Metadata-Version: 2.1
Name: bioregistry
Version: 0.1.7
Summary: Integrated registry of biological databases and nomenclatures
Home-page: https://github.com/bioregistry/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/bioregistry/bioregistry/releases
Project-URL: Bug Tracker, https://github.com/bioregistry/bioregistry/issues
Description: <p align="center">
          <img src="https://github.com/bioregistry/bioregistry/raw/main/docs/source/logo.png" height="150">
        </p>
        
        <h1 align="center">
            Bioregistry
        </h1>
        
        <p align="center">
            <a href="https://github.com/bioregistry/bioregistry/actions?query=workflow%3ATests">
                <img alt="Tests" src="https://github.com/bioregistry/bioregistry/workflows/Tests/badge.svg" />
            </a>
            <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/bioregistry/bioregistry/blob/main/LICENSE">
                <img alt="PyPI - License" src="https://img.shields.io/pypi/l/bioregistry" />
            </a>
            <a href='https://bioregistry.readthedocs.io/en/latest/?badge=latest'>
                <img src='https://readthedocs.org/projects/bioregistry/badge/?version=latest' alt='Documentation Status' />
            </a>
            <a href="https://zenodo.org/badge/latestdoi/319481281">
                <img src="https://zenodo.org/badge/319481281.svg" alt="DOI">
            </a>
        </p>
        
        <p align="center">
           A community-driven integrative meta-registry of biological databases, ontologies, and other resources.
           <br />More information <a href="https://bioregistry.io/summary/">here</a>.
        </p>
        
        ## ⬇️ Download
        
        The bioregistry database can be downloaded directly
        from [here](https://github.com/bioregistry/bioregistry/blob/main/src/bioregistry/data/bioregistry.json).
        
        The manually curated portions of these data are available under the CC0 1.0 Universal License.
        
        ## 🙏 Contributing
        
        There haven't been any external contributors yet, but if you want to get involved, you can make edits directly to
        the [bioregistry.json](https://github.com/bioregistry/bioregistry/blob/main/src/bioregistry/data/bioregistry.json)
        file through the GitHub interface.
        
        Things that would be helpful:
        
        1. For all entries, add a `["wikidata"]["database"]` entry. Many ontologies and databases don't have a property in
           Wikidata because the process of adding a new property is incredibly cautious. However, anyone can add a database as
           normal Wikidata item with a Q prefix. One example is UniPathway, whose Wikidata database item
           is [Q85719315](https://www.wikidata.org/wiki/Q85719315). If there's no database item on Wikidata, you can even make
           one! Note: don't mix this up with a paper describing the
           resource, [Q35631060](https://www.wikidata.org/wiki/Q35631060). If you see there's a paper, you can add it under
           the `["wikidata"]["paper"]` key.
        2. Adding `["homepage"]` entry for any entry that doesn't have an external reference
        
        A full list of curation to-do's is automatically generated as a web page
        [here](https://bioregistry.github.io/bioregistry/curation/). This page also has a more in-depth tutorial on how to contribute.
        
        ## 🚀 Installation
        
        The Bioregistry can be installed from [PyPI](https://pypi.org/project/bioregistry/) with:
        
        ```bash
        $ pip install bioregistry
        ```
        
        It can be installed in development mode for local curation with:
        
        ```bash
        $ git clone https://github.com/bioregistry/bioregistry.git
        $ cd bioregistry
        $ pip install -e .
        ```
        
        ## 💪 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
        ```
        
        The pattern for an entry in the Bioregistry can be looked up quickly with `get_pattern()` if
        it exists. It prefers the custom curated, then MIRIAM, then Wikidata pattern.
        
        ```python
        import bioregistry
        
        assert '^GO:\\d{7}$' == bioregistry.get_pattern('go')
        ```
        
        Entries in the Bioregistry can be checked for deprecation with the `is_deprecated()` function. MIRIAM and OBO Foundry
        don't often agree - OBO Foundry takes precedence since it seems to be updated more often.
        
        ```python
        import bioregistry
        
        assert bioregistry.is_deprecated('nmr')
        assert not bioregistry.is_deprecated('efo')
        ```
        
        Entries in the Bioregistry can be looked up with the `get()` function.
        
        ```python
        import bioregistry
        
        entry = bioregistry.get('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_registry()
        ```
        
        ## 🕸️ Resolver App
        
        After installing with the `[web]` extras, run the resolver CLI with
        
        ```shell
        $ bioregistry web
        ```
        
        to run a web app that functions like Identifiers.org, but backed by the Bioregistry.
        A public instance of this app is hosted by the [INDRA Lab](https://indralab.github.io) at 
        https://bioregistry.io.
        
        ## ♻️ Update
        
        The database is automatically updated daily thanks to scheduled workflows in GitHub Actions. The workflow's
        configuration can be found [here](https://github.com/bioregistry/bioregistry/blob/main/.github/workflows/update.yml)
        and the last run can be seen [here](https://github.com/bioregistry/bioregistry/actions?query=workflow%3A%22Update+Data%22).
        Further, a [changelog](https://github.com/bioregistry/bioregistry/commits?author=actions-user) can be recapitulated from the
        commits of the GitHub Actions bot.
        
        If you want to manually update the database after installing in development mode, run the following:
        
        ```bash
        $ bioregistry update
        ```
        
        ## ⚖️ License
        
        The code in this repository is licensed under the
        [MIT License](https://github.com/bioregistry/bioregistry/blob/main/LICENSE).
        
        ## 📖 Citation
        
        Hopefully there will be a paper describing this resource on *bioRxiv* sometime in 2021! Until then, you can use the
        Zenodo [BibTeX](https://zenodo.org/record/4404608/export/hx) or [CSL](https://zenodo.org/record/4404608/export/csl).
        
        ## 💰 Funding
        
        The development of the Bioregistry is funded by the DARPA Young Faculty Award W911NF2010255 (PI: Benjamin M. Gyori).
        
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
Provides-Extra: docs
Provides-Extra: charts
Provides-Extra: web
