biomappings 0.3.7

Description:

biomappings 0.3.7

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

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.

🌐 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:

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.

⬇️ 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:

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
Packages the code in both a tar archive and a wheel using build
Uploads to PyPI using twine. Be sure to have a .pypirc file configured to avoid the need for manual input at this
step
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 minor after.