Metadata-Version: 2.1
Name: bioregistry
Version: 0.0.2
Summary: Integrated registry of biological databases and nomenclatures
Home-page: https://github.com/cthoyt/bioregistry
Author: Charles Tapley Hoyt
Author-email: cthoyt@gmail.com
Maintainer: Charles Tapley Hoyt
Maintainer-email: cthoyt@gmail.com
License: MIT
Download-URL: https://github.com/cthoyt/bioregistry/releases
Project-URL: Bug Tracker, https://github.com/cthoyt/bioregistry/issues
Description: <p align="center">
          <img src="docs/source/logo.png" height="150">
        </p>
        
        <h1 align="center">
            Bioregistry
        </h1>
        
        <p align="center">
            <a href="https://pypi.org/project/bioregistry">
                <img alt="PyPI" src="https://img.shields.io/pypi/v/bioregistry" />
            </a>
            <a href="https://pypi.org/project/bioregistry">
                <img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/bioregistry" />
            </a>
            <a href="https://github.com/cthoyt/bioregistry/blob/main/LICENSE">
                <img alt="PyPI - License" src="https://img.shields.io/pypi/l/bioregistry" />
            </a>
            <a href="https://zenodo.org/badge/latestdoi/319481281">
                <img src="https://zenodo.org/badge/319481281.svg" alt="DOI">
            </a>
        </p>
        
        An integrative registry of biological databases, ontologies, and nomenclatures.
        
        ## ⬇️ Download
        
        The bioregistry database can be downloaded directly
        from [here](https://github.com/cthoyt/bioregistry/blob/main/src/bioregistry/data/bioregistry.json)
        
        ## 🚀 Installation
        
        ```bash
        $ pip install git+https://github.com/cthoyt/bioregistry.git
        ```
        
        ## Usage
        
        The Bioregistry can be used to normalize prefixes across MIRIAM and all the (very plentiful) variants that pop up in
        ontologies in OBO Foundry and the OLS with the `normalize_prefix()` function.
        
        ```python
        import bioregistry
        
        # This works for synonym prefixes, like:
        assert 'ncbitaxon' == bioregistry.normalize_prefix('taxonomy')
        
        # This works for common mistaken prefixes, like:
        assert 'chembl.compound' == bioregistry.normalize_prefix('chembl')
        
        # This works for prefixes that are often written many ways, like:
        assert 'eccode' == bioregistry.normalize_prefix('ec-code')
        assert 'eccode' == bioregistry.normalize_prefix('EC_CODE')
        
        # If a prefix is not registered, it gives back `None`
        assert bioregistry.normalize_prefix('not a real key') is None
        ```
        
        Entries in the Bioregistry can be looked up with the `get()` function.
        
        ```python
        import bioregistry
        
        entry = bioregistry.normalize_prefix('taxonomy')
        # there are lots of mysteries to discover in this dictionary!
        ```
        
        The full Bioregistry can be read in a Python project using:
        
        ```python
        import bioregistry
        
        registry = bioregistry.read_bioregistry()
        ```
        
        ## Update
        
        ```bash
        $ bioregistry update
        ```
        
Keywords: databases,biological databases,biomedical databases
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3 :: Only
Requires-Python: >=3.6
Description-Content-Type: text/markdown
