LOINC-on-OWL

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

LOINC-on-OWL

Campbell, James R
At Nebraska we are preparing extract code to publish a LOINC-on-OWL subset taken from an inferred view of SNOMED CT which we enhanced with a LOINC code map from SNOMED Observable Entities.  At this time we are compiling an exhaustive list of all LOINC concepts and the Grouper concepts that we need to extract a hierarchically complete subset view of LOINC.  We intend to extract Axioms for Concept declaration, Equivalence, Subtype and Properties of Annotations for the set of concepts.  

Given that Equivalence axioms have structured reference to defining attribute-value pairs taken from SNOMED hierarchies other than Observable Entity, do we have to include concept declarations and/or additional axioms or Properties for the defining attribute and/or value concepts in the extract in order to be able to load and browse the LOINC-on-OWL ontology in Protege?
Jim Campbell

The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: LOINC-on-OWL

samsontu
Hi Jim,

On Jun 22, 2019, at 11:04 AM, Campbell, James R <[hidden email]> wrote:

At Nebraska we are preparing extract code to publish a LOINC-on-OWL subset taken from an inferred view of SNOMED CT which we enhanced with a LOINC code map from SNOMED Observable Entities.  At this time we are compiling an exhaustive list of all LOINC concepts and the Grouper concepts that we need to extract a hierarchically complete subset view of LOINC.  We intend to extract Axioms for Concept declaration, Equivalence, Subtype and Properties of Annotations for the set of concepts.  

Given that Equivalence axioms have structured reference to defining attribute-value pairs taken from SNOMED hierarchies other than Observable Entity, do we have to include concept declarations and/or additional axioms or Properties for the defining attribute and/or value concepts in the extract in order to be able to load and browse the LOINC-on-OWL ontology in Protege?

You don’t need to have class declarations for referenced concepts for your extract to be loadable into Protege. Presumably these referenced concepts are recognizable from their usage contexts that they are classes. Protege will show these referenced classes as a flat list of subclasses of owl:Thing. 

For properties, the same thing should apply, as long as their usages allow the OWL parser to recognize them as data, object, or annotation properties. If there is any ambiguity about a property’s role, it will default to be an annotation property.

You may want to export some annotations, such as those of rtfs:label, so that concepts have human-readable labels.

I myself haven’t used the Protege export much. Others can add their advices or corrections. You may also look at ROBOT


With best regards,
Samson



_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

smime.p7s (1K) Download Attachment