[go] mapping between DB_Object_ID and DB_Object_Symbol

[David Hill]

O.K. my misunderstanding. Sorry.

Valerie Wood wrote:
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> Hi David,
>
> Chris is refering to our (GeneDB) odd practice of repeating the names 
> in the synonyms column, so the gene name might be repeated in the 
> synonym field for a single gene) Rather than between genes (which is 
> OK for synonyms).
>
> The reason we did this  is explained in later e-mail
>
> Val
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> David Hill wrote:
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>>
>>>
>>>
>>> I think it's best not to repeat symbols as synonyms, as you lead 
>>> people to believe that these will always be present, which may 
>>> potentially lead to them implementing buggy software (if they are 
>>> extremely sloppy). 
>>
>> But, synonyms for gene symbols are harvested directly from the 
>> literature. Unfortunately, bench scientists don't often consider 
>> whether the 'handle' they are using for their gene is unique. This is 
>> a huge issue in mouse and often a lot of the work of a curator is to 
>> determine which gene an author is actually talking about. However, 
>> every official gene symbol should only correspond to one database 
>> gene ID. All other uses of symbols than the official symbol for a 
>> gene should go in the 'synonyms' field.
>>
>>> Those writing software correctly have to defensively implement some 
>>> kind of filter, if they want to avoid reporting back (mildly 
>>> confusing) duplicates to their users. Consistency is always a good 
>>> thing.
>>>
>>> I think the 1:1 violation is more serious though
>>>
>>> On Aug 9, 2007, at 7:38 PM, Gavin Sherlock wrote:
>>>
>>>> Hi all,
>>>>
>>>> An issue came up with GO::TermFinder, because it chokes on files 
>>>> where the relationship between DB_Object_ID and DB_Object_Symbol is 
>>>> not 1:1, and there are a number of files that have for instance a 
>>>> 1:2 relationship between these columns, e.g.:
>>>>
>>>> GeneDB_Spombe: SPCC777.13 maps to SPCC777.13, vps35
>>>> pseudocap: PA5429 maps to aspA, adhA
>>>> RGD: RGD:1359623 maps to Tuba4a, Tuba4
>>>> WB: WBGene00000386 maps to cdc-25.1, cdc25.1
>>>>
>>>> My question is, should this be a 1:1 relationship, and the 
>>>> annotation files checking script needs to reject files that deviate 
>>>> from that (presumably these additional names would become synonyms 
>>>> instead), or is a 1:2 or more relationship allowed between those 
>>>> columns, in which case, I'll have to modify GO::TermFinder 
>>>> appropriately.
>>>>
>>>> As an additional data point, the pombe file actually lists both 
>>>> SPCC777.13 and vps35 as synonyms for the gene too :
>>>>
>>>> whitbread 1001 % grep 'SPCC777.13' gene_association.GeneDB_Spombe
>>>> GeneDB_Spombe   SPCC777.13      SPCC777.13              
>>>> GO:0003674      GO_REF:0000015  ND              
>>>> F                       gene    taxon:4896      20070711GeneDB_Spombe
>>>> GeneDB_Spombe   SPCC777.13      vps35           GO:0005768      
>>>> PMID:16622069  IMP              C       retromer complex subunit 
>>>> Vps35  SPCC777.13|vps35       gene     taxon:4896      
>>>> 20060424        GeneDB_Spombe
>>>> GeneDB_Spombe   SPCC777.13      vps35           GO:0030904      
>>>> PMID:16622069  IMP              C       retromer complex subunit 
>>>> Vps35  SPCC777.13|vps35       gene     taxon:4896      
>>>> 20040625        GeneDB_Spombe
>>>> GeneDB_Spombe   SPCC777.13      vps35           GO:0030904      
>>>> PMID:16622069  ISS      SGD:S000003690  C       retromer complex 
>>>> subunit Vps35  SPCC777.13|vps35gene    taxon:4896      
>>>> 20040625        GeneDB_Spombe
>>>> GeneDB_Spombe   SPCC777.13      vps35           GO:0006886      
>>>> PMID:16622069  IMP              P       retromer complex subunit 
>>>> Vps35  SPCC777.13|vps35       gene     taxon:4896      
>>>> 20040625        GeneDB_Spombe
>>>> GeneDB_Spombe   SPCC777.13      vps35           GO:0042147      
>>>> PMID:16622069  IMP              P       retromer complex subunit 
>>>> Vps35  SPCC777.13|vps35       gene     taxon:4896      
>>>> 20060424        GeneDB_Spombe
>>>> GeneDB_Spombe   SPCC777.13      vps35           GO:0030437      
>>>> PMID:15189449  IMP              P       retromer complex subunit 
>>>> Vps35  SPCC777.13|vps35       gene     taxon:4896      
>>>> 20040625        GeneDB_Spombe
>>>> GeneDB_Spombe   SPCC777.13      vps35           GO:0005829      
>>>> PMID:16823372  IDA              C       retromer complex subunit 
>>>> Vps35  SPCC777.13|vps35       gene     taxon:4896      
>>>> 20060724        GeneDB_Spombe
>>>>
>>>> - is there a rule (I couldn't find one) that says the synonyms 
>>>> should not repeat the DB_Object_ID and DB_Object_Symbol, or should 
>>>> there be?  Would it save any space in the file sizes?
>>>>
>>>> Cheers,
>>>> Gavin
>>>> ________________________________________________________
>>>>
>>>> Gavin Sherlock
>>>> Dept. of Genetics
>>>> S201A, Grant Building,
>>>> Stanford University Medical School,
>>>> Stanford,
>>>> CA 94305-5120
>>>>
>>>> Tel: 650 498 6012
>>>> Fax: 650 724 3701
>>>>
>>>>
>>>
>>
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