This project uses the OWLApi perform different transformations of SNOMED CT representations.
Clone and build with:
mvn clean compile assembly:single
This will generate the executable JAR file: owl-test-x.x.x-SNAPSHOT-jar-with-dependencies.jar
Binaries are also available in the releases section of the github repository.
Run the executable from the command line, for example:
java -jar rf2-to-owl-x.x.x-SNAPSHOT-jar-with-dependencies.jar -help
Arguments help:
usage: rf2-to-owl
-cd Convert concepts to concrete domains
-cf <arg> Concepts file
-df <arg> Descriptions file
-help Prints help
-iri <arg> IRI for Owl Generation
-lf <arg> language refset file
-mode <arg> conversion mode, expected values: rf2-to-owl,
owl-to-refset, refset-to-owl
-of <arg> Owl file
-orf <arg> Owl Refset file
-output <arg> Output file
-rf <arg> Relationships file
-rf2Folder <arg> RF2 Folder
-syntax <arg> OWL Syntax, expected values: owlxml, functional,
manchester
-tf <arg> Text definition file
Arguments required for this mode:
java -jar rf2-to-owl-x.x.x-SNAPSHOT-jar-with-dependencies.jar -mode rf2-to-owl -rf2Folder /x/y/z/snapshot -output ontology.owl
Optional arguments:
If the RF2 files are not part of a standard release package, paths for the individual files can be passed using the arguments described in the arguments help.
The process generates the following OWL artifacts in the ontology:
Since the July 2017 release of the international edition, some relationships that specify numerical values are represented using concepts for the example:
Source: 318420003 | Product containing atenolol 50 mg/1 each oral tablet (virtual clinical drug) |
Attribute: 732947008 | Has presentation strength denominator unit (attribute) |
Destination: 732774003 | 50 (qualifier value) |
If the "Concrete domains conversion" parameter is sent as "TRUE", those relationships are converted into OWL Data Properties, instead of the normal OWL Object Properties. Classification results should be identical, but having actual values instead of concept references may allow for more detailed queries and computations.
Attributes that are currently converted as data properties:
732944001 | Has presentation strength numerator value (attribute) | - DataType: float
732946004 | Has presentation strength denominator value (attribute) | - DataType: float
Arguments required for this mode:
java -jar rf2-to-owl-x.x.x-SNAPSHOT-jar-with-dependencies.jar -mode owl-to-refset -of ontology.owl -output owlRefset.txt
Arguments required for this mode:
java -jar rf2-to-owl-x.x.x-SNAPSHOT-jar-with-dependencies.jar -mode refset-to-owl -orf owlRefset.txt -output ontology.owl