[BiO BB] GeneBank to SwissProt Mapping?

[Anand Kumar]

Dan,

We, with the Swissprot team, have begun to work in the area of bridging the gap between disease and gene products as a pilot project. This would help to bridge the gap between diseases and gene products, as it exists in OMIM. We are trying to address various granularities from clinical to molecular levels.
Are you doing the mapping for human proteins? That could help us since we already use the annotations present with GO to the respective gene products.

Kind Regards,
Anand.

Am Sa 15.05.2004 11:35, Dan Bolser <dmb at mrc-dunn.cam.ac.uk> schrieb:

> 
> Thanks Pamela for your suggestions, I have tried LocusLink (the 'loc2acc'
> file) but I find many missing swissprot / trembl accession numbers. I
> fear that the GO mapping could be incomplete for other resons too. 
> 
> Thanks Svensson for the offer of assistance below, but I am not sure how
> having PID will help me. (sorry for my ignorance).
> 
> I know sptrembl has a good PIR mapping, can we get to PIR from GI?
> 
> I am running blast jobs at the minuite as the bind sequence file isn't too
> big, but getting accurate 1-1 mapping means that I have to blast against
> the full datasets and not some non redundant version thereof.
> 
> 4 more days to go...
> 
> If anyone wants the data let me know.
> 
> Dan.
> 
> 
> 
> On 14 May 2004, Svensson, B.A.T. (HKG) wrote:
> 
> >
> >
> >
> >On Fri, 2004-05-14 at 15:28, Dan Bolser wrote:
> >> On 14 May 2004, Svensson, B.A.T. (HKG) wrote:
> >> 
> >> >What data do you have to start with?
> >> 
> >> BIND.... I am thinking that blast will get the job done if I use refseq...
> >
> >I don't know about BIND, but if you have refseq, then you will be able
> >to fetch the protein identifier (PID) as well as well as the official
> >gene symbol from NCBI's data set UniGene (pre-blasted as to say), this
> >should be enough to link to your data. If you need help with retrieving
> >PID's and gene symbols, let me know and I can make a query in my own
> >database to retrieve this data for you - or anything else you need from
> >UniGene.
> >
> >Precisely which EBI dataset would you like to link to?
> >
> >
> >> >On Fri, 2004-05-14 at 15:10, Dan Bolser wrote:
> >> >> Any body know how to map proteins from the NCBI to proteins from the EBI?
> >> >> 
> >> >> Cheers,
> >> >> Dan.
> >> >
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> >
> 
> 
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Anand Kumar MBBS, PhD
IFOMIS
Faculty of Medicine
University of Leipzig
Härtelstraße 16-18
04107 Leipzig
Germany
http://www.uni-leipzig.de/~akumar/