[Gramene] Use of the 'with' field in the Gramene GAF

[Rachael Huntley]

Hi Pankaj,

Sorry for the delay in responding. Thank you for letting us know your 
plans regarding your upcoming change to using gene/locus instead of 
UniProtKB accessions.

I'm sorry that you have been having problems with submitting your GO 
annotations, I'm not sure why this would be the case, so could you 
please give me some more details about what specific problems you have 
been facing and maybe we can assist you further. We are trying to 
improve our electronic annotation pipelines so that species that do not 
have resources for manual curation will be catered for, so this is 
something we are aware of and, hopefully, will be able to continually 
improve.

Best wishes,
Rachael.

On 09/03/2011 19:15, Pankaj Jaiswal (OSU) wrote:
>
> Rachel,
>
> We will be looking at these issues and the WITH column in subsequent 
> releases. Essentially we will be starting to move away from our 
> Uniprot based annotation to the respective species genome based 
> annotation, with gene/locus being the common denominator. Uniprot IDs 
> would be mapped to the gene IDs.
>
> On the other hand we have also realized that we are unable to submit 
> our annotations regularly because of the stringency posted by GO 
> annotation guidelines on IEAs and now IPI, IEA and RCAs. remember, not 
> every genome database especially plants has enough number of hands to 
> do manual curation. Now we have many more plant genomes than just the 
> reference. Much of the work will remain in the IEA, IEP, IMP and IPI 
> via genome scale interactomes.
>
> Pankaj
>
>
> On 3/9/2011 1:48 AM, Rachael Huntley wrote:
>> Hello,
>>
>> I am writing on behalf of the UniProtKB-GOA group at EBI to ask if it
>> would it be possible for you to help us with some Gramene gene
>> association file questions we have?
>>
>> We're currently trying to improve the GO annotation we integrate into
>> UniProtKB from external MODs, by looking at including the MOD
>> identifiers used in the 'with' field (column 8) of externally generated
>> annotations; at the moment we ignore any 'with' field data that doesn't
>> use a GO identifier or UniProtKB accession, and so integrate these
>> annotations into our set with an empty 'with' field, which obviously is
>> not ideal.
>> Therefore we would very much like to include Gramene identifiers that
>> match the following regular expressions:
>>
>> (GR):([A-Z]\d[\d\w]{3}\d)
>> (GR_PROTEIN):([A-Z]\d[\d\w]{3}\d)
>>
>> Do these look reasonable to you?
>>
>> We have come across a couple of errors in the contents of the 'with'
>> column of the Gramene gene association file, which I have listed below
>> together with the reasons why they have been rejected.
>>
>> Rejected:
>> [IPI GR_protein:O24435]
>> [IPI GR_protein:Q2XPP5]
>> Reason: The accessions shown are UniProtKB accessions and so should have
>> a 'UniProtKB:' prefix.
>>
>> Rejected:
>> [RCA UniProt:Q69F95]
>> Reason:
>> The 'with' field should not be filled with an RCA annotation.
>>
>> If you agree with these reasons, would you be able to make the changes
>> to your file?
>>
>> Your help in this is much appreciated.
>>
>> Best wishes,
>> Rachael.
>>


-- 
GOA and IntAct Curator
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge, CB10 1SD
UK

Tel: 01223 492515
Fax: 01223 494468
Email: huntley at ebi.ac.uk
GOA: http://www.ebi.ac.uk/GOA
IntAct: http://www.ebi.ac.uk/intact