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ontology/document networks

Todd F. Peterson tfp at ncgr.org
Wed Dec 3 09:05:55 PST 2003


Hello,

We are developing tools that allow creation of networks from GO and the
Medical Subject Headings ontology (MeSH) based upon co-occurence of terms
in PubMed documents. The resulting graph my be viewed using the Graph
Visualization Framework (GVF, http://sourceforge.net/projects/gvf/).
Various metrics may be applied to the network to enhance the
visualization by coloring nodes and edges. Additional metrics are being
developed as well as analysis routines to aid in the understanding and
mining of document databases that are indexed by ontology terms.

These tools are not publicly available yet, but we could provide more
information or early beta versions upon request.

Todd Peterson
Sr. Software Developer
The National Center for Genome Resources
Santa Fe, New Mexico


On Wed, 3 Dec 2003, Evelyn Camon wrote:

> Hi,
>
> Might also interest people to know that in QuickGO you can also display
> annotation to 2 or more species. Just type two Swiss-Prot
> accession numbers in the QuickGO search field, chose Swiss-Prot ID option
> eg. P51587 P97929 which display human and mouse GO annotations.
> You can also display GO annotation to more than one InterPro entry at a time
> choosing the InterPro Id option and IPR000424 IPR000635.
>
> cheers
> Evelyn.
>
>
> "Dr. Scot E. Dowd" wrote:
>
> > Hello,
> > We have a new graphical frontend for AMIGO and the go database.  This allows
> > you to see as many ontology graphed values side by side on the same page.
> > Thanks to a nice suggestion we have added a textual feature as well.  This
> > first implimentation shows only level 3 but we are in the last stages of
> > developing a recursive level query feature that will allow for viewing of
> > any level into the ontology.
> >
> > http://199.133.147.101/cgi-bin/species/index.pl
> >
> > Have a look around this is version 1.0.  Let us know your thoughts.
> > Scot
> >
> > Dr. Scot E. Dowd Ph.D.
> > Research Microbiologist
> > USDA-ARS Livestock Issues Research Unit
> > RT3 Box 215 FM 1294
> > Lubbock, TX 79403
> >
> > 806-746-5356 ext 241
> > mobile 806-832-0659
> > fax 806-744-4402
> >
> > -----Original Message-----
> > From: owner-gofriends at genome.stanford.edu
> > [mailto:owner-gofriends at genome.stanford.edu] On Behalf Of Dr. Scot E. Dowd
> > Sent: Wednesday, December 03, 2003 9:36 AM
> > To: go-friends at genome.stanford.edu
> > Subject: Forum
> >
> > Hello,
> > We started a forum/message board for Gene Ontology.  It can be found at
> > http://199.133.147.108/forum/  Because we see that so many people have the
> > same questions and mail lists (even with archives) are difficult to search
> > perhaps our forum can bring together these questions and answers.  I hope
> > this is not to presumptious ;-) Scot
> >
> > Dr. Scot E. Dowd Ph.D.
> > Research Microbiologist
> > USDA-ARS Livestock Issues Research Unit
> > RT3 Box 215 FM 1294
> > Lubbock, TX 79403
> >
> > 806-746-5356 ext 241
> > mobile 806-832-0659
> > fax 806-744-4402
> >
> > -----Original Message-----
> > From: owner-gofriends at genome.stanford.edu
> > [mailto:owner-gofriends at genome.stanford.edu] On Behalf Of Midori Harris
> > Sent: Wednesday, December 03, 2003 7:35 AM
> > To: Peter Hornbeck
> > Cc: go-friends at genome.stanford.edu
> > Subject: Re: your mail
> >
> > Hello,
> >
> > GO documentation is available on the web; see
> > http://www.geneontology.org/GO.contents.doc.html for a list. There is also a
> > small collection of tutorial materials available by TFP from
> > ftp://ftp.geneontology.org/pub/go/teaching_resources.
> >
> > I don't know the answer to your second question.
> >
> > Regards,
> > Midori
> >
> > ============================
> > Midori A. Harris, Ph.D.
> > GO Editor
> > EMBL - EBI
> > Wellcome Trust Genome Campus
> > Hinxton
> > Cambridge CB10 1SD UK
> >
> > Tel: +44 (0) 1223 494667
> > Fax: +44 (0) 1223 494468
> > Email: midori at ebi.ac.uk
> >
> > On Wed, 26 Nov 2003, Peter Hornbeck wrote:
> >
> > > 1) What resources (courses and documentation) would you recommend to
> > > newcomers to GO?
> > >
> > > 2) Are GO terms used in developing nodes for graphical networking
> > > visualization tools?
> > >
> > >
> > >
> > > P. Hornbeck
> > > Magnolia, MA
> > >
> > >       "If it sounds good, it is good."       -Duke Ellington
> > >
> > >
> > >
> > >
> > >
> >
> > --
> > 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/
> >
> > --
> > 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/
>


--
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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