Common Fund Tools¶
CFDE Search Portal¶
The NIH Common Fund (CF) has funded a wide variety of data types and studies that are of interest to clinical and biomedical researchers, however those datasets are hosted on an equally large number of websites, with varying query systems. The Common Fund Data Ecosystem (CFDE) Portal is a unified system for searching across the entire CF portfolio in a single search, and is the first step in addressing the goal of making CF data more Find-able, Accessible, Interoperable and Reusable (FAIR). The wide range of data types, models and formats used by Common Fund Programs are being harmonized using well-defined metadata, common controlled vocabularies using the Crosscut Metadata Model.
Human Microbiome Project Use Case¶
| Est. Time | Lesson name | Description |
|---|---|---|
| 30 mins | Using the CFDE Search Portal to Find Files | Find Human Microbiome Project (HMP) data with DRS IDs |
| 10 mins | Creating a CATATICA Account | Add files to CAVATICA using DRS IDs |
| 10 mins | Adding files to CAVATICA with DRS IDs | Add files to CAVATICA using DRS IDs |
Kids First & CAVATICA Lessons¶
The NIH Common Fund-supported Gabriella Miller Kids First (KF) Data Resource Center (DRC) enables researchers, clinicians, and patients to work together to accelerate research and promote new discoveries for children affected with cancer and structural birth defects. Data from over 16,000 individuals, including DNA and RNA sequence data, is available to empower your research today. Data collected from more than 30,000 samples are expected to be available in the next few years.
Our aim is to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain. The goal of this training module is to enable clinicians and researchers to use the data portal to build cohorts, and to move that data to an analysis platform (CAVATICA).
Setting up your KF Portal Permissions¶
| Est. Time | Lesson name | Description |
|---|---|---|
| 5 mins | The Setup | Introduction |
| 20 mins | KF Portal Registration | Register for KF portal access |
| 20 mins | Cavatica Registration | Register for Cavatica access |
| 20 mins | Connecting Accounts | Connect KF and Cavatica |
| 20 mins | Accessing Data | Set up data access authorization |
Exploring Data in the KF Portal¶
| Est. Time | Lesson name | Description |
|---|---|---|
| 10 mins | Explore | Explore KF dashboard |
| 10 mins | Filtering | Filter data from the dashboard |
| 10 mins | Plots | Explore dashboard plots |
| 10 mins | Resetting | Reset search queries |
Advanced KF Portal Queries¶
| Est. Time | Lesson name | Description |
|---|---|---|
| 10 mins | Advanced Queries | Filter with advanced queries |
| 10 mins | Ands & Ors | Use conditional statements to filter |
| 10 mins | Joint Queries | Link multiple filters as joint queries |
| 10 mins | Checking Queries | Interpret query results |
| 10 mins | Saving Queries | Save participant sets or search term combinations |
Importing and downloading KF Data¶
| Est. Time | Lesson name | Description |
|---|---|---|
| 10 mins | Push to Cavatica | Move KF data to Cavatica |
| 10 mins | Data Download Options | Options for downloading data to your local computer |
| 10 mins | Data Download via KF Portal | Local download from the KF portal |
| 20 mins | Data Download via Cavatica | Local download from Cavatica |
| 30 mins | Data Upload to Cavatica | Using the Command Line Uploader tool to move files from AWS to Cavatica |
Learning Objectives
- learn how to search the CFDE Portal to find data
- learn how to use DRS IDs to access data
- learn how to connect your Kids First, CAVATICA, and protected access accounts
- learn how to find and filter Kids First data sets
- learn how to move your chosen cohort to Cavatica for analysis
- learn how to apply for access to new data sets
This training assumes a basic background in human medicine. For this tutorial, you'll need a modern web browser (e.g., Chrome, Firefox, Safari). You'll also need 1) either ORCID or Google account and 2) eRA Commons ID credentials to login and connect portals.
IDG Tutorials¶
Members of Illuminating the Druggable Genome (IDG) Common Fund Program have created video tutorials for a variety of IDG tools and resources.