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HUPO-PSI / proxi-schemas

ProXI: Schema definitions for the Proteomics eXpression Interface
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Do we need Psm accession? #55

Closed edeutsch closed 4 years ago

edeutsch commented 4 years ago

Psm is defined in the YAML as:

Psm: required:

I like the usi. But what is the accession? Does anyone plan on filling in some other kind of accession for a PSM?

Related, the output does not have datasetIdentifier. All the other components needed to build a USI are part of the output. Except datasetIdentifier. Seems like we should have it. Maybe that's what accession was supposed to be?

ypriverol commented 4 years ago

Psm is defined in the YAML as:

Psm: required:

  • peptideSequence properties: accession: type: string description: Accession of the PSM usi: type: string description: The USI representation for the PSM ...

I like the usi. But what is the accession? Does anyone plan on filling in some other kind of accession for a PSM?

Originally this was here to make the difference between to PSMs that share the same USI. In PRIDE we don't have that use case anymore, probably @jjcarver still wants to keep it? If not we can remove it.

Related, the output does not have datasetIdentifier. All the other components needed to build a USI are part of the output. Except datasetIdentifier. Seems like we should have it. Maybe that's what accession was supposed to be?

Agree. We should have a dataset accession for easy recovery. What about: 

datasetAccession

   type: string 
   description: Dataset accession

If everyone agree with a +1, I can added it to the schema.

edeutsch commented 4 years ago

I rather like datasetIdentifier better than datasetAccession, but datasetAccession is okay if that's what everyone else likes. Better than plain accession.

ypriverol commented 4 years ago

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