Re: OWL and RDF lists

Molstly protégé, and other OWL-capable tools like StarDog. I'd like to
figure out for FHIR whether to use RDF lists, but I think it's
important for the SemWeb as a whole to solve this. As it stands, it
looks like one should never use RDF lists.

Given that way more RDF data processing happens with SPARQL than with
OWL, and SPARQL *can* access lists (albeit awkwardly), it sounds crazy
to forgo using lists just because someone someday might want to do OWL
inference over the entities in the list. Voilà the dilema.

It would also be really nice to understand if there is a fundamental
reason for this limitation in OWL. I beleieve that Jim's research
shows that at least OWL-API can be updated to allow lists. If this is
the case, and this can be replicated in other OWL implementations,
then perhaps the answer is a period of civil disobedience where folks
violate the spec, use tools that support that violation, and
eventually update the OWL spec. This interim solution could be made
official with an OWL 1.1. errata stating that rdf:first/rest *can* be
used in axioms.


On Thu, Aug 11, 2022 at 08:47:27PM +0000, Mark Wallace wrote:
> Eric, are you looking for a solution that runs Within protege? Within a triple store?
> 
> ________________________________
> From: Eric Prud'hommeaux <eric@w3.org>
> Sent: Thursday, August 11, 2022 8:26 AM
> To: semantic-web@w3.org <semantic-web@w3.org>
> Cc: Jim Balhoff <balhoff@renci.org>; dbooth@dbooth.org <dbooth@dbooth.org>
> Subject: OWL and RDF lists
> 
> RDF lists (technically "collections" ¹) have terse abbreviations in
> Turtle/SPARQL and a "ladder" representation as triples.
> 
> <https://en.wikipedia.org/wiki/Flag_of_France> :orderedColors _:1 .
> _:1 rdf:first "blue" .
> _:1 rdf:rest _:2 .
> _:2 rdf:first "white" .
> _:2 rdf:rest _:3 .
> _:3 rdf:first "red" .
> _:3 rdf:rest rdf:nil .
> 
> The SPARQL 1.2 WG is wrestling with lists ², and JSON-LD 1.1 has added
> support for them ³. OWL however, specifically disables them by
> prohibiting inferences across predicates in the rdf: namespace à la
> Jim Balhoff's example ⁴;
> [[
> :contains rdf:type owl:ObjectProperty ;
>   owl:propertyChainAxiom ( rdf:rest :contains ) .
> ]]
> 
> FHIR is a set of models for clinical record. It has representations in
> XML, JSON and RDF. There's a playground ⁵ to explore alternatives
> which illustrates alternatives, including whether to use
> rdf:Collections (see button at top-right). With collections turned
> off, we have to roll our own order (fhir:index 0, 1, 2...), which
> kinda goes against RDF standards.
> 
> I put together a gist which illustrates three observations we might
> encounter in a patient's record. The codes for the first two appear in
> a SNOMED hieararchy you might query for evidence of bone density loss
> (clinical example, balancing corticosteroids against osteoporosis).
> 
> https://fhircat.github.io/fhir-rdf-playground/?axes=rdvCh&manifestURL=https://gist.githubusercontent.com/ericprud/8e53eef196ccdc2c43f40238fdd06691/raw/224261f5055a3980acd79570fe5caeaf4a4b2d84/osteo-manifest.json
> 
> 
> Solbrig et al demonstrate how the SNOMED hierarchy can be used for
> valuable clinical insights ⁶ *iff* we can work write OWL axioms which
> simultaneously access the SNOEMD hierarchy and the codes in the
> paitent data. But as Jim demonstrated, that requires OWL axioms that
> reference the forbidden rdf: namespace.
> 
> Thoughts? Advice?
> 
> 
> ¹ https://www.w3.org/TR/rdf-primer/#collections
> ² https://github.com/w3c/sparql-12/issues/46
> ³ https://www.w3.org/TR/json-ld11/#example-82-specifying-that-a-collection-is-ordered-in-the-context
> ⁴ https://gist.github.com/balhoff/62fb8f2c1e29bc0d4d27c3df0d005154
> ⁵ https://fhircat.github.io/fhir-rdf-playground/
> ⁶ https://github.com/BD2KOnFHIR/BLENDINGFHIRandRDF
>

Received on Friday, 12 August 2022 12:25:26 UTC