Re: OWL and RDF lists

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<mailto: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<mailto:eric@w3.org>>
Sent: Thursday, August 11, 2022 8:26 AM
To: semantic-web@w3.org<mailto:semantic-web@w3.org> <semantic-web@w3.org<mailto:semantic-web@w3.org>>
Cc: Jim Balhoff <balhoff@renci.org<mailto:balhoff@renci.org>>; dbooth@dbooth.org<mailto:dbooth@dbooth.org> <dbooth@dbooth.org<mailto: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