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HUPO-PSI / proxi-schemas

ProXI: Schema definitions for the Proteomics eXpression Interface
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is startPosition and endPosition really needed? #57

Closed edeutsch closed 4 years ago

edeutsch commented 4 years ago

ProteinIdentification: required:

Is the startPosition and endPosition really required here? We don't have it trivially available at the moment, so are lying with -1 and -1. We can get it and will, I guess. but I'm questioning if we really should have these required. Most proteomics data output doesn't normally capture this?

ypriverol commented 4 years ago

I think the idea is to capture the position of the peptide identification in protein identification. This is well-documented and traces in formats like mzIdentML and mzTab. I don't know if the information is available for complete submissions in PRIDE and MassIVE we should remove that information from the API.

My vote +1 is to make this optional fields in that case you don't need to provide -1. Please @jjcarver @edeutsch let me know with a +1 if you like the idea.

edeutsch commented 4 years ago

+1, I vote startPosition and endPosition should be optional

ypriverol commented 4 years ago

Solve in this PR https://github.com/HUPO-PSI/proxi-schemas/pull/52