[Go] Alert: proposal to obsolete several molecular function terms that impacts existing annotations (fwd)

[Midori Harris]

Hi,

I just realized that this alert apparently didn't reach the list when I 
first sent it. In case the attached text file was the problem, I've 
removed it, but will send it off-list to anyone who wants to see it.

I'll also revise the comment deadline to October 7th.

Midori

---------- Forwarded message ----------
Date: Wed, 10 Sep 2008 11:42:23 +0100 (BST)
From: Midori Harris <midori at ebi.ac.uk>
To: GO Mailing List <go at geneontology.org>
Subject: Alert: proposal to obsolete several molecular function terms that
     impacts existing annotations

Dear GO,

The proposal has been made to obsolete

chemokine receptor-like receptor activity ; GO:0001598
corticotrophin-releasing factor gastric inhibitory peptide-like receptor 
activity ; GO:0001636
dopamine D1 receptor-like receptor activity ; GO:0001588
dopamine D2 receptor-like receptor activity ; GO:0001591
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

SourceForge link:
https://sourceforge.net/tracker/index.php?func=detail&aid=2092506&group_id=36855&atid=440764

Annotations to these terms exist as listed below:

gene_association.dictyBase.gz
GO ID	IEA	non-IEA	total
GO:0001584	1	2	3
GO:0008067	0	1	1

gene_association.fb.gz
GO ID	IEA	non-IEA	total
GO:0001584	28	3	31
GO:0001588	0	1	1
GO:0001591	0	2	2
GO:0001633	0	5	5
GO:0008067	2	6	8

gene_association.GeneDB_Lmajor.gz
GO ID	IEA	non-IEA	total
GO:0001584	9	0	9

gene_association.GeneDB_Pfalciparum.gz
GO ID	IEA	non-IEA	total
GO:0001584	4	0	4

gene_association.goa_chicken.gz
GO ID	IEA	non-IEA	total
GO:0001584	351	0	351
GO:0008067	14	0	14

gene_association.goa_cow.gz
GO ID	IEA	non-IEA	total
GO:0001584	378	0	378
GO:0008067	13	0	13

gene_association.goa_human.gz
GO ID	IEA	non-IEA	total
GO:0001584	406	1	407
GO:0008067	20	8	28

gene_association.goa_uniprot.gz
GO ID	IEA	non-IEA	total
GO:0001584	18346	0	18346
GO:0008067	128	0	128

gene_association.goa_zebrafish.gz
GO ID	IEA	non-IEA	total

gene_association.gramene_oryza.gz
GO ID	IEA	non-IEA	total

gene_association.mgi.gz
GO ID	IEA	non-IEA	total
GO:0001584	385	1	386
GO:0001591	0	3	3
GO:0001615	0	1	1
GO:0008067	8	2	10
GO:0015058	0	1	1

gene_association.rgd.gz
GO ID	IEA	non-IEA	total
GO:0001584	436	13	449
GO:0001591	0	3	3
GO:0001615	0	1	1
GO:0001633	0	1	1
GO:0008067	15	0	15

gene_association.tair.gz
GO ID	IEA	non-IEA	total
GO:0001584	2	0	2

gene_association.wb.gz
GO ID	IEA	non-IEA	total
GO:0001584	191	0	191
GO:0001588	0	5	5
GO:0001591	0	1	1
GO:0008067	3	0	3

gene_association.zfin.gz
GO ID	IEA	non-IEA	total
GO:0001584	411	0	411
GO:0001591	0	3	3
GO:0008067	5	0	5


The reason for obsoleting these terms is that they represent gene products -- 
the "-like" refers to some sort of resemblance, usually sequence similarity, 
between the protein features of the receptors. Also, most of these terms are 
undefined.

Annotations should be transferred to a parent, as will be indicated for each 
term in consider or replaced_by tags. For most of the terms the recommended 
parent is:

   G-protein coupled receptor activity ; GO:0004930

GO:0001584 is in the prokaryotic subset; none of the other terms are in any 
subset maintained in the GO .obo files. A few of the terms are used in external 
mappings, as indicated in the attached text file.

SourceForge link:
https://sourceforge.net/tracker/index.php?func=detail&aid=2092506&group_id=36855&atid=440764

Comment period ends on September 24, 2008.

*** Unless objections are received by September 24,
      we will assume that you agree to this change. ***

Thanks,
Midori