Ontology Based Profile Matching
Clone or download
Latest commit 8cce7d7 Jul 26, 2018



Ontology Based Profile Matching

Build Status Coverage Status Documentation Status

This will eventually replace sim2 currently distributed as part of owltools

Reference Implementation

Monarch owlsim instance:


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:


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:

  - owlsim-core/src/test/resources/simple-pheno-with-negation.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.


or for some versions of dropwizard:

Example query using default config:


Build with Docker

Run those commands from the root directory (with Docker >= 1.9):

mvn package
docker build -t owlsim-all . # by default contains all the species
docker run -e JAVA_OPTS='-Xmx10g' -p 8080:8080 owlsim-all

To restrict to specific species:

docker build --build-arg species=all -t owlsim-all . # default if no args is provided or not matching any species
docker build --build-arg species=Hs -t owlsim-human .
docker build --build-arg species=Hs,Mm -t owlsim-multi .
# supported species: Hs,Mm,Dr,Dm,Ce