suggesting two new terms

[gocentral]

Hi GO team,

Below is the description of the suggested terms, respective GO IDs, and the supporting pubmed id.

Suggested terms: ligand-dependent GPCR activity (from pubmed id: 17379646)(new child term) steroid hormone receptor like activity (from pubmed id: 17379646)(new child term)

Hierarchy: Parent Term: Receptor activity (GO ID 4872)->ligand-dependent GPCR activity (from pubmed id: 17379646)(new child term) ->steroid hormone receptor like activity (from pubmed id: 17379646)(new child term)->estrogen receptor activity (GO ID 30284)(Existing child term)

Suggested Term: estrogen receptor like activity ( from the pubmed id: 17379646)

Hierarchy Parent Term: Receptor activity (GO ID 4872)-> Child Term :transmembrane receptor activity (GO ID 4888)-> Child Term : G-protein coupled receptor activity (GO ID 4930)-> estrogen receptor like activity ( from the pubmed id: 17379646)(suggested child term)

With best regards, Jesintha.

Reported by: awg1

Original Ticket: "geneontology/ontology-requests/5383":https://sourceforge.net/p/geneontology/ontology-requests/5383

[gocentral]

Logged In: YES user_id=865072 Originator: NO

I would like to suggest the term "ligand-dependent GPCR activity" is essentially redundant with the well-used existing term "G-protein coupled receptor activity ; GO:0004930", defined as "A receptor that binds an extracellular ligand and transmits the signal to a heterotrimeric G-protein complex. These receptors are characteristically seven-transmembrane receptors and are made up of hetero- or homodimers."

How would ligand-dependent GPCR activity be defined differently? Is there some kind of ligand-independent GPCR activity not captured in the GO?

I'm afraid I don't support the "steroid hormone receptor like activity" and the "estrogen receptor like activity" terms at all, as no definitions are given, and ideally receptor activity terms should be named according to the ligand or class of ligands that are bound, not based on structural similarities to other proteins. For this reason, I am also opposed to the existing GO terms "rhodopsin-like receptor activity ; GO:0001584" and "secretin-like receptor activity ; GO:0001633". These are at least grouping terms for GPCR terms with known ligands, but I would still prefer that these terms should be obsoleted.

Thanks,

Alex

Original comment by: addiehl

[gocentral]

I can add a synonym to GO:0004930, unless there is any evidence to respond to Alex's questions.

I agree with Alex about the terms with "-like" in the names. The "like" refers to some sort of resemblance, usually sequence similarity, between the protein features of the receptors. Although this kind of information is interesting and important in molecular biology, it lies outside the scope of GO.

Alex - there are several more "-like" receptor terms in the ontology; most of them are not grouping terms and have no definitions. I'd be quite willing to make them obsolete, and will look up annotation stats and send an alert email to the GO list.

GO:0001598 chemokine receptor-like receptor activity GO:0001636 corticotrophin-releasing factor gastric inhibitory peptide-like receptor activity GO:0001588 dopamine D1 receptor-like receptor activity GO:0001591 dopamine D2 receptor-like receptor activity GO:0015058 epidermal growth factor-like module containing hormone receptor activity GO:0001629 G-protein receptor 45-like receptor activity GO:0001630 GP40-like receptor activity GO:0001606 GPR37/endothelin B-like receptor activity GO:0001617 growth hormone secretagogue-like receptor activity GO:0001627 leucine-rich G-protein receptor-like receptor activity GO:0008067 metabotropic glutamate, GABA-B-like receptor activity GO:0001584 rhodopsin-like receptor activity GO:0001633 secretin-like receptor activity GO:0001615 thyrotropin releasing hormone and secretagogue-like receptors activity GO:0001603 vasopressin-like receptor activity

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> gomidori

Original comment by: mah11

[gocentral]

obsolete-alert email sent

Original comment by: mah11

[gocentral]

Midori,

I agree with your decision to obsolete these "-like" terms. I'm sorry not to have responded earlier, but for some reason I am rarely if ever getting any SF emails these days -- don't know if it's SF itself or an overactive spam filter.

Thanks,

Alex

Original comment by: addiehl

[gocentral]

It's definitely not my spam filter -- just search through ~1800 messages for the past two weeks -- anyone else having problems getting emails from SF?

Thanks,

Alex

Original comment by: addiehl

[gocentral]

I've done the work on this now:

added synonym for GO:0004930

renamed: GO:0001588 now 'dopamine receptor coupled via Gs' GO:0001591 now 'dopamine receptor coupled via Gi/Go'

obsolete: chemokine receptor-like receptor activity ; GO:0001598 corticotrophin-releasing factor gastric inhibitory peptide-like receptor activity ; GO:0001636 epidermal growth factor-like module containing hormone receptor activity ; GO:0015058 G-protein receptor 45-like receptor activity ; GO:0001629 GP40-like receptor activity ; GO:0001630 GPR37/endothelin B-like receptor activity ; GO:0001606 growth hormone secretagogue-like receptor activity ; GO:0001617 leucine-rich G-protein receptor-like receptor activity ; GO:0001627 metabotropic glutamate, GABA-B-like receptor activity ; GO:0008067 rhodopsin-like receptor activity ; GO:0001584 secretin-like receptor activity ; GO:0001633 thyrotropin releasing hormone and secretagogue-like receptors activity ; GO:0001615 vasopressin-like receptor activity ; GO:0001603

Original comment by: mah11

[gocentral]

• status: open --> closed-fixed

Original comment by: mah11