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

[E Dimmer]

Hi,

The SPKW2GO mapping has now been updated, as per Alex's recommendations 
- so that the GPI-anchor keyword maps now to 'anchored to membrane'.
Thanks Alex,

Emily

Midori Harris wrote:
> Hi Alex,
>
> My comment on the keyword mapping was not intended to mean that the 
> 'GPI-anchor' shouldn't be mapped to any GO term at all; I meant only 
> that it should not be mapped to the new, correctly defined and 
> applied, 'GPI anchor binding term'. Sorry if that wasn't clear.
>
> m
>
> On Fri, 18 Jan 2008, Alexander Diehl wrote:
>
>> 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
>>
>>
>>


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------------------------------------------------------------------ 

    Emily Dimmer
    GOA Coordinator
    EMBL-EBI
    Wellcome Trust Genome Campus
    Hinxton
    Cambridge CB10 1SD, U.K.
    Tel:     +44 1223 494654
    Fax:    +44 1223 494468
    email:  edimmer at ebi.ac.uk
    URL:    http://www.ebi.ac.uk/goa