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HUPO-PSI / psi-mi-CV

Molecular Interactions Controll Vocabulary
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GenPept as new database? #208

Closed noedelta closed 8 years ago

noedelta commented 14 years ago

We have a data provider (Phosphosite) who wants to export some proteins that are from GenPept and seemingly nowhere else. Could we add GenPept as a child of 'sequence database' under 'participant database' under 'database citation'?

Thanks, Gary

Reported by: gbader

noedelta commented 14 years ago

Hi ary

Sorry missed this - there is already a term under Source Database MI:0851 - protein genbank identifier. I don't like the name of the term so may look at improving that, but it was basically added to allow reference to genpept entries

Original comment by: orchard

noedelta commented 14 years ago

Hi Gary

Sorry missed this - there is already a term under Source Database MI:0851 - protein genbank identifier. I don't like the name of the term so may look at improving that, but it was basically added to allow reference to genpept entries

Sandra

Original comment by: orchard

noedelta commented 14 years ago

Hi Sandra - we eventually figured out that the correct MI term to use in this case is GenBank. GenPept is not an official database name, though it is a format and referred to internally in NCBI. Also, the sequences are in UniProt/trembl. An example accession is AAC52059. This is not a protein genbank identifier, which are integers e.g. 2947031

Thanks, Gary

Original comment by: gbader

noedelta commented 14 years ago

Original comment by: orchard