[go] mapping between DB_Object_ID and DB_Object_Symbol

[David Hill]

>
>
> 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
>>
>>
>