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Re: Protein representation with a Bioschemas context ()

From: Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>
Date: Thu, 9 Nov 2017 14:25:24 +0000
To: Leyla Garcia <ljgarcia@ebi.ac.uk>
CC: Carole Goble <carole.goble@manchester.ac.uk>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>, Dan Brickley <danbri@danbri.org>, Anders Riutta <anders.riutta@gladstone.ucsf.edu>
Message-ID: <E50D38AF-A58E-4BA9-AC50-CC9110ABDF84@hw.ac.uk>
Hi

Unless I’m mistaken, the decision is now about presentation. Options 1 and 2 are both equivalent when you expand them out.

I personally like 2 as it makes the json-ld very readable and also explicitly declares where each property is from.
https://github.com/BioSchemas/specifications/blob/master/Protein/examples/ProteinEntity-with-context.json

Alasdair

On 9 Nov 2017, at 13:44, Leyla Garcia <ljgarcia@ebi.ac.uk<mailto:ljgarcia@ebi.ac.uk>> wrote:

Hi,

In that case, our options are reduced to:

1. eliminate the long property names by introducing shorthands in the context, something like the latest commit to my example
https://github.com/BioSchemas/specifications/blob/master/PhysicalEntity/examples/BioChemEntityAlt-min%2Brec.jsonld<https://github.com/BioSchemas/specifications/blob/master/PhysicalEntity/examples/BioChemEntityAlt-min+rec.jsonld>

2. using a context with  predefined aliases linking to the preferred ontology by the data provider (see https://github.com/BioSchemas/specifications/blob/master/Protein/examples/ProteinEntity-with-context.json).

Any preferences?

Regards,

On 09/11/2017 13:31, Carole Goble wrote:


Bioschemas has already been publicly accused of running parallel ontology efforts and we were very clear that we were not going to reinvent ontologies.
So I am very reticent about doing so.

Rafa and I are already involved in a Researchschemas initiative with EOSC and have lines of enquiry for joining up with initiatives in biodiversity and geosciences. It would be good if we didn’t end up with many many parallel activities. But instead a converged one

Carole




Sent from my iPhone by
Professor Carole Goble
The University of Manchester
UK

On 9 Nov 2017, at 11:13, Leyla Garcia <ljgarcia@ebi.ac.uk<mailto:ljgarcia@ebi.ac.uk>> wrote:

Hi all,

On 09/11/2017 10:47, Gray, Alasdair J G wrote:
Hi All,

Leyla, thanks for providing a concrete example from which we can base our discussions.

Points in favour of Leyla’s proposal:
- Properties and types defined in Bioschemas namespace
- json-ld validates using the structured data markup tool
It will depending on whether schema.org<http://schema.org/> is before (validates but all schema terms are moved to the bioschemas namespace) or after (does not validate but the namespace are correctly conserved)

- We don’t need to choose one ontology over another

Points against Leyla’s proposal
- We are minting our own ontology terms

We can avoid that by using a context with just predefined aliases (see https://github.com/BioSchemas/specifications/blob/master/Protein/examples/ProteinEntity-with-context.json). But then, Google does not know anything about all those possible types that could be associated to the aliases.

Minting our own terms (I would not say ontology) makes things easier as Google would need to know only schema.org<http://schema.org/> and Bioschemas. BUT, then maybe Google does not want to open that door as Bioschemas would become a somehow parallel vocabulary and other projects/groups might want to do something similar... OR maybe Google will prefer all to be moved as proper types to schema.org<http://schema.org/>.

Also, keep in mind that schema.org<http://schema.org/> mints terms already covered by ontologies. Citations for instance are covered by the Bibliographic Ontology (BIBO) and the Semantic Publishing and Referencing (SPAR) ontologies.

Regards,


We can of course eliminate the long property names by introducing shorthands in the context, something like the latest commit to my example
https://github.com/BioSchemas/specifications/blob/master/PhysicalEntity/examples/BioChemEntityAlt-min%2Brec.jsonld<https://github.com/BioSchemas/specifications/blob/master/PhysicalEntity/examples/BioChemEntityAlt-min+rec.jsonld>
This could be expanded to something similar to the full context that Leyla used, but instead of creating new Bioschema terms, we would reused terms from existing ontologies

Points in favour of Alasdair's proposal:
- We are not minting our own ontology terms
- With full context like Leyla’s the example would validate

Points against Alasdair's proposal
- We have to select terms from existing ontologies, i.e. we will be selecting one ontology over another

Ultimately, with all these proposals someone adopting will need to edit the same number of characters, and we should highlight somehow what these are.

I think we are in broad agreement that we can move away from using the additionalProperties.

What we still need to determine is are we going to mint terms in the Bioschemas namespace (that could eventually be pushed to schema.org<http://schema.org/>) or select terms from existing ontologies. Opinions on this last point please.

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<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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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
Received on Thursday, 9 November 2017 14:25:57 UTC

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