- 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 >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> */Heriot-Watt University is The Times & The Sunday Times >>>> International University of the Year 2018/* >>>> >>>> Founded in 1821, Heriot-Watt is a leader in ideas and solutions. >>>> With campuses and students across the entire globe we span the >>>> world, delivering innovation and educational excellence in >>>> business, engineering, design and the physical, social and life >>>> sciences. >>>> >>>> This email is generated from the Heriot-Watt University Group, >>>> which includes: >>>> >>>> 1. Heriot-Watt University, a Scottish charity registered under >>>> number SC000278 >>>> 2. Edinburgh Business School a Charity Registered in Scotland, >>>> SC026900. Edinburgh Business School is a company limited by >>>> guarantee, registered in Scotland with registered number >>>> SC173556 and registered office at Heriot-Watt University >>>> Finance Office, Riccarton, Currie, Midlothian, EH14 4AS >>>> 3. Heriot- Watt Services Limited (Oriam), Scotland's national >>>> performance centre for sport. Heriot-Watt Services Limited is a >>>> private limited company registered is Scotland with registered >>>> number SC271030 and registered office at Research & Enterprise >>>> Services Heriot-Watt University, Riccarton, Edinburgh, EH14 4AS. >>>> >>>> The contents (including any attachments) are confidential. If you >>>> are not the intended recipient of this e-mail, any disclosure, >>>> copying, distribution or use of its contents is strictly >>>> prohibited, and you should please notify the sender immediately and >>>> then delete it (including any attachments) from your system. >>>> >>> >>> 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