Metadata-Version: 2.1
Name: biomappings
Version: 0.0.2
Summary: Curated and predicted mappings between biomedical identifiers in different namespaces
Home-page: https://github.com/biomappings/biomappings
License: MIT
Download-URL: https://github.com/biomappings/biomappings/releases
Project-URL: Bug Tracker, https://github.com/biomappings/biomappings/issues
Description: <p align="center">
          <img src="docs/source/logo.png" height="150">
        </p>
        
        <h1 align="center">
          Biomappings
        </h1>
        
        <p align="center">
            <a href="https://github.com/biomappings/biomappings/actions?query=workflow%3A%22Check+mappings%22">
                <img alt="Check mappings" src="https://github.com/biomappings/biomappings/workflows/Check%20mappings/badge.svg" />
            </a>
            <a href="https://pypi.org/project/biomappings">
                <img alt="PyPI" src="https://img.shields.io/pypi/v/biomappings" />
            </a>
            <a href="https://pypi.org/project/biomappings">
                <img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/biomappings" />
            </a>
            <a href="https://github.com/biomappings/biomappings/blob/main/LICENSE">
                <img alt="PyPI - License" src="https://img.shields.io/pypi/l/biomappings" />
            </a>
            <a href="https://zenodo.org/badge/latestdoi/285352907">
                <img src="https://zenodo.org/badge/285352907.svg" alt="DOI">
            </a>
        </p>
        
        Community curated and predicted equivalences and related mappings between named biological entities that are not
        available from primary sources.
        
        Human-curated true mappings are
        in [`src/biomappings/resources/mappings.tsv`](https://github.com/biomappings/biomappings/raw/master/src/biomappings/resources/mappings.tsv)
        , and automatically predicted mappings are
        in [`src/biomappings/resources/predictions.tsv`](https://github.com/biomappings/biomappings/raw/master/src/biomappings/resources/predictions.tsv)
        Human-curated *false* (i.e., incorrect) mappings that are non-trivial are
        in [`src/biomappings/resources/incorrect.tsv`](https://github.com/biomappings/biomappings/raw/master/src/biomappings/resources/incorrect.tsv)
        .
        
        Equivalences and related mappings that are available from the OBO Foundry and other primary sources can be accessed
        through [Inspector Javert's Xref Database](https://zenodo.org/record/3757266)
        on Zenodo which was described in [this blog post](https://cthoyt.com/2020/04/19/inspector-javerts-xref-database.html).
        
        ## ⬇️ Installation
        
        The most recent release can be installed from
        [PyPI](https://pypi.org/project/biomappings/) with:
        
        ```bash
        $ pip install biomappings
        ```
        
        The most recent code and data can be installed directly from GitHub with:
        
        ```bash
        $ pip install git+https://github.com/biomappings/biomappings.git
        ```
        
        To install in development mode, use the following:
        
        ```bash
        $ git clone git+https://github.com/biomappings/biomappings.git
        $ cd biomappings
        $ pip install -e .
        ```
        
        ## 🙏 Contributing Curations
        
        ### GitHub Web Interface
        
        GitHub has an interface for editing files directly in the browser. It will take care of creating a branch for you and
        creating a pull request. After logging into GitHub, click one of the following links to be brought to the editing
        interface:
        
        - [True Mappings](https://github.com/biomappings/biomappings/edit/master/src/biomappings/resources/mappings.tsv)
        - [False Mappings](https://github.com/biomappings/biomappings/edit/master/src/biomappings/resources/mappings.tsv)
        - [Predictions](https://github.com/biomappings/biomappings/edit/master/src/biomappings/resources/mappings.tsv)
        
        This has the caveat that you can only edit one file at a time. It's possible to navigate to your own forked version of
        the repository after, to the correct branch (will not be the default one), then edit other files in the web interface as
        well. However, if you would like to do this, then it's probably better to see the following instructions on contributing
        locally.
        
        ### Locally
        
        1. Fork the repository at https://github.com/biomappings/biomappings, clone locally, and make a new branch
        2. Edit one or more of the resource files (mappings.tsv, incorrect.tsv, predictions.tsv)
        3. Commit to your branch, push, and create a pull request back to the upstream repository.
        
        ## 🌐 Web Curation Interface
        
        Rather than editing files locally, this repository also comes with a web-based curation interface. Install the code in
        development mode with the `web` option (which installs `flask` and `flask-bootstrap`) using:
        
        ```bash
        $ git clone git+https://github.com/biomappings/biomappings.git
        $ cd biomappings
        $ pip install -e .[web]
        ```
        
        The web application can be run with:
        
        ```bash
        $ biomappings web
        ```
        
        It has a button for creating commits, but you'll also have to make pushes from the repository yourself after reviewing
        the changes.
        
        **Note** if you've installed `biomappings` via PyPI, then running the web curation interface doesn't make much sense,
        since it's non-trivial for most users to find the location of the resources within your Python installation's
        `site-packages` folder, and you won't be able to contribute them back.
        
        ## ⚖️ License
        
        Code is licensed under the MIT License. Data is licensed under the CC0 1.0 Universal License.
        
Keywords: biology
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
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
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Provides-Extra: tests
Provides-Extra: web
