[go] Alert: Proposal to obsolete GO:0048503 (function ontology) that impacts existing annotation

[Alexander Diehl]

Midori,

I did not and do not agree that the SwissProt mapping should disappear.  
At a minimum I would like to see the SwissProt keyword, 'GPI-anchor', 
mapped to 'anchored to membrane ; GO:0031225'.  Per PMID:17361015, I 
believe this is an entirely correct mapping.

See 
http://sourceforge.net/tracker/index.php?func=detail&aid=1873999&group_id=36855&atid=440764 
for my extended comments and suggested replacement terms.

--Alex


Midori Harris wrote:
> Hello,
>
> The proposal has been made to obsolete
>
>   GPI anchor binding ; GO:0048503
>
> Annotations to this term exist at present as follows:
>
>   DB        total    non-IEA
>   GeneDB_Spombe    10    10
>   GOA_chicken    25    2
>   GOA_cow    30    4
>   GOA_human    128    9
>   GOA_uniprot    280    4
>   MGI        123    8
>   RGD        59    5
>   ZFIN        11    0
>
> This term is not used in any GO slim set maintained within the OBO flat
> file.
>
> This term is used in one external mapping:
> spkw2go: SP_KW:KW-0336 GPI-anchor > GO:GPI anchor binding ; GO:0048503
>
> Note that this mapping should be deleted (and not replaced when the 
> new term becomes available), because the Swiss-Prot keyword is used 
> for proteins that have been modified by the addition of a GPI anchor.
>
> The reason for this proposal is this term has been widely, and 
> incorrectly, used to annotate proteins that have GPI anchors 
> covalently attached. A new term will be created that can be used to 
> annotate gene products that interact non-covalently with GPI anchors.
>
> The discussion has taken place on the annotation mailing list; a 
> summary has been lodged in SourceForge:
> https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1873999&group_id=36855 
>
>
> The two-week comment period ends on Friday, February 1, 2008.
>
> *** Unless objections are received by February 1,
>     we will assume that you agree to this change. ***
>
> Midori


-- 
Alexander Diehl, Ph.D.
Senior Scientific Curator
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609

email:  adiehl at informatics.jax.org
work:  +1 (207) 288-6427
fax:  +1 (207) 288-6131