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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

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.

Last update: June 24, 2022