vivarium-gbd-mapping

Mapping of Global Burden of Disease (GBD) entities to their metadata.

There are two packages offered in this distribution. The first, the gbd_mapping_generator is a set of scripts that define templates and data gathering code used to produce the second, the gbd_mapping. The gbd_mapping_generator package will not function without access to the IHME cluster and some of our internally used data access libraries. Mapping updates are managed by an automated toolchain, so this shouldn’t be an issue.

The gbd_mapping is a programmatically accessible (and TAB-complete-able) set of mappings for GBD entities including:

Causes

Risks

Covariates

Etiologies

Sequelae

Supported Python versions: 3.10, 3.11

You can install vivarium-gbd-mapping from PyPI with pip:

pip install vivarium-gbd-mapping

or build it from source by cloning the monorepo and installing this package:

git clone https://github.com/ihmeuw/vivarium-suite.git
cd vivarium-suite
pip install libs/gbd-mapping

Development and Mapping Generation

In order to generate or regenerate the mappings from data, you must have access to the Institute for Health Metrics and Evaluation cluster and internal PyPI server. Contact the vivarium developers at vivarium.dev@gmail.com or open an issue at https://github.com/ihmeuw/vivarium-suite for further instructions.

Given proper permissions, you can set up this library in development mode with

git clone https://github.com/ihmeuw/vivarium-suite.git
cd vivarium-suite
pip install -e 'libs/gbd-mapping[dev]'

Check out the docs!

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