{"id":21731110,"url":"https://github.com/biopragmatics/biomappings","last_synced_at":"2026-04-12T09:58:59.325Z","repository":{"id":39492064,"uuid":"285352907","full_name":"biopragmatics/biomappings","owner":"biopragmatics","description":"πŸ—ΊοΈ Community curated and predicted equivalences and related mappings between named biological entities that are not available from primary sources.","archived":false,"fork":false,"pushed_at":"2025-03-24T10:36:08.000Z","size":89031,"stargazers_count":52,"open_issues_count":36,"forks_count":14,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-03-29T12:03:51.614Z","etag":null,"topics":["biocuration","biopragmatics","bioregistry","mappings","ontology","semantics"],"latest_commit_sha":null,"homepage":"https://biopragmatics.github.io/biomappings/","language":"Jupyter 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Notebook","funding_links":["https://github.com/sponsors/cthoyt"],"categories":[],"sub_categories":[],"readme":"\u003cp align=\"center\"\u003e\n \u003cimg src=\"https://github.com/biopragmatics/biomappings/raw/master/docs/source/logo.png\" height=\"150\"\u003e\n\u003c/p\u003e\n\n\u003ch1 align=\"center\"\u003e\n Biomappings\n\u003c/h1\u003e\n\n\u003cp align=\"center\"\u003e\n \u003ca href=\"https://github.com/biopragmatics/biomappings/actions/workflows/tests.yml\"\u003e\n \u003cimg alt=\"Tests\" src=\"https://github.com/biopragmatics/biomappings/actions/workflows/tests.yml/badge.svg\" /\u003e\u003c/a\u003e\n \u003ca href=\"https://pypi.org/project/biomappings\"\u003e\n \u003cimg alt=\"PyPI\" src=\"https://img.shields.io/pypi/v/biomappings\" /\u003e\u003c/a\u003e\n \u003ca href=\"https://pypi.org/project/biomappings\"\u003e\n \u003cimg alt=\"PyPI - Python Version\" src=\"https://img.shields.io/pypi/pyversions/biomappings\" /\u003e\u003c/a\u003e\n \u003ca 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src=\"https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json\" alt=\"Ruff\" style=\"max-width:100%;\"\u003e\u003c/a\u003e\n \u003ca href=\"https://github.com/biopragmatics/bioregistry\"\u003e\n \u003cimg alt=\"Powered by the Bioregistry\" 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/\u003e\u003c/a\u003e\n \u003ca href=\"https://github.com/biopragmatics/biomappings/blob/main/.github/CODE_OF_CONDUCT.md\"\u003e\n \u003cimg src=\"https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg\" alt=\"Contributor Covenant\"/\u003e\u003c/a\u003e\n \u003ca href=\"https://zenodo.org/badge/latestdoi/285352907\"\u003e\n \u003cimg src=\"https://zenodo.org/badge/285352907.svg\" alt=\"DOI\"\u003e\u003c/a\u003e\n\u003c/p\u003e\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![](docs/img/mappings_screenshot.png)\n\n## πŸ’Ύ 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### πŸ₯’ 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### πŸ“Š 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[![Summary statistics](docs/img/summary.svg)](https://biopragmatics.github.io/biomappings)\n\n## πŸ™ 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### ✍️ 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### 🌐 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```console\n$ git clone https://github.com/biopragmatics/biomappings.git\n$ cd biomappings\n$ git checkout -b your-branch-name\n$ UV_PREVIEW=1 python3 -m pip install -e .[web]\n```\n\nThe web application can be run with:\n\n```console\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## πŸš€ Installation\n\nThe most recent release can be installed from\n[PyPI](https://pypi.org/project/biomappings/) with:\n\n```console\npython3 -m pip install biomappings\n```\n\nThe most recent code and data can be installed directly from GitHub with:\n\n```console\npython3 -m 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```console\n$ git clone https://github.com/biopragmatics/biomappings.git\n$ cd biomappings\n$ UV_PREVIEW=1 python3 -m pip install -e .\n```\n\n## πŸ’ͺ 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## πŸ‘‹ Attribution\n\n### βš–οΈ License\n\nThe code in this package is licensed under the MIT License. Data are licensed under the CC0 License.\n\n### πŸ“– Citation\n\n\u003e [Prediction and Curation of Missing Biomedical Identifier Mappings with Biomappings](https://doi.org/10.1093/bioinformatics/btad130)\n\u003e \u003cbr /\u003eHoyt, C. T., Hoyt, A. L., and Gyori, B. M. (2022)\n\u003e \u003cbr /\u003e*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### 🎁 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### πŸ’° Funding\n\nThe development of the Bioregistry is funded by the DARPA Young Faculty Award W911NF2010255 (PI:\nBenjamin M. Gyori).\n\n### πŸͺ 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## πŸ› οΈ For Developers\n\n\u003cdetails\u003e\n \u003csummary\u003eSee developer instructions\u003c/summary\u003e\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```console\n$ git clone git+https://github.com/biopragmatics/biomappings.git\n$ cd biomappings\n$ uv --preview pip install -e .\n```\n\nAlternatively, install using legacy pip with `UV_PREVIEW` mode enabled\nuntil the uv build backend becomes a stable feature:\n\n```console\n$ UV_PREVIEW=1 python3 -m pip install -e .\n```\n\n### Updating Package Boilerplate\n\nThis project uses `cruft` to keep boilerplate (i.e., configuration, contribution guidelines, documentation\nconfiguration)\nup-to-date with the upstream cookiecutter package. Update with the following:\n\n```console\npython3 -m pip install cruft\ncruft update\n```\n\nMore info on Cruft's update command is\navailable [here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project).\n\n### πŸ₯Ό Testing\n\nAfter cloning the repository and installing `tox` with\n`python3 -m pip install tox tox-uv`,\nthe unit tests in the `tests/` folder can be run reproducibly with:\n\n```console\ntox -e py\n```\n\nAdditionally, these tests are automatically re-run with each commit in a\n[GitHub Action](https://github.com/biopragmatics/biomappings/actions?query=workflow%3ATests).\n\n### πŸ“– Building the Documentation\n\nThe documentation can be built locally using the following:\n\n```console\ngit clone git+https://github.com/biopragmatics/biomappings.git\ncd biomappings\ntox -e docs\nopen docs/build/html/index.html\n```\n\nThe documentation automatically installs the package as well as the `docs`\nextra specified in the [`pyproject.toml`](pyproject.toml). `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\nThe documentation can be deployed to [ReadTheDocs](https://readthedocs.io) using\n[this guide](https://docs.readthedocs.io/en/stable/intro/import-guide.html).\nThe [`.readthedocs.yml`](.readthedocs.yml) YAML file contains all the configuration you'll need.\nYou can also set up continuous integration on GitHub to check not only that\nSphinx can build the documentation in an isolated environment (i.e., with `tox -e docs-test`)\nbut also that [ReadTheDocs can build it too](https://docs.readthedocs.io/en/stable/pull-requests.html).\n\n#### Configuring ReadTheDocs\n\n1. Log in to ReadTheDocs with your GitHub account to install the integration\n at https://readthedocs.org/accounts/login/?next=/dashboard/\n2. Import your project by navigating to https://readthedocs.org/dashboard/import then clicking the plus icon next to\n your repository\n3. You can rename the repository on the next screen using a more stylized name (i.e., with spaces and capital letters)\n4. Click next, and you're good to go!\n\n### πŸ“¦ Making a Release\n\n#### Configuring Zenodo\n\n[Zenodo](https://zenodo.org) is a long-term archival system that assigns a DOI to each release of your package.\n\n1. Log in to Zenodo via GitHub with this link: https://zenodo.org/oauth/login/github/?next=%2F. This brings you to a\n page that lists all of your organizations and asks you to approve installing the Zenodo app on GitHub. Click \"grant\"\n next to any organizations you want to enable the integration for, then click the big green \"approve\" button. This\n step only needs to be done once.\n2. Navigate to https://zenodo.org/account/settings/github/, which lists all of your GitHub repositories (both in your\n username and any organizations you enabled). Click the on/off toggle for any relevant repositories. When you make\n a new repository, you'll have to come back to this\n\nAfter these steps, you're ready to go! After you make \"release\" on GitHub (steps for this are below), you can navigate\nto https://zenodo.org/account/settings/github/repository/biopragmatics/biomappings\nto see the DOI for the release and link to the Zenodo record for it.\n\n#### Registering with the Python Package Index (PyPI)\n\nYou only have to do the following steps once.\n\n1. Register for an account on the [Python Package Index (PyPI)](https://pypi.org/account/register)\n2. Navigate to https://pypi.org/manage/account and make sure you have verified your email address. A verification email\n might not have been sent by default, so you might have to click the \"options\" dropdown next to your address to get to\n the \"re-send verification email\" button\n3. 2-Factor authentication is required for PyPI since the end of 2023 (see\n this [blog post from PyPI](https://blog.pypi.org/posts/2023-05-25-securing-pypi-with-2fa/)). This means\n you have to first issue account recovery codes, then set up 2-factor authentication\n4. Issue an API token from https://pypi.org/manage/account/token\n\n#### Configuring your machine's connection to PyPI\n\nYou have to do the following steps once per machine.\n\n```console\n$ uv tool install keyring\n$ keyring set https://upload.pypi.org/legacy/ __token__\n$ keyring set https://test.pypi.org/legacy/ __token__\n```\n\nNote that this deprecates previous workflows using `.pypirc`.\n\n#### Uploading to PyPI\n\nAfter installing the package in development mode and installing\n`tox` with `python3 -m pip install tox tox-uv`,\nrun the following from the console:\n\n```console\ntox -e finish\n```\n\nThis script does the following:\n\n1. Uses [bump-my-version](https://github.com/callowayproject/bump-my-version) to switch the version number in\n the `pyproject.toml`, `CITATION.cff`, `src/biomappings/version.py`,\n 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\n [`uv build`](https://docs.astral.sh/uv/guides/publish/#building-your-package)\n3. Uploads to PyPI using [`uv publish`](https://docs.astral.sh/uv/guides/publish/#publishing-your-package).\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\n#### Releasing on GitHub\n\n1. Navigate\n to https://github.com/biopragmatics/biomappings/releases/new\n to draft a new release\n2. Click the \"Choose a Tag\" dropdown and select the tag corresponding to the release you just made\n3. Click the \"Generate Release Notes\" button to get a quick outline of recent changes. Modify the title and description\n as you see fit\n4. Click the big green \"Publish Release\" button\n\nThis will trigger Zenodo to assign a DOI to your release as well.\n\n\u003c/details\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiopragmatics%2Fbiomappings","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiopragmatics%2Fbiomappings","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiopragmatics%2Fbiomappings/lists"}