CFDE Portal Overview¶
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, and common controlled vocabularies using the Crosscut Metadata Model.
The CFDE Search Portal uses the Crosscut Metadata Model (C2M2) a flexible metadata standard for describing experimental resources in biomedicine and related fields. This portal supports faceted search of metadata concepts such as anatomical location, species, and assay type, across a wide variety of datasets using a controlled vocabulary (we do not currently support protected metadata). This allows researchers to find a wide variety of data that would otherwise need to be searched individually, using varying nomenclatures. The portal only accepts C2M2 data packages from Common Fund Programs.
This tutorial focuses on the Human Microbiome Project (HMP). The goal of this tutorial is to identify small FASTQ files with persistent identifiers from a longitudinal multi-omics study.
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 CAVATICA Account||Add files to CAVATICA using DRS IDs|
|10 mins||Adding files to CAVATICA with DRS IDs||Add files to CAVATICA using DRS IDs|
In this tutorial you will learn:
- How to search the CFDE Portal to find data
- How to use DRS IDs to add data to CAVATICA
Please refer to the Portal User Guide for a detailed description of all portal features.
- Access to MacOS, Windows, or Linux
- Access to the internet and a web browser