Biomappings

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 TSV files using the Simple Standard for Sharing Ontology Mappings (SSSOM) format that look like this:

💾 Data

The data are available through the following four files on the biopragmatics/biomappings GitHub repository.

Curated	Description	Link
Yes	Human-curated true mappings	src/biomappings/resources/positive.sssom.tsv
Yes	Human-curated non-trivial false (i.e., incorrect) mappings	src/biomappings/resources/negative.sssom.tsv
Yes	Mappings that have been checked but not yet decided	src/biomappings/resources/unsure.sssom.tsv
No	Automatically predicted mappings	src/biomappings/resources/predictions.sssom.tsv

The primary and derived data in this repository are both available under the CC0 1.0 Universal License.

Predictions are generated by scripts in the scripts/ folder. Each uses the utilities from the biomappings.resources module to programmatically interact with the mappings files, e.g., to add predictions.

🥒 Derived

An aggregation of positive, negative, and predicted mappings are collated in the SSSOM (here) 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.

Equivalences and related mappings that are available from the OBO Foundry and other primary sources can be accessed through Inspector Javert's Xref Database on Zenodo which was described in this blog post.

📊 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.

💪 Getting Started

There are three main functions exposed from biomappings. Each loads a list of dictionaries with the mappings in each.

import biomappings

positive_mappings = biomappings.load_mappings()
negative_mappings = biomappings.load_false_mappings()
predicted_mappings = biomappings.load_predictions()

Full documentation can be found on ReadTheDocs.

🚀 Installation

The most recent release can be installed from PyPI with uv:

$ uv pip install biomappings

or with pip:

$ python3 -m pip install biomappings

The most recent code and data can be installed directly from GitHub with uv:

$ uv pip install git+https://github.com/biopragmatics/biomappings.git

or with pip:

$ python3 -m pip install git+https://github.com/biopragmatics/biomappings.git

👐 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.sssom.tsv file into either the positive mappings file (positive.sssom.tsv), negative mappings file (negative.sssom.tsv), or the unsure mappings file (unsure.sssom.tsv). Additionally, the confidence column should be removed, a mapping_justification column should be added with an appropriate value from the SEMAPV vocabulary, such as
the value semapv:ManualMappingCuration, and your ORCiD identifier should be written as a CURIE (e.g., orcid:0000-0003-1307-2508) in the author_id column.

Novel mappings can be curated by adding a full row to the positive mappings file (positive.sssom.tsv) following the format of the previous lines.

While Biomappings is generally able to use any predicate written as a compact URI (CURIE), it's preferred to use predicates from the Simple Knowledge Organization System (SKOS) to denote hierarchical relationships. The three most common predicates that are useful for curating mappings are:

Predicate	Description
skos:exactMatch	The two terms can be used interchangeably
skos:broadMatch	The object term is a super-class of the subject
skos: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:

• Positive Mappings
• Negative Mappings
• Unsure Mappings
• Predicted Mappings

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 (positive.sssom.tsv, negative.sssom.tsv, unsure.sssom.tsv, predictions.sssom.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:

$ git clone https://github.com/biopragmatics/biomappings.git
$ cd biomappings
$ git checkout -b your-branch-name
$ python3 -m pip install -e .[web]

The web application can be run with:

$ 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, 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 groups and counts contributions curator
3. A curation leaderboard is under construction at APICURON, though note that this is not up-to-date.

👋 Attribution

⚖️ License

The code in this package is licensed under the MIT License. Data are licensed under the CC0 License.

📖 Citation

Prediction and Curation of Missing Biomedical Identifier Mappings with Biomappings
Hoyt, C. T., Hoyt, A. L., and Gyori, B. M. (2022)
Bioinformatics, btad130.

@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, a part of the Laboratory of Systems Pharmacology and the Harvard Program in Therapeutic Science (HiTS) at Harvard Medical School.

💰 Funding

The development of this project has been funded in part by the DARPA Young Faculty Award W911NF2010255 (PI: Benjamin M. Gyori).

🍪 Cookiecutter

This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.

🛠️ For Developers

See developer instructions

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:

$ git clone git+https://github.com/biopragmatics/biomappings.git
$ cd biomappings
$ uv pip install -e .

Alternatively, install using pip:

$ python3 -m pip install -e .

🥼 Testing

After cloning the repository and installing tox with uv tool install tox --with tox-uv or python3 -m pip install tox tox-uv, the unit tests in the tests/ folder can be run reproducibly with:

$ tox -e py

Additionally, these tests are automatically re-run with each commit in a GitHub Action.

📖 Building the Documentation

The documentation can be built locally using the following:

$ 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 pyproject.toml. sphinx plugins like texext can be added there. Additionally, they need to be added to the extensions list in docs/source/conf.py.

The documentation can be deployed to ReadTheDocs using this guide. The .readthedocs.yml YAML file contains all the configuration you'll need. You can also set up continuous integration on GitHub to check not only that Sphinx can build the documentation in an isolated environment (i.e., with tox -e docs-test) but also that ReadTheDocs can build it too.

🧑‍💻 For Maintainers

See maintainer instructions

Initial Configuration

Configuring ReadTheDocs

ReadTheDocs is an external documentation hosting service that integrates with GitHub's CI/CD. Do the following for each repository:

1. Log in to ReadTheDocs with your GitHub account to install the integration at https://readthedocs.org/accounts/login/?next=/dashboard/
2. Import your project by navigating to https://readthedocs.org/dashboard/import then clicking the plus icon next to your repository
3. You can rename the repository on the next screen using a more stylized name (i.e., with spaces and capital letters)
4. Click next, and you're good to go!

Configuring Archival on Zenodo

Zenodo is a long-term archival system that assigns a DOI to each release of your package. Do the following for each repository:

1. Log in to Zenodo via GitHub with this link: https://zenodo.org/oauth/login/github/?next=%2F. This brings you to a page that lists all of your organizations and asks you to approve installing the Zenodo app on GitHub. Click "grant" next to any organizations you want to enable the integration for, then click the big green "approve" button. This step only needs to be done once.
2. Navigate to https://zenodo.org/account/settings/github/, which lists all of your GitHub repositories (both in your username and any organizations you enabled). Click the on/off toggle for any relevant repositories. When you make a new repository, you'll have to come back to this

After these steps, you're ready to go! After you make "release" on GitHub (steps for this are below), you can navigate to https://zenodo.org/account/settings/github/repository/biopragmatics/biomappings to see the DOI for the release and link to the Zenodo record for it.

Registering with the Python Package Index (PyPI)

The Python Package Index (PyPI) hosts packages so they can be easily installed with pip, uv, and equivalent tools.

1. Register for an account here
2. Navigate to https://pypi.org/manage/account and make sure you have verified your email address. A verification email might not have been sent by default, so you might have to click the "options" dropdown next to your address to get to the "re-send verification email" button
3. 2-Factor authentication is required for PyPI since the end of 2023 (see this blog post from PyPI). This means you have to first issue account recovery codes, then set up 2-factor authentication
4. Issue an API token from https://pypi.org/manage/account/token

This only needs to be done once per developer.

Configuring your machine's connection to PyPI

This needs to be done once per machine.

$ uv tool install keyring
$ keyring set https://upload.pypi.org/legacy/ __token__
$ keyring set https://test.pypi.org/legacy/ __token__

Note that this deprecates previous workflows using .pypirc.

📦 Making a Release

Uploading to PyPI

After installing the package in development mode and installing tox with uv tool install tox --with tox-uv or python3 -m pip install tox tox-uv, run the following from the console:

$ tox -e finish

This script does the following:

1. Uses bump-my-version to switch the version number in the pyproject.toml, CITATION.cff, src/biomappings/version.py, and docs/source/conf.py to not have the -dev suffix
2. Packages the code in both a tar archive and a wheel using uv build
3. Uploads to PyPI using uv publish.
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.

Releasing on GitHub

1. Navigate to https://github.com/biopragmatics/biomappings/releases/new to draft a new release
2. Click the "Choose a Tag" dropdown and select the tag corresponding to the release you just made
3. Click the "Generate Release Notes" button to get a quick outline of recent changes. Modify the title and description as you see fit
4. Click the big green "Publish Release" button

This will trigger Zenodo to assign a DOI to your release as well.

Updating Package Boilerplate

This project uses cruft to keep boilerplate (i.e., configuration, contribution guidelines, documentation configuration) up-to-date with the upstream cookiecutter package. Install cruft with either uv tool install cruft or python3 -m pip install cruft then run:

$ cruft update

More info on Cruft's update command is available here.