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Re: Protein representation with a Bioschemas context ()

From: Justin Clark-Casey <jc955@cam.ac.uk>
Date: Tue, 14 Nov 2017 18:21:33 +0000
To: Leyla Garcia <ljgarcia@ebi.ac.uk>, public-bioschemas@w3.org
Message-ID: <18ba2d2d-eb04-1b9e-6b08-e6295704c1c6@cam.ac.uk>
+1

On 14/11/17 13:57, Leyla Garcia wrote:
> Hi,
> 
> Nice to get that many comments!
> 
> So, it looks like we are talking about something like https://github.com/BioSchemas/specifications/blob/master/Protein/examples/ProteinEntity-with-context.json 
> where the context containing Gene and so will become the Bioschemas context and the IRIs will be agreed and then fixed. That example includes a third-party 
> property which is always possible whenever schema.org or Bioschemas do not provide a better option.
> 
> Regards
> 
> 
> On 14/11/2017 12:41, Justin Clark-Casey wrote:
>> I agree.  As Alasdair and Franck say, I feel that a major benefit of schema.org is in providing agreed upon minimal terms that aid findability.
>>
>> Pragmatically, data sources would always be free to use their own terms and additionalTypes (I don't think that bioschemas can or should forbid this), but 
>> they should be aware that there are agreed upon terms that will make their data findable/usable by a distributed community, rather than only by a few 
>> applications that are especially aware of their markup.
>>
>> I also agree with Stephen that relying on a central collator is too much overhead.  To me, this introduces a single point of failure that conflicts with the 
>> spirit of the web.
>>
>> -- Justin Clark-Casey
>>
>> On 14/11/17 12:02, Gray, Alasdair J G wrote:
>>> Dear All,
>>>
>>> I think Franck’s email clearly explains the situation here.
>>>
>>> Schema.org <http://schema.org> is about everyone buying in to use a common set of terms to markup their content. If they buy-in to that then they get the 
>>> benefit. Otherwise you are just on the linked data web.
>>>
>>> Bioschemas is about making Schema.org <http://schema.org> relevant for the life sciences. We have agreed as a community that we prefer to reuse an existing 
>>> ontology term than mint our own. However, to me, it means that we do need to select a single ontology term. It is through this agreement that we will see 
>>> benefit whilst also keeping the route to adoption straightforward.
>>>
>>> Alasdair
>>>
>>>> On 14 Nov 2017, at 10:21, Franck Michel <franck.michel@cnrs.fr <mailto:franck.michel@cnrs.fr>> wrote:
>>>>
>>>> Dear all,
>>>>
>>>> I'd like to bring a few elements into the discussion wrt. aliases.
>>>>
>>>> In JSON-LD, aliases are just a handy short-cut notation with a local scope: an alias just applies within the scope of the context where it is defined. And 
>>>> more importantly, an alias should not bear any meaning. The first thing a consumer app does with JSON-LD is to expand all terms, which immediately removes 
>>>> all aliases.
>>>>
>>>> Hence, if I use theBioschemas.org <http://bioschemas.org/>default context:
>>>> @context {  "Gene": { "@id":"http://purl.obolibrary.org/obo/SO_0000704"} ... }
>>>> I will typically write:  "@type": [ "BioChemEntity", "Gene" ]
>>>>
>>>> But I may well write a document with a custom alias:
>>>> @context {  "GeneAlias": { "@id":"http://purl.obolibrary.org/obo/SO_0000704"} ... }
>>>> and write:   "@type": [ "BioChemEntity", "GeneAlias" ]
>>>> With:
>>>> @context {  "obo": {  "@id":"http://purl.obolibrary.org/obo/"} ... }
>>>> I would write:   "@type": [ "BioChemEntity", "obo:SO_0000704" ]
>>>> Or I could even not use any alias:   "@type": [ "BioChemEntity","http://purl.obolibrary.org/obo/SO_0000704"]
>>>>
>>>> These are all equivalent from the point of view of a data consumer.
>>>>
>>>> In my view, the default context should be a useful guide for those annotating data withBioschemas.org <http://bioschemas.org/>markup, but alias names should 
>>>> not matter at all. What matters is the URIs to which aliases resolve.
>>>>
>>>> I feel like the solution of agreed pre-defined URIs, whatever the aliases used, is more sustainable. After all,schema.org <http://schema.org/>advocates for 
>>>> the use of specific agreed-upton terms. If one uses them, their pages are more likely to be discoverable. They can chose to use other terms if this is 
>>>> convenient for them, but then there is not guarantee that the pages will be discovered as easily.
>>>>
>>>> Franck.
>>>
>>> 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
>>> ORCID: http://orcid.org/0000-0002-5711-4872
>>> Office: Earl Mountbatten Building 1.39
>>> Twitter: @gray_alasdair
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
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>>
> 
Received on Tuesday, 14 November 2017 18:22:00 UTC

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