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Re: Protein representation with a Bioschemas context ()

From: Leyla Garcia <ljgarcia@ebi.ac.uk>
Date: Thu, 9 Nov 2017 16:00:47 +0000
To: "Gray, Alasdair J G" <A.J.G.Gray@hw.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: <931fcbab-c914-367f-1d8f-286585b605a8@ebi.ac.uk>
Hi,

On 09/11/2017 14:25, Gray, Alasdair J G wrote:
> Hi
>
> Unless I’m mistaken, the decision is now about presentation. Options 1 
> and 2 are both equivalent when you expand them out.
>
Mmm, maybe it is not just about presentation. In order to make easier 
things for tools and validators, we would need to agree on a set of 
predefined the aliases. Let's suppose Bioschemas recommends the aliases 
"Protein" and "transcribedFrom" but a mark up uses "EnzymeProtein" and 
"comesFromGene". The Bioschemas validation and tools would not know what 
to do with those "unknown" aliases.

If we do not want to impose any predefined aliases, then yes, the two 
options are the same. And then Bioschemas tools and validators will need 
to come up with a strategy to figure it out what corresponds to one 
profile or the other and when two different aliases refer to the same 
concept.

Regards,


> 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 <http://www.macs.hw.ac.uk/%7Eajg33>
> ORCID: http://orcid.org/0000-0002-5711-4872
> Office: Earl Mountbatten Building 1.39
> Twitter: @gray_alasdair
>
>
>
>
>
>
>
>
>
>
Received on Thursday, 9 November 2017 16:01:15 UTC

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