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Re: Bioschemas Taxon profile specification

From: Franck Michel <franck.michel@cnrs.fr>
Date: Fri, 29 Jun 2018 12:24:25 +0200
To: Justin Clark-Casey <justinccdev@gmail.com>, Leyla Garcia <ljgarcia@ebi.ac.uk>
Cc: Melanie Courtot <mcourtot@ebi.ac.uk>, "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>, Franck Michel <fmichel@i3s.unice.fr>, public-bioschemas@w3.org
Message-ID: <49d587ab-b7ef-3c8b-3330-b7a7502e83f0@cnrs.fr>
Dear all,

Thanks for your inputs. I will try to summarize the discussion so far 
(hope I don't forget anyone's input).

To make it easier to follow, I'll split this into two sub-threads. right 
after this email...


Le 28/06/2018 à 19:40, Justin Clark-Casey a écrit :
> On Thu, 28 Jun 2018 at 16:42, ljgarcia <ljgarcia@ebi.ac.uk 
> <mailto:ljgarcia@ebi.ac.uk>> wrote:
>
>     Hi,
>
>     What Melanie suggests is useful to describe profiles, they would
>     become
>     a DefinedTerm. That would help as well to avoid type/profile
>     confusion.
>     We would talk then about DefinedTerms. If we find a way to also
>     described the properties accepted with their restrictions, that
>     would be
>     even better. That might be a good subject for a different discussion.
>
>
> This means there will have to be special Bioschemas code that knows to 
> look in a DefinedTerm somewhere for this information.  I still think 
> using a subtype to signify a profile will be simpler.
>
> I also disagree with Alasdair in that I think there should be a 
> http://bioschema.org/Protein type.  This would be an empty type that 
> just signifies we're talking about a Bioschemas defined protein. so it 
> isn't treading on anybodies toes.  This would have information saying 
> it's defined by http://purl.obolibrary.org/obo/PR_000000001 and it's 
> same as terms.  Without this, there's not much point having a 
> bioschemas context, and requiring people to use this specific string 
> every time is cumbersome, especially if every group chooses something 
> from a different ontology.  This makes writing and consuming markup 
> harder.
>
>
>     The question remains. How do we choose a term over others to
>     associate
>     it to a profile/DefinedTerm?
>
>
> I suggest having members of each specification group propose which 
> term they want and then come to consensus via discussion and/or vote.
>
>
>     Regards,
>
>
>     On 2018-06-28 15:45, Melanie Courtot wrote:
>     > Hi,
>     >
>     > We could consider using the defined terms,
>     >
>     https://dataliberate.com/2018/06/18/schema-org-introduces-defined-terms/,
>     > to do that.
>     >
>     > So have a protein be defined as
>     >
>     >            "@type": "DefinedTerm",
>     >             "@id": "http://purl.obolibrary.org/obo/PR_000000001",
>     >             "name": "Protein",
>     >             "inDefinedTermSet": "http://bioschemas.org/terms",
>     >             "description": "An amino acid chain that is produced de
>     > novo by ribosome-mediated translation of a genetically-encoded
>     mRNA.",
>     >             "sameAs": "http://purl.obolibrary.org/obo/NCIT_C17021",
>     >             "sameAs":
>     "http://semanticscience.org/resource/SIO_010043"
>     >
>     > (Using random examples of sameAs from
>     > https://www.ebi.ac.uk/ols/search?q=protein)
>     >
>     > Cheers,
>     > Melanie
>     >
>     > ---
>     > Melanie Courtot, PhD
>     > EMBL-EBI
>     > GA4GH/BioSamples project lead
>     >
>     >> On 28 Jun 2018, at 15:18, ljgarcia <ljgarcia@ebi.ac.uk
>     <mailto:ljgarcia@ebi.ac.uk>> wrote:
>     >> Hi,
>     >>
>     >> I understood Franck's question in a different way.
>     >>
>     >> Alasdair says
>     >>
>     >>> I also agree that a context file should be provided which has the
>     >>> chosen types and terms in it, i.e. the context file would define
>     >>> Protein to be the URI http://purl.obolibrary.org/obo/PR_000000001.
>     >>
>     >> I think what Franck is asking is how to choose
>     >> http://purl.obolibrary.org/obo/PR_000000001 over other possible
>     >> terms to define a Protein. For the taxon case, same as it happens
>     >> with proteins, there are multiple possibilities. Franck, is this
>     >> your question? If it is, I do not think there is any agreement on
>     >> how to choose, other than going for well-known ontologies broadly
>     >> accepted by the community of interest, even better if the term is
>     >> mapped to other possible ones.
>     >>
>     >> Regards,
>     >>
>     >> On 2018-06-28 11:50, Gray, Alasdair J G wrote:
>     >> On 27 Jun 2018, at 19:19, Justin Clark-Casey
>     <justinccdev@gmail.com <mailto:justinccdev@gmail.com>>
>     >> wrote:
>     >> I think we should have mandatory known @types and properties.  In
>     >> my view, Bioschemas should be as easy as possible to write and
>     >> consume.  Multiple options will increase cognitive load on writers
>     >> (which one do I choose?  Why are these 2 examples using these
>     >> different terms?) and open the door to greater inconsistency.
>     >> Non-mandatory types will also raise the barriers for writing
>     >> Bioschemas software that will have to be aware of equivalent
>     >> mappings.
>     >> I completely agree that we should have a single approved type for
>     >> each profile, and likewise for each property a single chosen term.
>     >> This is the whole point of having the profiles.
>     >> I would go one step further and say that Bioschemas should provide
>     >> an http://bioschemas.org [1] [1]context that will define types such
>     >> as
>     >> Taxon, rather than blessing particular ontology terms.
>     >> I also agree that a context file should be provided which has the
>     >> chosen types and terms in it, i.e. the context file would define
>     >> Protein to be the URI http://purl.obolibrary.org/obo/PR_000000001.
>     >> To
>     >> be completely explicit, we would not be defining a type in the
>     >> bioschemas namespace, e.g. http://bioschemas.org/Protein.
>     >> This context can also document equivalent terms in different
>     >> ontologies.
>     >> I like the idea that this also contains mappings to the equivalent
>     >> terms in other ontologies.
>     >> 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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Received on Friday, 29 June 2018 10:24:53 UTC

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