Re: OWL and RDF lists

Hi all,

I just stumbled upon this thread. Last year I co-authored a paper that
analysed the impact of alternative design patterns for lists on the
efficiency of list-relevant operations in SPARQL. OWL was not a topic of
the paper, although we also considered OWL-compliant solutions, in the
analysis. One conclusion was that the rdf:List model was very inefficient
for many of the operations, and managing indexing in properties or using
container membership properties was generally preferable. I am aware this
goes against the OWL requirements but drop the ball nevertheless, in case
this is useful. The article is [1].

Best wishes

Enrico


[1] Daga, Enrico, Albert Meroño-Peñuela, and Enrico Motta. "Sequential
linked data: The state of affairs." *Semantic Web* Preprint (2021): 1-36.
--
Enrico Daga
http://about.me/enridaga


On Mon, 15 Aug 2022 at 19:02, Balhoff, Jim <balhoff@renci.org> wrote:

> I proposed a change to OWL API that would allow parsing certain lists into
> Abox axioms: https://github.com/owlcs/owlapi/pull/1074
>
> This would only be active if the ontology is specifically using the RDF
> list predicates as object properties. That change would be helpful for
> loading the proposed FHIR data model into Protégé and then being able to
> access items in lists (assuming that OWL API version makes its way
> into Protégé).
>
> I think outside of Protégé/OWL API, dealing with list data might not be as
> much of a problem, like if using an RDF rule engine to make inferences.
>
> On Aug 12, 2022, at 8:25 AM, Eric Prud'hommeaux <eric@w3.org> wrote:
>
> 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
>
>
>