https://github.com/monarch-initiative/phenol

phenol: Phenotype ontology library
https://github.com/monarch-initiative/phenol

genomics human-phenotype-ontology java mammalian-phenotype-ontology monarchinitiative ontologies phenomics phenotypes

Last synced: 3 months ago
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phenol: Phenotype ontology library

• Host: GitHub
• URL: https://github.com/monarch-initiative/phenol
• Owner: monarch-initiative
• License: bsd-3-clause
• Created: 2018-01-27T14:14:30.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2024-07-10T19:08:32.000Z (10 months ago)
• Last Synced: 2024-07-10T22:56:06.755Z (10 months ago)
• Topics: genomics, human-phenotype-ontology, java, mammalian-phenotype-ontology, monarchinitiative, ontologies, phenomics, phenotypes
• Language: Java
• Homepage: https://phenol.readthedocs.io/en/latest/
• Size: 18.5 MB
• Stars: 22
• Watchers: 9
• Forks: 4
• Open Issues: 7
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.rst
  • License: LICENSE

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# Phenol: Ontology Library for Phenomics and Genomics

A Java library for working with JSON phenotype ontologies including especially

the [Human Phenotype Ontology](https://www.human-phenotype-ontology.org) and the

[Mammalian Phenotype Ontology](http://www.informatics.jax.org/vocab/mp_ontology) and

associate phenotype annotation files.

## In Brief

- **Language/Platform:** Java >=11

- **License:** BSD 3-Clause Clear

- **Authors:**

    - Sebastian Bauer

    - Peter N. Robinson

    - Sebastian Koehler

    - Max Schubach

    - Manuel Holtgrewe

    - HyeongSik Kim

    - Michael Gargano

    - Daniel Danis

    - Jules Jacobsen

- **Availability:**

    - `phenol-core` for dealing with (biological) ontologies.

    - `phenol-io` for reading ontologies from JSON files.

    - `phenol-annotations` for reading computational disease models of the HPO project

    - `phenol-analysis` several demo apps showing how to use phenol.

    - `phenol-cli` for performing empirical score distribution computation as a stand-alone program.

## Usage

We recommend importing the `phenol` modules that are needed for your application.

For instance:

```xml

    org.monarchinitiative.phenol

    phenol-core

    ${phenol.version}

  org.monarchinitiative.phenol

  phenol-io

${phenol.version}

```

where `${phenol.version}` corresponds to the desired version, such as `2.1.0`.

## History

Phenol was initially forked from [ontolib]([https://github.com/Phenomics/ontolib) in February 2018, but was

extensively refactored and extended. The API of phenol and ontolib are not compatible with each other.