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

[Pankaj Jaiswal (OSU)]

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.
>