W3C home > Mailing lists > Public > public-bioschemas@w3.org > November 2017

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 
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) 


> 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
> ------------------------------------------------------------------------
> */Heriot-Watt University is The Times & The Sunday Times International 
> University of the Year 2018/*
> Founded in 1821, Heriot-Watt is a leader in ideas and solutions. With 
> campuses and students across the entire globe we span the world, 
> delivering innovation and educational excellence in business, 
> engineering, design and the physical, social and life sciences.
> This email is generated from the Heriot-Watt University Group, which 
> includes:
>  1. Heriot-Watt University, a Scottish charity registered under number
>     SC000278
>  2. Edinburgh Business School a Charity Registered in Scotland,
>     SC026900. Edinburgh Business School is a company limited by
>     guarantee, registered in Scotland with registered number SC173556
>     and registered office at Heriot-Watt University Finance Office,
>     Riccarton, Currie, Midlothian, EH14 4AS
>  3. Heriot- Watt Services Limited (Oriam), Scotland's national
>     performance centre for sport. Heriot-Watt Services Limited is a
>     private limited company registered is Scotland with registered
>     number SC271030 and registered office at Research & Enterprise
>     Services Heriot-Watt University, Riccarton, Edinburgh, EH14 4AS.
> The contents (including any attachments) are confidential. If you are 
> not the intended recipient of this e-mail, any disclosure, copying, 
> distribution or use of its contents is strictly prohibited, and you 
> should please notify the sender immediately and then delete it 
> (including any attachments) from your system.
Received on Thursday, 9 November 2017 11:12:15 UTC

This archive was generated by hypermail 2.4.0 : Friday, 17 January 2020 19:08:00 UTC