owlsim-v3

Ontology Based Profile Matching

This will eventually replace sim2 currently distributed as part of owltools

Documentation

For now you must do this:

mvn javadoc:javadoc

And then open target/site/apidocs/index.html in a browser

Running it

To become more familiar with the code, please run the junit tests in eclipse.

Also try the performance/integration tests in owlsim.compute.matcher.perf - these will need extra files downloaded see the Makefile for details.

To run the REST services:

mvn package

produces a standalone Dropwizard jar:

owlsim-services/target/owlsim-services-3.0-SNAPSHOT.jar

which runs with:

cd owlsim-services
java -jar target/owlsim-services-3.0-SNAPSHOT.jar server src/test/resources/test-configuration.yaml

where configuration.yaml describes the desired ontologies:

ontologyUris:
  - owlsim-core/src/test/resources/species.owl
ontologyDataUris: []

and then browse the REST documentation.

If you prefer to run the REST services from your IDE launch: org.monarchinitiative.owlsim.services.OwlSimServiceApplication as a main class with server and an appropriate YAML configuration as arguments.