[Biopython-dev] Uniprot parsers

[Renato Alves]

Actually I just tested the Uniprot-XML parser and it seems to suffer
from the same issue...

It ignores the following XML "properties":

<dbReference type="Ensembl" id="ENST00000353703" key="75">
<property type="protein sequence ID" value="ENSP00000300161" />
<property type="gene ID" value="ENSG00000166913" />
</dbReference>


Quoting Renato Alves on 11/11/2010 10:06 PM:
> Hi everyone,
> 
> With the arrival of the Uniprot XML parser, is the swiss format still
> going to be maintained?
> 
> I just clashed with a 'swiss' format parsing problem present in the
> 1.55b release (and previous releases). Seems like the format might have
> changed.
> 
> One random case is [1] where all of the 2nd and following IDs are
> ignored by the parser. In Ensembl, for instance, the parser only
> collects the ENST (the 1st) but not the ENSP (2nd) and ENSG (3rd)
> identifiers.
> 
> Is this a known issue?
> 
> Regards,
> Renato
> 
> [1] http://www.uniprot.org/uniprot/P31946.txt

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