[Bioperl-l] Extracting Gene Names Genome Ontology (GO) with Perl

Spiros Denaxas spiros at lokku.com
Mon Apr 16 11:21:40 EDT 2007


Nope, I don't have a CPAN module for it, and to be honest, I don't
think I will release one for it until I actually finish my PhD. The
code is really scruffy at some parts, lacks documentation and might
not work under all setups. My plan is to take some time after and
clean it up and release a proper version of it to the public.

What you are talking about however, if I understand correctly, is a
much much bigger project. Different genome databases have different
formats and a potential module must take them all into consideration.
Then the issue of the different evidence codes GO annotators use
throughout different genomes and which you consider of higher or lower
quality respective.

If you happen to stumble upon such a module, please share it, it would
be very interesting !

spiros

On 4/16/07, Wijaya Edward <ewijaya at i2r.a-star.edu.sg> wrote:
>
> Hi Spiros,
>
> Thanks for your reply. I am interested to apply it for
> all the kind of organisms related to that particular GO ID.
>
> Do you have a CPAN module for that?
> --
> Edward WIJAYA
> SINGAPORE
>
> ________________________________
>
> From: s.denaxas at gmail.com on behalf of Spiros Denaxas
> Sent: Mon 4/16/2007 11:10 PM
> To: Wijaya Edward
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Extracting Gene Names Genome Ontology (GO) with Perl
>
>
>
> Hi Edward,
>
> What organism are you interested in? I have some code from my PhD
> based on the Saccharomyces cerevisiae genome. Basically uses the SGD
> flat files and a local MySQL instance of GO. Might be worth turning
> into modules if people are interested in it, although it is pretty
> organism oriented and the lack of abstraction might introduce a number
> of problems.
>
> Spiros
>
> On 4/16/07, Wijaya Edward <ewijaya at i2r.a-star.edu.sg> wrote:
> >
> > Dear all,
> >
> > Given a GO id, is there a way to extract all
> > the related gene names from that id with Perl?
> >
> > Anybody has experience with that?
> > I've looked through GO module in CPAN, but can't seem
> > to find any tool that facilitated that searc
> >
> > Look forward very much for your advice.
> >
> > --
> > Edward WIJAYA
> > SINGAPORE
> >
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