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Gene identifier synonym table standard and/or repository?

Pankaj Jaiswal pj37 at cornell.edu
Thu Feb 20 08:06:55 PST 2003


Gramene will be populating the synonyms in Column 11 of GO association table
(gene_association.gramene_oryza) in its next updates.
-Pankaj

Suzanna Lewis wrote:
> 
> I'll do what I can to have FlyBase comply and add synonyms to
> column 11.
> 
> -S
> 
> On Thursday, February 20, 2003, at 12:19 AM, Gabriel Berriz wrote:
> 
> > Thanks for all of the responses to our earlier question (Fritz's post)
> > about synonym tables!
> >
> > We will go with column 11 in the GO gene association tables and
> > support those model organisms that make use of it.  We may also
> > supplement with Ensembl (although see Ensembl NOTE below).
> >
> > One comment on obtaining synonyms from the association tables rather
> > than a stand-alone synonym file.  Shortcomings include:
> > 1) No synonyms for genes that are not annotated.
> > 2) Since synonyms are stored in a "denormalized" way, there is
> > potential for inconsistencies between records for the same gene
> > (although this is less of an issue if the files are automatically
> > generated from a normalized database).
> >
> > FYI, the following association files (from
> > ftp.geneontology.org/pub/go/gene_associations/) do not use column 11:
> > gene_association.GeneDB_Pfalciparum
> > gene_association.GeneDB_Tbrucei
> > gene_association.GeneDB_tsetse
> > gene_association.compugen.Genbank
> > gene_association.compugen.Swissprot
> > gene_association.fb
> > gene_association.gramene_oryza
> > gene_association.zfin
> >
> > These do:
> > gene_association.GeneDB_Spombe          890   synonyms; 3765   genes
> > gene_association.goa_human                      19727 synonyms; 19727
> > genes
> > gene_association.goa_sptr                       28397 synonyms; 566342
> > genes
> > gene_association.mgi                            10080 synonyms; 9088
> > genes
> > gene_association.rgd                            522   synonyms; 1424
> > genes
> > gene_association.sgd                            6573  synonyms; 6905
> > genes
> > gene_association.tair                           45327 synonyms; 18771
> > genes
> > gene_association.tigr_Tbrucei_chr2      2     synonyms; 289    genes
> > gene_association.tigr_ath                       269   synonyms; 5749
> > genes
> > gene_association.tigr_shewanella                1233  synonyms; 3767
> > genes
> > gene_association.tigr_vibrio            1415  synonyms; 2924   genes
> > gene_association.vida                           19    synonyms; 83
> > genes
> > gene_association.wb                             1319  synonyms; 6833
> > genes
> >
> > It would be a great help to have similar standardized lists of all
> > "annotatable" genes for each GO organism.  In principle the
> > association tables could serve as the source of all "annotatable"
> > genes if they always included at least one annotation--possibly to
> > attributes of type "unknown"--for each annotatable gene id (or is this
> > the case now?).  As far as I know, there is no easy way to determine
> > whether this is the case for any given association table.
> >
> > Ensembl NOTE: Ensembl looks to be quite useful for us, and will get us
> > a more normalized table of synonyms, but we did some spot-checking in
> > fly and couldn't get an Ensembl list of synonyms to include
> > full-length gene names (e.g., Wingless, Kruppel) in addition to gene
> > symbols (Wg, Kr).  In both human and fly we never saw more than one
> > synonym for any given gene.  Are we doing something wrong?
> >
> > Thanks again for all of your help!
> >
> > Best Regards,
> > Gabriel Berriz
> >
> > At 10:19 AM 2/13/2003 -0800, 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
> >
> >
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