Synonym file

[Katica Ilic]

I aggree, synonym types are becoming really important, now that all
of the nodes are nearly done, and the next step is mapping.

That's why this is on the agenda for tomorrow as well.

Katica

On Thu, 1 Apr 2004, Sue Rhee wrote:

> I am not sure if I would agree with this. I think as soon as the OBO
> format and Dag-Edit is stablized (I would say another 2-4 weeks or so
> since GO recently went OBO), we should switch. Two reasons: 1. OBO
> supports the synonym type that we absolutely will depend on. 2. Dag-Edit
> enhancements will probably focus on the OBO format.
>
> Sue
>
> On Thu, 1 Apr 2004, Pankaj Jaiswal wrote:
>
> > I suggest sticking with the existing format until we start doing things
> > differently. We can think about it at the time of making the first
> > release.
> >
> > Pankaj
> >
> > Katica Ilic said:
> > >
> > >
> > > ...which means we should be swithcing to OBO sooner rather than later,
> > > right?
> > >
> > > Katica
> > >
> > > On Thu, 1 Apr 2004, Pankaj Jaiswal wrote:
> > >
> > >> GO did it at the time they were trying to switch over to the new synonym
> > >> formats to become compatible with the UMLS system. This method is no
> > >> more
> > >> required because the new OBO format takes care of it in a very nice
> > >> format.
> > >>
> > >> Managing a separate file is no more required.
> > >>
> > >> Pankaj
> > >>
> > >> Katica Ilic said:
> > >> > Pankaj,
> > >> >
> > >> > Another question: I noticed that GO has a separate txt file with
> > >> synonyms,
> > >> > describing exact type of the synonyms, IDs and relationships. This
> > >> file is
> > >> > created manually, and now that GO has switched to OBO, it is no longer
> > >> > needed.
> > >> >
> > >> > How about us at POC, currently we are not using any other type of
> > >> synonyms
> > >> > but the exact one (which has a lot of disadvantages). Should we stick
> > >> to
> > >> > this till we move on to OBO, or do we need such a file very soon?
> > >> >
> > >> > Any thoughts on this?
> > >> >
> > >> > Katica
> > >> > --------------------------------------------------------------------------
> > >> > Katica Ilic             		katica at acoma.stanford.edu
> > >> > The Arabidopsis Information Resource 	Tel: (650) 325-1521 ext. 253
> > >> > Carnegie Institution of Washington 	FAX: (650) 325-6857
> > >> > Department of Plant Biology 		URL: http://arabidopsis.org/
> > >> > 260 Panama St.
> > >> > Stanford, CA 94305
> > >> > U.S.A.
> > >> > --------------------------------------------------------------------------
> > >> >
> > >> >
> > >> >
> > >>
> > >>
> > >> --
> > >> Pankaj Jaiswal
> > >> Gramene Database
> > >> www.gramene.org
> > >>
> > >
> > > --------------------------------------------------------------------------
> > > Katica Ilic             		katica at acoma.stanford.edu
> > > The Arabidopsis Information Resource 	Tel: (650) 325-1521 ext. 253
> > > Carnegie Institution of Washington 	FAX: (650) 325-6857
> > > Department of Plant Biology 		URL: http://arabidopsis.org/
> > > 260 Panama St.
> > > Stanford, CA 94305
> > > U.S.A.
> > > --------------------------------------------------------------------------
> > >
> > >
> > >
> >
> >
> > --
> > Pankaj Jaiswal
> > Gramene Database
> > www.gramene.org
> >
>
> -----------------------------------------------------------------------------
> Sue Rhee                         	rhee at acoma.stanford.edu
> The Arabidopsis Information Resource	URL: www.arabidopsis.org
> Carnegie Institution of Washington	FAX: +1-650-325-6857
> Department of Plant Biology		Tel: +1-650-325-1521 ext. 251
> 260 Panama St.
> Stanford, CA 94305
> U.S.A.
> -----------------------------------------------------------------------------
>

--------------------------------------------------------------------------
Katica Ilic             		katica at acoma.stanford.edu
The Arabidopsis Information Resource 	Tel: (650) 325-1521 ext. 253
Carnegie Institution of Washington 	FAX: (650) 325-6857
Department of Plant Biology 		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
U.S.A.
--------------------------------------------------------------------------