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HUPO-PSI / proxi-schemas

ProXI: Schema definitions for the Proteomics eXpression Interface
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peptide vs peptidoform conflation #49

Closed edeutsch closed 4 years ago

edeutsch commented 4 years ago

We are totally conflating the terms peptide and peptidoform. From the /peptides YAML doc: http://www.peptideatlas.org/api/proxi/v0.1/ui/#/

"The peptide entry point returns global peptidoform statistics across an entire resource. Each peptide contains a summary of the statistics of the peptidoform across the entire resource."

We should aim to be clear and precise. If this endpoint is dealing in peptidoforms (and it does because there are ptms there), then I think we should call it: /peptidoforms

Do we also want to have /peptides entry point that is scrubbed of all mass mods? i.e. the /peptides entry point is agnostic to mass mods the /peptidoforms endpoint requires full handling of mass mods

What do you think?

ypriverol commented 4 years ago

Agree 100%. I will change the endpoint.

edeutsch commented 4 years ago

great, thanks. while you're making changes, two other things I note:

1) In the spec, peptidoform is sometimes written peptidoForm. It seems unnecessary and undesirable to have a camel hump in the middle of a word

2) Although the psm class has a proteinAccessions, the peptidoform class does not have a proteinAccessions. I assume it should? Or is there a reason not to?

edeutsch commented 4 years ago

Okay, I approved and merged the pull request. BUT, what about my items 1 and 2 immediately above this one? These were not addressed by the pull request.

edeutsch commented 4 years ago

@ypriverol would you consider items 1 and 2 above and create another pull request?

ypriverol commented 4 years ago

@edeutsch this line contains the proteinAccessions for the peptidoform. https://github.com/HUPO-PSI/proxi-schemas/pull/51/files#diff-2b41f0819ffcbd181875ee501a7daed0R629

edeutsch commented 4 years ago

oops, you are right, I missed it. everything looks good then, thanks.

ypriverol commented 4 years ago

Addressed in PR.