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Re: Protein representation with and without BioChemEntity

From: Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>
Date: Mon, 6 Nov 2017 10:00:09 +0000
To: Leyla Garcia <ljgarcia@ebi.ac.uk>
CC: Melanie Courtot <mcourtot@ebi.ac.uk>, Justin Clark-Casey <justinccdev@gmail.com>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>, Michel Dumontier <michel.dumontier@gmail.com>
Message-ID: <8FE6A27B-AF8A-49CB-A4CE-ADBB4684FA98@hw.ac.uk>
Hi Leyla,

On 3 Nov 2017, at 10:14, Leyla Garcia <ljgarcia@ebi.ac.uk<mailto:ljgarcia@ebi.ac.uk>> wrote:

@Alasdair, @Dan. Would not be even cleaner adding a second context to the mark up where we define aliases for the third party terms and types?

Yes adding aliases would be a sensible approach to making the json-ld more readable.

If we do so, then, as far as the same aliases are used, maybe what third party ontology is used becomes not that relevant anymore? Then people could use either one. And, just in case, Bioschemas would collate somewhere what ontologies are in used for each profile and corresponding properties. Aliases of course would be defined by the profile itself, at least those minimum and recommended ones which will be used for validation. It is always possible to add more properties but then would not be parsed for Bioschemas (or schema.org<http://schema.org/> I suppose).

The alias would only have scope within the given document. When comparing two documents these would be expanded. If different expansions were given for the alias then they would not be the same.

In effect, this proposal is to have our tooling add implicit equivalence mappings. While this could work for Bioschemas, it would have no meaning beyond our community. Thus meaning that if someone uses a standard tool, they will not get the equivalences that we intend.

If you think adding a second context makes things easier, I could work on some examples. They would look similar tohttps://github.com/BioSchemas/specifications/blob/master/PhysicalEntity/examples/BioChemEntityAlt-min+rec.jsonld but with aliases defined in the second context for "http://semanticscience.org/resource/is-transcribed-from"<http://semanticscience.org/resource/is-transcribed-from> and so on.

Please just edit the examples in GitHub. That way we don’t end up with too many different files and we can use the diffs to see what is happening.

Best regards


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 10:00:35 UTC

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