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Re: Bioschemas Taxon profile specification

From: Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>
Date: Thu, 28 Jun 2018 10:50:53 +0000
To: Justin Clark-Casey <justinccdev@gmail.com>
CC: "fmichel@i3s.unice.fr" <fmichel@i3s.unice.fr>, LJ Garcia Castro <ljgarcia@ebi.ac.uk>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>
Message-ID: <F274805F-F716-4CD9-A7B1-3656B552C31A@hw.ac.uk>

On 27 Jun 2018, at 19:19, Justin Clark-Casey <justinccdev@gmail.com<mailto:justinccdev@gmail.com>> wrote:

I think we should have mandatory known @types and properties.  In my view, Bioschemas should be as easy as possible to write and consume.  Multiple options will increase cognitive load on writers (which one do I choose?  Why are these 2 examples using these different terms?) and open the door to greater inconsistency.  Non-mandatory types will also raise the barriers for writing Bioschemas software that will have to be aware of equivalent mappings.

I completely agree that we should have a single approved type for each profile, and likewise for each property a single chosen term. This is the whole point of having the profiles.

I would go one step further and say that Bioschemas should provide an http://bioschemas.org<http://bioschemas.org/>context that will define types such as Taxon, rather than blessing particular ontology terms.

I also agree that a context file should be provided which has the chosen types and terms in it, i.e. the context file would define Protein to be the URI http://purl.obolibrary.org/obo/PR_000000001. To be completely explicit, we would not be defining a type in the bioschemas namespace, e.g. http://bioschemas.org/Protein.

This context can also document equivalent terms in different ontologies.

I like the idea that this also contains mappings to the equivalent terms in other ontologies.

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, 28 June 2018 10:51:20 UTC

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