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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Merge GO:0019933 cAMP-mediated signaling & regulation children GO:0010737 protein kinase A signaling & regulation children #26899

Open pgaudet opened 9 months ago

pgaudet commented 9 months ago

We would like to 'merge' these two processes: GO:0019933 cAMP-mediated signaling & regulation children GO:0010737 protein kinase A signaling & regulation children

That would capture the signaling cassette that consists of cAMP and PKA. The definition would be :

An intracellular signaling cassette that starts with the production of cAMP by adenylate cyclase, which releases the inhibition of protein kinase A (PKA) by its regulatory subunits, and activates downstream effectors, including the CREB transcription factor. cAMP can be produced by adenylate cyclase within a G protein-coupled receptor signaling pathway, or by a soluble adenylate cyclase.

We probably need to obsolete and create a new term, because these term have been used inconsistently for upstream pathways, and regulation of the pathway.

Please review your annotations https://github.com/geneontology/go-annotation/issues/4961 and https://github.com/geneontology/go-annotation/issues/4960 and let us know whether this seems like the correct solution.

Thanks, @hattrill and Pascale

pgaudet commented 9 months ago

+[Term] +id: GO:0141156 +name: cAMP/PKA signal transduction +namespace: biological_process +def: "An intracellular signaling cassette that starts with production of cyclic AMP (cAMP) by adenylate cyclase (either transmembrane or soluble), which activates protein kinase A, and ends with activation of downstream effectors such as the transcription factor CREB that further transmit the signal within the cell." [PMID:23209152] +synonym: "cAMP signaling" BROAD [] +synonym: "cAMP/PKA signaling cassette" EXACT [] +synonym: "PKA signaling" BROAD [] +synonym: "protein kinase A signaling" BROAD [] +is_a: GO:0141124 ! intracellular signaling cassette +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26899" xsd:anyURI +created_by: pg +creation_date: 2024-02-01T08:21:03Z

pgaudet commented 9 months ago

+[Term] +id: GO:0141161 +name: regulation of cAMP/PKA signal transduction +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of cAMP/PKA signal transduction. " [GOC:curators] +synonym: "regulation of cAMP/PKA signaling" EXACT [] +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0141156 ! cAMP/PKA signal transduction +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26899" xsd:anyURI +created_by: pg +creation_date: 2024-02-12T12:38:23Z + +[Term] +id: GO:0141162 +name: negative regulation of cAMP/PKA signal transduction +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of cAMP/PKA signal transduction." [PMID:17376027] +synonym: "negative regulation of cAMP/PKA signaling" EXACT [] +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0141156 ! cAMP/PKA signal transduction +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26899" xsd:anyURI +created_by: pg +creation_date: 2024-02-12T12:50:43Z

+[Term] +id: GO:0141163 +name: positive regulation of cAMP/PKA signal transduction +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of cAMP/PKA signal transduction." [PMID:21585352] +synonym: "positive regulation of cAMP/PKA signaling" EXACT [] +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0141156 ! cAMP/PKA signal transduction +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26899" xsd:anyURI +created_by: pg +creation_date: 2024-02-12T12:51:33Z