[go] mapping between DB_Object_ID and DB_Object_Symbol

[Chris Mungall]

I think it should be 1:1 for any one DB. Our model is that every  
distinct annotated entity has a single designated preferred symbol,  
the rest should go in the synonyms.

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). 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
>
>