMID:11542087
has db xref: PMID:11760965
has db xref: PMID:12054223
has db xref: PMID:2112744
has db xref: PMID:270744
has db xref: PMID:8123559
has db xref: PMID:8590690
has db xref: PMID:9103655
has db xref: PMID:9336922
has related synonym: Procaryotae
has related synonym: Prokaryota
has related synonym: Prokaryotae
has related synonym: bacteria
has exact synonym: eubacteria
has OBO namespace: ncbi_taxonomy
has related synonym: not Bacteria Haeckel 1894
term from ontology: obi.owl
term from ontology: pro.owl
has related synonym: prokaryote
has related synonym: prokaryotes
has_rank: NCBITaxon superkingdom
imported from: ncbitaxon.owl

Archaea
type: Class
subclass of: organism
has related synonym: Archaebacteria
has db xref: GC_ID:11
has related synonym: Mendosicutes
has related synonym: Metabacteria
has related synonym: Monera
has db xref: PMID:10425795
has db xref: PMID:10425796
has db xref: PMID:10425797
has db xref: PMID:10490293
has db xref: PMID:10843050
has db xref: PMID:10939651
has db xref: PMID:10939673
has db xref: PMID:10939677
has db xref: PMID:11211268
has db xref: PMID:11321083
has db xref: PMID:11321113
has db xref: PMID:11411719
has db xref: PMID:11540071
has db xref: PMID:11541975
has db xref: PMID:11542064
has db xref: PMID:11542149
has db xref: PMID:11760965
has db xref: PMID:12054223
has db xref: PMID:2112744
has db xref: PMID:25527841
has db xref: PMID:270744
has db xref: PMID:8123559
has db xref: PMID:8590690
has db xref: PMID:9103655
has db xref: PMID:9336922
has related synonym: Procaryotae
has related synonym: Prokaryota
has related synonym: Prokaryotae
has related synonym: archaea
has OBO namespace: ncbi_taxonomy
term from ontology: obi.owl
term from ontology: pro.owl
has related synonym: prokaryote
has related synonym: prokaryotes
has_rank: NCBITaxon superkingdom
imported from: ncbitaxon.owl

Eukaryota
type: Class
subclass of: organism
has related synonym: Eucarya
has related synonym: Eucaryotae
has related synonym: Eukarya
has related synonym: Eukaryotae
has db xref: GC_ID:1
has db xref: PMID:23020233
has exact synonym: eucaryotes
has exact synonym: eukaryotes
has related synonym: eukaryotes
has OBO namespace: ncbi_taxonomy
term from ontology: obi.owl
term from ontology: pro.owl
has_rank: NCBITaxon superkingdom
imported from: ncbitaxon.owl

Euarchontoglires
type: Class
subclass of: Mammalia
has db xref: GC_ID:1
has db xref: PMID:11214319
has db xref: PMID:12082125
has db xref: PMID:12878460
has db xref: PMID:15522813
has OBO namespace: ncbi_taxonomy
has_rank: NCBITaxon superorder
imported from: ncbitaxon.owl

Amniota
type: Class
subclass of: Euteleostomi
has db xref: GC_ID:1
has exact synonym: amniotes
has OBO namespace: ncbi_taxonomy
imported from: ncbitaxon.owl

Viridiplantae
type: Class
subclass of: Eukaryota
has related synonym: Chlorobionta
has related synonym: Chlorophyta/Embryophyta group
has db xref: GC_ID:1
has related synonym: chlorophyte/embryophyte group
has exact synonym: green plants
has related synonym: green plants
has OBO namespace: ncbi_taxonomy
term from ontology: po.owl
term from ontology: pro.owl
has_rank: NCBITaxon kingdom
imported from: ncbitaxon.owl

Opisthokonta
type: Class
subclass of: Eukaryota
has related synonym: Fungi/Metazoa group
has db xref: GC_ID:1
has OBO namespace: ncbi_taxonomy
term from ontology: obi.owl
has related synonym: opisthokonts
term from ontology: pro.owl
imported from: ncbitaxon.owl

Bilateria
type: Class
subclass of: Opisthokonta
has db xref: GC_ID:1
has OBO namespace: ncbi_taxonomy
imported from: ncbitaxon.owl

Arabidopsis thaliana
type: Class
subclass of: Viridiplantae
has related synonym: Arabidopsis thaliana (thale cress)
has related synonym: Arabidopsis_thaliana
has related synonym: Arbisopsis thaliana
has db xref: GC_ID:1
has exact synonym: mouse-ear cress
has OBO namespace: ncbi_taxonomy
term from ontology: obi.owl
term from ontology: pro.owl
has exact synonym: thale cress
has exact synonym: thale-cress
has_rank: NCBITaxon species
imported from: ncbitaxon.owl

Murinae
type: Class
subclass of: Rodentia
has db xref: GC_ID:1
has alternative id: NCBITaxon:109679
has OBO namespace: ncbi_taxonomy
has_rank: NCBITaxon subfamily
imported from: ncbitaxon.owl

Mammalia
type: Class
subclass of: Amniota
has db xref: GC_ID:1
has exact synonym: mammals
has related synonym: mammals
has OBO namespace: ncbi_taxonomy
term from ontology: obi.owl
term from ontology: pro.owl
has_rank: NCBITaxon class
imported from: ncbitaxon.owl

Dictyostelium discoideum
type: Class
subclass of: Eukaryota
has db xref: GC_ID:1
has OBO namespace: ncbi_taxonomy
term from ontology: obi.owl
term from ontology: pro.owl
has_rank: NCBITaxon species
imported from: ncbitaxon.owl

Ascomycota
type: Class
subclass of: Opisthokonta
has db xref: GC_ID:1
has db xref: PMID:17572334
has related synonym: ascomycetes
has exact synonym: ascomycetes
has OBO namespace: ncbi_taxonomy
has exact synonym: sac fungi
has_rank: NCBITaxon phylum
imported from: ncbitaxon.owl

Schizosaccharomyces pombe
type: Class
subclass of: Ascomycota
has db xref: GC_ID:1
has alternative id: NCBITaxon:45042
has related synonym: Schizosaccharomyces malidevorans
has related synonym: Schizosaccharomyces pombeP
has exact synonym: fission yeast
has OBO namespace: ncbi_taxonomy
term from ontology: obi.owl
term from ontology: pro.owl
has_rank: NCBITaxon species
imported from: ncbitaxon.owl

Saccharomyces cerevisiae
type: Class
subclass of: Ascomycota
has related synonym: Candida robusta
has db xref: GC_ID:1
has related synonym: Saccaromyces cerevisiae
has related synonym: Saccharomyce cerevisiae
has related synonym: Saccharomyces capensis
has related synonym: Saccharomyces italicus
has related synonym: Saccharomyces oviformis
has related synonym: Saccharomyces uvarum var. melibiosus
has related synonym: Saccharomyes cerevisiae
has related synonym: Sccharomyces cerevisiae
has exact synonym: baker's yeast
has exact synonym: brewer's yeast
has exact synonym: lager beer yeast
has OBO namespace: ncbi_taxonomy
term from ontology: obi.owl
term from ontology: pro.owl
has exact synonym: yeast
has_rank: NCBITaxon species
imported from: ncbitaxon.owl

Plasmodium falciparum
type: Class
subclass of: Eukaryota
has db xref: GC_ID:1
has related synonym: Plasmodium (Laverania) falciparum
term from ontology: doid.owl
has exact synonym: malaria parasite P. falciparum
has OBO namespace: ncbi_taxonomy
term from ontology: pro.owl
has_rank: NCBITaxon species
imported from: ncbitaxon.owl

Caenorhabditis elegans
type: Class
subclass of: Ecdysozoa
has db xref: GC_ID:1
has related synonym: Rhabditis elegans
has OBO namespace: ncbi_taxonomy
term from ontology: obi.owl
term from ontology: pro.owl
has exact synonym: roundworm
has_rank: NCBITaxon species
imported from: ncbitaxon.owl

Drosophila melanogaster
type: Class
subclass of: Ecdysozoa
has related synonym: Drosophila melangaster
has db xref: GC_ID:1
has related synonym: Sophophora melanogaster
has exact synonym: fruit fly
has OBO namespace: ncbi_taxonomy
term from ontology: obi.owl
term from ontology: pro.owl
has_rank: NCBITaxon species
imported from: ncbitaxon.owl

Danio rerio
type: Class
subclass of: Clupeocephala
has related synonym: Brachidanio rerio
has related synonym: Brachydanio rerio
has related synonym: Brachydanio rerio frankei
has related synonym: Cyprinus rerio
has related synonym: Danio frankei
has related synonym: Danio rerio frankei
has db xref: GC_ID:1
has alternative id: NCBITaxon:27702
has alternative id: NCBITaxon:37966
term from ontology: doid.owl
has exact synonym: leopard danio
has OBO namespace: ncbi_taxonomy
term from ontology: obi.owl
term from ontology: pro.owl
has exact synonym: zebra danio
has exact synonym: zebra fish
has exact synonym: zebrafish
has_rank: NCBITaxon species
imported from: ncbitaxon.owl

Salmo salar
type: Class
subclass of: Clupeocephala
has exact synonym: Atlantic salmon
has db xref: GC_ID:1
term from ontology: doid.owl
has OBO namespace: ncbi_taxonomy
term from ontology: pro.owl
has_rank: NCBITaxon species
imported from: ncbitaxon.owl

Gallus gallus
type: Class
subclass of: Amniota
has db xref: GC_ID:1
has related synonym: Gallus domesticus
has related synonym: Gallus gallus domesticus
has exact synonym: bantam
has exact synonym: chicken
has exact synonym: chickens
has OBO namespace: ncbi_taxonomy
term from ontology: obi.owl
term from ontology: pro.owl
has_rank: NCBITaxon species
imported from: ncbitaxon.owl

Homo sapiens
type: Class
subclass of: Euarchontoglires
has db xref: GC_ID:1
has exact synonym: human
has exact synonym: man
has OBO namespace: ncbi_taxonomy
term from ontology: obi.owl
term from ontology: pro.owl
has_rank: NCBITaxon species
imported from: ncbitaxon.owl

Rodentia
type: Class
subclass of: Euarchontoglires
has db xref: GC_ID:1
has OBO namespace: ncbi_taxonomy
term from ontology: obi.owl
term from ontology: pro.owl
has exact synonym: rodent
has related synonym: rodents
has_rank: NCBITaxon order
imported from: ncbitaxon.owl

organism
type: Class
equivalent class: Class
  union of: Viruses
  union of: Bacteria
  union of: Archaea
  union of: Eukaryota
subclass of: material entity
editor note: 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
editor note: 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
term editor: GROUP: OBI Biomaterial Branch
term from ontology: obi.owl
term from ontology: pro.owl
definition: A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
definition source: WEB: http://en.wikipedia.org/wiki/Organism
example of usage: animal
example of usage: fungus
editor preferred label: organism
example of usage: plant
example of usage: virus
has curation status: IAO_0000122
imported from: obi.owl

age
type: Class
subclass of: physical quality
definition: A time quality inhering in a bearer by virtue of how long the bearer has existed.
id: PATO:0000011
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: attribute slim
in subset: attribute slim
in_subset: scalar slim
in subset: scalar slim

fluorescence
type: Class
subclass of: radiation quality
definition: A luminous flux quality inhering in a bearer by virtue of the bearer's emitting longer wavelength light following the absorption of shorter wavelength radiation; fluorescence is common with aromatic compounds with several rings joined together.
id: PATO:0000018
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in subset: attribute slim
in_subset: attribute slim

biological sex
type: Class
subclass of: organismal quality
definition: An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
id: PATO:0000047
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in subset: attribute slim
in_subset: attribute slim

morphology
type: Class
subclass of: physical object quality
definition: A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
id: PATO:0000051
has OBO namespace: quality
imported from: pato.owl
in subset: attribute slim

size
type: Class
subclass of: morphology
definition: A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
id: PATO:0000117
has OBO namespace: quality
imported from: pato.owl
in subset: attribute slim
in subset: scalar slim

length
type: Class
subclass of: size
definition: A 1-D extent quality which is equal to the distance between two points.
id: PATO:0000122
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in subset: attribute slim
in_subset: attribute slim
in_subset: mpath slim
in subset: mpath slim
in subset: scalar slim
in_subset: scalar slim

mass
type: Class
subclass of: physical quality
definition: A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
id: PATO:0000125
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in subset: attribute slim
in_subset: attribute slim
in subset: relational slim
in_subset: relational slim
in_subset: scalar slim
in subset: scalar slim

position
type: Class
subclass of: physical quality
definition: A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
id: PATO:0000140
has alternative id: PATO:0001032
has alternative id: PATO:0001631
has exact synonym: location
has exact synonym: placement
has OBO namespace: quality
has exact synonym: relational spatial quality
imported from: pato.owl
in subset: attribute slim

structure
type: Class
subclass of: morphology
definition: A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.
id: PATO:0000141
has alternative id: PATO:0001452
has broad synonym: conformation
has OBO namespace: quality
has exact synonym: relational structural quality
imported from: pato.owl
in subset: attribute slim

temperature
type: Class
subclass of: physical quality
definition: A physical quality of the thermal energy of a system.
id: PATO:0000146
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: attribute slim
in subset: attribute slim
in_subset: scalar slim
in subset: scalar slim

viability
type: Class
subclass of: organismal quality
definition: An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population.
id: PATO:0000169
has OBO namespace: quality
imported from: pato.owl
in subset: attribute slim
in subset: disposition slim

behavioral quality
type: Class
subclass of: organismal quality
definition: An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation.
id: PATO:0000186
has alternative id: PATO:0001722
has exact synonym: behavioural quality
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl

female
type: Class
subclass of: phenotypic sex
definition: A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
id: PATO:0000383
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: mpath slim
in subset: mpath slim
in subset: value slim
in_subset: value slim

male
type: Class
subclass of: phenotypic sex
definition: A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
id: PATO:0000384
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: mpath slim
in subset: mpath slim
in_subset: value slim
in subset: value slim

volume
type: Class
subclass of: size
definition: A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies.
id: PATO:0000918
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: attribute slim
in subset: attribute slim
in_subset: mpath slim
in subset: mpath slim
in_subset: scalar slim
in subset: scalar slim

physical quality
type: Class
subclass of: physical object quality
definition: A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
id: PATO:0001018
has alternative id: PATO:0002079
has db xref: Wikipedia:Physical_property
has OBO namespace: quality
has exact synonym: relational physical quality
imported from: pato.owl
in subset: attribute slim

pressure
type: Class
subclass of: physical quality
definition: A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts.
id: PATO:0001025
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in subset: attribute slim
in_subset: attribute slim

diluted
type: Class
subclass of: physical object quality
definition: A concentration which relatively low.
id: PATO:0001161
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: relational slim
in subset: relational slim
in_subset: value slim
in subset: value slim

damaged
type: Class
subclass of: structure
definition: A structural quality inhering in a bearer by virtue of the bearer being harmed or injured or spoiled, such that its functionality is impaired.
id: PATO:0001167
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
is opposite_of: PATO_0001168
imported from: pato.owl
in subset: value slim
in_subset: value slim

lateral to
type: Class
subclass of: position
definition: A spatial quality inhering in a bearer by virtue of the bearer's being located toward the side relative to another entity.
id: PATO:0001193
has exact synonym: lateral
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: mpath slim
in subset: mpath slim
in_subset: relational slim
in subset: relational slim
in_subset: value slim
in subset: value slim

ventral to
type: Class
subclass of: position
definition: A spatial quality inhering in a bearer by virtue of the bearer's being located toward the abdomen of an organism relative to another entity.
id: PATO:0001196
has exact synonym: anterior_ to
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in subset: mpath slim
in_subset: mpath slim
in subset: relational slim
in_subset: relational slim
in subset: value slim
in_subset: value slim

dorsal to
type: Class
subclass of: position
definition: A spatial quality inhering in a bearer by virtue of the bearer's being located toward the back or upper surface of an organism relative to another entity.
id: PATO:0001233
has exact synonym: dorsal
term from ontology: obi.owl
term from ontology: pato.owl
has exact synonym: posterior_to (human torso)
has OBO namespace: quality
has exact synonym: superior_to (human head)
is opposite_of: PATO_0001234
imported from: pato.owl
in_subset: relational slim
in subset: relational slim
in_subset: value slim
in subset: value slim

PATO_0001237
type: Class
term from ontology: obi.owl
term from ontology: pato.owl
deprecated: true
has obsolescence reason: IAO_0000227
term replaced by: physical object quality
imported from: pato.owl

PATO_0001238
type: Class
term from ontology: obi.owl
term from ontology: pato.owl
deprecated: true
has obsolescence reason: IAO_0000227
term replaced by: physical object quality
imported from: pato.owl

physical object quality
type: Class
subclass of: quality
definition: A quality which inheres in a continuant.
has alternative id: PATO:0001237
has alternative id: PATO:0001238
id: PATO:0001241
comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.
has exact synonym: monadic quality of a continuant
has narrow synonym: monadic quality of an object
has narrow synonym: monadic quality of continuant
has exact synonym: multiply inhering quality of a physical entity
has OBO namespace: quality
has exact synonym: quality of a continuant
has exact synonym: quality of a single physical entity
has exact synonym: quality of an object
has exact synonym: quality of continuant
has db xref: snap:Quality
imported from: pato.owl

bacterial mating type
type: Class
subclass of: mating type
definition: A mating type that indicates whether the F plasmid has integrated into the chromosome.
id: PATO:0001335
has OBO namespace: quality
imported from: pato.owl
in subset: attribute slim

yeast mating type
type: Class
subclass of: mating type
definition: A yeast mating type.
id: PATO:0001337
has OBO namespace: quality
imported from: pato.owl
in subset: attribute slim

mixed sex
type: Class
subclass of: physical object quality
definition: A biological sex quality inhering in a population of multiple sexes.
comment: For example a mixture of females and male or males and hermaphrodites.
id: PATO:0001338
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in subset: value slim
in_subset: value slim

biomaterial purity
type: Class
subclass of: structure
definition: A composition quality inhering in an bearer by virtue of the bearer's homogeneity of a biomaterial.
id: PATO:0001339
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: attribute slim
in subset: attribute slim
in_subset: scalar slim
in subset: scalar slim

hermaphrodite
type: Class
subclass of: phenotypic sex
definition: A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual.
id: PATO:0001340
has exact synonym: intersex
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: value slim
in subset: value slim

a mating type (yeast)
type: Class
subclass of: Saccharomyces cerevisiae mating type
definition: A S. cerevisiae mating type cells that secrete a pheromone that in alpha haploids stimulates processes that lead to mating.
id: PATO:0001341
has broad synonym: a
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: value slim
in subset: value slim

Saccharomyces cerevisiae mating type
type: Class
subclass of: yeast mating type
definition: A S. cerevisiae mating type.
id: PATO:0001342
has OBO namespace: quality
imported from: pato.owl
in subset: attribute slim

Schizosaccharomyces pombe mating type
type: Class
subclass of: yeast mating type
definition: A S. pombe mating type determined by the gene configuration on the mat1 locus.
id: PATO:0001343
has OBO namespace: quality
imported from: pato.owl
in subset: attribute slim

alpha mating type (yeast)
type: Class
subclass of: Saccharomyces cerevisiae mating type
definition: A S. cerevisiae mating type cells that secrete a pheromone that stimulates a haploids.
id: PATO:0001344
has broad synonym: alpha
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in subset: value slim
in_subset: value slim

h minus
type: Class
subclass of: Schizosaccharomyces pombe mating type
definition: A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus.
has exact synonym: M
id: PATO:0001345
has exact synonym: h -
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: value slim
in subset: value slim

h plus
type: Class
subclass of: Schizosaccharomyces pombe mating type
definition: A S. pombe mating type determined by the mat1-Pc and mat1-Pi on the mat1 locus.
has exact synonym: P
id: PATO:0001346
has exact synonym: h+
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in subset: value slim
in_subset: value slim

F mating type
type: Class
subclass of: bacterial mating type
definition: A bacterial mating type indicating the presence of F plasmid in a bacterial cell.
id: PATO:0001347
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: value slim
in subset: value slim

F minus mating type
type: Class
subclass of: bacterial mating type
definition: A bacterial mating type indicating the absence of F plasmid in a bacterial cell.
has exact synonym: F-
id: PATO:0001348
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: value slim
in subset: value slim

ploidy
type: Class
subclass of: cellular quality
definition: A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism.
id: PATO:0001374
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: attribute slim
in subset: attribute slim

haploid
type: Class
subclass of: euploid
definition: A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes.
id: PATO:0001375
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: cell quality
in subset: cell quality
in subset: value slim
in_subset: value slim

polyploid
type: Class
subclass of: euploid
definition: A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes.
id: PATO:0001377
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: cell quality
in subset: cell quality
in_subset: value slim
in subset: value slim

aneuploid
type: Class
subclass of: ploidy
definition: A ploidy quality inhering in a bearer by virtue of the bearer's containing a non-integral multiple of the monoploid number, due to extra or missing chromosomes.
id: PATO:0001385
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in subset: cell quality
in_subset: cell quality
in subset: value slim
in_subset: value slim

euploid
type: Class
subclass of: ploidy
definition: A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes.
id: PATO:0001393
has OBO namespace: quality
imported from: pato.owl
in subset: cell quality
in subset: value slim

diploid
type: Class
subclass of: euploid
definition: A ploidy quality inhering in a bearer by virtue of the bearer's having two copies (homologs) of each chromosome, usually one from the mother and one from the father.
id: PATO:0001394
comment: The exact number may be one or two different from the 2n number and still be classified as diploidy (although with aneuploidy). Nearly all mammals are diploid organisms, although all individuals have some small fracton of cells that are polyploidy.
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: cell quality
in subset: cell quality
in_subset: value slim
in subset: value slim

cellular quality
type: Class
subclass of: physical object quality
definition: A monadic quality of continuant that exists at the cellular level of organisation.
id: PATO:0001396
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl

alive
type: Class
subclass of: viability
definition: A viability quality inhering in a bearer by virtue of the bearer's condition before death.
id: PATO:0001421
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: value slim
in subset: value slim

dead
type: Class
subclass of: viability
definition: A viability quality inhering in a bearer by virtue of the cessation of the bearer's life.
id: PATO:0001422
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: value slim
in subset: value slim

quality of a solid
type: Class
subclass of: quality of a substance
definition: A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable.
id: PATO:0001546
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
has exact synonym: solidity
imported from: pato.owl
in subset: attribute slim
in_subset: attribute slim

quality of a gas
type: Class
subclass of: quality of a substance
definition: A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape.
id: PATO:0001547
has exact synonym: gaseous
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: attribute slim
in subset: attribute slim

quality of a liquid
type: Class
subclass of: quality of a substance
definition: A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape.
id: PATO:0001548
has exact synonym: liquidity
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in subset: attribute slim
in_subset: attribute slim

PATO_0001631
type: Class
term from ontology: obi.owl
term from ontology: pato.owl
deprecated: true
has obsolescence reason: IAO_0000227
term replaced by: position
imported from: pato.owl

anterior to
type: Class
subclass of: position
definition: A spatial quality inhering in a bearer by virtue of the bearer's being located toward the front of an organism relative to another entity.
id: PATO:0001632
term from ontology: obi.owl
term from ontology: pato.owl
has exact synonym: preceding
has OBO namespace: quality
has exact synonym: ventral_to
imported from: pato.owl
in_subset: mpath slim
in subset: mpath slim
in_subset: relational slim
in subset: relational slim
in subset: value slim
in_subset: value slim

radiation quality
type: Class
subclass of: physical quality
definition: A quality that inheres in an bearer by virtue of how that bearer interacts with radiation.
id: PATO:0001739
has OBO namespace: quality
imported from: pato.owl
in subset: attribute slim

radioactive
type: Class
subclass of: radiation quality
definition: A radiation quality inhering in bearer by virtue of the bearer's exhibiting or being caused by radioactivity.
id: PATO:0001741
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: value slim
in subset: value slim

left side of
type: Class
subclass of: position
definition: A spatial quality inhering in a bearer by virtue of the bearer's being located on left side of from the a another entity.
id: PATO:0001792
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: mpath slim
in subset: mpath slim
in_subset: relational slim
in subset: relational slim
in_subset: value slim
in subset: value slim

right side of
type: Class
subclass of: position
definition: A spatial quality inhering in a bearer by virtue of the bearer's being located on right side of a another entity.
id: PATO:0001793
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: mpath slim
in subset: mpath slim
in_subset: relational slim
in subset: relational slim
in_subset: value slim
in subset: value slim

phenotypic sex
type: Class
subclass of: biological sex
id: PATO:0001894
has OBO namespace: quality
imported from: pato.owl
in subset: attribute slim

mating type
type: Class
subclass of: biological sex
definition: A biological sex quality inhering in an individual or a population that undergo sexual reproduction.
id: PATO:0001895
has OBO namespace: quality
imported from: pato.owl
in subset: attribute slim

frozen
type: Class
subclass of: temperature
definition: A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point.
id: PATO:0001985
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in subset: value slim
in_subset: value slim

organismal quality
type: Class
subclass of: physical object quality
definition: A quality that inheres in an entire organism or part of an organism.
id: PATO:0001995
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl

quality of a substance
type: Class
subclass of: physical quality
creation date: 2010-03-15T04:35:27Z
definition: A quality inhering in a bearer by virtue of its constitution.
created by: George Gkoutos
id: PATO:0002198
has OBO namespace: quality
imported from: pato.owl
in subset: attribute slim

handedness
type: Class
subclass of: behavioral quality
creation date: 2010-03-22T05:48:33Z
definition: A behavioral quality inhering ina bearer by virtue of the bearer's unequal distribution of fine motor skill between its left and right hands or feet.
comment: Adapted from Wikipedia and the birnlex term that is dbxref'd. Added on behalf of OBI at March 2010 workshop.
id: PATO:0002201
created by: haendel
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: attribute slim
in subset: attribute slim
in subset: disposition slim
in_subset: disposition slim

left handedness
type: Class
subclass of: handedness
creation date: 2010-03-22T05:49:06Z
definition: Handedness where the organism preferentially uses the left hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot.
id: PATO:0002202
created by: haendel
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in subset: disposition slim
in_subset: disposition slim
in subset: value slim
in_subset: value slim

right handedness
type: Class
subclass of: handedness
creation date: 2010-03-22T05:49:19Z
definition: Handedness where the organism preferentially uses the right hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot.
id: PATO:0002203
created by: haendel
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: disposition slim
in subset: disposition slim
in subset: value slim
in_subset: value slim

ambidextrous handedness
type: Class
subclass of: handedness
creation date: 2010-03-22T05:49:30Z
definition: Handedness where the organism exhibits no overall dominance in the use of right or left hand or foot in the performance of tasks that require one hand or foot or a dominant hand or foot.
id: PATO:0002204
created by: haendel
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
imported from: pato.owl
in_subset: disposition slim
in subset: disposition slim
in_subset: value slim
in subset: value slim

fluid flow rate
type: Class
subclass of: physical quality
creation date: 2010-07-28T03:00:20Z
definition: A physical quality inhering in a fluid (liquid or gas) by virtue of the amount of fluid which passes through a given surface per unit time.
id: PATO:0002243
created by: george
term from ontology: obi.owl
term from ontology: pato.owl
has OBO namespace: quality
has exact synonym: volume flow rate
has exact synonym: volumetric flow rate
imported from: pato.owl
in subset: attribute slim
in_subset: attribute slim
in subset: scalar slim
in_subset: scalar slim

plant structure development stage
type: Class
subclass of: life cycle stage
definition: A stage in the life of a plant structure (PO:0009011) during which the plant structure undergoes developmental processes.
has related synonym: Arabidopsis growth (related)
has alternative id: PO:0007021
id: PO:0009012
has db xref: PO_GIT:185
comment: Refers to GO:0032502 (developmental process), including growth, differentiation, and senescence.
has exact synonym: etapa de desarrollo de estructura vegetal (Spanish, exact)
has exact synonym: plant growth and development stage (exact)
has OBO namespace: plant_structure_development_stage
imported from: po.owl
in subset: TraitNet

plant anatomical entity
type: Class
subclass of: anatomical entity
creation date: 2010-11-15T11:41:38Z
definition: An anatomical entity that is or was part of a plant.
comment: Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 anatomical entity is defined as: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
id: PO:0025131
has db xref: PO_GIT:224
has exact synonym: entidad anat&#243mica vegetal (Spanish, exact)
has OBO namespace: plant_anatomy
created by: rwalls
has exact synonym: 植物 解剖学（形態）的実体 (Japanese, exact)
imported from: po.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.
id: PR:000000001
comment: Proteins 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].
term from ontology: obi.owl
term from ontology: pro.owl
has OBO namespace: protein
imported from: pr.owl

CD4 molecule
type: Class
subclass of: protein
definition: A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence.
has exact synonym: CD4
comment: Category=gene. Requested by=CL.
has db xref: PIRSF:PIRSF001977
id: PR:000001004
has exact synonym: T-cell differentiation antigen L3T4
has exact synonym: T-cell surface antigen T4/Leu-3
has exact synonym: T-cell surface glycoprotein CD4
term from ontology: obi.owl
term from ontology: pro.owl
has OBO namespace: protein
imported from: pr.owl

CD3 subunit with immunoglobulin domain
type: Class
subclass of: protein
definition: A protein with a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response.
has exact synonym: CD3 subunit with Ig-like domain
comment: Category=family.
has db xref: PIRSF:PIRSF001993
id: PR:000001018
term from ontology: obi.owl
term from ontology: pro.owl
has OBO namespace: protein
imported from: pr.owl

antithrombin-III
type: Class
subclass of: protein
definition: A serpin that is a translation product of the human SERPINC1 gene or a 1:1 ortholog thereof.
has related synonym: AT3
has exact synonym: ATIII
comment: Category=gene.
id: PR:000003252
has exact synonym: SERPINC1
term from ontology: obi.owl
term from ontology: pro.owl
has OBO namespace: protein
has exact synonym: serpin C1
imported from: pr.owl

double-stranded RNA-specific adenosine deaminase
type: Class
subclass of: protein
has exact synonym: 136 kDa double-stranded RNA-binding protein
definition: A protein that is a translation product of the human ADAR gene or a 1:1 ortholog thereof.
has exact synonym: ADAR
has related synonym: ADAR1
comment: Category=gene.
has exact synonym: DRADA
has related synonym: DSRAD
has related synonym: G1P1
has exact synonym: IFI-4
has related synonym: IFI4
has exact synonym: K88DSRBP
id: PR:000003745
has exact synonym: RNA adenosine deaminase 1
has exact synonym: interferon-inducible protein 4
term from ontology: obi.owl
has broad synonym: p136
term from ontology: pro.owl
has OBO namespace: protein
imported from: pr.owl

deoxyribonuclease-1
type: Class
subclass of: protein
definition: A protein that is a translation product of the human DNASE1 gene or a 1:1 ortholog thereof.
comment: Category=gene.
has exact synonym: DNASE1
has related synonym: DNL1
has exact synonym: DNase I
has related synonym: DRNI
id: PR:000006592
has exact synonym: deoxyribonuclease I
has exact synonym: dornase alfa
term from ontology: obi.owl
term from ontology: pro.owl
has OBO namespace: protein
imported from: pr.owl

glial cell line-derived neurotrophic factor
type: Class
subclass of: protein
definition: A protein that is a translation product of the human GDNF gene or a 1:1 ortholog thereof.
has exact synonym: ATF
comment: Category=gene.
has exact synonym: GDNF
id: PR:000007928
has exact synonym: astrocyte-derived trophic factor
term from ontology: obi.owl
term from ontology: pro.owl
has OBO namespace: protein
imported from: pr.owl

ribonuclease T2
type: Class
subclass of: protein
definition: A protein that is a translation product of the human RNASET2 gene or a 1:1 ortholog thereof.
comment: Category=gene.
id: PR:000014060
has related synonym: RNASE6PL
has exact synonym: RNASET2
term from ontology: obi.owl
term from ontology: pro.owl
has OBO namespace: protein
has exact synonym: ribonuclease 6
imported from: pr.owl

DNA ligase
type: Class
subclass of: protein
definition: A protein that is a translation product of the Escherichia coli K-12 ligA gene or a 1:1 ortholog thereof.
comment: Category=gene.
id: PR:000023089
has related synonym: dnaL
has related synonym: lig
has exact synonym: ligA
has related synonym: lop
term from ontology: obi.owl
has related synonym: pdeC
has exact synonym: polydeoxyribonucleotide synthase [NAD(+)]
term from ontology: pro.owl
has OBO namespace: protein
imported from: pr.owl

T cell receptor co-receptor CD8
type: Class
subclass of: molecular entity
definition: A protein complex that is a membrane-bound heterodimeric co-receptor for MHC class-I antigen/T-cell receptor interaction.
has exact synonym: CD8alphabeta
comment: Category=complex. Requested by=CL.
id: PR:000025402
has exact synonym: TCR co-receptor CD8
term from ontology: obi.owl
term from ontology: pro.owl
has OBO namespace: protein
imported from: pr.owl

guanyl-specific ribonuclease T1
type: Class
subclass of: protein
definition: A protein that is a translation product of the Aspergillus oryzae rntA gene or a 1:1 ortholog thereof.
comment: Category=gene.
id: PR:000025467
has exact synonym: RNase T1
term from ontology: obi.owl
term from ontology: pro.owl
has OBO namespace: protein
has exact synonym: rntA
imported from: pr.owl

nuclease S1
type: Class
subclass of: protein
definition: A protein that is a translation product of the Aspergillus oryzae nucS gene or a 1:1 ortholog thereof.
comment: Category=gene.
id: PR:000025471
has exact synonym: deoxyribonuclease S1
has exact synonym: endonuclease S1
has exact synonym: nucS
term from ontology: obi.owl
term from ontology: pro.owl
has OBO namespace: protein
has exact synonym: single-stranded-nucleate endonuclease
imported from: pr.owl

ribonuclease U2
type: Class
subclass of: protein
definition: A protein that is a translation product of the Ustilago sphaerogena RNU2 gene or a 1:1 ortholog thereof.
comment: Category=gene.
id: PR:000025475
has exact synonym: RNU2
has exact synonym: RNase U2
term from ontology: obi.owl
term from ontology: pro.owl
has OBO namespace: protein
imported from: pr.owl

ribonuclease V1
type: Class
subclass of: protein
definition: A protein with ribonuclease activity that is a constituent of cobra venom.
comment: Category=gene.
id: PR:000025477
has exact synonym: RNase V1
term from ontology: obi.owl
term from ontology: pro.owl
has OBO namespace: protein
imported from: pr.owl

ribonuclease CL3
type: Class
subclass of: protein
definition: A protein with ribonuclease activity that is purified from chicken liver.
comment: Category=gene.
id: PR:000025478
has exact synonym: RNase CL3
term from ontology: obi.owl
term from ontology: pro.owl
has OBO namespace: protein
imported from: pr.owl

vessel
type: Class
subclass of: multicellular anatomical structure
definition: A tubular structure that contains, conveys body fluid, such as blood or lymph.
id: UBERON:0000055
has OBO namespace: uberon
imported from: uberon.owl
in subset: grouping class
in subset: pheno slim

anatomical structure
type: Class
subclass of: anatomical entity
has db xref: AAO:0010825
has db xref: AEO:0000003
has db xref: BILA:0000003
has db xref: CARO:0000003
has db xref: EHDAA2:0003003
has db xref: EMAPA:0
has db xref: FBbt:00007001
has db xref: FMA:305751
has db xref: FMA:67135
has db xref: GAID:781
has db xref: HAO:0000003
has db xref: MA:0003000
has db xref: MESH:D000825
definition: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
has db xref: TAO:0000037
has db xref: TGMA:0001823
id: UBERON:0000061
has db xref: VHOG:0001759
has db xref: WBbt:0000100
has db xref: XAO:0003000
has db xref: ZFA:0000037
has exact synonym: biological structure
has exact synonym: connected biological structure
has OBO namespace: uberon
has db xref: AnatomicalStructure
imported from: uberon.owl
in subset: upper level
has db xref: http://www.snomedbrowser.com/Codes/Details/362889002

organ
type: Class
subclass of: multicellular anatomical structure
definition: Anatomical structure that performs a specific function or group of functions [WP].
external_ontology_notes: CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4
has db xref: CARO:0020004
has db xref: EFO:0000634
has db xref: EMAPA:35949
has db xref: ENVO:01000162
has db xref: FMA:67498
has db xref: MA:0003001
has db xref: OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA
has db xref: OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA
external_definition: Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
id: UBERON:0000062
has db xref: UMLS:C0178784
has db xref: WBbt:0003760
has related synonym: anatomical unit
has related synonym: body organ
has related synonym: element
has OBO namespace: uberon
has db xref: Organ (anatomy)
has db xref: http://linkedlifedata.com/resource/umls/id/C0178784
has db xref: C13018
imported from: uberon.owl
in subset: upper level
has db xref: birnlex 4
has db xref: http://www.snomedbrowser.com/Codes/Details/272625005

life cycle stage
type: Class
subclass of: process
definition: A spatiotemporal region encompassing some part of the life cycle of an organism.
has db xref: BILS:0000105
has db xref: EFO:0000399
has db xref: FBdv:00007012
has db xref: FMA:24120
has db xref: HsapDv:0000000
has db xref: MmusDv:0000000
has db xref: OlatDv:0000010
has db xref: PdumDv:0000090
id: UBERON:0000105
has db xref: WBls:0000002
has db xref: XAO:1000000
has db xref: ZFS:0000000
has db xref: ZFS:0100000
has narrow synonym: developmental stage
has db xref: ncithesaurus:Developmental_Stage
has narrow synonym: stage
external_ontology_notes: the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
editor note: this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
has OBO namespace: uberon
external_ontology_notes: we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
imported from: uberon.owl
in subset: efo slim
in subset: upper level

breast
type: Class
subclass of: multicellular anatomical structure
has db xref: BTO:0000149
has db xref: CALOHA:TS-2083
has db xref: EV:0100124
has db xref: FMA:9601
has db xref: GAID:33
has db xref: MESH:D001940
has db xref: OpenCyc:Mx4rvVjV7ZwpEbGdrcN5Y29ycA
taxon_notes: The breasts of a female primate's body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's.
definition: The upper ventral region of an animal's torso.
id: UBERON:0000310
has db xref: UMLS:C0006141
term from ontology: doid.owl
has db xref: galen:Breast
has related synonym: mamma
has exact synonym: mammary part of chest
has exact synonym: mammary region
term from ontology: obi.owl
has OBO namespace: uberon
has db xref: Breast
has db xref: http://linkedlifedata.com/resource/umls/id/C0006141
has db xref: C12971
imported from: uberon.owl
in subset: pheno slim
has db xref: http://www.snomedbrowser.com/Codes/Details/181131000

heart
type: Class
subclass of: anatomical structure
subclass of: organ
subclass of: mesoderm-derived structure
subclass of: trunk region element
definition: A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
has db xref: AAO:0010210
homology_notes: As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]
has db xref: BILA:0000020
has db xref: BTO:0000562
external_definition: Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]
has db xref: CALOHA:TS-0445
has db xref: EFO:0000815
has db xref: EHDAA2:0000738
has db xref: EHDAA:420
has db xref: EMAPA:16105
has db xref: EV:0100018
has db xref: FMA:7088
has db xref: GAID:174
has related synonym: Herz@de
has db xref: MA:0000072
has db xref: MAT:0000036
has db xref: MESH:D006321
has db xref: MIAA:0000036
has db xref: OpenCyc:Mx4rvVjvDpwpEbGdrcN5Y29ycA
external_definition: Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]
has db xref: TAO:0000114
comment: Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" http://dx.doi.org/10.1101/gad.1485706
id: UBERON:0000948
has db xref: UMLS:C0018787
has db xref: VHOG:0000276
has db xref: XAO:0000064
has db xref: ZFA:0000114
has narrow synonym: branchial heart
has_relational_adjective: cardiac
has related synonym: cardium
has exact synonym: chambered heart
term from ontology: doid.owl
has db xref: galen:Heart
term from ontology: obi.owl
axiom_lost_from_external_ontology: relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]
has OBO namespace: uberon
has exact synonym: vertebrate heart
has db xref: Heart
has db xref: http://linkedlifedata.com/resource/umls/id/C0018787
has db xref: C12727
imported from: uberon.owl
in subset: efo slim
in subset: major organ
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core
has db xref: http://www.snomedbrowser.com/Codes/Details/302509004

brain
type: Class
subclass of: anatomical structure
subclass of: organ
homology_notes: (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]
has db xref: AAO:0010478
has db xref: ABA:Brain
has db xref: BAMS:Br
has db xref: BAMS:Brain
has db xref: BILA:0000135
has db xref: BTO:0000142
has db xref: CALOHA:TS-0095
external_definition: Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]
has db xref: DHBA:10155
has db xref: EFO:0000302
has db xref: EHDAA2:0000183
has db xref: EHDAA:2641
has db xref: EHDAA:6485
has db xref: EMAPA:16894
has db xref: EV:0100164
has db xref: FBbt:00005095
has db xref: FMA:50801
has db xref: GAID:571
has db xref: HBA:4005
has db xref: MA:0000168
has db xref: MAT:0000098
has db xref: MBA:8
has db xref: MBA:997
has db xref: MESH:D001921
has db xref: MIAA:0000098
has db xref: OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA
has db xref: PBA:3999
external_definition: Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]
has db xref: TAO:0000008
definition: The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
external_definition: The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)
id: UBERON:0000955
has db xref: UMLS:C0006104
has db xref: UMLS:C1269537
has db xref: VHOG:0000157
has db xref: XAO:0000010
has db xref: ZFA:0000008
term from ontology: doid.owl
has related synonym: encephalon
has db xref: galen:Brain
has db xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx
term from ontology: obi.owl
editor note: requires review for applicability to invertebrate structures, e.g. synganglion
has related synonym: suprasegmental levels of nervous system
has related synonym: suprasegmental structures
has related synonym: synganglion
has related synonym: the brain
has OBO namespace: uberon
has db xref: Brain
has db xref: http://linkedlifedata.com/resource/umls/id/C0006104
has db xref: http://linkedlifedata.com/resource/umls/id/C1269537
has db xref: C12439
imported from: uberon.owl
in subset: cumbo
in subset: efo slim
in subset: major organ
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core
has db xref: birnlex 796
has db xref: http://www.snomedbrowser.com/Codes/Details/258335003
contributor: cmungall

anatomical entity
type: Class
subclass of: material entity
has db xref: AAO:0010841
has db xref: AEO:0000000
has db xref: BILA:0000000
definition: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
has db xref: CARO:0000000
has db xref: EHDAA2:0002229
has db xref: FBbt:10000000
has db xref: FBbt_root:00000000
has db xref: FMA:62955
has db xref: HAO:0000000
has db xref: MA:0000001
has db xref: TAO:0100000
has db xref: TGMA:0001822
id: UBERON:0001062
has db xref: UMLS:C1515976
has db xref: XAO:0000000
has db xref: ZFA:0100000
has OBO namespace: uberon
has db xref: http://linkedlifedata.com/resource/umls/id/C1515976
has db xref: C12219
imported from: uberon.owl
in subset: upper level
has db xref: birnlex 6

skeletal muscle tissue
type: Class
subclass of: muscle tissue
has db xref: EMAPA:32716
has db xref: FMA:14069
has db xref: MA:0002439
definition: Muscle tissue that consists primarily of skeletal muscle fibers.
external_definition: Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]
editor note: TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle.
homology_notes: This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG]
external_definition: Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]
id: UBERON:0001134
has db xref: UMLS:C0242692
term from ontology: doid.owl
term from ontology: obi.owl
has broad synonym: skeletal muscle
has related synonym: skeletal muscle system
has related synonym: somatic muscle
has OBO namespace: uberon
has db xref: Skeletal striated muscle
has db xref: http://linkedlifedata.com/resource/umls/id/C0242692
has db xref: C13050
imported from: uberon.owl
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core
has db xref: http://www.snomedbrowser.com/Codes/Details/426215008
contributor: RDruzinsky
contributor: cmungall
contributor: dosumis
contributor: mellybelly

tibial nerve
type: Class
subclass of: anatomical entity
has db xref: EMAPA:36512
has db xref: FMA:19035
has db xref: GAID:854
has db xref: MA:0001173
has db xref: MESH:D013979
has db xref: OpenCyc:Mx4rwNya8JwpEbGdrcN5Y29ycA
definition: The tibial nerve is a branch of the sciatic nerve. The tibial nerve passes through the popliteal fossa to pass below the arch of soleus. In the popliteal fossa the nerve gives off branches to gastrocnemius, popliteus, soleus and plantaris muscles, an articular branch to the knee joint, and a cutaneous branch that will become the sural nerve. The sural nerve is joined by fibres from the common peroneal nerve and runs down the calf to supply the lateral side of the foot. Below the soleus muscle the nerve lies close to the tibia and supplies the tibialis posterior, the flexor digitorum longus and the flexor hallucis longus. The nerve passes into the foot running posterior to the medial malleolus. Here it is bound down by the flexor retinaculum in company with the posterior tibial artery. [WP,unvetted].
id: UBERON:0001323
has db xref: UMLS:C0040186
term from ontology: doid.owl
has exact synonym: medial popliteal nerve
has related synonym: n. tibialis
term from ontology: obi.owl
has OBO namespace: uberon
has db xref: Tibial nerve
has db xref: http://linkedlifedata.com/resource/umls/id/C0040186
has db xref: C52809
imported from: uberon.owl
in subset: uberon slim
has db xref: http://www.snomedbrowser.com/Codes/Details/181078002

coronary artery
type: Class
subclass of: blood vessel
subclass of: heart blood vessel
definition: An artery that supplies the myocardium.
has db xref: BTO:0000290
has db xref: CALOHA:TS-0176
has db xref: EFO:0002551
has db xref: EMAPA:19160
has db xref: EMAPA:25968
has db xref: EV:0100383
has db xref: FMA:49893
has db xref: MA:0002453
has db xref: OpenCyc:Mx4rvoL56ZwpEbGdrcN5Y29ycA
id: UBERON:0001621
has db xref: UMLS:C0205042
has db xref: VHOG:0001557
has db xref: ZFA:0005812
has exact synonym: coronary arterial tree
has related synonym: coronary vessel
term from ontology: doid.owl
has db xref: galen:CoronaryArtery
term from ontology: obi.owl
has OBO namespace: uberon
has db xref: Coronary anatomy
has db xref: http://linkedlifedata.com/resource/umls/id/C0205042
has db xref: C12843
imported from: uberon.owl
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
has db xref: http://www.snomedbrowser.com/Codes/Details/181294004

blood vessel
type: Class
subclass of: vessel
subclass of: mesoderm-derived structure
definition: A vessel through which blood circulates in the body.
has db xref: AAO:0011004
has db xref: AEO:0000207
external_definition: Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]
external_definition: Any of the vessels through which blood circulates in the body.[AAO]
has db xref: BTO:0001102
has db xref: CALOHA:TS-0080
has db xref: EFO:0000817
has db xref: EHDAA2:0003252
has db xref: EHDAA:240
has db xref: EMAPA:32743
has db xref: EMAPA:35993
has db xref: FMA:50722
has db xref: FMA:63183
external_ontology_notes: FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX
has db xref: GAID:169
has db xref: MA:0000060
has db xref: MAT:0000393
has db xref: MESH:D001808
has db xref: OpenCyc:Mx4rvVjxlpwpEbGdrcN5Y29ycA
has db xref: TAO:0002137
homology_notes: The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
id: UBERON:0001981
has db xref: UMLS:C0005847
has db xref: VHOG:0001250
has db xref: XAO:0001011
has db xref: ZFA:0005314
taxon_notes: annelids have blood vessels, but this class is not applicable to annelids.
editor note: consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus
has exact synonym: region of vascular tree organ
has OBO namespace: uberon
has related synonym: vas sanguineum
has broad synonym: vascular element
has exact synonym: vascular tree organ region
has db xref: Blood vessel
has db xref: http://linkedlifedata.com/resource/umls/id/C0005847
has db xref: C12679
imported from: uberon.owl
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core
has db xref: nlx anat 090901
has db xref: http://www.snomedbrowser.com/Codes/Details/361097006

liver
type: Class
subclass of: anatomical structure
subclass of: gland
subclass of: trunk region element
subclass of: digestive gland
has db xref: AAO:0010111
homology_notes: All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG]
definition: An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
taxon_notes: An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003).
has db xref: BTO:0000759
has db xref: CALOHA:TS-0564
has db xref: EFO:0000887
has db xref: EHDAA2:0000997
has db xref: EHDAA:2197
has db xref: EMAPA:16846
has db xref: EV:0100089
has db xref: FMA:7197
has db xref: GAID:288
has db xref: MA:0000358
has db xref: MAT:0000097
has db xref: MESH:D008099
has db xref: MIAA:0000097
external_ontology_notes: Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function.
has db xref: OpenCyc:Mx4rvVimppwpEbGdrcN5Y29ycA
external_definition: Organ which secretes bile and participates in formation of certain blood proteins.[AAO]
has db xref: TAO:0000123
taxon_notes: The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates.
id: UBERON:0002107
has db xref: UMLS:C0023884
has db xref: VHOG:0000257
has db xref: XAO:0000133
has db xref: ZFA:0000123
term from ontology: doid.owl
has db xref: galen:Liver
has_relational_adjective: hepatic
has related synonym: iecur
has related synonym: jecur
term from ontology: obi.owl
axiom_lost_from_external_ontology: relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]
function_notes: secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
has OBO namespace: uberon
has db xref: Liver
has db xref: http://linkedlifedata.com/resource/umls/id/C0023884
has db xref: C12392
imported from: uberon.owl
in subset: efo slim
in subset: major organ
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core
has db xref: http://www.snomedbrowser.com/Codes/Details/181268008

muscle tissue
type: Class
subclass of: mesoderm-derived structure
subclass of: multicellular anatomical structure
has db xref: AAO:0000306
has db xref: AEO:0000122
has db xref: CALOHA:TS-0642
has db xref: EHDAA2:0003122
has db xref: EMAPA:32715
has db xref: FMA:9641
has db xref: MA:0002437
has db xref: MESH:D009132
definition: Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].
external_definition: One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]
id: UBERON:0002385
has db xref: UMLS:C2328219
comment: Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach.
has db xref: galen:MuscleTissue
has exact synonym: muscular tissue
has exact synonym: portion of muscle tissue
has exact synonym: textus muscularis
has OBO namespace: uberon
has db xref: Muscle tissue
has db xref: http://linkedlifedata.com/resource/umls/id/C2328219
has db xref: C12435
imported from: uberon.owl
in subset: uberon slim
has db xref: http://www.snomedbrowser.com/Codes/Details/91727004

gland
type: Class
subclass of: organ
has db xref: AAO:0000212
has db xref: AEO:0000096
has db xref: BTO:0000522
has related synonym: Druese
has db xref: EFO:0000797
has db xref: EHDAA2:0003096
has db xref: EHDAA:2161
has db xref: EHDAA:4475
has db xref: EHDAA:6522
has db xref: EMAPA:18425
has db xref: FBbt:00100317
has db xref: FMA:7146
has db xref: FMA:86294
has db xref: HAO:0000375
has db xref: MA:0003038
has db xref: MAT:0000021
has db xref: MIAA:0000021
has db xref: OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA
id: UBERON:0002530
has alternative id: UBERON:MIAA_0000021
has db xref: UMLS:C1285092
has db xref: WikipediaCategory:Glands
definition: an organ that functions as a secretory or excretory organ
has db xref: galen:Gland
has related synonym: glandula
has_relational_adjective: glandular
has exact synonym: glandular organ
has OBO namespace: uberon
has db xref: Gland
has db xref: http://linkedlifedata.com/resource/umls/id/C1285092
has db xref: C13319
imported from: uberon.owl
in subset: efo slim
in subset: pheno slim
in subset: uberon slim
has db xref: http://www.snomedbrowser.com/Codes/Details/134358001

heart blood vessel
type: Class
subclass of: blood vessel
subclass of: coronary vessel
definition: A blood vessel that is part of a heart [Automatically generated definition].
has db xref: EMAPA:35397
has db xref: MA:0002483
id: UBERON:0003498
has exact synonym: blood vessel of heart
has related synonym: cardiac blood vessel
has OBO namespace: uberon
imported from: uberon.owl
in subset: pheno slim

mesoderm-derived structure
type: Class
subclass of: anatomical structure
definition: An anatomical structure that develops (entirely or partially) from the mesoderm.
has db xref: FBbt:00025998
curator notes: Grouping term for query purposes
id: UBERON:0004120
has exact synonym: mesodermal derivative
has OBO namespace: uberon
imported from: uberon.owl
in subset: grouping class

trunk region element
type: Class
subclass of: organ
definition: An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.
has db xref: MA:0000516
id: UBERON:0005177
has exact synonym: trunk organ
has OBO namespace: uberon
imported from: uberon.owl
in subset: non informative
in subset: organ slim

coronary vessel
type: Class
subclass of: vessel
subclass of: mesoderm-derived structure
definition: Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation
has db xref: MESH:D003331
editor note: TODO - change relation from part_of
id: UBERON:0005985
has OBO namespace: uberon
has db xref: Coronary circulation
imported from: uberon.owl
in subset: pheno slim

digestive gland
type: Class
subclass of: organ
subclass of: gland
definition: A gland, such as the liver or pancreas, that secretes into the alimentary canal substances necessary for digestion.
has db xref: AAO:0000130
has db xref: BTO:0000345
id: UBERON:0006925
has exact synonym: digestive system gland
has OBO namespace: uberon
imported from: uberon.owl
in subset: organ slim

multicellular anatomical structure
type: Class
subclass of: anatomical structure
definition: An anatomical structure that has more than one cell as a part.
has db xref: CARO:0010000
has db xref: FBbt:00100313
id: UBERON:0010000
has exact synonym: multicellular structure
has OBO namespace: uberon
imported from: uberon.owl
in subset: upper level

Xenopus anatomical entity
type: Class
subclass of: anatomical entity
has db xref: CARO:0000000
definition: Entity that is either an individual member of Xenopus or constitutes the structural organization of an individual member Xenopus.
id: XAO:0000000
has OBO namespace: xenopus_anatomy
imported from: xao.owl

Xenopus developmental stage
type: Class
subclass of: life cycle stage
definition: A temporal interval that defines Xenopus life from unfertilized egg to adult and death stages.
id: XAO:1000000
has OBO namespace: xenopus_developmental_stage
imported from: xao.owl

zebrafish anatomical entity
type: Class
subclass of: anatomical entity
id: ZFA:0100000
has OBO namespace: zebrafish_anatomy
imported from: zfa.owl

Stages
type: Class
subclass of: life cycle stage
id: ZFS:0100000
has OBO namespace: zebrafish_stages
imported from: zfa.owl