OHDSI Geographic Informations Systems (GIS)


Mission

Improve the health of populations by generating reliable evidence from integrated geospatial and person-level health data.


Updates

All updates


Collaboration Approach

Like most of OHDSI, we use Github and MS Teams for collaboration, version control, etc. There are no perfect options for supporting collaboration. We’ll help you accomodate to ours as best we can. In particular, we use Github for managing tasks like defining and monitoring progress on OHDSI studies, infrastructure roadmaps, technical issues, etc.

We review progress and get input from the broader group at weekly meetings on Thursdays. Leaders of specific projects within the GIS workgroup schedule and hold meetings with subgroups outside the main Thursday meeting. Those other meetings are where most of the work on use cases and advancing technical infrastructure gets done.

To see what the group is working on, check the use case and dataset status page, which tracks the status of use cases and dataset requests.

Apart from the groups’ offical leadership, many members make fundamental contributions to the group’s decisions, strategies, and products.

All are welcome. We’d love to work with you. Please see our page on proposing new use cases. If you are new and are considering using the GIS toolchain to do research or contibuting to the group’s work, we will schedule a separate meeting with you to help you figure out what manner of participation makes sense for you.

New to OHDSI? First sign up for an OHDSI MS Teams account here. It’s easy peasy. Already have an OHDSI Teams account? Great. Just sign up for the GIS Workgroup here.

The main workgroup call is on MS Teams every Thursday at 10 AM US Eastern Time (Meeting Link). We are always looking for better ways to accomodate the time constraints of valued members around the world. Please let us know if this schedule is an obstacle.


GIS Toolchain

The GIS toolchain consists of extensions to the OMOP schema, extensions to the OMOP Vocabulary, and GIS-specific software for acquiring and working with geospatial data. Together, these enable researchers to use health-related attributes of the regions where patients live in OHDSI study cohort definitions. For example, you can use the GIS toolchain to define cohorts that include regional data on exposure to toxicants or social deprivation along with EHR data on relevant health outcomes. The toolchain also includes informatics resources that support integration with the main OHDSI tool stack (HADES) and integration with externally supported solutions for geocoding and for finding and deriving relevant data sources from catalogs of available data sources.

Importantly, the toolchain allows integrated analysis of geospatial and EHR data without sharing any sensitive patient location data.

OMOP GIS schema extensions

The External_Exposure table is an extension to the main OMOP schema. It holds data on things that can affect health that are associated with the places where patients live. The Location_History table contains information on patient’s residence and the dates during which they lived in that location. The DDLs and associated documentation for the External_Exposure table and the Location_History table are here and here respectively. The entity-relationship diagram showing the joins between these tables and the main OMOP schema is here.

OMOP Vocabulary extensions

The GIS extensions to the OMOP Vocabulary cover geometries, toxicants, and social determinants. They are used to represent a very large set of entities that can affect health and their relationships. The vocabularies are built and released from the Custom Vocabulary Builder repository (see the vocabulary documentation). They are based on mature existing ontologies and were developed by GIS workgroup members who are part of the OHDSI Core Vocabulary team in accordance with the guiding principles for OMOP vocabulary development, quality assurance, and integration. Current work on their validation in real use cases is expected to support their eventual acceptance as versioned community-maintained extensions of the core OMOP Vocabulary.

gaiaCore

The gaiaDB schema supports specification of attributes and geographic shapes in publicly available datasets, which allows the tables in the GIS schema extension to be joined with patient-level clinical data stored in the main OMOP schema. The gaiaCore R package runs this pipeline from R (ingestion, location loading, the spatial-temporal join), checks the derived exposure, copies it into the OMOP CDM, and provides exposure analytics. The package and its documentation are here.

Guidance

The GIS toolchain requires patient addresses to be geocoded into representations that GIS software expects; for example, the latitude and longitude coordinates of street addresses or the coordinates of the lines that define a postal region. The OHDSI GIS workgroup does not develop geocoding software. Two open-source geocoders, DeGAUSS and the PostGIS TIGER geocoder, are available as optional components of the Gaia Docker deployment and run locally, so no address data leaves the institution. The GIS Workgroup provides guidance about privacy-preserving options for geocoding address information, a benchmark of four geocoders, and considerations for using available open-source and commercial geocoding approaches. The workgroup is also developing guidance to aid researchers in making informed decisions about selecting and working with alternative geospatial data sources that are relevant to addressing a research question.

Support for integration with OHDSI’s technical ecosytem

The GIS Workgroup provides a containerized deployment of the toolchain (gaiaDocker, following the OHDSI Broadsea approach) and an ohdsi/gaia-core image with HADES, gaiaCore and the extension packages (CaprForExtensions and FeatureExtractionForExtensions) installed. A hands-on tutorial, first run at the 2026 OHDSI Global Symposium, carries one example study end to end on a synthetic 10,000-person OMOP dataset with real county PM2.5. The generators and benchmark scripts are archived on Zenodo. The workgroup is developing a robust approach to working with available geospatial data sources via catalogs. The approach uses schema.org-compliant standards and federated metadata sharing methods widely used in the GIS community to share information about available datasets.


In short: place data are described once in the catalog and mapped to standard concepts; inside the data holder’s own environment, residence histories are geocoded locally and joined to that place data by gaiaDB and gaiaCore, which produces person-level exposure records beside the clinical data; and OHDSI tools then analyze both together. Addresses and individual records stay at the data holder, and only aggregate results are shared.


Goals

The OHDSI GIS Workgroup carries out work in support of its mission by pursuing the following goals:

  • Support OHDSI studies that use the GIS toolchain
  • Conduct studies that use the GIS toolchain
  • Advance the development of the GIS toolchain
  • Facilitate the use of externally supported privacy-protecting geocoding software
  • Develop data cataloging resources and guidance that enable reuse of specific geospatial datasets in OHDSI studies


Publications/Presentations

Agentic AI-Assisted Harmonization of CHoRUS/PostGIS Exposure Variables for OHDSI GIS Observational Research (2026 OHDSI Global Symposium Poster, Brief report)

Development of Multi-Language Connectors Using GaiaDB (2026 OHDSI Global Symposium Poster, Brief report)

Metadata standards in OMOP to increase reproducibility in exposomics studies (2026 OHDSI Global Symposium Poster)

Integrating geospatial data into the OMOP CDM: a hands-on tutorial with the OHDSI GIS toolchain (2026 OHDSI Global Symposium, October 20, 2026; materials on the tutorial pages)

OHDSI GIS Workgroup 2026 Objectives and Key Results (slides)

OHDSI GIS Workgroup 2024 Accomplishments and 2025 Goals (slides)

OMOP GIS Vocabulary Package for Observational Studies in Health Care and Public Health (2024 OHDSI Symposium Poster, Abstract)

OHDSI GIS Toolchain Live Demonstration (2024 OHDSI Symposium Video)

OHDSI GIS Infrastructure (2023 OHDSI Symposium Poster, Abstract)

Toxins Vocabulary (2023 OHDSI Symposium Poster, Abstract)

Leveraging the OMOP Common Data Model to Support Distributed Health Equity Research (2023 OHDSI Symposium Poster)

OHDSI GIS Workgroup October 10, 2023 Update (Video)

OHDSI GIS Workgroup 2023 Objectives and Key Results (Video, slides)

Leveraging Location Data in OMOP to Incorporate Area Deprivation Index (2022 OHDSI Symposium Poster, Abstract)

OHDSI GIS Workgroup August 23, 2022 Update (Video)

OHDSI GIS (2016 OHDSI Symposium Poster abstract)

Related OHDSI geospatial work from the wider community

Spatial Analysis Tool Based on OMOP CDM: Geospatial functionality support in OHDSI ATLAS (2020 OHDSI Global Symposium Poster, Video)

Application for Epidemiological Geographic Information System (AEGIS): an open source spatial analysis tool based on CDM (2018 OHDSI Symposium Software demonstration, Code)

AEGIS: Tool for semi-automatic creating medical map based on GUI (2017 OHDSI Symposium Software demonstration)