OWL refsets preview
The OWL refsets have been developed for the international release in July 2018. The OWL axiom refset only contains the logic definitions that cannot be represented in the RF2 stated relationship file. Please note, descriptions are included on this Confluence page for readability, but they are not part of the OWL refset files.
USE WITHIN CLINICAL SYSTEMS CANNOT BE SUPPORTED AT THIS TIME.
The Preview represents a proof of concept and is distributed for evaluation purposes only. It is not for use in production clinical systems or in clinical settings.
The limited scope of OWL refsets will allow sufficient time for users to develop and update their tooling and systems. The plan is to have full representation of all definitions in the OWL axiom refset in January 2019 release. The stated relationship file will be deprecated after the January 2019 release. Please provide your feedback as comments on this page.
OWL Ontology Reference Set in 2018 July International release
Id | owlExpression | |||||
|---|---|---|---|---|---|---|
709e618d-9434-4c3b-b437-200e9aa26d59 | 20180731 | 1 | 900000000000012004 |
|
| Prefix(:=<http://snomed.info/id/>) |
ba81d0bf-1703-4edf-a641-4bf7ae336a7c | 20180731 | 1 | 900000000000012004 |
| Prefix(owl:=<http://www.w3.org/2002/07/owl#>) | |
2992ad4c-c5f8-4235-8e6b-36be3cacca57 | 20180731 | 1 | 900000000000012004 |
| Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>) | |
beefaa9e-a868-4a36-9ca8-b301cd6ae17f | 20180731 | 1 | 900000000000012004 |
| Prefix(xml:=<http://www.w3.org/XML/1998/namespace>) | |
3c566f2c-b38f-40bb-a6cb-7ea114ce8cf9 | 20180731 | 1 | 900000000000012004 |
| Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>) | |
3b0c7f58-388d-4956-84d5-fbff44197018 | 20180731 | 1 | 900000000000012004 |
| Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>) | |
f81c24fb-c40a-4b28-9adb-85f748f71395 | 20180731 | 1 | 900000000000012004 | Ontology(<http://snomed.info/sct/900000000000207008>) |
OWL Axiom Reference Set in 2018 July International release
Id | owlExpression | |||||
|---|---|---|---|---|---|---|
bcc83805-c402-4c02-ac6b-4ce8efd47773 | 20180731 | 1 | 900000000000012004 | TransitiveObjectProperty(:733930001) | ||
fb90eade-26b7-4747-bf6a-c9c235c1802d | 20180731 | 1 | 900000000000012004 | TransitiveObjectProperty(:738774007) | ||
8164a2fc-cac3-4b54-9d9e-f9c597a115ea | 20180731 | 1 | 900000000000012004 | TransitiveObjectProperty(:123005000) | ||
c1200e3f-c808-4dc8-8904-fec1c7b26280 | 20180731 | 1 | 900000000000012004 | SubObjectPropertyOf(ObjectPropertyChain(:363701004 :738774007) :363701004) | ||
0a4047c5-0d6b-4e71-a786-21658377eecf | 20180731 | 1 | 900000000000012004 | SubObjectPropertyOf(ObjectPropertyChain(:424361007 :738774007) :424361007) | ||
37c61ae4-e371-4d90-b635-5934c0777890 | 20180731 | 1 | 900000000000012004 | TransitiveObjectProperty(:733928003) | ||
bcba6a63-15c7-4109-930d-bf561d98321d | 20180731 | 1 | 900000000000012004 | SubObjectPropertyOf(ObjectPropertyChain(:246075003 :738774007) :246075003) | ||
b8074e53-7157-4f2c-826f-c9019afbff88 | 20180731 | 1 | 900000000000012004 | SubObjectPropertyOf(ObjectPropertyChain(:246093002 :738774007) :246093002) | ||
b4b8c410-13af-46cc-b238-d132b7a79f1c | 20180731 | 1 | 900000000000012004 | ReflexiveObjectProperty(:738774007) | ||
34a2b4fd-093f-41c0-81c9-c68f3dc76bec | 20180731 | 1 | 900000000000012004 | ReflexiveObjectProperty(:733928003) | ||
70c580eb-e0b2-4ac3-815f-8a9b1be45bb3 | 20180731 | 1 | 900000000000012004 | SubObjectPropertyOf(ObjectPropertyChain(:127489000 :738774007) :127489000) |
The content of OWL Axiom refset will be updated according to the requirement from content projects. For the 2018 July release, we anticipate the property chains, property axioms (transitive and reflxive) for the drug and substance projects.
The files can be downloaded at the following links
- This is not a standard file for release. This file is provided for the convienence of visualisation of the snapshot in an ontology tool, such as Protégé.
The linkes to specifications and related documents
Comments
@michael lawley You are right that the Snomed OWL Toolkit is not currently using the OWLOntology reference set and it should.
I will update the toolkit in the develop branch and ask for your feedback in the next few days.
Thank you for your feedback!
Many thanks @michael lawley, I had a discussion with Kai and updated the OWL refset specification to clarify it further.
The OWL ontology refset should only have a single active entry for OWL ontology header. Extension will need to add a new OWL ontology header and inactivate the one from the international release.
It is possible that modules in SNOMED CT can be directly translated into OWL ontologies. Extensions can import the ontology of SNOMED CT core module since the content in the model component module has already been included. The new OWL ontology header should include extension module identifier and import statement(s). This approach could avoid accidental changes to the imported ontology, however, it also won’t allow extensions to fix critical errors in the imported ontology. The implementation could be more complicated than the representation of an edition as a single ontology. Therefore, ontology import is not recommended at the current stage.
Please let us know your feedback.
@michael lawley I've updated the RF2 to OWL implementation in the develop branch of the Snomed OWL Toolkit to take the information from the OWL Ontology reference sets.
The URI is extracted from the ontology header reference set member and used in the owl output file.
Any prefixes in addition to the standard ones will be added to the owl output file however these are not used in any useful way.
There is a unit test and RF2 file showing how an extension should make the International ontology header inactive and provide their own.
I welcome your feedback on this Snomed OWL Toolkit implementation before it is released. (This functionality is not yet available in the executable jar on the release pages.)
It is not clear to me how the OWLOntology and OWLAxiom reference sets are supposed to be combined to produce the resulting OWL Functional Syntax rendering.
Specifically, the OWLOntology reference set contains an entry like:
Ontology(<http://snomed.info/sct/900000000000207008>)but the axioms themselves need to be syntactically embedded inside this giving something like the following (only some data from above included for brevity):Prefix(:=<http://snomed.info/id/>)Prefix(owl:=<http://www.w3.org/2002/07/owl#>)Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)Ontology(<http://snomed.info/sct/900000000000207008>TransitiveObjectProperty(:733930001)SubObjectPropertyOf(ObjectPropertyChain(:363701004 :738774007) :363701004))Looking at the snomed-owl-toolkit code it seems that it hacks around this issue and loads/parses every axiom separately and independently of the actually-supplied OWLOntology content.
To make matters more complicated, it's not clear what should happen with extensions. I think (based on OWL Reference Set Specification (draft)) that the expectation is that the OWLOntology reference set would contain an additional entry:
xxxxxxx
20180731
1
32506021000036107
762103008 |OWL ontology reference set|
734147008 |OWL ontology header|
Ontology(<http://snomed.info/sct/32506021000036107>)
But now there are two Ontology declarations - how do the axioms get handled; how do we know which Ontology declaration to use in the rendering(s) (there can only be one per file)? Should there also be an Imports entry?