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Revised protein profile (was Re: Bioschemas at SWAT4LS)

From: Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>
Date: Mon, 11 Dec 2017 10:47:20 +0000
To: Leyla Garcia <ljgarcia@ebi.ac.uk>
CC: "public-bioschemas@w3.org" <public-bioschemas@w3.org>
Message-ID: <AB0E331D-9377-42D8-B5B6-D8722153813A@hw.ac.uk>
Hi Leyla

On 8 Dec 2017, at 16:53, Leyla Garcia <ljgarcia@ebi.ac.uk<mailto:ljgarcia@ebi.ac.uk>> wrote:

We also had a hackathon on the last day. I used the time to update the protein specification (spreadsheet mapping), a protein example [1] and creating some ShEX shapes to validate proteins [2].

I’ve had a look at your revised protein profile (0.4-draft.1)

I’m confused by the properties bioschemas:associatedDisease and bioschemas:transcribedFrom.

At the moment you have put in the description an existing ontology term that should be used http://purl.obolibrary.org/obo/so#associated_with and http://semanticscience.org/resource/SIO_010081.rdf respectively. I think these term URIs should appear in the first column, i.e. they should be the recommended term for this profile.

Another issue is the isContainedIn term. This term does not appear in schema.org<http://schema.org>, but the way it is presented here implies that it does. Presumably this is a term that we are proposing for adoption in schema.org<http://schema.org>. In this case, the schema.org<http://schema.org> description should be empty, as there is no existing definition. The proposed definition should then appear in the Bioschemas section. A question here would be is there an existing ontology term that could be used?

Best regards


[1] https://github.com/BioSchemas/specifications/blob/master/Protein/examples/ProteinEntity-with-context.json (please keep in mind that the context will be actually provided by Bioschemas)

[2] https://github.com/BioSchemas/specifications/blob/master/Protein/ProteinEntity-with-context.shex

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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Received on Monday, 11 December 2017 10:48:06 UTC

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