https://github.com/monarch-initiative/owlsim-v3
Ontology Based Profile Matching
https://github.com/monarch-initiative/owlsim-v3
java monarchinitiative ontology owlsim profile-matching semantic-similarity
Last synced: 6 months ago
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Ontology Based Profile Matching
- Host: GitHub
- URL: https://github.com/monarch-initiative/owlsim-v3
- Owner: monarch-initiative
- Created: 2014-08-25T14:57:36.000Z (about 11 years ago)
- Default Branch: master
- Last Pushed: 2022-05-20T20:53:18.000Z (over 3 years ago)
- Last Synced: 2025-04-14T23:08:06.141Z (6 months ago)
- Topics: java, monarchinitiative, ontology, owlsim, profile-matching, semantic-similarity
- Language: JavaScript
- Size: 6.74 MB
- Stars: 17
- Watchers: 15
- Forks: 5
- Open Issues: 65
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# owlsim-v3
Ontology Based Profile Matching
[](https://travis-ci.org/monarch-initiative/owlsim-v3)
[](https://coveralls.io/github/monarch-initiative/owlsim-v3?branch=master)
[](http://owlsim.readthedocs.org/en/latest/?badge=latest)
## 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](http://localhost:8080/api/docs/).
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:
* http://localhost:8080/api/docs/
* http://localhost:8080/api/match/matchers
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 -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
```