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Re: Bioschemas Taxon profile specification

From: Justin Clark-Casey <justinccdev@gmail.com>
Date: Wed, 4 Jul 2018 18:31:54 +0100
Message-ID: <CAME9NR9TDWzQGZw4KQpbYAaP6tvn0raVmv7mzwWimvews8L2Zw@mail.gmail.com>
To: cboettig@gmail.com
Cc: Franck Michel <fmichel@i3s.unice.fr>, Leyla Garcia <ljgarcia@ebi.ac.uk>, Melanie Courtot <mcourtot@ebi.ac.uk>, "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>, public-bioschemas@w3.org
Yeah, I don't think you would define equivalent terms in the context.  As
Carl says, I think it's actually in an out-of-band document (rdfa for
schema.org, maybe even placeable in the yaml that generates the spec pages
on Bioschemas.org).  However, at least having this in JSON-LD or equivalent
will make the relations readable for software, even if the format is
bespoke to us (hopefully we could be very close to the schema.org approach).

And the 'sparing different communities sensitivity' is actually why I
propose having Bioschemas define an empty signalling type (e.g.
http://bioschemas.org/taxon) and the sameas stuff in the out-of-band
JSON-LD file.  Then many term equivalences can be listed without upsetting
any particular community.  The empty Bioschemas type is not a term, it's
just a device for simplifying Bioschemas markup and avoiding damaging
debates.  It would contain absolutely no term definition or description
itself and would merely have sameas links to other ontologies.

On Fri, 29 Jun 2018 at 17:32, Carl Boettiger <cboettig@gmail.com> wrote:

> 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
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>>> >> Office: Earl Mountbatten Building 1.39
>>> >> Twitter: @gray_alasdair
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>> --
>
> http://carlboettiger.info
>
Received on Wednesday, 4 July 2018 17:32:55 UTC

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