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

[Rachael Huntley]

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
Welcome 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