biomappings 0.3.7

Curated and predicted mappings between biomedical identifiers in different namespaces

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 a simple TSV file that looks 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/mappings.tsv
Yes	Human-curated non-trivial false (i.e., incorrect) mappings	src/biomappings/resources/incorrect.tsv
Yes	Mappings that have been checked but not yet decided	src/biomappings/resources/unsure.tsv
No	Automatically predicted mappings	src/biomappings/resources/predictions.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

The mappings are distributed in the Simple Standard for Sharing Ontology Mappings (SSSOM) format (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.

🙏 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), 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:

• True Mappings
• False Mappings
• Unsure Mappings
• Predictions

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:

$ 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:

$ 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 automatically uploaded to APICURON.

⬇️ Installation

The most recent release can be installed from PyPI with:

$ pip install biomappings

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

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

To install in development mode and create a new branch, use the following:

$ 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.

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 graphs with the following functions:

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.

👋 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
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 the Bioregistry is funded 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
$ 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:

$ tox

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 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.

📦 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:

$ tox -e finish

This script does the following:

1. Uses Bump2Version to switch the version number in the setup.cfg, 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 build
3. Uploads to PyPI using 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.