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DAGeditor and new ontologies

Hannick, Linda lhannick at
Tue Mar 26 07:08:28 PST 2002

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?

Linda Hannick

-----Original Message-----
From: Charles Lu [mailto:clu at] 
Sent: Tuesday, March 26, 2002 9:05 AM
To: Hannick, Linda
Subject: Re: GO-control


    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


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
web  :

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