Re: OWL and RDF lists

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