[Bioperl-l] Relations

Hilmar Lapp hlapp at gmx.net
Tue Jan 6 11:50:57 EST 2004

I've heard someone wanted to code this up half a year ago, but AFAIK 
the script never made it into the repository. I think this would be 
very useful to have.

The GO associations for RefSeq are present in RefSeq most of the time 
but obfuscated in the feature table. I wrote a SeqProcessor that 
promotes them to annotations, but RefSeq keeps changing the format of 
that on me, so even though possible it's not an approach that warms 
your heart. Note that LL also comes with GO links in the records, which 
are extracted fairly well by the parser.


On Monday, January 5, 2004, at 04:15  PM, Holland, Richard wrote:

> Me again! Sorry about this heap of messages from me today, I'm having a
> couple of BioPerl days to hammer out all the things my boss wants done
> before the end of the month...
> Has anyone got a script to load GO term associations into BioSQL
> bioentry_qualifier_value with? If not I'll put one together and post it
> when it's done, but I don't want to write one if one already exists. 
> I'm
> interested in linking GO terms to RefSeqs (not sure where to get the
> associations from there though), GO to InterPro, and GO to SwissProt.
> Also InterPro to SwissProt if possible.
> cheers,
> Richard
> ---
> Richard Holland
> Bioinformatics Database Developer
> ITS, Agresearch Invermay x3279
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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