{
    "info": {
        "author": "Martin Larralde",
        "author_email": "martin.larralde@embl.de",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Intended Audience :: Developers",
            "Intended Audience :: Healthcare Industry",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Programming Language :: Python :: 3.8",
            "Programming Language :: Python :: 3.9",
            "Programming Language :: Python :: 3.10",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Software Development :: Libraries :: Python Modules",
            "Typing :: Typed"
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        "description": "# `pronto` [![Stars](https://img.shields.io/github/stars/althonos/pronto.svg?style=social&maxAge=3600&label=Star)](https://github.com/althonos/pronto/stargazers)\n\n*A Python frontend to ontologies.*\n\n[![Actions](https://img.shields.io/github/workflow/status/althonos/pronto/Test/master?logo=github&style=flat-square&maxAge=300)](https://github.com/althonos/pronto/actions)\n[![License](https://img.shields.io/badge/license-MIT-blue.svg?style=flat-square&maxAge=2678400)](https://choosealicense.com/licenses/mit/)\n[![Source](https://img.shields.io/badge/source-GitHub-303030.svg?maxAge=2678400&style=flat-square)](https://github.com/althonos/pronto/)\n[![Docs](https://img.shields.io/readthedocs/pronto?style=flat-square&maxAge=3600)](http://pronto.readthedocs.io/en/stable/?badge=stable)\n[![Coverage](https://img.shields.io/codecov/c/gh/althonos/pronto?style=flat-square&maxAge=3600)](https://codecov.io/gh/althonos/pronto/)\n[![Sanity](https://img.shields.io/codacy/grade/157b5fd24e5648ea80580f28399e79a4.svg?style=flat-square&maxAge=3600)](https://codacy.com/app/althonos/pronto)\n[![PyPI](https://img.shields.io/pypi/v/pronto.svg?style=flat-square&maxAge=3600)](https://pypi.python.org/pypi/pronto)\n[![Bioconda](https://img.shields.io/conda/vn/bioconda/pronto?style=flat-square&maxAge=3600)](https://anaconda.org/bioconda/pronto)\n[![Versions](https://img.shields.io/pypi/pyversions/pronto.svg?style=flat-square&maxAge=3600)](https://pypi.org/project/pronto/#files)\n[![Wheel](https://img.shields.io/pypi/wheel/pronto?style=flat-square&maxAge=3600)](https://pypi.org/project/pronto/#files)\n[![Changelog](https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400&style=flat-square)](https://github.com/althonos/pronto/blob/master/CHANGELOG.md)\n[![GitHub issues](https://img.shields.io/github/issues/althonos/pronto.svg?style=flat-square&maxAge=600)](https://github.com/althonos/pronto/issues)\n[![DOI](https://img.shields.io/badge/doi-10.5281%2Fzenodo.595572-purple?style=flat-square&maxAge=2678400)](https://doi.org/10.5281/zenodo.595572)\n[![Downloads](https://img.shields.io/badge/dynamic/json?style=flat-square&color=303f9f&maxAge=86400&label=downloads&query=%24.total_downloads&url=https%3A%2F%2Fapi.pepy.tech%2Fapi%2Fprojects%2Fpronto)](https://pepy.tech/project/pronto)\n\n## \ud83d\udea9 Table of Contents\n\n- [Overview](#%EF%B8%8F-overview)\n- [Supported Languages](#%EF%B8%8F-supported-languages)\n- [Installing](#-installing)\n- [Examples](#-examples)\n- [API Reference](#-api-reference)\n- [License](#-license)\n\n## \ud83d\uddfa\ufe0f Overview\n\nPronto is a Python library to parse, browse, create, and export\nontologies, supporting several ontology languages and formats. It\nimplement the specifications of the\n[Open Biomedical Ontologies 1.4](http://owlcollab.github.io/oboformat/doc/obo-syntax.html)\nin the form of an safe high-level interface. *If you're only interested in\nparsing OBO or OBO Graphs document, you may wish to consider\n[`fastobo`](https://pypi.org/project/fastobo) instead.*\n\n\n## \ud83c\udff3\ufe0f Supported Languages\n\n- [Open Biomedical Ontologies 1.4](http://owlcollab.github.io/oboformat/doc/GO.format.obo-1_4.html).\n  *Because this format is fairly new, not all OBO ontologies can be parsed at the\n  moment. See the [OBO Foundry roadmap](https://github.com/orgs/fastobo/projects/2)\n  listing the compliant ontologies, and don't hesitate to contact their developers\n  to push adoption forward.*\n- [OBO Graphs](https://github.com/geneontology/obographs) in [JSON](http://json.org/)\n  format. *The format is not yet stabilized to the results may change from file\n  to file.*\n- [Ontology Web Language 2](https://www.w3.org/TR/owl2-overview/)\n  in [RDF/XML format](https://www.w3.org/TR/2012/REC-owl2-mapping-to-rdf-20121211/).\n  *OWL2 ontologies are reverse translated to OBO using the mapping defined in the\n  [OBO 1.4 Semantics](http://owlcollab.github.io/oboformat/doc/obo-syntax.html).*\n\n## \ud83d\udd27 Installing\n\n\nInstalling with `pip` is the easiest:\n```console\n# pip install pronto          # if you have the admin rights\n$ pip install pronto --user   # install it in a user-site directory\n```\n\nThere is also a `conda` recipe in the `bioconda` channel:\n```console\n$ conda install -c bioconda pronto\n```\n\nFinally, a development version can be installed from GitHub\nusing `setuptools`, provided you have the right dependencies\ninstalled already:\n```console\n$ git clone https://github.com/althonos/pronto\n$ cd pronto\n# python setup.py install\n```\n\n## \ud83d\udca1 Examples\n\nIf you're only reading ontologies, you'll only use the `Ontology`\nclass, which is the main entry point.\n\n```python\n>>> from pronto import Ontology\n```\n\nIt can be instantiated from a path to an ontology in one of the supported\nformats, even if the file is compressed:\n```python\n>>> go = Ontology(\"tests/data/go.obo.gz\")\n```\n\nLoading a file from a persistent URL is also supported, although you may also\nwant to use the `Ontology.from_obo_library` method if you're using persistent\nURLs a lot:\n```python\n>>> cl = Ontology(\"http://purl.obolibrary.org/obo/cl.obo\")\n>>> stato = Ontology.from_obo_library(\"stato.owl\")\n```\n\n### \ud83c\udff7\ufe0f Get a term by accession\n\n`Ontology` objects can be used as mappings to access any entity\nthey contain from their identifier in compact form:\n```python\n>>> cl['CL:0002116']\nTerm('CL:0002116', name='B220-low CD38-positive unswitched memory B cell')\n```\n\nNote that when loading an OWL ontology, URIs will be compacted to CURIEs\nwhenever possible:\n\n```python\n>>> aeo = Ontology.from_obo_library(\"aeo.owl\")\n>>> aeo[\"AEO:0000078\"]\nTerm('AEO:0000078', name='lumen of tube')\n```\n\n### \ud83d\udd8a\ufe0f Create a new term from scratch\n\nWe can load an ontology, and edit it locally. Here, we add a new protein class\nto the Protein Ontology.\n```python\n>>> pr = Ontology.from_obo_library(\"pr.obo\")\n>>> brh = ms.create_term(\"PR:XXXXXXXX\")\n>>> brh.name = \"Bacteriorhodopsin\"\n>>> brh.superclasses().add(pr[\"PR:000001094\"])  # is a rhodopsin-like G-protein\n>>> brh.disjoint_from.add(pr[\"PR:000036194\"])   # disjoint from eukaryotic proteins\n```\n\n### \u270f\ufe0f Convert an OWL ontology to OBO format\n\nThe `Ontology.dump` method can be used to serialize an ontology to any of the\nsupported formats (currently OBO and OBO JSON):\n```python\n>>> edam = Ontology(\"http://edamontology.org/EDAM.owl\")\n>>> with open(\"edam.obo\", \"wb\") as f:\n...     edam.dump(f, format=\"obo\")\n```\n\n### \ud83c\udf3f Find ontology terms without subclasses\n\nThe `terms` method of `Ontology` instances can be used to\niterate over all the terms in the ontology (including the\nones that are imported). We can then use the `is_leaf`\nmethod of `Term` objects to check is the term is a leaf in the\nclass inclusion graph.\n\n```python\n>>> ms = Ontology(\"ms.obo\")\n>>> for term in ms.terms():\n...     if term.is_leaf():\n...         print(term.id)\nMS:0000000\nMS:1000001\n...\n```\n\n<!-- ### \ud83e\udd1d Merging several ontologies -->\n\n## \ud83d\udcd6 API Reference\n\nA complete API reference can be found in the\n[online documentation](https://pronto.readthedocs.io/en/latest/api.html), or\ndirectly from the command line using `pydoc`:\n```console\n$ pydoc pronto.Ontology\n```\n\n## \ud83d\udcdc License\n\nThis library is provided under the open-source\n[MIT license](https://choosealicense.com/licenses/mit/).\nPlease cite this library if you are using it in a scientific\ncontext using the following DOI:\n[**10.5281/zenodo.595572**](https://doi.org/10.5281/zenodo.595572)\n\n\n",
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