obsolete GO:0030374 and GO:0140536, replaced with GO:0003713 and GO:0…

[edwong57]

…03714; Fixes #29150

[github-actions[bot]]

Here's a diff of how these changes impact the classified ontology:

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/go.owl
• Version IRI: http://purl.obolibrary.org/obo/go/releases/2024-11-13/go.owl
• Loaded from: file:/__w/go-ontology/go-ontology/src/ontology/../../reasoned-master.owl/reasoned.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/go.owl
• Version IRI: http://purl.obolibrary.org/obo/go/releases/2024-11-13/go.owl
• Loaded from: file:/__w/go-ontology/go-ontology/src/ontology/../../reasoned-pr.owl/reasoned.owl

Ontology imports

Ontology annotations

nuclear receptor coactivator activity http://purl.obolibrary.org/obo/GO_0030374

Removed

• nuclear receptor coactivator activity label "nuclear receptor coactivator activity"

• nuclear receptor coactivator activity definition "A transcription coactivator activity that activates or increases the transcription of specific gene sets via binding to a DNA-bound nuclear receptor, either on its own or as part of a complex. Coactivators often act by altering chromatin structure and modifications. For example, one class of transcription coregulators modifies chromatin structure through covalent modification of histones. A second class remodels the conformation of chromatin in an ATP-dependent fashion. A third class modulates interactions of DNA-bound DNA-binding transcription factors with other transcription coregulators. A fourth class of coactivator activity is the bridging of a DNA-binding transcription factor to the general (basal) transcription machinery. The Mediator complex, which bridges sequence-specific DNA binding transcription factors and RNA polymerase, is also a transcription coactivator."

  • database_cross_reference "GOC:dph"

  • database_cross_reference "GOC:tb"

• nuclear receptor coactivator activity comment "For usage guidance, see comment in GO:0003712 ; transcription coregulator activity."

• nuclear receptor coactivator activity SubClassOf transcription coactivator activity

Added

• nuclear receptor coactivator activity term replaced by "GO:0003713"

• nuclear receptor coactivator activity term tracker item "https://github.com/geneontology/go-ontology/issues/29150"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• nuclear receptor coactivator activity comment "The reason for obsoletion is that these activities are not necessarily specific for nuclear receptors subclass of dbTFs, so that distinction leads to misannotations."

• nuclear receptor coactivator activity label "obsolete nuclear receptor coactivator activity"

• nuclear receptor coactivator activity definition "OBSOLETE. A transcription coactivator activity that activates or increases the transcription of specific gene sets via binding to a DNA-bound nuclear receptor, either on its own or as part of a complex. Coactivators often act by altering chromatin structure and modifications. For example, one class of transcription coregulators modifies chromatin structure through covalent modification of histones. A second class remodels the conformation of chromatin in an ATP-dependent fashion. A third class modulates interactions of DNA-bound DNA-binding transcription factors with other transcription coregulators. A fourth class of coactivator activity is the bridging of a DNA-binding transcription factor to the general (basal) transcription machinery. The Mediator complex, which bridges sequence-specific DNA binding transcription factors and RNA polymerase, is also a transcription coactivator."

  • database_cross_reference "GOC:dph"

  • database_cross_reference "GOC:tb"

• nuclear receptor coactivator activity deprecated true

nuclear receptor corepressor activity http://purl.obolibrary.org/obo/GO_0140536

Removed

• nuclear receptor corepressor activity definition "A transcription corepressor activity that represses or decreases the transcription of specific gene sets via binding to a DNA-bound nuclear receptor, either on its own or as part of a complex. Nuclear receptor corepressors often act by altering chromatin structure and modifications. For example, one class of transcription nuclear receptor corepressors modifies chromatin structure through covalent modification of histones. A second class remodels the conformation of chromatin in an ATP-dependent fashion. A third class modulates interactions of DNA-bound DNA-binding transcription factors with other transcription coregulators."

  • database_cross_reference "PMID:9238851"

  • database_cross_reference "PMID:7566114"

  • database_cross_reference "PMID:7566126"

• nuclear receptor corepressor activity label "nuclear receptor corepressor activity"

• nuclear receptor corepressor activity comment "For usage guidance, see comment in GO:0003712 ; transcription coregulator activity."

• nuclear receptor corepressor activity SubClassOf transcription corepressor activity

• nuclear receptor corepressor activity SubClassOf part of some negative regulation of transcription by RNA polymerase II

Added

• nuclear receptor corepressor activity label "obsolete nuclear receptor corepressor activity"

• nuclear receptor corepressor activity comment "The reason for obsoletion is that these activities are not necessarily specific for nuclear receptors subclass of dbTFs, so that distinction leads to misannotations."

• nuclear receptor corepressor activity term tracker item "https://github.com/geneontology/go-ontology/issues/29150"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI)

• nuclear receptor corepressor activity term replaced by "GO:0003714"

• nuclear receptor corepressor activity deprecated true

• nuclear receptor corepressor activity definition "OBSOLETE. A transcription corepressor activity that represses or decreases the transcription of specific gene sets via binding to a DNA-bound nuclear receptor, either on its own or as part of a complex. Nuclear receptor corepressors often act by altering chromatin structure and modifications. For example, one class of transcription nuclear receptor corepressors modifies chromatin structure through covalent modification of histones. A second class remodels the conformation of chromatin in an ATP-dependent fashion. A third class modulates interactions of DNA-bound DNA-binding transcription factors with other transcription coregulators."

  • database_cross_reference "PMID:9238851"

  • database_cross_reference "PMID:7566114"

  • database_cross_reference "PMID:7566126"