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Re: Bioschemas profile specification: multiple candidate terms from various ontologies

From: Franck Michel <franck.michel@cnrs.fr>
Date: Mon, 2 Jul 2018 10:20:43 +0200
To: Carl Boettiger <cboettig@gmail.com>, public-bioschemas@w3.org
Message-ID: <fd89e99d-55c2-d520-983d-070236fbdb81@cnrs.fr>
Hi Carl,

Thanks for your response, I answer in the other thread with a relevant 
title.

Good point. As you suggest indeed, we would provide in the context the 
terms selected for each profile, while optional mappings would be 
provided within _companion files_ like the schema.org shema.rdfa that 
you mention.

Regarding the syntax, I would say we can choose whatever RDF 
serialization we deem most appropriate (JSON-LD, Turtle...), possibly 
several. Below, I give an example context and mapping graph in JSON-LD.

Context:
{  "@context": [
"http://schema.org/",
         {  "tc": "http://rs.tdwg.org/ontology/voc/TaxonConcept#",
             "tc:rank": { "@type": "@id" } }
     ],
     "tc:rank": "http://rs.tdwg.org/ontology/voc/TaxonRank#Species"
}

Mappings:
{
   "@context": {...},
   "@graph": [
      {  "@id": "tc:rank",
         "owl:equivalentProperty": 
"http://www.wikidata.org/prop/direct/P105",
         "sameAs": "https://www.wikidata.org/wiki/Property:P105"
      },
      ...
    ]
}

Note that the "profile mappings file" inherits the profile context.

Does this sound right to you guys?

Franck.

Le 29/06/2018 à 18:32, Carl Boettiger a écrit :
> 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 <http://schema.org> itself, it does not define any 
> owl:equivalentProperty in the schema.org <http://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".


Le 29/06/2018 à 12:28, Franck Michel a écrit :
> (hit the send button too fast: I renamed this one to split the threads.)
>
> *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/",
>         {
>             "tc": "http://rs.tdwg.org/ontology/voc/TaxonConcept#",
>             "tc:rank": {
>                 "@type": "@id",
>                 "owl:equivalentProperty": 
> "http://www.wikidata.org/prop/direct/P105",
>                 "sameAs": "https://www.wikidata.org/wiki/Property:P105"
>             }
>         }
>     ],
>     "tc:rank": "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 
>> <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 Monday, 2 July 2018 08:21:14 UTC

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