<p align="center">
<img src="https://github.com/biopragmatics/biomappings/raw/master/docs/source/logo.png" height="150">
</p>
<h1 align="center">
Biomappings
</h1>
<p align="center">
<a href="https://github.com/biopragmatics/biomappings/actions?query=workflow%3A%22Check+mappings%22">
<img alt="Check mappings" src="https://github.com/biopragmatics/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/biopragmatics/biomappings/blob/main/LICENSE">
<img alt="PyPI - License" src="https://img.shields.io/pypi/l/biomappings" />
</a>
<a href='https://biomappings.readthedocs.io/en/latest/?badge=latest'>
<img src='https://readthedocs.org/projects/biomappings/badge/?version=latest' alt='Documentation Status' />
</a>
<a href="https://zenodo.org/badge/latestdoi/285352907">
<img src="https://zenodo.org/badge/285352907.svg" alt="DOI">
</a>
<a href="https://github.com/psf/black">
<img src="https://img.shields.io/badge/code%20style-black-000000.svg" alt="Code style: black">
</a>
<a href="https://github.com/biopragmatics/bioregistry">
<img alt="Powered by the Bioregistry" src="https://img.shields.io/static/v1?label=Powered%20by&message=Bioregistry&color=BA274A&style=flat&logo=image/png;base64,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" />
</a>
<a href="https://github.com/biopragmatics/biomappings/blob/master/docs/CODE_OF_CONDUCT.md">
<img alt="Contributor Covenant" src="https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg" />
</a>
</p>
Biomappings is a repository of community curated and predicted equivalences and
related mappings between named biological entities that are not available from
primary sources. It's also a place where anyone can contribute curations
of predicted mappings or their own novel mappings. Ultimately, we hope that
primary resources will integrate these mappings and distribute them themselves.
Mappings are stored in a simple TSV file that looks like this:
## 💾 Data
The data are available through the following four files on
the [biopragmatics/biomappings](https://github.com/biopragmatics/biomappings) GitHub repository.
| Curated | Description | Link |
| ------- |--------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------|
| Yes | Human-curated true mappings | [`src/biomappings/resources/mappings.tsv`](https://github.com/biopragmatics/biomappings/raw/master/src/biomappings/resources/mappings.tsv) |
| Yes | Human-curated *non-trivial* false (i.e., incorrect) mappings | [`src/biomappings/resources/incorrect.tsv`](https://github.com/biopragmatics/biomappings/raw/master/src/biomappings/resources/incorrect.tsv) |
| Yes | Mappings that have been checked but not yet decided | [`src/biomappings/resources/unsure.tsv`](https://github.com/biopragmatics/biomappings/raw/master/src/biomappings/resources/unsure.tsv) |
| No | Automatically predicted mappings | [`src/biomappings/resources/predictions.tsv`](https://github.com/biopragmatics/biomappings/raw/master/src/biomappings/resources/predictions.tsv) |
The primary and derived data in this repository are both available under
the [CC0 1.0 Universal License](https://github.com/biopragmatics/biomappings/blob/master/LICENSE).
Predictions are generated by scripts in the [`scripts/`](scripts) folder. Each
uses the utilities from the `biomappings.resources` module to programmatically
interact with the mappings files, e.g., to add predictions.
### 🥒 Derived
The mappings are distributed in the [Simple Standard for Sharing Ontology Mappings
(SSSOM)](https://github.com/mapping-commons/sssom) format
([here](https://github.com/biopragmatics/biomappings/blob/master/docs/_data/sssom))
and can be referenced by PURL such as https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv.
The positive mappings are also available as a network through
[NDEx](https://www.ndexbio.org/#/network/402d1fd6-49d6-11eb-9e72-0ac135e8bacf).
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).
### 📊 Summary
Summary statistics of the manually curated mappings and predicted mappings
are automatically generated nightly and deployed as a website with GitHub
Actions to https://biopragmatics.github.io/biomappings.
[](https://biopragmatics.github.io/biomappings)
## 🙏 Contributing
We welcome contributions in the form of curations to any of the four primary TSV
files in this repository via a pull request to the main Biomappings repository
at https://github.com/biopragmatics/biomappings.
Predicted mappings can be curated by moving a row in the `predictions.tsv` file
into either the positive mappings file (`mappings.tsv`), negative mappings file
(`incorrect.tsv`), or the unsure mappings file (`unsure.tsv`). Additionally,
the `confidence` column should be removed, a `type` column should be added with
the value `manually_reviewed`, and the `source` column should be changed from
the prediction script's URI to your ORCiD identifier written as a CURIE
(e.g., `orcid:0000-0003-1307-2508`).
Novel mappings can be curated by adding a full row to the positive mappings
file (`mappings.tsv`) following the format of the previous lines.
While Biomappings is generally able to use any predicate written as a [compact URI (CURIE)](http://www.w3.org/TR/curie),
it's preferred to use predicates from the [Simple Knowledge Organization System (SKOS)](https://www.w3.org/2004/02/skos/)
to denote hierarchical relationships. The three most common predicates that are
useful for curating mappings are:
| Predicate | Description |
|---------------------------------------------------------------------------------------|-------------------------------------------------|
| [`skos:exactMatch`](https://www.w3.org/2009/08/skos-reference/skos.html#exactMatch) | The two terms can be used interchangeably |
| [`skos:broadMatch`](https://www.w3.org/2009/08/skos-reference/skos.html#broadMatch) | The object term is a super-class of the subject |
| [`skos:narrowMatch`](https://www.w3.org/2009/08/skos-reference/skos.html#narrowMatch) | The object term is a sub-class of the subject |
### Online via 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/biopragmatics/biomappings/edit/master/src/biomappings/resources/mappings.tsv)
- [False Mappings](https://github.com/biopragmatics/biomappings/edit/master/src/biomappings/resources/incorrect.tsv)
- [Unsure Mappings](https://github.com/biopragmatics/biomappings/edit/master/src/biomappings/resources/unsure.tsv)
- [Predictions](https://github.com/biopragmatics/biomappings/edit/master/src/biomappings/resources/predictions.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.
### ✍️ Local via a Text Editor
1. Fork the repository at https://github.com/biopragmatics/biomappings, clone locally, and make a new branch (see below)
2. Edit one or more of the resource files (`mappings.tsv`, `incorrect.tsv`, `unsure.tsv`, `predictions.tsv`)
3. Commit to your branch, push, and create a pull request back to the upstream repository.
### 🌐 Local via the 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/biopragmatics/biomappings.git
$ cd biomappings
$ git checkout -b your-branch-name
$ pip install -e .[web]
```
The web application can be run with:
```bash
$ biomappings web
```
It can be accessed by navigating to http://localhost:5000/ in your browser.
After you do some curations, the web application takes care of interacting with
the git repository from which you installed `biomappings` via the "commit and
push" button.
**Note** if you've installed `biomappings` via [PyPI](https://pypi.org/project/biomappings/),
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.
### Curation Attribution
There are three places where curators of Biomappings are credited:
1. ORCiD identifiers of curators are stored in each mapping
2. The [summary website](https://biopragmatics.github.io/biomappings) groups
and counts contributions curator
3. A curation leaderboard is automatically uploaded to [APICURON](https://apicuron.org/database?resource_uri=https:%2F%2Fbiomappings.github.io%2Fbiomappings%2F).
## ⬇️ 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/biopragmatics/biomappings.git
```
To install in development mode and create a new branch, use the following:
```bash
$ git clone git+https://github.com/biopragmatics/biomappings.git
$ cd biomappings
$ pip install -e .
```
## 💪 Usage
There are three main functions exposed from `biomappings`. Each loads a list of dictionaries with the mappings in each.
```python
import biomappings
true_mappings = biomappings.load_mappings()
false_mappings = biomappings.load_false_mappings()
predictions = biomappings.load_predictions()
```
Alternatively, you can use the above links to the TSVs on GitHub in with the library or programming language of your
choice.
The data can also be loaded as [networkx](https://networkx.org/) graphs with the following functions:
```python
import biomappings
true_graph = biomappings.get_true_graph()
false_graph = biomappings.get_false_graph()
predictions_graph = biomappings.get_predictions_graph()
```
Full documentation can be found on [ReadTheDocs](https://biomappings.readthedocs.io).
## 👋 Attribution
### ⚖️ License
Code is licensed under the MIT License. Data are licensed under the CC0 License.
### 📖 Citation
> [Prediction and Curation of Missing Biomedical Identifier Mappings with Biomappings](https://doi.org/10.1093/bioinformatics/btad130)
> <br />Hoyt, C. T., Hoyt, A. L., and Gyori, B. M. (2022)
> <br />*Bioinformatics*, btad130.
```bibtex
@article{Hoyt2022,
title = {{Prediction and Curation of Missing Biomedical Identifier Mappings with Biomappings}},
author = {Hoyt, Charles Tapley and Hoyt, Amelia L and Gyori, Benjamin M},
journal = {Bioinformatics},
year = {2023},
month = {03},
issn = {1367-4811},
doi = {10.1093/bioinformatics/btad130},
url = {https://doi.org/10.1093/bioinformatics/btad130},
note = {btad130},
eprint = {https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad130/49521613/btad130.pdf},
}
```
### 🎁 Support
Biomappings was developed by the [INDRA Lab](https://indralab.github.io), a part of the
[Laboratory of Systems Pharmacology](https://hits.harvard.edu/the-program/laboratory-of-systems-pharmacology/about/)
and the [Harvard Program in Therapeutic Science (HiTS)](https://hits.harvard.edu)
at [Harvard Medical School](https://hms.harvard.edu/).
### 💰 Funding
The development of the Bioregistry is funded by the DARPA Young Faculty Award W911NF2010255 (PI:
Benjamin M. Gyori).
### 🍪 Cookiecutter
This package was created with [@audreyfeldroy](https://github.com/audreyfeldroy)'s
[cookiecutter](https://github.com/cookiecutter/cookiecutter) package using [@cthoyt](https://github.com/cthoyt)'s
[cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack) template.
## 🛠️ For Developers
<details>
<summary>See developer instructions</summary>
The final section of the README is for if you want to get involved by making a code contribution.
### Development Installation
To install in development mode, use the following:
```bash
$ git clone git+https://github.com/biopragmatics/biomappings.git
$ cd biomappings
$ pip install -e .
```
### 🥼 Testing
After cloning the repository and installing `tox` with `pip install tox`, the unit tests in the `tests/` folder can be
run reproducibly with:
```shell
$ tox
```
Additionally, these tests are automatically re-run with each commit in a [GitHub Action](https://github.com/biopragmatics/biomappings/actions?query=workflow%3ATests).
### 📖 Building the Documentation
The documentation can be built locally using the following:
```shell
$ git clone git+https://github.com/biopragmatics/biomappings.git
$ cd biomappings
$ tox -e docs
$ open docs/build/html/index.html
```
The documentation automatically installs the package as well as the `docs`
extra specified in the [`setup.cfg`](setup.cfg). `sphinx` plugins
like `texext` can be added there. Additionally, they need to be added to the
`extensions` list in [`docs/source/conf.py`](docs/source/conf.py).
### 📦 Making a Release
After installing the package in development mode and installing
`tox` with `pip install tox`, the commands for making a new release are contained within the `finish` environment
in `tox.ini`. Run the following from the shell:
```shell
$ tox -e finish
```
This script does the following:
1. Uses [Bump2Version](https://github.com/c4urself/bump2version) to switch the version number in the `setup.cfg`,
`src/biomappings/version.py`, and [`docs/source/conf.py`](docs/source/conf.py) to not have the `-dev` suffix
2. Packages the code in both a tar archive and a wheel using [`build`](https://github.com/pypa/build)
3. Uploads to PyPI using [`twine`](https://github.com/pypa/twine). Be sure to have a `.pypirc` file configured to avoid the need for manual input at this
step
4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can
use `tox -e bumpversion minor` after.
</details>
Raw data
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"maintainer": "Charles Tapley Hoyt",
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"maintainer_email": "cthoyt@gmail.com",
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"author": "Charles Tapley Hoyt",
"author_email": "cthoyt@gmail.com",
"download_url": "https://files.pythonhosted.org/packages/d7/51/1ba54b40221a985f2038df58f57d8176d2dbfa08533c1f854b0e24c19fa2/biomappings-0.3.7.tar.gz",
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"description": "<p align=\"center\">\n <img src=\"https://github.com/biopragmatics/biomappings/raw/master/docs/source/logo.png\" height=\"150\">\n</p>\n\n<h1 align=\"center\">\n Biomappings\n</h1>\n\n<p align=\"center\">\n <a href=\"https://github.com/biopragmatics/biomappings/actions?query=workflow%3A%22Check+mappings%22\">\n <img alt=\"Check mappings\" src=\"https://github.com/biopragmatics/biomappings/workflows/Check%20mappings/badge.svg\" />\n </a>\n <a href=\"https://pypi.org/project/biomappings\">\n <img alt=\"PyPI\" src=\"https://img.shields.io/pypi/v/biomappings\" />\n </a>\n <a href=\"https://pypi.org/project/biomappings\">\n <img alt=\"PyPI - Python Version\" src=\"https://img.shields.io/pypi/pyversions/biomappings\" />\n </a>\n <a href=\"https://github.com/biopragmatics/biomappings/blob/main/LICENSE\">\n <img alt=\"PyPI - License\" src=\"https://img.shields.io/pypi/l/biomappings\" />\n </a>\n <a href='https://biomappings.readthedocs.io/en/latest/?badge=latest'>\n <img src='https://readthedocs.org/projects/biomappings/badge/?version=latest' alt='Documentation Status' />\n </a>\n <a href=\"https://zenodo.org/badge/latestdoi/285352907\">\n <img src=\"https://zenodo.org/badge/285352907.svg\" alt=\"DOI\">\n </a>\n <a href=\"https://github.com/psf/black\">\n <img src=\"https://img.shields.io/badge/code%20style-black-000000.svg\" alt=\"Code style: black\">\n </a>\n <a href=\"https://github.com/biopragmatics/bioregistry\">\n <img alt=\"Powered by the Bioregistry\" src=\"https://img.shields.io/static/v1?label=Powered%20by&message=Bioregistry&color=BA274A&style=flat&logo=image/png;base64,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\" />\n </a>\n <a href=\"https://github.com/biopragmatics/biomappings/blob/master/docs/CODE_OF_CONDUCT.md\">\n <img alt=\"Contributor Covenant\" src=\"https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg\" />\n </a>\n</p>\n\nBiomappings is a repository of community curated and predicted equivalences and\nrelated mappings between named biological entities that are not available from\nprimary sources. It's also a place where anyone can contribute curations\nof predicted mappings or their own novel mappings. Ultimately, we hope that\nprimary resources will integrate these mappings and distribute them themselves.\n\nMappings are stored in a simple TSV file that looks like this:\n\n\n\n## \ud83d\udcbe Data\n\nThe data are available through the following four files on\nthe [biopragmatics/biomappings](https://github.com/biopragmatics/biomappings) GitHub repository.\n\n| Curated | Description | Link |\n| ------- |--------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------|\n| Yes | Human-curated true mappings | [`src/biomappings/resources/mappings.tsv`](https://github.com/biopragmatics/biomappings/raw/master/src/biomappings/resources/mappings.tsv) |\n| Yes | Human-curated *non-trivial* false (i.e., incorrect) mappings | [`src/biomappings/resources/incorrect.tsv`](https://github.com/biopragmatics/biomappings/raw/master/src/biomappings/resources/incorrect.tsv) |\n| Yes | Mappings that have been checked but not yet decided | [`src/biomappings/resources/unsure.tsv`](https://github.com/biopragmatics/biomappings/raw/master/src/biomappings/resources/unsure.tsv) |\n| No | Automatically predicted mappings | [`src/biomappings/resources/predictions.tsv`](https://github.com/biopragmatics/biomappings/raw/master/src/biomappings/resources/predictions.tsv) |\n\nThe primary and derived data in this repository are both available under\nthe [CC0 1.0 Universal License](https://github.com/biopragmatics/biomappings/blob/master/LICENSE).\n\nPredictions are generated by scripts in the [`scripts/`](scripts) folder. Each\nuses the utilities from the `biomappings.resources` module to programmatically\ninteract with the mappings files, e.g., to add predictions.\n\n### \ud83e\udd52 Derived\n\nThe mappings are distributed in the [Simple Standard for Sharing Ontology Mappings\n(SSSOM)](https://github.com/mapping-commons/sssom) format\n([here](https://github.com/biopragmatics/biomappings/blob/master/docs/_data/sssom))\nand can be referenced by PURL such as https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv.\nThe positive mappings are also available as a network through\n[NDEx](https://www.ndexbio.org/#/network/402d1fd6-49d6-11eb-9e72-0ac135e8bacf).\n\nEquivalences and related mappings that are available from the OBO Foundry and other primary sources can be accessed\nthrough [Inspector Javert's Xref Database](https://zenodo.org/record/3757266)\non Zenodo which was described in [this blog post](https://cthoyt.com/2020/04/19/inspector-javerts-xref-database.html).\n\n### \ud83d\udcca Summary\n\nSummary statistics of the manually curated mappings and predicted mappings\nare automatically generated nightly and deployed as a website with GitHub\nActions to https://biopragmatics.github.io/biomappings.\n\n[](https://biopragmatics.github.io/biomappings)\n\n## \ud83d\ude4f Contributing\n\nWe welcome contributions in the form of curations to any of the four primary TSV\nfiles in this repository via a pull request to the main Biomappings repository\nat https://github.com/biopragmatics/biomappings.\n\nPredicted mappings can be curated by moving a row in the `predictions.tsv` file\ninto either the positive mappings file (`mappings.tsv`), negative mappings file\n(`incorrect.tsv`), or the unsure mappings file (`unsure.tsv`). Additionally,\nthe `confidence` column should be removed, a `type` column should be added with\nthe value `manually_reviewed`, and the `source` column should be changed from\nthe prediction script's URI to your ORCiD identifier written as a CURIE\n(e.g., `orcid:0000-0003-1307-2508`).\n\nNovel mappings can be curated by adding a full row to the positive mappings\nfile (`mappings.tsv`) following the format of the previous lines.\n\nWhile Biomappings is generally able to use any predicate written as a [compact URI (CURIE)](http://www.w3.org/TR/curie),\nit's preferred to use predicates from the [Simple Knowledge Organization System (SKOS)](https://www.w3.org/2004/02/skos/)\nto denote hierarchical relationships. The three most common predicates that are\nuseful for curating mappings are:\n\n| Predicate | Description |\n|---------------------------------------------------------------------------------------|-------------------------------------------------|\n| [`skos:exactMatch`](https://www.w3.org/2009/08/skos-reference/skos.html#exactMatch) | The two terms can be used interchangeably |\n| [`skos:broadMatch`](https://www.w3.org/2009/08/skos-reference/skos.html#broadMatch) | The object term is a super-class of the subject |\n| [`skos:narrowMatch`](https://www.w3.org/2009/08/skos-reference/skos.html#narrowMatch) | The object term is a sub-class of the subject |\n\n### Online via GitHub Web Interface\n\nGitHub has an interface for editing files directly in the browser. It will take care of creating a branch for you and\ncreating a pull request. After logging into GitHub, click one of the following links to be brought to the editing\ninterface:\n\n- [True Mappings](https://github.com/biopragmatics/biomappings/edit/master/src/biomappings/resources/mappings.tsv)\n- [False Mappings](https://github.com/biopragmatics/biomappings/edit/master/src/biomappings/resources/incorrect.tsv)\n- [Unsure Mappings](https://github.com/biopragmatics/biomappings/edit/master/src/biomappings/resources/unsure.tsv)\n- [Predictions](https://github.com/biopragmatics/biomappings/edit/master/src/biomappings/resources/predictions.tsv)\n\nThis has the caveat that you can only edit one file at a time. It's possible to navigate to your own forked version of\nthe repository after, to the correct branch (will not be the default one), then edit other files in the web interface as\nwell. However, if you would like to do this, then it's probably better to see the following instructions on contributing\nlocally.\n\n### \u270d\ufe0f Local via a Text Editor\n\n1. Fork the repository at https://github.com/biopragmatics/biomappings, clone locally, and make a new branch (see below)\n2. Edit one or more of the resource files (`mappings.tsv`, `incorrect.tsv`, `unsure.tsv`, `predictions.tsv`)\n3. Commit to your branch, push, and create a pull request back to the upstream repository.\n\n### \ud83c\udf10 Local via the Web Curation Interface\n\nRather than editing files locally, this repository also comes with a web-based curation interface. Install the code in\ndevelopment mode with the `web` option (which installs `flask` and `flask-bootstrap`) using:\n\n```bash\n$ git clone git+https://github.com/biopragmatics/biomappings.git\n$ cd biomappings\n$ git checkout -b your-branch-name\n$ pip install -e .[web]\n```\n\nThe web application can be run with:\n\n```bash\n$ biomappings web\n```\n\nIt can be accessed by navigating to http://localhost:5000/ in your browser.\nAfter you do some curations, the web application takes care of interacting with\nthe git repository from which you installed `biomappings` via the \"commit and\npush\" button.\n\n**Note** if you've installed `biomappings` via [PyPI](https://pypi.org/project/biomappings/),\nthen running the web curation interface doesn't make much sense,\nsince it's non-trivial for most users to find the location of the resources within your Python installation's\n`site-packages` folder, and you won't be able to contribute them back.\n\n### Curation Attribution\n\nThere are three places where curators of Biomappings are credited:\n\n1. ORCiD identifiers of curators are stored in each mapping\n2. The [summary website](https://biopragmatics.github.io/biomappings) groups\n and counts contributions curator\n3. A curation leaderboard is automatically uploaded to [APICURON](https://apicuron.org/database?resource_uri=https:%2F%2Fbiomappings.github.io%2Fbiomappings%2F).\n\n## \u2b07\ufe0f Installation\n\nThe most recent release can be installed from\n[PyPI](https://pypi.org/project/biomappings/) with:\n\n```bash\n$ pip install biomappings\n```\n\nThe most recent code and data can be installed directly from GitHub with:\n\n```bash\n$ pip install git+https://github.com/biopragmatics/biomappings.git\n```\n\nTo install in development mode and create a new branch, use the following:\n\n```bash\n$ git clone git+https://github.com/biopragmatics/biomappings.git\n$ cd biomappings\n$ pip install -e .\n```\n\n## \ud83d\udcaa Usage\n\nThere are three main functions exposed from `biomappings`. Each loads a list of dictionaries with the mappings in each.\n\n```python\nimport biomappings\n\ntrue_mappings = biomappings.load_mappings()\n\nfalse_mappings = biomappings.load_false_mappings()\n\npredictions = biomappings.load_predictions()\n```\n\nAlternatively, you can use the above links to the TSVs on GitHub in with the library or programming language of your\nchoice.\n\nThe data can also be loaded as [networkx](https://networkx.org/) graphs with the following functions:\n\n```python\nimport biomappings\n\ntrue_graph = biomappings.get_true_graph()\n\nfalse_graph = biomappings.get_false_graph()\n\npredictions_graph = biomappings.get_predictions_graph()\n```\n\nFull documentation can be found on [ReadTheDocs](https://biomappings.readthedocs.io).\n\n## \ud83d\udc4b Attribution\n\n### \u2696\ufe0f License\n\nCode is licensed under the MIT License. Data are licensed under the CC0 License.\n\n### \ud83d\udcd6 Citation\n\n> [Prediction and Curation of Missing Biomedical Identifier Mappings with Biomappings](https://doi.org/10.1093/bioinformatics/btad130)\n> <br />Hoyt, C. T., Hoyt, A. L., and Gyori, B. M. (2022)\n> <br />*Bioinformatics*, btad130. \n\n```bibtex\n@article{Hoyt2022,\n title = {{Prediction and Curation of Missing Biomedical Identifier Mappings with Biomappings}},\n author = {Hoyt, Charles Tapley and Hoyt, Amelia L and Gyori, Benjamin M},\n journal = {Bioinformatics},\n year = {2023},\n month = {03},\n issn = {1367-4811},\n doi = {10.1093/bioinformatics/btad130},\n url = {https://doi.org/10.1093/bioinformatics/btad130},\n note = {btad130},\n eprint = {https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad130/49521613/btad130.pdf},\n}\n```\n\n### \ud83c\udf81 Support\n\nBiomappings was developed by the [INDRA Lab](https://indralab.github.io), a part of the\n[Laboratory of Systems Pharmacology](https://hits.harvard.edu/the-program/laboratory-of-systems-pharmacology/about/)\nand the [Harvard Program in Therapeutic Science (HiTS)](https://hits.harvard.edu)\nat [Harvard Medical School](https://hms.harvard.edu/).\n\n### \ud83d\udcb0 Funding\n\nThe development of the Bioregistry is funded by the DARPA Young Faculty Award W911NF2010255 (PI:\nBenjamin M. Gyori).\n\n### \ud83c\udf6a Cookiecutter\n\nThis package was created with [@audreyfeldroy](https://github.com/audreyfeldroy)'s\n[cookiecutter](https://github.com/cookiecutter/cookiecutter) package using [@cthoyt](https://github.com/cthoyt)'s\n[cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack) template.\n\n## \ud83d\udee0\ufe0f For Developers\n\n<details>\n <summary>See developer instructions</summary>\n\n\nThe final section of the README is for if you want to get involved by making a code contribution.\n\n### Development Installation\n\nTo install in development mode, use the following:\n\n```bash\n$ git clone git+https://github.com/biopragmatics/biomappings.git\n$ cd biomappings\n$ pip install -e .\n```\n\n### \ud83e\udd7c Testing\n\nAfter cloning the repository and installing `tox` with `pip install tox`, the unit tests in the `tests/` folder can be\nrun reproducibly with:\n\n```shell\n$ tox\n```\n\nAdditionally, these tests are automatically re-run with each commit in a [GitHub Action](https://github.com/biopragmatics/biomappings/actions?query=workflow%3ATests).\n\n### \ud83d\udcd6 Building the Documentation\n\nThe documentation can be built locally using the following:\n\n```shell\n$ git clone git+https://github.com/biopragmatics/biomappings.git\n$ cd biomappings\n$ tox -e docs\n$ open docs/build/html/index.html\n``` \n\nThe documentation automatically installs the package as well as the `docs`\nextra specified in the [`setup.cfg`](setup.cfg). `sphinx` plugins\nlike `texext` can be added there. Additionally, they need to be added to the\n`extensions` list in [`docs/source/conf.py`](docs/source/conf.py).\n\n### \ud83d\udce6 Making a Release\n\nAfter installing the package in development mode and installing\n`tox` with `pip install tox`, the commands for making a new release are contained within the `finish` environment\nin `tox.ini`. Run the following from the shell:\n\n```shell\n$ tox -e finish\n```\n\nThis script does the following:\n\n1. Uses [Bump2Version](https://github.com/c4urself/bump2version) to switch the version number in the `setup.cfg`,\n `src/biomappings/version.py`, and [`docs/source/conf.py`](docs/source/conf.py) to not have the `-dev` suffix\n2. Packages the code in both a tar archive and a wheel using [`build`](https://github.com/pypa/build)\n3. Uploads to PyPI using [`twine`](https://github.com/pypa/twine). Be sure to have a `.pypirc` file configured to avoid the need for manual input at this\n step\n4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped.\n5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can\n use `tox -e bumpversion minor` after.\n</details>\n",
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