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Re: Protein representation with a Bioschemas context ()

From: Melanie Courtot <mcourtot@ebi.ac.uk>
Date: Fri, 10 Nov 2017 10:14:28 +0000
To: public-bioschemas@w3.org
Message-ID: <aad125da-4bf1-b711-e9f4-303e28efe8d2@ebi.ac.uk>

I thought we were converging towards defining aliases such as 
"transcribedfrom" and then have the context point to possible ontologies 
where "transcribedFrom" could be defined, but the emails excerpts below 
seem to indicate a preferred IRI would need to be chosen?

Would it be possible to have an example with the latest consensus? It 
would be easier to make sure we are all on the same page to comment on.


On 10/11/2017 09:50, Leyla Garcia wrote:
> Hello,
> It seems that we have at least three votes (Alasdair's, Anders', mine) 
> for Bioschemas contexts defining aliases that would point to any 
> preferred existing ontology term. Please correct me if I am wrong.
> For groups to work on deliverable 3 "Create a proof of concept client 
> integrating annotation from several resources", we should first have 
> an agreement about the specifications so it would be great to hear 
> from more people on  the list. Any thoughts?
> Regards,
> On 10/11/2017 09:38, Gray, Alasdair J G wrote:
>> Hi All
>>> On 9 Nov 2017, at 22:11, Anders Riutta 
>>> <anders.riutta@gladstone.ucsf.edu 
>>> <mailto:anders.riutta@gladstone.ucsf.edu>> wrote:
>>> The Bioschemas JSON-LD context could be a single file, or it could 
>>> be a combined context, where "http://bioschemas.org/context.jsonld" 
>>> might point to a collection of contexts  like this:
>>>     [ 
>>>     "http://schema.org/",
>>>     "http://bioschemas.org/Protein/context.jsonld",
>>>     "http://bioschemas.org/LabProtocol/context.jsonld",
>>>         ... 
>>>     ]
>> I like this suggestion from Anders of Bioschemas serving suitable 
>> json-ld context files for each of the profiles and these being 
>> referenced in the examples.
>> I suggest that we add as an output of the profile creation activity 
>> that they must provide a context file for the profile.
>> Is there best practice for versioning these context files?
>>> > We have to select terms from existing ontologies, i.e. we will be 
>>> selecting one ontology over another
>>> Alasdair's concern above is justified, because doing this can be 
>>> sensitive, and it can be tricky to accommodate the subtle variations 
>>> in meaning that different sub-communities attach to certain terms, 
>>> especially when there are multiple IRIs with a 98% overlap in 
>>> meaning but a 2% difference that is just enough to prevent them from 
>>> being exactMatches. However, judiciously endorsing selected IRIs as 
>>> well-thought out and reflective of existing practice could actually 
>>> be a significant source of value that the Bioschemas community could 
>>> provide, because it would be an efficient and transparent process 
>>> for recognizing and forming consensus. Note that we don't have to 
>>> choose one ontology in toto over another; we can pick and choose 
>>> terms from multiple ontologies, as appropriate.
>> I agree that we can mix and match terms from different ontologies. 
>> Also, for the search and lightweight exchange use cases that we are 
>> focusing on we are in the 98% case so hopefully consensus will not be 
>> too difficult but that is up to each of the working groups.
>> Best regards
>> 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 Friday, 10 November 2017 10:14:53 UTC

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