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

Re: Protein representation with and without BioChemEntity

From: Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>
Date: Mon, 6 Nov 2017 10:16:50 +0000
To: Melanie Courtot <mcourtot@ebi.ac.uk>
CC: Michel Dumontier <michel.dumontier@gmail.com>, Leyla Garcia <ljgarcia@ebi.ac.uk>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>
Message-ID: <A175F4DA-B2F1-49D2-B7C2-94CCAFF8B347@hw.ac.uk>
Hi

I appreciate the argument for not wanting to say that one ontology term is better than another, and also that we do not want to get into the area of defining our own terms.

However, the benefit of Bioschemas comes from us agreeing as a community that we are going to use a particular subset of terms.

Thus I believe that a profile should select a particular term to use. Where possible this should be from schema.org<http://schema.org>, but where such a term does not exist we should be selecting one, hopefully using a widely used term.

With the Proteins profile we have selected several terms for use and stating these with additionalProperty.

Of course, people are free to use equivalence of terms to convert these for ingestion, but I believed that we do need to keep the profiles simple to encourage take up.

Alasdair

On 3 Nov 2017, at 13:43, Melanie Courtot <mcourtot@ebi.ac.uk<mailto:mcourtot@ebi.ac.uk>> wrote:

+1
As said below, either existing mappings or some tools - OxO, BioPortal or else; I didn't mean to add a constraint there.

For the relations at least users will need to make sure there is a way to get to a "known" entity for validation. Do we know how that could look like?
Let's say for example some datasets use "http://semanticscience.org/resource/is-transcribed-from"<http://semanticscience.org/resource/is-transcribed-from> and some use "http://purl.obolibrary.org/obo/RO_0002510" (and I'm sure there are other relations than SIO and RO, using those as working examples, not saying either SIO or RO should be required), how would that work for the protein profile?

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 Monday, 6 November 2017 10:17:22 UTC

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