Re: Bioschemas Taxon profile specification

Hi Franck,

I'm not an expert in OWL, but I don't think the context is the correct
place to define the OWL relationships.  If you consider the examples of
schema.org itself, it does not define any owl:equivalentProperty in the
schema.org definitions themselves, but rather includes them in the offical
schema.rdfa document where the class definitions are also specified, e.g.
https://github.com/schemaorg/schemaorg/blob/master/data/schema.rdfa#L4545
defines
 that schema:description is the owl:equivalentProperty to dc:description,
just as you would expect.

I'm not actually sure if the bioschemas definitions are defined in
identical format to the schema.rdfa (personally I find rdfa hard to read
and tend to convert that to JSON-LD first for my own use cases), but if so,
it seems like that is where we should put the owl:equivalentProperty
statements, rather than in the context?



Note that the invalid error you see is not specific to sameAs or
owl:equivalentProperty; I believe a context cannot have any 'non-special'
terms.  Perhaps you want instead:

{
  "@context": [
    "http://schema.org/",
    {
      "tc": "http://rs.tdwg.org/ontology/voc/TaxonConcept#",
      "wdt": "http://www.wikidata.org/prop/direct/",
      "tc:rank": {
        "@type": "@id",
        "@id": "https://www.wikidata.org/wiki/Property:P105"
      }
    }
  ],
  "tc:rank": "http://rs.tdwg.org/ontology/voc/TaxonRank#Species"
}


Obviously this is a slightly different statement, since it does not define
a property and equivalent property, but literally uses the wikidata URI as
the expanded URI definition of "tc:rank".

On Fri, Jun 29, 2018 at 3:26 AM Franck Michel <franck.michel@cnrs.fr> wrote:

> First sub-thread:  *What do we do when there are multiple candidate terms
> from various ontologies?*
>
> I guess there is a consensus here: each specification group proposes a
> single approved term for each type and each property, that represents the
> group consensus.
> The only difficulty may be to reach this consensus while sparing different
> communities' sensitivity.
>
> It's been suggested that the context may document mappings to equivalent
> terms in other ontologies. Although the idea is compelling, I'm not sure
> how this can be achieved technically. I have tried the [invalid] example
> below. Let us assume the Biodiversity group chooses the TDWG rank property
> (tc:rank) to denote the taxonomic rank. The context names this property
> while providing the equivalent Wikidata property (owl:equivalentProperty)
> and webpage thereof (remember that schema:sameAs gives the "URL of a
> reference Web page that unambiguously indicates the item's identity (...)".
> {
>     "@context": [
>         "http://schema.org/" <http://schema.org/>,
>         {
>             "tc": "http://rs.tdwg.org/ontology/voc/TaxonConcept#"
> <http://rs.tdwg.org/ontology/voc/TaxonConcept#>,
>             "tc:rank": {
>                 "@type": "@id",
>                 "owl:equivalentProperty":
> "http://www.wikidata.org/prop/direct/P105"
> <http://www.wikidata.org/prop/direct/P105>,
>                 "sameAs": "https://www.wikidata.org/wiki/Property:P105"
> <https://www.wikidata.org/wiki/Property:P105>
>             }
>         }
>     ],
>     "tc:rank": "http://rs.tdwg.org/ontology/voc/TaxonRank#Species"
> <http://rs.tdwg.org/ontology/voc/TaxonRank#Species>
> }
>
> Unfortunately, this example is invalid
> <https://json-ld.org/playground/#startTab=tab-expanded&json-ld=%7B%22%40context%22%3A%5B%22http%3A%2F%2Fschema.org%2F%22%2C%7B%22tc%22%3A%22http%3A%2F%2Frs.tdwg.org%2Fontology%2Fvoc%2FTaxonConcept%23%22%2C%22wdt%22%3A%22http%3A%2F%2Fwww.wikidata.org%2Fprop%2Fdirect%2F%22%2C%22tc%3Arank%22%3A%7B%22%40type%22%3A%22%40id%22%2C%22owl%3AequivalentProperty%22%3A%22wdt%3AP105%22%2C%22sameAs%22%3A%22https%3A%2F%2Fwww.wikidata.org%2Fwiki%2FProperty%3AP105%22%7D%7D%5D%2C%22tc%3Arank%22%3A%22http%3A%2F%2Frs.tdwg.org%2Fontology%2Fvoc%2FTaxonRank%23Species%22%7D>
> because a JSON-LD term definition cannot contain a sameAs or owl:equivalent
> property.
> Can you think of other ways to express this mapping?
>
>
> Franck.
>
>
> 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> 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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