W3C home > Mailing lists > Public > public-bioschemas@w3.org > November 2017

Re: Protein representation with a Bioschemas context ()

From: Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>
Date: Thu, 9 Nov 2017 10:47:36 +0000
To: Leyla Garcia <ljgarcia@ebi.ac.uk>
CC: "public-bioschemas@w3.org" <public-bioschemas@w3.org>, Dan Brickley <danbri@danbri.org>, Anders Riutta <anders.riutta@gladstone.ucsf.edu>
Message-ID: <3F2425BC-E84A-487E-AF29-9C6CFA63C9AA@hw.ac.uk>
Hi All,

Leyla, thanks for providing a concrete example from which we can base our discussions.

Points in favour of Leyla’s proposal:
- Properties and types defined in Bioschemas namespace
- json-ld validates using the structured data markup tool
- We don’t need to choose one ontology over another

Points against Leyla’s proposal
- We are minting our own ontology terms

We can of course eliminate the long property names by introducing shorthands in the context, something like the latest commit to my example
https://github.com/BioSchemas/specifications/blob/master/PhysicalEntity/examples/BioChemEntityAlt-min%2Brec.jsonld<https://github.com/BioSchemas/specifications/blob/master/PhysicalEntity/examples/BioChemEntityAlt-min+rec.jsonld>
This could be expanded to something similar to the full context that Leyla used, but instead of creating new Bioschema terms, we would reused terms from existing ontologies

Points in favour of Alasdair's proposal:
- We are not minting our own ontology terms
- With full context like Leyla’s the example would validate

Points against Alasdair's proposal
- We have to select terms from existing ontologies, i.e. we will be selecting one ontology over another

Ultimately, with all these proposals someone adopting will need to edit the same number of characters, and we should highlight somehow what these are.

I think we are in broad agreement that we can move away from using the additionalProperties.

What we still need to determine is are we going to mint terms in the Bioschemas namespace (that could eventually be pushed to schema.org<http://schema.org>) or select terms from existing ontologies. Opinions on this last point please.

Alasdair

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 Thursday, 9 November 2017 10:48:08 UTC

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