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:
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.
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 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.
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 |
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:
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.
- Fork the repository at https://github.com/biopragmatics/biomappings, clone locally, and make a new branch (see below)
- Edit one or more of the resource files (
mappings.tsv,incorrect.tsv,unsure.tsv,predictions.tsv) - Commit to your branch, push, and create a pull request back to the upstream repository.
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
$ UV_PREVIEW=1 python3 -m pip install -e .[web]The web application can be run with:
$ biomappings webIt 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.
There are three places where curators of Biomappings are credited:
- ORCiD identifiers of curators are stored in each mapping
- The summary website groups and counts contributions curator
- A curation leaderboard is automatically uploaded to APICURON.
The most recent release can be installed from PyPI with:
python3 -m pip install biomappingsThe most recent code and data can be installed directly from GitHub with:
python3 -m pip install git+https://github.com/biopragmatics/biomappings.gitTo install in development mode and create a new branch, use the following:
$ git clone https://github.com/biopragmatics/biomappings.git
$ cd biomappings
$ UV_PREVIEW=1 python3 -m pip install -e .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.
The code in this package is licensed under the MIT License. Data are licensed under the CC0 License.
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},
}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.
The development of the Bioregistry is funded by the DARPA Young Faculty Award W911NF2010255 (PI: Benjamin M. Gyori).
This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.
See developer instructions
The final section of the README is for if you want to get involved by making a code contribution.
To install in development mode, use the following:
$ git clone git+https://github.com/biopragmatics/biomappings.git
$ cd biomappings
$ uv --preview pip install -e .Alternatively, install using legacy pip with UV_PREVIEW mode enabled
until the uv build backend becomes a stable feature:
$ UV_PREVIEW=1 python3 -m pip install -e .This project uses cruft to keep boilerplate (i.e., configuration, contribution guidelines, documentation
configuration)
up-to-date with the upstream cookiecutter package. Update with the following:
python3 -m pip install cruft
cruft updateMore info on Cruft's update command is available here.
After cloning the repository and installing tox with
python3 -m pip install tox tox-uv,
the unit tests in the tests/ folder can be run reproducibly with:
tox -e pyAdditionally, these tests are automatically re-run with each commit in a GitHub Action.
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.htmlThe 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.
- Log in to ReadTheDocs with your GitHub account to install the integration at https://readthedocs.org/accounts/login/?next=/dashboard/
- Import your project by navigating to https://readthedocs.org/dashboard/import then clicking the plus icon next to your repository
- You can rename the repository on the next screen using a more stylized name (i.e., with spaces and capital letters)
- Click next, and you're good to go!
Zenodo is a long-term archival system that assigns a DOI to each release of your package.
- 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.
- 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.
You only have to do the following steps once.
- Register for an account on the Python Package Index (PyPI)
- 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
- 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
- Issue an API token from https://pypi.org/manage/account/token
You have to do the following steps 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.
After installing the package in development mode and installing
tox with python3 -m pip install tox tox-uv,
run the following from the console:
tox -e finishThis script does the following:
- Uses bump-my-version to switch the version number in
the
pyproject.toml,CITATION.cff,src/biomappings/version.py, anddocs/source/conf.pyto not have the-devsuffix - Packages the code in both a tar archive and a wheel using
uv build - Uploads to PyPI using
uv publish. - Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
- 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 -- minorafter.
- Navigate to https://github.com/biopragmatics/biomappings/releases/new to draft a new release
- Click the "Choose a Tag" dropdown and select the tag corresponding to the release you just made
- Click the "Generate Release Notes" button to get a quick outline of recent changes. Modify the title and description as you see fit
- Click the big green "Publish Release" button
This will trigger Zenodo to assign a DOI to your release as well.