- 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