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nucleus.yaml
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nucleus.yaml
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---
graphs:
- id: "http://purl.obolibrary.org/obo/go-test.owl"
meta:
basicPropertyValues:
- pred: "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion"
val: "1.2"
version: "http://purl.obolibrary.org/obo/go-test/releases/2016-10-22/go-test.owl"
nodes:
- id: "http://purl.obolibrary.org/obo/GO_0005575"
lbl: "cellular_component"
type: "CLASS"
meta:
definition:
val: "The part of a cell or its extracellular environment 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."
xrefs:
- "GOC:go_curators"
- "NIF_Subcellular:sao-1337158144"
comments:
- "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."
subsets:
- "http://purl.obolibrary.org/obo/go-test#goslim_aspergillus"
- "http://purl.obolibrary.org/obo/go-test#goslim_candida"
- "http://purl.obolibrary.org/obo/go-test#goslim_chembl"
- "http://purl.obolibrary.org/obo/go-test#goslim_generic"
- "http://purl.obolibrary.org/obo/go-test#goslim_metagenomics"
- "http://purl.obolibrary.org/obo/go-test#goslim_pir"
- "http://purl.obolibrary.org/obo/go-test#goslim_plant"
- "http://purl.obolibrary.org/obo/go-test#goslim_yeast"
- "http://purl.obolibrary.org/obo/go-test#gosubset_prok"
synonyms:
- pred: "hasExactSynonym"
val: "cell or subcellular entity"
- synonymType: "http://purl.obolibrary.org/obo/go-test#systematic_synonym"
pred: "hasExactSynonym"
val: "cellular component"
- pred: "hasRelatedSynonym"
val: "subcellular entity"
xrefs:
- "NIF_Subcellular:nlx_subcell_100315"
xrefs:
- val: "NIF_Subcellular:sao-1337158144"
- val: "NIF_Subcellular:sao1337158144"
basicPropertyValues:
- pred: "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId"
val: "GO:0008372"
- pred: "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace"
val: "cellular_component"
- id: "http://purl.obolibrary.org/obo/GO_0005622"
lbl: "intracellular"
type: "CLASS"
meta:
definition:
val: "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."
xrefs:
- "ISBN:0198506732"
subsets:
- "http://purl.obolibrary.org/obo/go-test#goslim_chembl"
- "http://purl.obolibrary.org/obo/go-test#goslim_generic"
- "http://purl.obolibrary.org/obo/go-test#goslim_metagenomics"
- "http://purl.obolibrary.org/obo/go-test#goslim_pir"
- "http://purl.obolibrary.org/obo/go-test#goslim_plant"
- "http://purl.obolibrary.org/obo/go-test#gosubset_prok"
synonyms:
- pred: "hasExactSynonym"
val: "internal to cell"
- pred: "hasExactSynonym"
val: "protoplasm"
- pred: "hasRelatedSynonym"
val: "nucleocytoplasm"
xrefs:
- "GOC:mah"
- pred: "hasRelatedSynonym"
val: "protoplast"
xrefs:
- "GOC:mah"
xrefs:
- val: "Wikipedia:Intracellular"
basicPropertyValues:
- pred: "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace"
val: "cellular_component"
- id: "http://purl.obolibrary.org/obo/GO_0005623"
lbl: "cell"
type: "CLASS"
meta:
definition:
val: "The basic structural and functional unit of all organisms. Includes\
\ the plasma membrane and any external encapsulating structures such as\
\ the cell wall and cell envelope."
xrefs:
- "GOC:go_curators"
subsets:
- "http://purl.obolibrary.org/obo/go-test#goslim_chembl"
- "http://purl.obolibrary.org/obo/go-test#goslim_generic"
- "http://purl.obolibrary.org/obo/go-test#goslim_plant"
- "http://purl.obolibrary.org/obo/go-test#gosubset_prok"
xrefs:
- val: "NIF_Subcellular:sao1813327414"
- val: "Wikipedia:Cell_(biology)"
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000589"
val: "cell and encapsulating structures"
- pred: "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace"
val: "cellular_component"
- id: "http://purl.obolibrary.org/obo/GO_0005634"
lbl: "nucleus"
type: "CLASS"
meta:
definition:
val: "A membrane-bounded organelle of eukaryotic cells in which chromosomes\
\ are housed and replicated. In most cells, the nucleus contains all of\
\ the cell's chromosomes except the organellar chromosomes, and is the site\
\ of RNA synthesis and processing. In some species, or in specialized cell\
\ types, RNA metabolism or DNA replication may be absent."
xrefs:
- "GOC:go_curators"
subsets:
- "http://purl.obolibrary.org/obo/go-test#goslim_aspergillus"
- "http://purl.obolibrary.org/obo/go-test#goslim_candida"
- "http://purl.obolibrary.org/obo/go-test#goslim_chembl"
- "http://purl.obolibrary.org/obo/go-test#goslim_generic"
- "http://purl.obolibrary.org/obo/go-test#goslim_metagenomics"
- "http://purl.obolibrary.org/obo/go-test#goslim_pir"
- "http://purl.obolibrary.org/obo/go-test#goslim_plant"
- "http://purl.obolibrary.org/obo/go-test#goslim_yeast"
synonyms:
- synonymType: "http://purl.obolibrary.org/obo/go-test#systematic_synonym"
pred: "hasExactSynonym"
val: "cell nucleus"
xrefs:
- val: "NIF_Subcellular:sao1702920020"
- val: "Wikipedia:Cell_nucleus"
basicPropertyValues:
- pred: "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace"
val: "cellular_component"
- id: "http://purl.obolibrary.org/obo/GO_0008372"
type: "CLASS"
meta:
basicPropertyValues:
- pred: "http://purl.obolibrary.org/obo/IAO_0000231"
val: "http://purl.obolibrary.org/obo/IAO_0000227"
- pred: "http://purl.obolibrary.org/obo/IAO_0100001"
val: "http://purl.obolibrary.org/obo/GO_0005575"
deprecated: true
- id: "http://purl.obolibrary.org/obo/GO_0043226"
lbl: "organelle"
type: "CLASS"
meta:
definition:
val: "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."
xrefs:
- "GOC:go_curators"
subsets:
- "http://purl.obolibrary.org/obo/go-test#goslim_chembl"
- "http://purl.obolibrary.org/obo/go-test#goslim_generic"
- "http://purl.obolibrary.org/obo/go-test#goslim_pir"
- "http://purl.obolibrary.org/obo/go-test#gosubset_prok"
xrefs:
- val: "NIF_Subcellular:sao1539965131"
- val: "Wikipedia:Organelle"
basicPropertyValues:
- pred: "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace"
val: "cellular_component"
- id: "http://purl.obolibrary.org/obo/GO_0043227"
lbl: "membrane-bounded organelle"
type: "CLASS"
meta:
definition:
val: "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."
xrefs:
- "GOC:go_curators"
subsets:
- "http://purl.obolibrary.org/obo/go-test#gosubset_prok"
synonyms:
- pred: "hasExactSynonym"
val: "membrane-enclosed organelle"
xrefs:
- val: "NIF_Subcellular:sao414196390"
basicPropertyValues:
- pred: "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace"
val: "cellular_component"
- id: "http://purl.obolibrary.org/obo/GO_0043229"
lbl: "intracellular organelle"
type: "CLASS"
meta:
definition:
val: "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."
xrefs:
- "GOC:go_curators"
subsets:
- "http://purl.obolibrary.org/obo/go-test#goslim_pir"
- "http://purl.obolibrary.org/obo/go-test#gosubset_prok"
basicPropertyValues:
- pred: "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace"
val: "cellular_component"
- id: "http://purl.obolibrary.org/obo/GO_0043231"
lbl: "intracellular membrane-bounded organelle"
type: "CLASS"
meta:
definition:
val: "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."
xrefs:
- "GOC:go_curators"
subsets:
- "http://purl.obolibrary.org/obo/go-test#goslim_pir"
- "http://purl.obolibrary.org/obo/go-test#gosubset_prok"
synonyms:
- pred: "hasExactSynonym"
val: "intracellular membrane-enclosed organelle"
basicPropertyValues:
- pred: "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace"
val: "cellular_component"
- id: "http://purl.obolibrary.org/obo/GO_0044424"
lbl: "intracellular part"
type: "CLASS"
meta:
definition:
val: "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."
xrefs:
- "GOC:jl"
comments:
- "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."
subsets:
- "http://purl.obolibrary.org/obo/go-test#goantislim_grouping"
- "http://purl.obolibrary.org/obo/go-test#gocheck_do_not_annotate"
- "http://purl.obolibrary.org/obo/go-test#gosubset_prok"
basicPropertyValues:
- pred: "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace"
val: "cellular_component"
- id: "http://purl.obolibrary.org/obo/GO_0044464"
lbl: "cell part"
type: "CLASS"
meta:
definition:
val: "Any constituent part of a cell, the basic structural and functional\
\ unit of all organisms."
xrefs:
- "GOC:jl"
comments:
- "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."
subsets:
- "http://purl.obolibrary.org/obo/go-test#goantislim_grouping"
- "http://purl.obolibrary.org/obo/go-test#gocheck_do_not_annotate"
- "http://purl.obolibrary.org/obo/go-test#goslim_pir"
- "http://purl.obolibrary.org/obo/go-test#gosubset_prok"
synonyms:
- pred: "hasExactSynonym"
val: "cellular subcomponent"
xrefs:
- "NIF_Subcellular:sao628508602"
- pred: "hasRelatedSynonym"
val: "protoplast"
xrefs:
- "GOC:mah"
xrefs:
- val: "NIF_Subcellular:sao628508602"
basicPropertyValues:
- pred: "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace"
val: "cellular_component"
- id: "http://purl.obolibrary.org/obo/BFO_0000050"
lbl: "part of"
type: "PROPERTY"
propertyType: "OBJECT"
meta:
xrefs:
- val: "BFO:0000050"
basicPropertyValues:
- pred: "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace"
val: "external"
- pred: "http://www.geneontology.org/formats/oboInOwl#shorthand"
val: "part_of"
- id: "http://purl.obolibrary.org/obo/IAO_0000115"
lbl: "definition"
type: "PROPERTY"
propertyType: "ANNOTATION"
- id: "http://www.geneontology.org/formats/oboInOwl#SubsetProperty"
lbl: "subset_property"
type: "PROPERTY"
propertyType: "ANNOTATION"
- id: "http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"
lbl: "synonym_type_property"
type: "PROPERTY"
propertyType: "ANNOTATION"
- id: "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId"
lbl: "has_alternative_id"
type: "PROPERTY"
propertyType: "ANNOTATION"
- id: "http://www.geneontology.org/formats/oboInOwl#hasDbXref"
lbl: "database_cross_reference"
type: "PROPERTY"
propertyType: "ANNOTATION"
- id: "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"
lbl: "has_exact_synonym"
type: "PROPERTY"
propertyType: "ANNOTATION"
- id: "http://www.geneontology.org/formats/oboInOwl#hasOBOFormatVersion"
lbl: "has_obo_format_version"
type: "PROPERTY"
propertyType: "ANNOTATION"
- id: "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace"
lbl: "has_obo_namespace"
type: "PROPERTY"
propertyType: "ANNOTATION"
- id: "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"
lbl: "has_related_synonym"
type: "PROPERTY"
propertyType: "ANNOTATION"
- id: "http://www.geneontology.org/formats/oboInOwl#hasScope"
lbl: "has_scope"
type: "PROPERTY"
propertyType: "ANNOTATION"
- id: "http://www.geneontology.org/formats/oboInOwl#hasSynonymType"
lbl: "has_synonym_type"
type: "PROPERTY"
propertyType: "ANNOTATION"
- id: "http://www.geneontology.org/formats/oboInOwl#id"
type: "PROPERTY"
propertyType: "ANNOTATION"
- id: "http://www.geneontology.org/formats/oboInOwl#inSubset"
lbl: "in_subset"
type: "PROPERTY"
propertyType: "ANNOTATION"
- id: "http://www.geneontology.org/formats/oboInOwl#shorthand"
lbl: "shorthand"
type: "PROPERTY"
propertyType: "ANNOTATION"
- id: "http://www.w3.org/2000/01/rdf-schema#comment"
type: "PROPERTY"
propertyType: "ANNOTATION"
- id: "http://www.w3.org/2000/01/rdf-schema#label"
type: "PROPERTY"
propertyType: "ANNOTATION"
- id: "http://purl.obolibrary.org/obo/go-test#goantislim_grouping"
meta:
comments:
- "Grouping classes that can be excluded"
- id: "http://purl.obolibrary.org/obo/go-test#gocheck_do_not_annotate"
meta:
comments:
- "Term not to be used for direct annotation"
- id: "http://purl.obolibrary.org/obo/go-test#gocheck_do_not_manually_annotate"
meta:
comments:
- "Term not to be used for direct manual annotation"
- id: "http://purl.obolibrary.org/obo/go-test#goslim_aspergillus"
meta:
comments:
- "Aspergillus GO slim"
- id: "http://purl.obolibrary.org/obo/go-test#goslim_candida"
meta:
comments:
- "Candida GO slim"
- id: "http://purl.obolibrary.org/obo/go-test#goslim_chembl"
meta:
comments:
- "ChEMBL protein targets summary"
- id: "http://purl.obolibrary.org/obo/go-test#goslim_generic"
meta:
comments:
- "Generic GO slim"
- id: "http://purl.obolibrary.org/obo/go-test#goslim_goa"
meta:
comments:
- "GOA and proteome slim"
- id: "http://purl.obolibrary.org/obo/go-test#goslim_metagenomics"
meta:
comments:
- "Metagenomics GO slim"
- id: "http://purl.obolibrary.org/obo/go-test#goslim_pir"
meta:
comments:
- "PIR GO slim"
- id: "http://purl.obolibrary.org/obo/go-test#goslim_plant"
meta:
comments:
- "Plant GO slim"
- id: "http://purl.obolibrary.org/obo/go-test#goslim_pombe"
meta:
comments:
- "Fission yeast GO slim"
- id: "http://purl.obolibrary.org/obo/go-test#goslim_synapse"
meta:
comments:
- "synapse GO slim"
- id: "http://purl.obolibrary.org/obo/go-test#goslim_virus"
meta:
comments:
- "Viral GO slim"
- id: "http://purl.obolibrary.org/obo/go-test#goslim_yeast"
meta:
comments:
- "Yeast GO slim"
- id: "http://purl.obolibrary.org/obo/go-test#gosubset_prok"
meta:
comments:
- "Prokaryotic GO subset"
- id: "http://purl.obolibrary.org/obo/go-test#mf_needs_review"
meta:
comments:
- "Catalytic activity terms in need of attention"
- id: "http://purl.obolibrary.org/obo/go-test#syngo_official_label"
lbl: "label approved by the SynGO project"
- id: "http://purl.obolibrary.org/obo/go-test#systematic_synonym"
lbl: "Systematic synonym"
meta:
basicPropertyValues:
- pred: "http://www.geneontology.org/formats/oboInOwl#hasScope"
val: "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"
- id: "http://purl.obolibrary.org/obo/go-test#termgenie_unvetted"
meta:
comments:
- "Terms created by TermGenie that do not follow a template and require additional\
\ vetting by editors"
- id: "http://purl.obolibrary.org/obo/go-test#virus_checked"
meta:
comments:
- "Viral overhaul terms"
edges:
- sub: "http://purl.obolibrary.org/obo/GO_0005622"
pred: "is_a"
obj: "http://purl.obolibrary.org/obo/GO_0044464"
- sub: "http://purl.obolibrary.org/obo/GO_0005623"
pred: "is_a"
obj: "http://purl.obolibrary.org/obo/GO_0005575"
- sub: "http://purl.obolibrary.org/obo/GO_0005634"
pred: "is_a"
obj: "http://purl.obolibrary.org/obo/GO_0043231"
- sub: "http://purl.obolibrary.org/obo/GO_0043226"
pred: "is_a"
obj: "http://purl.obolibrary.org/obo/GO_0005575"
- sub: "http://purl.obolibrary.org/obo/GO_0043227"
pred: "is_a"
obj: "http://purl.obolibrary.org/obo/GO_0043226"
- sub: "http://purl.obolibrary.org/obo/GO_0043229"
pred: "is_a"
obj: "http://purl.obolibrary.org/obo/GO_0043226"
- sub: "http://purl.obolibrary.org/obo/GO_0043229"
pred: "is_a"
obj: "http://purl.obolibrary.org/obo/GO_0044424"
- sub: "http://purl.obolibrary.org/obo/GO_0043231"
pred: "is_a"
obj: "http://purl.obolibrary.org/obo/GO_0043227"
- sub: "http://purl.obolibrary.org/obo/GO_0043231"
pred: "is_a"
obj: "http://purl.obolibrary.org/obo/GO_0043229"
- sub: "http://purl.obolibrary.org/obo/GO_0044424"
pred: "is_a"
obj: "http://purl.obolibrary.org/obo/GO_0044464"
- sub: "http://purl.obolibrary.org/obo/GO_0044424"
pred: "http://purl.obolibrary.org/obo/BFO_0000050"
obj: "http://purl.obolibrary.org/obo/GO_0005622"
- sub: "http://purl.obolibrary.org/obo/GO_0044464"
pred: "is_a"
obj: "http://purl.obolibrary.org/obo/GO_0005575"
- sub: "http://purl.obolibrary.org/obo/GO_0044464"
pred: "http://purl.obolibrary.org/obo/BFO_0000050"
obj: "http://purl.obolibrary.org/obo/GO_0005623"
- sub: "http://purl.obolibrary.org/obo/BFO_0000050"
pred: "inverseOf"
obj: "http://purl.obolibrary.org/obo/go-test#has_part"
logicalDefinitionAxioms:
- definedClassId: "http://purl.obolibrary.org/obo/GO_0044424"
genusIds:
- "http://purl.obolibrary.org/obo/GO_0005575"
restrictions:
- propertyId: "http://purl.obolibrary.org/obo/BFO_0000050"
fillerId: "http://purl.obolibrary.org/obo/GO_0005622"
- definedClassId: "http://purl.obolibrary.org/obo/GO_0044464"
genusIds:
- "http://purl.obolibrary.org/obo/GO_0005575"
restrictions:
- propertyId: "http://purl.obolibrary.org/obo/BFO_0000050"
fillerId: "http://purl.obolibrary.org/obo/GO_0005623"