Gen3 Data Dictionary Gallery

• Canine
  • This is the dictionary used for the Canine Data Commons, which is the "demo" Commons given on the Gen3 Home page.
  • It allows for longitudinal data through its "Follow Up" node.
• Account
• AnVIL
  • Used by the NHGRI Genomic Data Science Analysis, Visualization and Informatics Lab-space (AnVIL)
  • In terms of number of nodes, this is a "minimal" dictionary. At the same time, there are 216 properties in the subject node.
• Covid-19
• Data Commons Framework (DCF)
  • This is the "baseline" dictionary that comes with Compose Services. It does not allow for longitudinal data.
• Gtex
  You can go here for an NIH program snapshot of the Genotype-Tissue Expression (GTEx) Program
• NCI-GDC (National Cancer Institute - Genomic Data Commons)
• NDH
• RERF

Purpose

This page can give us some ideas about how we can structure our own Gen3 data dictionaries for the BLSA and other projects.

Comments

This was created by crawling through the UC-CDIS Github Page for all of the Gen3 data dictionaries they have made available.

The dictionaries are written in YAML, but we can convert them to JSON with some help from this repo. Once they are in JSON, we can visualize them using this React app.

In some cases, the Github repos for these dictionaries would reveal some extra information about the projects behind the dictionaries. In other cases, the repos simply hosted the YAML files. I have tried to summarize whatever information I could find here.

The Gen3 developers are in the process of updating the format of their data dictionaries. I have the impression that the React app was made with the older format in mind. Consequently, the React app wasn't able to successfully visualize all of the data dictionaries that are on the UC-CDIS Github page. The dictionaries provided here are the ones that could be visualized successfully.