W3C home > Mailing lists > Public > public-bioschemas@w3.org > June 2018

Re: Bioschemas Taxon profile specification

From: Justin Clark-Casey <justinccdev@gmail.com>
Date: Thu, 28 Jun 2018 18:40:56 +0100
Message-ID: <CAME9NR_YwG-JJ2_vd5YG5y5UCsyeTedon6X=FZ8dwY9kuPF8NQ@mail.gmail.com>
To: 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
On Thu, 28 Jun 2018 at 16:42, ljgarcia <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> 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>
> >> 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
> >> 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 Thursday, 28 June 2018 17:41:59 UTC

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