Gene identifier synonym table standard and/or repository?

[Suzanna Lewis]

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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