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Gene identifier synonym table standard and/or repository?

Evelyn Camon camon at ebi.ac.uk
Fri Feb 14 02:03:14 PST 2003


Hi,

>Synonym
>Gene_symbol [or other text]
>Here: International Protein Index identifier (section 5).
>Example: IPI00010440

In the GOAReadme we explain that we use synonym column 11
of the 'gene association file' for our IPI identifier. Is this still OK?

Evelyn


Suzanna Lewis wrote:

> Hi,
>
> I'm double-checking here that we are getting this loaded
> into the DB as well. They don't currently appear in amigo,
> nor can they be searched, but Brad and I are talking about
> how to do that.
>
> -S
>
> On Thursday, February 13, 2003, at 09:33 AM, Valerie Wood wrote:
>
> >
> >
> > i utilize this column for S. pombe too. btw I use "|" to separate
> > multiple
> > synonyms, is this correct?
> >
> >
> >
> > On Thu, 13 Feb 2003, Tanya Berardini wrote:
> >
> >>
> >> In the TAIR gene_association file, column 11 is populated with
> >> synonyms/aliases for the annotated object.  These may include
> >> BAC-based
> >> names from the genome sequencing phase, full names for the lettered
> >> abbreviations (e.g. EMF1 is embryonic flower 1), other aliases for
> >> that
> >> gene (e.g. ATROP4 = ROP4 = ATGP3 = ARAC5), Arabidopsis Genome
> >> Initiative
> >> (AGI) locus names (of the format ATxgXXXXX), and gene product names.
> >>
> >> Tanya
> >>
> >>
> >> On Thu, 13 Feb 2003, Suzanna Lewis wrote:
> >>
> >>> In the gene associations table the 11th column is listed
> >>> as DB_object_synonym. I believe that this column was
> >>> added especially to address this issue. It allows for
> >>> white space and has a cardinality of 0, 1, or >1. I think
> >>> this is a more a problem of the organism databases not
> >>> having made the switch to providing this information
> >>> when the gene associations are submitted. Column 12
> >>> is the db object type (is it a gene, or a protein, or a .....)
> >>> and column 13 is the taxon. I think if these were being
> >>> populated it would perhaps help you.
> >>>
> >>> Any chance of this being put into practice annotators??
> >>>
> >>> -S
> >>>
> >>> On Thursday, February 13, 2003, at 07:54 AM, Fritz Roth wrote:
> >>>
> >>>> Greetings GOphiles,
> >>>>
> >>>> We are working on some new software that uses GO annotation, and we
> >>>> would really like it to support all GO-annotated organisms.  Our
> >>>> chief
> >>>> barrier to doing this is the lack of gene identifier synonym tables
> >>>> for each organism (so that users can enter gene names rather than
> >>>> being restricted to MOD IDS, e.g., SGD or MGI IDs).
> >>>>
> >>>> Is there an agreed GO Consortium standard for gene identifier
> >>>> synonym
> >>>> tables (could be as simple as tab-delimited text with a
> >>>> synonym-uniqueID pair on each line).  If so, is there a repository
> >>>> for
> >>>> such files?  Or is this a GMOD question?
> >>>>
> >>>> Thanks!
> >>>> Fritz Roth
> >>>>
> >>>> -------------------------------------------------
> >>>> Frederick P. Roth, Asst. Professor
> >>>> Harvard Medical School
> >>>> Dept. of Biological Chemistry and Molecular Pharmacology
> >>>> 250 Longwood Avenue, SGMB-322, Boston, MA 02115
> >>>> (617) 432-3551 phone            (617) 432-3557 FAX
> >>>> froth at hms.harvard.edu           http://llama.med.harvard.edu
> >>>> -------------------------------------------------
> >>>>
> >>>>
> >>>> --
> >>>> This message is from the GOFriends moderated mailing list.  A list
> >>>> of
> >>>> public
> >>>> announcements and discussion of the Gene Ontology (GO) project.
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> >>>
> >>>
> >>> --
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> >>>
> >>
> >> ----------------------------------------------------------------------
> >> ---------
> >> Tanya Berardini, Ph.D.                       tberardi at acoma.stanford.edu
> >> The Arabidopsis Information Resource FAX: (650) 325-6857
> >> Carnegie Institution of Washington   Tel: (650) 325-1521 ext. 325
> >> Department of Plant Biology          URL: http://arabidopsis.org/
> >> 260 Panama St.
> >> Stanford, CA 94305
> >> ----------------------------------------------------------------------
> >> ---------
> >>
> >>
> >> --
> >> 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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> >> gofriends-request at geneontology.org
> >> Web:          http://www.geneontology.org/
> >>
> >
> > -----------------------------------------------------------------------
> > -----------
> > Valerie Wood                 Tel: 01223 494954
> > S. Pombe Genome Project              Fax: 01223 494919
> > The Sanger Institute           email: val at sanger.ac.uk
> > Wellcome Trust Genome Campus   http://www.sanger.ac.uk/Projects/S_pombe
> > Cambridge
> > CB10 1SA
> >
> >
>
> --
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> announcements and discussion of the Gene Ontology (GO) project.
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