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

From: Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>
Date: Wed, 13 Dec 2017 14:57:20 +0000
To: Leyla Garcia <ljgarcia@ebi.ac.uk>
CC: "public-bioschemas@w3.org" <public-bioschemas@w3.org>
Message-ID: <B79E1938-FA56-4CFB-915C-DF1998302438@hw.ac.uk>
Hi Leyla,

On 12 Dec 2017, at 11:29, Leyla Garcia <ljgarcia@ebi.ac.uk<mailto:ljgarcia@ebi.ac.uk>> wrote:

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 usedhttp://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.

No worries, we are all feeling our way forward with this and what the mapping sheets are capable of providing. We are actively updating the instructions for the mapping files to help clarify these issues.

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?

That is a good question. First I would suggest that the profile should be defined independently of the context file, i.e. it should include the complete IRIs for the properties to be used. Based on that, I would suggest that the context files exist in the repository alongside the examples.


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<http://schema.org/>, I will update the mapping sheet.

Thanks.

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<http://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.

OK, but we need to understand this in the wider schema.org<http://schema.org> context. They already have a hasPart relationship on CreativeWork and the containedIn property that applied to Places has been superseded by containedInPlace. We should maybe consider something in the name that denotes the BioChemEntity aspect of this property.

@Dan, could you provide some guidance on this point?

Best regards,

Alasdair

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 Wednesday, 13 December 2017 14:58:01 UTC

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