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Re: Protein representation with a Bioschemas context ()

From: Leyla Garcia <ljgarcia@ebi.ac.uk>
Date: Thu, 9 Nov 2017 13:44:38 +0000
To: Carole Goble <carole.goble@manchester.ac.uk>
Cc: "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>, Dan Brickley <danbri@danbri.org>, Anders Riutta <anders.riutta@gladstone.ucsf.edu>
Message-ID: <87646d34-55e3-3a4e-df6c-8018f7430bfe@ebi.ac.uk>
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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Received on Thursday, 9 November 2017 13:45:08 UTC

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