OHDSI GIS

Introduction

An R package and RShiny app for working with OMOP CDM data in conjunction with geospatial data in a standardized format.

Features

• Ability to register desired geospatial data sources.
• Work with PHI in a local environment.

Technology

gaiaCore is an R package created by the OHDSI GIS work group. A Postgres/PostGIS database is used to store and maintain source records.

System Requirements

To set up the backbone schema, you must have a Postgres/PostGIS database

Getting Started

Installing the gaiaCore R package

1. See the instructions here for configuring your R environment, including RTools and Java.

2. You can install the development version of gaiaCore from GitHub with:

   # install.packages("devtools")
   devtools::install_github("OHDSI/GIS/packages/gaiaCore")

3. library(gaiaCore)

Installing the database

gaiaDB is a postgres database with PostGIS installed. If you don't have an existing postgres/PostGIS instance, you can create one in a docker container (see below).

If you already have a Postgres/PostGIS database, skip the Docker section.

Creating a Docker Container

1. You will need to have Docker and Docker Compose installed. The easiest way to install Docker and Docker Compose is by installing Docker Desktop.

2. Download the init directory from this repository.

3. From a terminal (Command Prompt or Powershell on Windows), make sure the init directory is your working directory.

4. Run command docker-compose up -d. This will build a docker image, install the database, load the data and variable sources, and expose the database at port 5432.

• Note: to change the port, open the file docker-compose.yml and edit line 10 from - "5432:5432" to - "X:5432" where X is the desired port.

5. You can now connect to the database from R using localhost, port 5432 (if not changed), username "postgres", and password "mysecretpassword"

• Note: to change your password, edit line 13 of the docker-compose.yml file. If you've already started the container, you will need to shut down the container, remove the volumes and image that were created, and redo step 4 for the password change to take effect.

6. The next section will highlight the steps to connect your PostGIS Docker container to R

Connecting the Database to R

1. Create the connectionDetails object

connectionDetails <- DatabaseConnector::createConnectionDetails(
  dbms = "postgresql",
  server = "", # server info, use localhost/gaiaDB if setting up from Docker
  port = 5432,
  user="postgres", # username to access server
  password = "mysecretpassword") 

2. Run the initializeDatabase(connectionDetails) function

Support

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

Contributing

Read here how you can contribute to this package.

License

GIS is licensed under Apache License 2.0

Development

gaiaCore is being developed in R Studio.

gaiaDB is being developed in Postgres/PostGIS

Development status

Under development