Synonym file

[Pankaj Jaiswal]

We haven't gone upto that stage of defining synonyms by their class. I
reiterate wait until the first release is ready to roll out. By that time
OBO format and the DAG-Editor handling it should become stable.

Pankaj

Katica Ilic said:
>
> 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.
> --------------------------------------------------------------------------
>
>
>


-- 
Pankaj Jaiswal
Gramene Database
www.gramene.org