Gen3 community members have created tools that facilitate interactions with a Gen3 Data Commons. These tools may be of use to both Gen3 users or operators. Any questions about their use should be directed to the maintainers of the particular tool.
The Gen3 Software Development Kit (SDK) for Python provides classes and functions for handling common tasks when interacting with a Gen3 commons. It also exposes a Command Line Interface (CLI). Created by the Center for Translational Data Science at the University of Chicago.
GitHub
Utilities for Gen3 management including validation tools. Created by the Center for Translational Data Science at the University of Chicago.
Gen3 Tracker (g3t) includes utilities to manage Gen3 schemas, projects and submissions. Tools include those to create and manage metadata, manipulate file manifests, status checks, metadata validation, user access, and others.
g3t_etl is a command-line tool and library designed to manage Gen3 metadata including transformations to and from FHIR formatted data. The tool provides various commands, each serving a specific purpose.
GitHub
Stand-alone tools developed to test and visualize Gen3 dictionaries. They allow for quicker testing of dictionary updates and do not require a full Gen3 deployment. Created by BioTeam.
GitHub
A python tool that uses Google Sheets for simple, automated and efficient dictionary development. The Gen3 schema mapping library enables an automated workflow to edit, test, validate and publish Gen3 Data Dictionaries, using a google sheet as input. Created by the Australian BioCommons.
Gen3 dictionary tools (Docker images) for conversion, visualization, testing and validation to allow for iterative development of Gen3 data dictionary schema locally. Created by the Genomics Platform Group at University of Melbourne Centre for Cancer Research (UMCCR).