[go] mapping between DB_Object_ID and DB_Object_Symbol

[Valerie Wood]

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





David Hill wrote:

>
>>
>>
>> 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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