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Re: Protein representation with a Bioschemas context ()

From: Anders Riutta <anders.riutta@gladstone.ucsf.edu>
Date: Tue, 14 Nov 2017 11:31:57 -0800
Message-ID: <CAJEHyTnUAZ=+Sxb9oBNBLSDcqu=PUY8dMZ7j=JJOG2qHFOZ84A@mail.gmail.com>
To: public-bioschemas@w3.org
>
> So, it looks like we are talking about something like
> https://github.com/BioSchemas/specifications/blob/master/Pro
> tein/examples/ProteinEntity-with-context.json where the context
> containing Gene and so will become the Bioschemas context and the IRIs will
> be agreed and then fixed. That example includes a third-party property
> which is always possible whenever schema.org or Bioschemas do not provide
> a better option.


To clarify, here's a list of what I'm hearing we'll have:

   1. Context published by Bioschemas, e.g., "
   http://bioschemas.org/context.jsonld"
   2. Data published by each data provider, e.g.,
   http://rest.ensembl.org/...
   <http://rest.ensembl.org/lookup/id/ENSG00000157764?content-type=application/json>
   3. Context published by each data provider, e.g., "
   http://ensembl.org/context.jsonld"
      - Option A: Data provider can re-use Bioschemas context: {"@context":
      "http://bioschemas.org/"}
      - Option B: Data provider can create their own context, but, whenever
      possible, will use the IRIs from the Bioschemas context

3A will probably only be possible if the data provider is creating a new
API.

Most data providers will need to use 3B, because their terms will not match
the terms from the Bioschemas context, e.g., "transcribedFrom" vs.
"comesFromGene". By re-using IRIs from the Bioschemas context, they will
make it possible for Bioschemas-compliant tools to work despite term
differences, because the data provider context and the Bioschemas context
will together make it clear that "comesFromGene" and "transcribedFrom" both
mean "http://semanticscience.org/resource/SIO_010081".
Received on Tuesday, 14 November 2017 19:32:24 UTC

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