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/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.
Paths:
- http://localhost:8080/api-docs/
- http://localhost:8080/match/matchers -- lists matchers
or for some versions of dropwizard:
Example query using default config:
http://localhost:8080/api/match/jaccard?id=X:heart-morphology&id=X:brain-morphology
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 -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=human -t owlsim-human