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

[Midori Harris]

Update: Alex has pointed out that two of these terms can be renamed and 
retained, because their definitions describe aspects of their activities:

   dopamine D1 receptor-like receptor activity ; GO:0001588
   dopamine D2 receptor-like receptor activity ; GO:0001591

m

On Thu, 25 Sep 2008, Midori Harris wrote:

> 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
> 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
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