{"id":25359646,"url":"https://github.com/monarch-initiative/phenol","last_synced_at":"2025-10-29T23:31:36.516Z","repository":{"id":38954894,"uuid":"119170338","full_name":"monarch-initiative/phenol","owner":"monarch-initiative","description":"phenol: Phenotype ontology library","archived":false,"fork":false,"pushed_at":"2024-07-10T19:08:32.000Z","size":19359,"stargazers_count":22,"open_issues_count":7,"forks_count":4,"subscribers_count":9,"default_branch":"master","last_synced_at":"2024-07-10T22:56:06.755Z","etag":null,"topics":["genomics","human-phenotype-ontology","java","mammalian-phenotype-ontology","monarchinitiative","ontologies","phenomics","phenotypes"],"latest_commit_sha":null,"homepage":"https://phenol.readthedocs.io/en/latest/","language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/monarch-initiative.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.rst","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2018-01-27T14:14:30.000Z","updated_at":"2024-05-09T10:32:27.000Z","dependencies_parsed_at":"2023-01-23T23:03:18.242Z","dependency_job_id":"e07a2789-7530-4c59-82b9-286487c24da1","html_url":"https://github.com/monarch-initiative/phenol","commit_stats":null,"previous_names":[],"tags_count":28,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/monarch-initiative%2Fphenol","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/monarch-initiative%2Fphenol/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/monarch-initiative%2Fphenol/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/monarch-initiative%2Fphenol/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/monarch-initiative","download_url":"https://codeload.github.com/monarch-initiative/phenol/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":238909492,"owners_count":19550845,"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":["genomics","human-phenotype-ontology","java","mammalian-phenotype-ontology","monarchinitiative","ontologies","phenomics","phenotypes"],"created_at":"2025-02-14T21:07:11.264Z","updated_at":"2025-10-29T23:31:30.050Z","avatar_url":"https://github.com/monarch-initiative.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![CI CD](https://github.com/monarch-initiative/phenol/actions/workflows/maven.yml/badge.svg)](https://github.com/monarch-initiative/phenol/actions/workflows/maven.yml/badge.svg)\n[![Documentation Status](https://readthedocs.org/projects/phenol/badge/?version=latest)](http://phenol.readthedocs.io/en/latest/?badge=latest)\n[![Maven Central](https://maven-badges.herokuapp.com/maven-central/org.monarchinitiative.phenol/phenol/badge.svg)](https://maven-badges.herokuapp.com/maven-central/org.monarchinitiative.phenol/phenol)\n\n# Phenol: Ontology Library for Phenomics and Genomics\n\nA Java library for working with JSON phenotype ontologies including especially\nthe [Human Phenotype Ontology](https://www.human-phenotype-ontology.org) and the\n[Mammalian Phenotype Ontology](http://www.informatics.jax.org/vocab/mp_ontology) and\nassociate phenotype annotation files.\n\n\n## In Brief\n\n- **Language/Platform:** Java \u003e=11\n- **License:** BSD 3-Clause Clear\n- **Authors:**\n    - Sebastian Bauer\n    - Peter N. Robinson\n    - Sebastian Koehler\n    - Max Schubach\n    - Manuel Holtgrewe\n    - HyeongSik Kim\n    - Michael Gargano\n    - Daniel Danis\n    - Jules Jacobsen\n\n- **Availability:**\n    - `phenol-core` for dealing with (biological) ontologies.\n    - `phenol-io` for reading ontologies from JSON files.\n    - `phenol-annotations` for reading computational disease models of the HPO project\n    - `phenol-analysis` several demo apps showing how to use phenol.\n    - `phenol-cli` for performing empirical score distribution computation as a stand-alone program.\n\n## Usage\nWe recommend importing the `phenol` modules that are needed for your application.\n\nFor instance:\n\n```xml\n\u003cdependency\u003e\n    \u003cgroupId\u003eorg.monarchinitiative.phenol\u003c/groupId\u003e\n    \u003cartifactId\u003ephenol-core\u003c/artifactId\u003e\n    \u003cversion\u003e${phenol.version}\u003c/version\u003e\n\u003c/dependency\u003e\n\u003cdependency\u003e\n  \u003cgroupId\u003eorg.monarchinitiative.phenol\u003c/groupId\u003e\n  \u003cartifactId\u003ephenol-io\u003c/artifactId\u003e\n\u003cversion\u003e${phenol.version}\u003c/version\u003e\n\u003c/dependency\u003e\n\u003c!-- ... and other modules --\u003e\n```\n\nwhere `${phenol.version}` corresponds to the desired version, such as `2.1.0`.\n\n## History\nPhenol was initially forked from [ontolib]([https://github.com/Phenomics/ontolib) in February 2018, but was\nextensively refactored and extended. The API of phenol and ontolib are not compatible with each other.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmonarch-initiative%2Fphenol","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmonarch-initiative%2Fphenol","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmonarch-initiative%2Fphenol/lists"}