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DAGeditor and new ontologies

Midori Harris midori at ebi.ac.uk
Tue Mar 26 07:30:56 PST 2002


Hi Linda,

You can choose an ID prefix for a new ontology: from the Plugins menu,
open the DAG-Edit Configuration Manager. Go to the Behavior tab, and edit
the default ID prefix field. The program will still be able to recognize
any ID prefix, but will assign your default prefix to any new terms you
add.

Jane Lomax has been working on documentation for DAG-Edit, and we hope it
will go online very soon.

Cheers,
Midori

On Tue, 26 Mar 2002, Hannick, Linda wrote:

> Michael,
> We have internally formulated a transposable element (TE) ontology to track
> transposable elements in Arabidopsis.  We also have a system for entering
> temporary terms (TI) that are awaiting approval as GO: terms.  When they are
> approved, we convert them to "GO:nnnnnnn".  We would like to be able to use
> the DAGeditor to view these ontologies by dumping flat *.ontology files from
> our database similar to process.ontology, function.ontology and
> component.ontology.  Our TI: terms would then come up in DAGeditor, and we
> could load our TE terms into DAGeditor for viewing and term searching.
> 
> So far, it appears that DAGeditor recognizes "GO" and "SO" prefixes on
> terms.  I do not know if it recognizes the plant ontology.  Can it be made
> more global, so we do not have to maintain a separate version in-house, and
> so the new ontologies that come along can easily be incorporated?
> 
> Is there any downside to this idea? I actually do not know who maintains the
> software... Should I direct this to someone else?
> 
> Thanks
> Linda Hannick
> 
> -----Original Message-----
> From: Charles Lu [mailto:clu at tigr.org] 
> Sent: Tuesday, March 26, 2002 9:05 AM
> To: Hannick, Linda
> Subject: Re: GO-control
> 
> Linda
> 
>     There are few things you need to find out before doing this.  First
> DAGeditor is a 3rd party software.  Therefore, it is not known for sure if
> it will read newly formatted flat files.  In other words, it might not
> work for TI, TEs.  We can't assume having just the right format will work
> since it might also look for specific keywords.
> 
>     If you want you can try it by making a copy of the ontology file and
> make few changes manually and see if it upsets the DAGeditor.  I myself
> have never used DAGeditor but does it do similar thing as through our web
> interface?
> 
> 
> charles
> 
> 
> On Mon, 25 Mar 2002, Hannick, Linda wrote:
> 
> > Charles,
> > The program "dageditor" reads the flat files process.ontology,
> > component.ontology and function.ontology.  It would be helpful to be
> > able to access everything in the Ontology set, including temporary TI:
> > ID's and transposable element TE: ID's.  To do this, we would need to
> > have a file generated out of our database after pulling down the new
> > terms each night.  I am envisioning a script that runs after the new
> > terms are loaded, which dumps the terms in our database to a flat file.
> > This flat file has the same format as the files at GO.
> >
> > Can you craft a script that will run in concert with the nightly
> > updates?
> > Thanks,
> > Linda
> >
> > P.S. I just put this into BITS.
> >
> >
> 
> -- 
> Charles Lu
> Bioinformatics Engineer
> The Institute for Genomic Research (TIGR)
> 9712 Medical Center Drive
> Rockville, MD 20850-0978
> Phone: 301-610-5957
> email: clu at tigr.org
> web  : http://www.tigr.org
> 
> --
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