Re: Protein representation with a Bioschemas context ()

Hi all,

I was under the same impression than Melanie. We agree on aliases but 
providers can decide what is their preferred IRI for any of them. A 
Bioschemas Protein context would just provide a default context that can 
also be used as a template where IRIs (but not aliases) can be modified. 
And of course, anyone could add more aliases, Bioschemas will just not 
parse those outside the default/template provided context.

I thought we did not want to impose any IRI. Is there any reason why we 
should?

Regards,



On 10/11/2017 11:27, Melanie Courtot wrote:
> Thanks, that great and really helpful.
>
> Why couldn't we allow different projects to define their own context? 
> For example, I modified the one provided in the example to use other 
> ontologies: http://tinyurl.com/yd5snze2
> (Note I'm not saying those should be used, I just picked alternative 
> to the existing ones for gene, protein and transcribedFrom as an example)
>
> Bioschemas can then offer a context by default while leaving the 
> possibility for others to chose alternatives. Would it be a problem 
> for the validators to only consider 
> https://github.com/ariutta/specifications/blob/ariutta-demo/Protein/examples/ProteinEntityNew.json 
> when checking whether entities comply with the profile?
>
> Cheers,
> Melanie
>
> On 10/11/2017 10:55, Gray, Alasdair J G wrote:
>> PS: The example is now working on the JSON-LD Playground site
>> http://tinyurl.com/y9mu423y
>>
>>> On 10 Nov 2017, at 10:38, Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk 
>>> <mailto:A.J.G.Gray@hw.ac.uk>> wrote:
>>>
>>>>
>>>> On 10 Nov 2017, at 10:14, Melanie Courtot <mcourtot@ebi.ac.uk 
>>>> <mailto:mcourtot@ebi.ac.uk>> wrote:
>>>>
>>>> Hi,
>>>>
>>>> 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?
>>>
>>> Each profile would need to choose a single IRI for each of the terms 
>>> used within it, i.e. in the case of transcribedFrom this is currently
>>> http://semanticscience.org/resource/SIO_010081
>>> It is having consensus on these terms that will provide the benefit 
>>> that we envision.
>>>
>>> By using a shared context we would simplify the creation of the 
>>> markup as people can just reference the common context.
>>>>
>>>> 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.
>>>
>>> The example Anders sent would be the current proposal
>>> https://github.com/ariutta/specifications/blob/ariutta-demo/Protein/examples/ProteinEntityNew.json
>>>
>>> With the context being
>>> https://github.com/ariutta/specifications/blob/ariutta-demo/context.jsonld
>>> I have deployed this context at the below but it is not quite 
>>> working yet.
>>> bioschemas.org/Protein/context.jsonld 
>>> <http://bioschemas.org/Protein/context.jsonld>
>>>
>>> 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
>>
>