Biolookup

Get metadata and ontological information about biomedical entities.

🕸️ Lookup App

After installing with the [web] extras, you can run the lookup app in local mode with:

$ biolookup web --lazy

This means that the in-memory data from pyobo are used. If you have a large external database, you can run in remote mode with the --sql flag:

$ biolookup web --sql --uri postgresql+psycopg2://postgres:biolookup@localhost:5434/biolookup

If --uri is not given for the web subcommand, it uses pystow.get_config("pyobo", "sqlalchemy_uri)to look up from PYOBO_SQLALCHEMY_URI or in ~/.config/pyobo.ini. If none is given, it defaults to a SQLite database in ~/.data/pyobo/pyobo.db.

🗂️ Load the Database

$ biolookup load  --uri postgresql+psycopg2://postgres:biolookup@localhost:5434/biolookup

If --uri is not given for the load subcommand, it uses pystow.get_config("pyobo", "sqlalchemy_uri) to look up from PYOBO_SQLALCHEMY_URI or in ~/.config/pyobo.ini. If none is given, it defaults to a SQLite database in ~/.data/pyobo/pyobo.db.

🚀 Installation

The most recent release can be installed from PyPI with:

$ pip install biolookup

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

$ pip install git+https://github.com/biolookup/biolookup.git

To install in development mode, use the following:

$ git clone git+https://github.com/biolookup/biolookup.git
$ cd biolookup
$ pip install -e .

👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.rst for more information on getting involved.

👀 Attribution

⚖️ License

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

🎁 Support

The Biolookup Service 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

This project has been supported by the following grants:

🍪 Cookiecutter

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