{"id":25073353,"url":"https://github.com/monarch-initiative/owlsim-v3","last_synced_at":"2026-02-27T08:35:01.528Z","repository":{"id":20049121,"uuid":"23317497","full_name":"monarch-initiative/owlsim-v3","owner":"monarch-initiative","description":"Ontology Based Profile Matching","archived":false,"fork":false,"pushed_at":"2022-05-20T20:53:18.000Z","size":7065,"stargazers_count":17,"open_issues_count":65,"forks_count":5,"subscribers_count":15,"default_branch":"master","last_synced_at":"2025-04-14T23:08:06.141Z","etag":null,"topics":["java","monarchinitiative","ontology","owlsim","profile-matching","semantic-similarity"],"latest_commit_sha":null,"homepage":null,"language":"JavaScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/monarch-initiative.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2014-08-25T14:57:36.000Z","updated_at":"2024-09-22T14:55:58.000Z","dependencies_parsed_at":"2022-08-31T13:41:42.268Z","dependency_job_id":null,"html_url":"https://github.com/monarch-initiative/owlsim-v3","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/monarch-initiative%2Fowlsim-v3","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/monarch-initiative%2Fowlsim-v3/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/monarch-initiative%2Fowlsim-v3/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/monarch-initiative%2Fowlsim-v3/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/monarch-initiative","download_url":"https://codeload.github.com/monarch-initiative/owlsim-v3/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248975316,"owners_count":21192209,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["java","monarchinitiative","ontology","owlsim","profile-matching","semantic-similarity"],"created_at":"2025-02-06T23:19:33.908Z","updated_at":"2026-02-27T08:34:56.484Z","avatar_url":"https://github.com/monarch-initiative.png","language":"JavaScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"# owlsim-v3\n\nOntology Based Profile Matching\n\n[![Build Status](https://travis-ci.org/monarch-initiative/owlsim-v3.svg?branch=master)](https://travis-ci.org/monarch-initiative/owlsim-v3)\n[![Coverage Status](https://coveralls.io/repos/monarch-initiative/owlsim-v3/badge.svg?branch=master\u0026service=github)](https://coveralls.io/github/monarch-initiative/owlsim-v3?branch=master)\n[![Documentation Status](https://readthedocs.org/projects/owlsim/badge/?version=latest)](http://owlsim.readthedocs.org/en/latest/?badge=latest)\n\n\n## Documentation\n\nFor now you must do this:\n\n    mvn javadoc:javadoc\n\nAnd then open target/site/apidocs/index.html in a browser\n\n## Running it\n\nTo become more familiar with the code, please run the junit tests in eclipse.\n\nAlso try the performance/integration tests in `owlsim.compute.matcher.perf` - these will need extra files downloaded\nsee the Makefile for details.\n\nTo run the REST services:\n\n    mvn package\n\nproduces a standalone Dropwizard jar:\n\n    owlsim-services/target/owlsim-services-3.0-SNAPSHOT.jar\n\nwhich runs with:\n\n    cd owlsim-services\n    java -jar target/owlsim-services-3.0-SNAPSHOT.jar server src/test/resources/test-configuration.yaml\n\nwhere configuration.yaml describes the desired ontologies:\n\n    ontologyUris:\n      - owlsim-core/src/test/resources/simple-pheno-with-negation.owl\n    ontologyDataUris: []\n\nand then browse the [REST documentation](http://localhost:8080/api/docs/).\n\nIf you prefer to run the REST services from your IDE launch:\n`org.monarchinitiative.owlsim.services.OwlSimServiceApplication` as a main\nclass with `server` and an appropriate YAML configuration as arguments.\n\nPaths:\n\n * http://localhost:8080/api-docs/\n * http://localhost:8080/match/matchers -- lists matchers\n\nor for some versions of dropwizard:\n\n * http://localhost:8080/api/docs/\n * http://localhost:8080/api/match/matchers\n\nExample query using default config:\n\nhttp://localhost:8080/api/match/jaccard?id=X:heart-morphology\u0026id=X:brain-morphology\n\n## Build with Docker\n\nRun those commands from the root directory (with Docker \u003e= 1.9):\n\n```\nmvn package\ndocker build -t owlsim-all . # by default contains all the species\ndocker run -e JAVA_OPTS='-Xmx10g' -p 8080:8080 owlsim-all\n```\n\nTo restrict to specific species:\n\n```\ndocker build --build-arg species=all -t owlsim-all . # default if no args is provided or not matching any species\ndocker build --build-arg species=Hs -t owlsim-human .\ndocker build --build-arg species=Hs,Mm -t owlsim-multi .\n# supported species: Hs,Mm,Dr,Dm,Ce\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmonarch-initiative%2Fowlsim-v3","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmonarch-initiative%2Fowlsim-v3","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmonarch-initiative%2Fowlsim-v3/lists"}