https://github.com/OHDSI/GIS
Last synced: 2 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/OHDSI/GIS
- Owner: OHDSI
- License: apache-2.0
- Created: 2016-10-28T18:13:40.000Z (about 9 years ago)
- Default Branch: main
- Last Pushed: 2024-12-05T06:35:35.000Z (12 months ago)
- Last Synced: 2024-12-24T16:51:26.078Z (11 months ago)
- Language: R
- Homepage: https://ohdsi.github.io/GIS
- Size: 111 MB
- Stars: 10
- Watchers: 15
- Forks: 9
- Open Issues: 64
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- License: LICENSE.md
Awesome Lists containing this project
- jimsghstars - OHDSI/GIS - (R)
README
# OHDSI GIS Workgroup
## Introduction
Please visit our [webpage](https://ohdsi.github.io/GIS/index.html) for more details and the most **up-to-date information** and **software documentation**.
For **project management**, see the [GIS Project Page](https://github.com/orgs/OHDSI/projects/26)
[Click here](https://github.com/OHDSI/GIS/issues/new?assignees=&labels=Use+Case&projects=&template=use-case.yaml&title=%5BUse+Case%5D%3A+) to propose a new **Use Case**.
## Our Work
### [OMOP GIS Vocabulary Package](https://ohdsi.github.io/GIS/vocabulary.html)
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
Find the Delta Vocabulary files for the Vocabulary Package [here](https://github.com/TuftsCTSI/CVB/tree/main/GIS/Ontology)
### [gaiaDB](https://github.com/ohdsi/gaiaDB)
A staging database and collection of transformation recipes for public place-based datasets
### [gaiaCore](https://github.com/ohdsi/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](https://ohdsi.github.io/GIS/getting-started.html)
### Docker Quick Start
> Prerequisite: this solution requires that you have Docker and Docker Compose installed. See [here](https://docs.docker.com/engine/install/).
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
```bash
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
```bash
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](https://github.com/ohdsi/gaiaDB).
The gaiaCore image is **built** from the Dockerfile in the docker directory in this repository.
```bash
# 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