A list of Gen3 features
Gen3 is an open-source platform that enables the standing-up of data commons for managing, analyzing, and sharing research data. Below you can find an exhaustive list of Gen3 features.
Dictionary and structured data
- Explore the graph in the dictionary page of Windmill:
- Search keywords
- Visualize possible paths between nodes
- Download JSON or TSV format for node templates
- Explore project graphs and nodes in Windmill:
- Visualize graph model
- Browse/download data for each node
- Structured data submission (create, update, delete records) in JSON, TSV or CSV:
- Submission page of Windmill
- Gen3 SDK (Python, R)
- Export structured data as a JSON, TSV or CSV file
- Structured data is stored in Postgres databases
- Flattened data:
- Structured data can be flattened and stored in Elasticsearch by using our ETL tool
- Explore the Elasticsearch structured data using Guppy
- Generate fake data specific to a dictionary for testing
- Import and export using the Portable Format for Biomedical Data (PFB): (Work in progress)
- Import and export a dictionary
- Import and export structured data
Data files
- Data upload through the Gen3 Client
- Indexing data files:
- Create data file records and mint GUIDs
- Index a new version of the same file
- Get the most recent version of a file
- Index data files that are stored outside of the Commons
- GUID resolver
- Data download:
- Core metadata endpoint to get information about a data file
- Metadata Service
Data exploration and analysis
Access management and security
- Gen3 follows the OpenID Connect (OIDC) specifications
- Gen3 supports logging in through Google, NIH, ORCID, Microsoft and Synapse
- Create precise roles, policies and groups of users to limit access to resources
- Assign policies to users:
- Individual users
- Groups of users
- All logged in users
- All anonymous users
Automation