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Re: Revised protein profile (was Re: Bioschemas at SWAT4LS)

From: Leyla Garcia <ljgarcia@ebi.ac.uk>
Date: Tue, 12 Dec 2017 11:29:19 +0000
To: "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>
Cc: "public-bioschemas@w3.org" <public-bioschemas@w3.org>
Message-ID: <593a5302-1b9f-ee94-29a4-b325fc6bc21a@ebi.ac.uk>
Hi Alasdair,

On 11/12/2017 10:47, Gray, Alasdair J G wrote:
> I’ve had a look at your revised protein profile (0.4-draft.1)
> http://bioschemas.org/devSpecs/Protein/specification/
> 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.

I did not know that was the way for third-party properties, I will 
update the mapping sheet accordingly.
One question about it. The Bioschemas context would have aliases for 
those properties, right? I know the aliases are not meaningful but still 
useful to create a compact version of a markup. So, how/where would 
those aliases be define in Bioschemas?

> 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.

It is indeed a property to be proposed to schema.org, I will update the 
mapping sheet.

> A question here would be is there an existing ontology term that could 
> be used?

Of course there is, but contains/isContainedIn are part of the 
properties to be proposed to schema.org and agreed by the community 
during our last meeting. Those properties in BioChemEntity are the ones 
that roughly applied to any bio/chem/biochem entity so they are part of 
the specification rather than a profile.

> Best regards
> Alasdair
>> [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 <http://www.macs.hw.ac.uk/%7Eajg33>
> ORCID: http://orcid.org/0000-0002-5711-4872
> Office: Earl Mountbatten Building 1.39
> Twitter: @gray_alasdair
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Received on Tuesday, 12 December 2017 11:30:22 UTC

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