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Gene identifier synonym table standard and/or repository?

Judy Sprague judys at vital-4.cs.uoregon.edu
Tue Feb 25 16:02:27 PST 2003


ZFIN is interested in learning how other databases are defining the column 11 
field 'synonym'.  Are these symbols that were formerly approved nomenclature or 
any symbol that has been used to refer to a given gene?

Judy


>X-Unix-From: gberriz at hms.harvard.edu  Wed Feb 19 08:23:49 2003
>X-Authentication-Warning: alberich.Stanford.EDU: majordom set sender to 
owner-gofriends at genome-mail.stanford.edu using -f
>X-Sender: gabriel_berriz at hms.harvard.edu
>Date: Wed, 19 Feb 2003 11:19:03 -0500
>To: gofriends at genome.stanford.edu
>From: Gabriel Berriz <gberriz at hms.harvard.edu>
>Subject: Re: Gene identifier synonym table standard and/or repository?
>Mime-Version: 1.0
>
>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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