[Bioperl-l] organ from est entry

[Win Hide]

eVOC providees a map of dbEST transcrpts to terms such a organ in its
anatomy vocabulary. Contact janet@sanbi.ac.za. It will be part of datamart,
and Arek also has his view on this. Win
----- Original Message -----
From: "Ewan Birney" <birney@ebi.ac.uk>
To: "Heikki Lehvaslaiho" <heikki@ebi.ac.uk>
Cc: "Wiepert, Mathieu" <Wiepert.Mathieu@mayo.edu>; <bioperl-l@bioperl.org>;
"Dr. Winston Hide" <winhide@sanbi.ac.za>
Sent: Friday, November 15, 2002 7:21 PM
Subject: Re: [Bioperl-l] organ from est entry


>
>
> On 15 Nov 2002, Heikki Lehvaslaiho wrote:
>
> > Matthiew,
> >
> > Check out the STACK database from SANBI. Win Hide and his merry fellows
> > have been working on an ontology for (EST related) anatomy. I am not
> > really up to date on this; I am sure someone else on the list knows
> > better.
>
> For sure. It is called eVoc and I think it is going to merrily come into
> the main Ensembl set as well. SANBI guys - Janet Kelso (???) are the
> people. I've cc'd win hide so he can give us the full story... over to
> win...
>
>
>
>
>  >
> > -Heikki
> >
> > On Fri, 2002-11-15 at 14:30, Wiepert, Mathieu wrote:
> > > Hi,
> > >
> > > Is it possible to get the organ that a tissue is from, given a genbank
entry for an EST?  I should say, the answer is yes if I parse the note tag
of the primary tag.  But I thought there would be a more obvious way to
categorize est.'s by organ, perhaps not?
> > >
> > > Is anyone interested in having the organ parsed, so if you have an est
sequence, you can ask for the organ?  Of course it is simple to parse it out
yourself, but it is a convenience to me to have a method parse it out, so I
am going to write one.  Just wasn't sure if it is useful to others.  It
looks like it is standard practice to put organ information in the note, or
is it much more obvious to get it somewhere else, maybe it is, I haven't
really looked past the genbank entries.
> > >
> > > -Mat
> > > _______________________________________________
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> > --
> > ______ _/      _/_____________________________________________________
> >       _/      _/                      http://www.ebi.ac.uk/mutations/
> >      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
> >     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
> >    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
> >   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
> >      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
> > ___ _/_/_/_/_/________________________________________________________
> >
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>
>
>