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Re: Protein representation with a Bioschemas context ()

From: Franck Michel <franck.michel@cnrs.fr>
Date: Tue, 14 Nov 2017 22:51:53 +0100
To: public-bioschemas@w3.org
Message-ID: <05eeeaef-6921-1f73-dfdb-2dfd9e95447e@cnrs.fr>
An option between 3A and 3B may consist in importing the Bioschemas 
context and extend it with an additional custom terms:

   "@context": [
     "http://bioschemas.org/context.jsonld",
     {
       "comesFromGene":"...",
     }
   ]

According to the specification it is even possible to override a term 
defined in a previously loaded context: 
https://json-ld.org/spec/latest/json-ld/#advanced-context-usage

Franck.

Le 14/11/2017 à 20:31, Anders Riutta a écrit :
>
>     So, it looks like we are talking about something like
>     https://github.com/BioSchemas/specifications/blob/master/Protein/examples/ProteinEntity-with-context.json
>     <https://github.com/BioSchemas/specifications/blob/master/Protein/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 <http://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 21:52:17 UTC

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