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HUPO-PSI / proxi-schemas

ProXI: Schema definitions for the Proteomics eXpression Interface
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What should /psms compact and full look like? #54

Open edeutsch opened 4 years ago

edeutsch commented 4 years ago

All endpoints have resultType=compact|full What should compact for /psms be? the YAML says: Psm: required:

but just a list of peptideSequences is useless. I thought just USIs would be a fine compact. But peptideSequence is required. so here's a possibility:

http://www.peptideatlas.org/api/proxi/v0.1/psms?resultType=compact&accession=PXD005942 [ { "peptideSequence": "LSSPATLNSR", "usi": "mzspec:PXD005942:030219_ywt_sf-39:scan:10:LSSPATLNSR/2" }, { "peptideSequence": "LSSPATLNSR", "usi": "mzspec:PXD005942:030219_ywt_sf-39:scan:13:LSSPATLNSR/2" }, { "peptideSequence": "LSSPATLNSR", "usi": "mzspec:PXD005942:030219_ywt_sf-40:scan:15:LSSPATLNSR/2" }, ...

Do we like that?

ypriverol commented 4 years ago

@edeutsch I think we add the peptideSequence as required for visualization purposes. The idea was that if we develop some kind of visualization tool like proteomecentral for PROXI would be great to have a table for projects where we show the peptide sequence + the usi. Probably, we need to add more information as required for this visualization use case such as the charge state precursor mass.

See this example from PRIDE as a table https://www.ebi.ac.uk/pride/archive/spectra

But if everyone agrees to remove it, we can discuss it in the next call.

edeutsch commented 4 years ago

I don't really know. I view the information needed to build the USI as the minimum useful information. But your table doesn't seem to have peptidoform and scan/index and it doesn't seem to useful to force you do provide it. I think I would say nothing is required and each implementer can choose what to provide. But that seems a bit weak, too. I don't know. A good discussion topic.