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'with' field contents for IPI annotations

Valerie Wood val at
Wed Mar 1 04:21:05 PST 2006

Hi Ev,

For S. pombe you can convert all

GeneDB_Spombe:SPCC1223.06 to the protein ID for all IPI's

I don't have separate gene and protein IDs (at present) but all IGIs are
genes and all IPIs are proteins.

I can think of instances in S. pombe where this would not work in the
future (i.e. post translationally cleaved into two proteins which only
have a single ID at present), but I'll deal with those when I have some
interaction data to map to them. In these cases I will make sure they
are two seperate entries in Uniprot and use the Uniprot ID instead.


Evelyn Camon wrote:
> thanks however..we integrate data from Consortium member association
> files so how data is added there and why is very important to us...
> ..the issue I was addressing was whether we should convert a gene id
> to a protein Id if we can map it or if a gene id should be left as it is
> provided as there were specific reasons why a protein id was not
> provided...curator not sure of interacting protein from publication...
> It is of course easier not to convert any ids from external sources...
> thanks
> Evelyn
> Midori Harris wrote:
> >>How will we know the difference between a group adding gene ids instead
> >>of protein Ids as the latter was not available and group adding a gene
> >>id for other reasons???
> >
> >
> > For the purposes of the gene_association file, I think it doesn't matter.
> > Of course if a database has trouble finding UniProt IDs, they should
> > communicate with UniProt to address the problem, but that should all
> > happen separately (and by human communication, not file parsing) -- i.e.,
> > there's no point trying to capture it in the gene_association file.
> >
> > m
> >
> >
> >>If Consortium member has difficultly getting Uniprot ids we should
> >>address these concerns and the appropriate contacts can be made.
> >>I appreciate these thing can take time and solution is needed in the
> >>interim.
> >
> >
> --
> Evelyn Camon
> GOA Coordinator
> Senior Scientific Curator
> European Bioinformatics Institute
> Tel:01223-494465
> Fax:01223-494468
> E-mail: camon at
> URL:

Valerie Wood		       Tel: 01223 494954
S. pombe Genome Project	       Fax: 01223 494919 		       
The Sanger Institute           email: val at
Wellcome Trust Genome Campus 
CB10 1SA

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