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File format question

Chris Mungall cjm at fruitfly.org
Tue Dec 21 09:51:29 PST 2004


Hi Victoria

The easiest way to convert between old goflat and the obo-text format is
to download dagedit and use the flat2obo and obo2flat programs that come
with it (you can of course use dagedit to load a file in one format and
save it in another format).

If you prefer perl, you can download the go-perl module from CPAN and use
the scripts that come with that to convert either way

Chris

On Tue, 21 Dec 2004, Victoria Petri wrote:

>
> Hello all,
> These days the GO text files are generated from the obo file. I was
> wondering if anyone knows of a way to go from a text file to the obo file
> format.
>
> Thanks,
>
> Victoria
>
> Victoria Petri, Ph.D.
> Scientific Curator for Gene Ontology
> Rat Genome Database (http://www.rgd.mcw.edu)
> Bioinformatics Research Center (http://www.brc.mcw.edu)
> Medical College of Wisconsin
> 8701 Watertown Plank Road
> Milwaukee, WI 53208
> (414) 456-7507
> (414) 456-6190 Fax
> vpetri at mcw.edu
> vpetri at mail.brc.mcw.edu
>
> -----Original Message-----
> From: Jane Lomax [mailto:jane at ebi.ac.uk]
> Sent: Monday, December 20, 2004 10:51 AM
> To: gofriends at genome.stanford.edu
> Subject: namespace change
>
> Hi - this is just a quick warning that we'll be changing the namespace
> field in the geneontology.obo file tomorrow. There has been some
> discussion about this on the go-database list (see
> http://mail.fruitfly.org/pipermail/go-database/2004-December/thread.html
> thread 'Term type changed?).
>
> The change will be from:
>
> namespace: process
> namespace: function
> namespace: component
>
> to:
>
> namespace: biological_process
> namespace: molecular_function
> namespace: cellular_component
>
> There will be no change to the old GO flat files (function.ontology,
> process.ontology, component.ontology and GO.defs).
>
> Let me know if anyone has any queries,
>
> Jane Lomax
> GO editorial office
>
>
> --
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>
> --
> This message is from the GOFriends moderated mailing list.  A list of public
> announcements and discussion of the Gene Ontology (GO) project.
> Problems with the list?           E-mail: owner-gofriends at geneontology.org
> Subscribing   send   "subscribe"   to   gofriends-request at geneontology.org
> Unsubscribing send   "unsubscribe"  to  gofriends-request at geneontology.org
> Web:          http://www.geneontology.org/
>

--
This message is from the GOFriends moderated mailing list.  A list of public
announcements and discussion of the Gene Ontology (GO) project.
Problems with the list?           E-mail: owner-gofriends at geneontology.org
Subscribing   send   "subscribe"   to   gofriends-request at geneontology.org
Unsubscribing send   "unsubscribe"  to  gofriends-request at geneontology.org
Web:          http://www.geneontology.org/



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