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HUPO-PSI / psi-mi-CV

Molecular Interactions Controll Vocabulary
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addition of \'sequence database\' term in CV database #72

Closed noedelta closed 8 years ago

noedelta commented 18 years ago

Currently CV database high level terms allow follow the structure of the PSI main elements (interaction, experiment, participant, feature, source). Within participant xref we there are number of databases able to describe whatever interactor type including small molecules. %participant database xref MI:0473 %cabri MI:0246 %chebi MI:0474 %cygd MI:0464 %ddbj/embl/genbank MI:0475 %ensembl MI:0476 %entrez gene/locuslink MI:0477 %flybase MI:0478 %huge MI:0249 %international protein index MI:0675 %kegg MI:0470 %mgd/mgi MI:0479 %newt MI:0247 %omim MI:0480 %refseq MI:0481 %resid MI:0248 %rfam MI:0482 %rgd MI:0483 %sequence ontology MI:0601 %sgd MI:0484 %uniparc MI:0485 %uniprot knowledge base MI:0486 %wormbase MI:0487

Sequence database would be a child of participant db xref and have as children all appropriate dbs :

%participant database xref MI:0473 %cabri MI:0246 %chebi MI:0474 %newt MI:0247 %resid MI:0248 %sequence ontology MI:0601 new Sequence database xref
%cygd MI:0464 %ddbj/embl/genbank MI:0475 %ensembl MI:0476 %entrez gene/locuslink MI:0477 %flybase MI:0478 %huge MI:0249 %international protein index MI:0675 %kegg MI:0470 %mgd/mgi MI:0479
%omim MI:0480 %refseq MI:0481
%rfam MI:0482 %rgd MI:0483
%sgd MI:0484 %uniparc MI:0485 %uniprot knowledge base MI:0486 %wormbase MI:0487

The main advantage would be an easier checking of that a sequence is provided for each participant within a PSI file (minimal requirment)

Reported by: luisa_montecchi

noedelta commented 18 years ago

Logged In: YES user_id=653048

Sorry the second list of db is identical to the first. Shall we add also 'small molecule xre'?

luisa

Original comment by: luisa_montecchi

noedelta commented 18 years ago

Logged In: YES user_id=653048

San Francisco PSI meeting: approved the addition of the term 'sequence database'.

Original comment by: luisa_montecchi

noedelta commented 18 years ago

Original comment by: luisa_montecchi