OHDSI GIS Workgroup

Introduction

Please visit our webpage for more details and the most up-to-date information and software documentation.

For project management, see the GIS Project Page

Click here to propose a new Use Case.

Our Work

OMOP GIS Vocabulary Package

The OMOP GIS (Geographic Information System) Vocabulary Package is designed to elevate data-driven healthcare research by enabling the integration of spatial, environmental, behavioral, socioeconomic, phenotypic, and toxin-related determinants of health into standardized data structures. Features:

• OMOP GIS Vocabulary
• OMOP Exposome Vocabulary
• OMOP SDoH (Social Determinants of Health) Vocabulary

gaiaDB

A staging database and collection of transformation recipes for public place-based datasets

gaiaCore

An R Package for interacting with gaiaDB - part of the OHDSI GIS Gaia toolchain

Quick Start

Instructions to quickly install and start using Gaia are here

Docker Quick Start

Prerequisite: this solution requires that you have Docker and Docker Compose installed. See here.

Containerized instances of gaiaDB (geospatial data store) and the gaiaCore R package (built in to Broadsea Hades and wrapped with an HTTP API via Plumber) can quickly be deployed and connected using Docker Compose

git clone git@github.com:OHDSI/GIS.git

cd GIS

docker compose -f ./docker/docker-compose.yaml up -d

The gaiaCore R Package is wrapped with an HTTP API. You can test that the service is started in running at the specified port with the /hello endpoint, or load a variable to gaiaDB with the /load endpoint

curl "http://localhost:8000/load?variable_id=1"

Configure database connection details and HTTP API port in the .env file in the docker directory.

At this time, images are not published and are built when docker compose is run:

The gaiaDB image is built from the Dockerfile in the gaiaDB repository.

The gaiaCore image is built from the Dockerfile in the docker directory in this repository.

# stop containers
docker compose -f ./docker/docker-compose.yaml down

Support

• Developer questions/comments/feedback: OHDSI Forum
• Please use the GitHub issue tracker for all bugs/issues/enhancements

Contributing

We are eager to engage with interested developers with interest or experience in frontend, backend, and geospatial development.

If you are interested in contributing and don't know where to begin, please join the OHDSI GIS WG or email at zollovenecek[at]ohdsi[dot]org