Welcome to UMLS RAT’s documentation!

UMLS RAT (REST API Tool) provides a reasonable interface to the UMLS Metathesaurus via the REST API. We cache responses using requests cache to speed things up. Ultimately, you will only end up downloading as much data as you need which for most use cases is a relatively small portion of the whole. If you need the entire Metathesaurus, this is not the best tool.

Install

pip install umls-rat

API Key

Before you get started, you first need to get an API key from UMLS. By default, your API key will be read from the environment variable UMLS_API_KEY. If this variable is not set, you must pass your key to the umlsrat.api.rat_session.MetaThesaurusSession constructor.

SSL

Note that you may need to add an SSL certificate which can be done by setting the REQUESTS_CA_BUNDLE environment variable. See here for more info.

Development

Install poetry environment.

poetry install

Execute unit tests. Set UMLS_API_KEY or pass in with --api-key arg.

poetry run python -m pytest -sv tests

Cached requests are stored in ~/.cache/umls-rat. Caching can be disabled when running the tests, with the --no-cache flag, eg

poetry run python -m pytest -sv tests --cache=False

The default version of UMLS used is a constant umlsrat.const.DEFAULT_UMLS_VERSION. The version used for testing can be modified at runtime with the --umls-version arg, eg

poetry run python -m pytest -sv tests --cache=False --umls-version current

Build Documentation

Install docs dependencies.

poetry install --with docs

Buidl the docs

poetry run make -C docs clean html

Indices and tables