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Re: Protein representation with a Bioschemas context ()

From: Leyla Garcia <ljgarcia@ebi.ac.uk>
Date: Thu, 9 Nov 2017 11:11:49 +0000
To: "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>
Cc: "public-bioschemas@w3.org" <public-bioschemas@w3.org>, Dan Brickley <danbri@danbri.org>, Anders Riutta <anders.riutta@gladstone.ucsf.edu>
Message-ID: <4566d966-1283-543a-1e62-e088039c7569@ebi.ac.uk>
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 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 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.

Also, keep in mind that 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
>
>
>
>
>
>
>
>
>
>
> Untitled Document
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Received on Thursday, 9 November 2017 11:12:15 UTC

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