Welcome to the OHDSI Geographic Information Systems (GIS) Working Group – the central hub for integrating geospatial and person-level health data within the OHDSI ecosystem.
Mission: Improve the health of populations by generating reliable evidence from integrated geospatial and person-level health data.
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.
The OHDSI GIS Working Group maintains and develops several interconnected repositories that together form the Gaia toolchain:
OHDSI/GIS (this repository)
- Central documentation and coordination hub
- OMOP GIS schema extensions
- Use case tracking and project management
- Developer guidelines and contribution workflows
- PostgreSQL/PostGIS database serving as the core data repository
- Geospatial data ingestion, management, and analysis
- SQL routines and PostGIS functionality
- OMOP CDM integration
- LinkML/JSON-LD metadata support
OHDSI/gaiaCore (TuftsCTSI/gaiaCore for development)
- Multi-language connector framework for gaiaDB
- RESTful API access via PostgREST
- Database and API paradigm support
- Language-specific client libraries (R, Python, etc.)
- Orchestrates functions and protocols defined in gaiaDB
- Metadata catalog for geospatial data sources
- Schema.org-compliant data discovery
- Federated metadata sharing
- Containerized deployment of Gaia toolchain
- Coordinated image builds and versioned releases
- Docker Compose orchestration
- Complete GIS stack deployment
- OMOP GIS Vocabulary Package delta files
- OMOP Exposome Vocabulary
- OMOP SDoH (Social Determinants of Health) Vocabulary
- Toxins and environmental exposure vocabularies
Find the Delta Vocabulary files for the Vocabulary Package here
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
The Gaia toolchain provides end-to-end support for integrating geospatial data with OMOP CDM:
- gaiaDB: PostgreSQL/PostGIS database with geospatial data processing, SQL routines, and OMOP integration
- gaiaCore: Multi-language connector framework providing RESTful API and database access to gaiaDB
- gaiaCatalog: Data discovery and metadata management
- gaiaDocker: Containerized deployment with coordinated image builds and versioned releases
Instructions to quickly install and start using Gaia are here
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 -dThe 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- Developer questions/comments/feedback: OHDSI Forum
- Please use the GitHub issue tracker for all bugs/issues/enhancements
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
See Developer Resources for detailed contributing guidelines.
This repository uses RMarkdown to generate documentation hosted on GitHub Pages. To build the site locally:
# Quick start
Rscript build-site.R
# Or using R console
setwd("rmd")
rmarkdown::render_site(encoding = "UTF-8")For detailed build instructions, see BUILD.md