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Re: Protein representation with and without BioChemEntity

From: Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>
Date: Thu, 2 Nov 2017 12:04:55 +0000
To: Melanie Courtot <mcourtot@ebi.ac.uk>
CC: Justin Clark-Casey <justinccdev@gmail.com>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>
Message-ID: <C2324C62-CBCB-42E5-85F8-8498A2DE50C0@hw.ac.uk>
Hi Melanie,

I think we are talking at cross purposes. The three examples show different ways of representing a protein.

My original motivation was to compare the BioChemEntity wrapper approach using additionProperty with an approach that would involve the Bioschemas community proposing multiple new types to schema.org<http://schema.org>*. When I discussed these two examples with Dan, he pointed out that we don’t need to use additionalProperty, we can just use the ontology terms directly. In the first and third example, i was just using the ontology terms that were proposed by the Protein Group in the Protein Profile. In the second example, I was playing with the idea that we create these properties in schema.org<http://schema.org>.

The markup in the first example, BioChemEntity with additionalProperty, is complex and increases the complexity of the tools needed for creating and consuming that markup. The third set of examples, using the ontology terms directly, gives us a simplified markup and therefore simplifies our tooling. It will also make adoption more straightforward. It would be up to the profiles to decide which are the appropriate ontology terms to use.

I hope this clears things up


*This approach was ruled out in the May meeting, but I felt that it was important to do a comparison of the two approaches with a concrete example

On 2 Nov 2017, at 10:34, Melanie Courtot <mcourtot@ebi.ac.uk<mailto:mcourtot@ebi.ac.uk>> wrote:

Hi Alastair,

I'm not sure I understand, are you talking about validating profiles? For validation purpose wouldn't it be equivalent to look for a string such as "isContainedIn" or a URI such as http://purl.obolibrary.org/obo/RO_0001018, where the latter has the advantage to not duplicate existing terms as well as offering dereferencing, hierarchy and flexibility?

I'll admit being a bit confused between the 3 examples, so I may be overlooking something.


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
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Twitter: @gray_alasdair


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Received on Thursday, 2 November 2017 12:05:22 UTC

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