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Re: Protein representation with a Bioschemas context ()

From: Leyla Garcia <ljgarcia@ebi.ac.uk>
Date: Fri, 10 Nov 2017 13:31:02 +0000
To: Melanie Courtot <mcourtot@ebi.ac.uk>, public-bioschemas@w3.org
Message-ID: <d8eeebbb-4f84-1065-cf89-701bb5a34a82@ebi.ac.uk>
Hi again,

And there would be a Bioschemas generic context/template as well. 
Aliases like "Gene" are needed in the Protein profile, but as there is 
no Gene Working Group, it should be Bioschemas covering those aliases.

Regards,

On 10/11/2017 13:28, Leyla Garcia wrote:
> 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
>>>
>>
>
Received on Friday, 10 November 2017 13:31:37 UTC

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