GPCR pathway project - Githubissues

ukemi commented 7 years ago

The following is the list of tasks for this project:

[x] cAMP receptor activity not a child of G-protein coupled receptor activity geneontology/go-ontology/issues/13881
[x] MP cell surface receptor signaling pathway geneontology/go-ontology/issues/13912
[x] GO:0007189 adenylate cyclase-activating G-protein coupled receptor signaling pathway... missing parent geneontology/go-ontology/issues/13903
[x] postive regulation of cAMP biosynthetic process geneontology/go-ontology/issues/13910
[x] Very similar to 13910 geneontology/go-ontology/issues/12890
[x] G-protein cycle / G-protein assembly and disassembly https://github.com/geneontology/go-ontology/issues/13978
[x] Create list of good references that support GPCR pathway
[x] Obsolete GO:0100019 regulation of cAMP-mediated signaling by transcription from RNA polymerase II promoter - Obsoletion notice sent Oct 31
[x] Merge GO:0007189 adenylate cyclase-activating G protein coupled receptor signaling pathway and GO:0010579 positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway https://github.com/geneontology/go-ontology/issues/14547

Annotation review

CYCLIC NUCLEOTIDE METABOLIC PROCESS REGULATION

[x] GO:0030819 positive regulation of cAMP biosynthetic process https://github.com/geneontology/go-annotation/issues/1691
[x] GO:0030818 negative regulation of cAMP biosynthetic process https://github.com/geneontology/go-annotation/issues/1691
[x] GO:0030820, GO:0030821, GO:0030822 regulation of cAMP catabolic process and + and - children https://github.com/geneontology/go-annotation/issues/1971
[ ] GO:0030814 regulation of cAMP metabolic process #1986
[ ] GO:0030816 positive regulation of cAMP metabolic process #2000
[x] regulation of cGMP metabolic/catabolic/biosynthetic process', and + and - children #1985
[x] GO:0030802 regulation of cyclic nucleotide biosynthetic process #1982
[x] GO:0030801 positive regulation of cyclic nucleotide metabolic process #1981
[ ] GO:0030803 negative regulation of cyclic nucleotide biosynthetic process #1983

CYCLIC NUCLEOTIDE METABOLIC PROCESS

[x] cAMP biosynthetic process https://github.com/geneontology/go-annotation/issues/1712
[ ] GO:0052653 3',5'-cyclic diguanylic acid metabolic process #1984
[ ] GO:0006182 cGMP biosynthetic process https://github.com/geneontology/go-annotation/issues/1977
[ ] GO:0009187 cyclic nucleotide metabolic process https://github.com/geneontology/go-annotation/issues/1978
[ ] GO:0009190 cyclic nucleotide biosynthetic process https://github.com/geneontology/go-annotation/issues/1979
[ ] GO:0006198 cAMP catabolic process https://github.com/geneontology/go-annotation/issues/1974

SIGNALING

[ ] GO:0043950 positive regulation of cAMP-mediated signaling https://github.com/geneontology/go-annotation/issues/1691
[ ] GO:0007194 negative regulation of adenylate cyclase activity https://github.com/geneontology/go-annotation/issues/1691

Ontology updates for the cAMP biosynthesis terms:

[x] Obsolete GO:0030817 regulation of cAMP biosynthetic process https://github.com/geneontology/go-ontology/issues/14718
[x] Obsolete GO:0030818 negative regulation of cAMP biosynthetic process https://github.com/geneontology/go-ontology/issues/14718
[x] Obsolete GO:0030819 positive regulation of cAMP biosynthetic process https://github.com/geneontology/go-ontology/issues/14718
[x] Obsolete regulation of cyclic nucleotide metabolic process and children https://github.com/geneontology/go-ontology/issues/15811

Ontology updates for G-protein signaling pathway children:

[x] Obsolete GO:0000757 signal transduction involved in regulation of conjugation with mutual genetic exchange https://github.com/geneontology/go-ontology/issues/15815
[x] Merge 'GO:0001789 G-protein coupled receptor signaling pathway, coupled to S1P second messenger' into 'GO:0003376 sphingosine-1-phosphate signaling pathway' https://github.com/geneontology/go-ontology/issues/15822

Ontology updates for other signaling terms