Review annotations to GO:0051767 nitric-oxide synthase biosynthetic process and regulation

[raymond91125]

Dear all,

The proposal has been made to obsolete GO:0051767 nitric-oxide synthase biosynthetic proces GO:0051771 negative regulation of nitric-oxide synthase biosynthetic process GO:0051770 positive regulation of nitric-oxide synthase biosynthetic process GO:0051769 regulation of nitric-oxide synthase biosynthetic process

see https://github.com/geneontology/go-ontology/issues/28860.

"The annotations to the regulation of NO synthase biosynthesis are to signaling molecules, indicating that they should instead be annotated to the appropriate signaling pathway, + 'acts upstream of, positive effect' (positive) GO:0141149 regulation of nitric oxide-cGMP mediated signal transduction"

Experimental annotations that need to be reviewed are here: https://docs.google.com/spreadsheets/d/153K3OPgtJPq6Y7LuPMHq7kSt2HHUaIM0FOnmhb_IaZs/edit?gid=0#gid=0

Impacted groups: ARUK-UCL 8 - done BHF-UCL 14 - done RGD 15 UniProt 2

** Group contacts: https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv

Mappings that need to be reviewed: (InterPro2GO, UniProt-Keywords, UniRule) None.

Thanks.

[slaulederkind]

Why does "nitric-oxide synthase biosynthetic process and regulation" get singled out for ontological treatment away from "translation". It's not part of a group of proteins like the MHC. There are also a handful of other individual proteins listed under "macromolecule biosynthetic process" (GO:0009059). Why?

[deustp01]

Why does "nitric-oxide synthase biosynthetic process and regulation" get singled out for ontological treatment

Because of its uniquely central role in mediating / regulating a number of other processes in mammals, maybe a larger range of multicellular animals, was the answer given in an earlier ontology discussion. And that answer was deemed insufficient to justify singling it out, hence the current obsoletion proposal.

[slaulederkind]

RGD finished.

[slaulederkind]

Thank you @deustp01.

[RLovering]

Note that NO has important for antibacterial etc properties and therefore its synthesis is not necessarily relevant to nitric oxide-cGMP mediated signal transduction and also NO is necessary for peptidyl-cysteine S-nitrosylation therefore regulation of NO levels is not just about regulation of nitric oxide-cGMP mediated signal transduction. Although I am sure that changing these annotations will encourage the annotation to these other processes which will be a good thing but unfortunately it is not simply a case of changing the existing annotations to the signaling term Ruth

[Antonialock]

uniprot updated

[pgaudet]

Thanks @RLovering

We should definitely look at these examples.

[RLovering]

Thanks @RLovering

We should definitely look at these examples.

I have made sure that the term inflammatory response is included where appropriate and changed term to regulation of gene expression has input NOS1/2/3 as required if appropriate

[pgaudet]

Great !