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Re: Protein representation with a Bioschemas context ()

From: Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>
Date: Tue, 14 Nov 2017 12:02:14 +0000
To: "public-bioschemas@w3.org" <public-bioschemas@w3.org>
Message-ID: <561C4181-A492-468D-98B7-A1DAD581B037@hw.ac.uk>
Dear All,

I think Franck’s email clearly explains the situation here.

Schema.org<http://schema.org> is about everyone buying in to use a common set of terms to markup their content. If they buy-in to that then they get the benefit. Otherwise you are just on the linked data web.

Bioschemas is about making Schema.org<http://schema.org> relevant for the life sciences. We have agreed as a community that we prefer to reuse an existing ontology term than mint our own. However, to me, it means that we do need to select a single ontology term. It is through this agreement that we will see benefit whilst also keeping the route to adoption straightforward.


On 14 Nov 2017, at 10:21, Franck Michel <franck.michel@cnrs.fr<mailto:franck.michel@cnrs.fr>> wrote:

Dear all,

I'd like to bring a few elements into the discussion wrt. aliases.

In JSON-LD, aliases are just a handy short-cut notation with a local scope: an alias just applies within the scope of the context where it is defined. And more importantly, an alias should not bear any meaning. The first thing a consumer app does with JSON-LD is to expand all terms, which immediately removes all aliases.

Hence, if I use the Bioschemas.org<http://bioschemas.org/> default context:
   @context {  "Gene": {  "@id": "http://purl.obolibrary.org/obo/SO_0000704"<http://purl.obolibrary.org/obo/SO_0000704>  } ... }
I will typically write:  "@type": [ "BioChemEntity", "Gene" ]

But I may well write a document with a custom alias:
    @context {  "GeneAlias": {  "@id": "http://purl.obolibrary.org/obo/SO_0000704"<http://purl.obolibrary.org/obo/SO_0000704>  } ... }
and write:   "@type": [ "BioChemEntity", "GeneAlias" ]
    @context {  "obo": {  "@id": "http://purl.obolibrary.org/obo/"<http://purl.obolibrary.org/obo/>  } ... }
I would write:   "@type": [ "BioChemEntity", "obo:SO_0000704" ]
Or I could even not use any alias:   "@type": [ "BioChemEntity", "http://purl.obolibrary.org/obo/SO_0000704"<http://purl.obolibrary.org/obo/SO_0000704> ]

These are all equivalent from the point of view of a data consumer.

In my view, the default context should be a useful guide for those annotating data with Bioschemas.org<http://bioschemas.org/> markup, but alias names should not matter at all. What matters is the URIs to which aliases resolve.

I feel like the solution of agreed pre-defined URIs, whatever the aliases used, is more sustainable. After all, schema.org<http://schema.org/> advocates for the use of specific agreed-upton terms. If one uses them, their pages are more likely to be discoverable. They can chose to use other terms if this is convenient for them, but then there is not guarantee that the pages will be discovered as easily.


Alasdair J G Gray
Fellow of the Higher Education Academy
Assistant Professor in Computer Science,
School of Mathematical and Computer Sciences
(Athena SWAN Bronze Award)
Heriot-Watt University, Edinburgh UK.

Email: A.J.G.Gray@hw.ac.uk<mailto:A.J.G.Gray@hw.ac.uk>
Web: http://www.macs.hw.ac.uk/~ajg33
ORCID: http://orcid.org/0000-0002-5711-4872
Office: Earl Mountbatten Building 1.39
Twitter: @gray_alasdair


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Received on Tuesday, 14 November 2017 12:02:52 UTC

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