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File format question

Jane Lomax jane at ebi.ac.uk
Thu Jan 6 02:57:46 PST 2005


Hi Victoria,

The DAG-Edit package comes with two scripts, flat2obo and obo2flat that 
you can use to switch between the two formats. Remember though that you'll 
lose information when you convert from flat -> obo because the obo format 
contains some extra information (e.g. synonym types, namespace).

Hope this helps,

Jane

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
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Web:          http://www.geneontology.org/



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