Learn how to access Terra-hosted datasets, curated showcase workspaces, and a workflow repository to build your workspace.
How to access the Terra Libraries
Click the main navigation menu (three horizontal lines icon) at the top left of any page and open the "Library" submenu.
Terra hosts both open- and controlled-access datasets. Some datasets have built-in data explorers for browsing, filtering, and searching the data. Explorers also let you use selection criteria to create custom subsets (cohorts) of data. Note: The number of available datasets - and the amount and type of data available in each - are growing, including public-access datasets.
Accessing controlled data from the Terra Data LibraryRegistering for Terra does not mean you can access all the hosted data. To access restricted data, you must be added to an Access policy for that resource. When you try to view data you cannot access, you'll be prompted to request access.
Terra Library datasets
Datasets have different explorers for filtering data to make custom cohorts. Note: Since the Data Library is always expanding, you may find additional datasets available on Terra.
AnVIL - CCDG, CMG, GTEx, eMERGE
The Genotype-Tissue Expression (GTEx) Program established a data resource and tissue bank to study the relationship between genetic variation and gene expression in multiple human tissues.
STAGE - TOPMedTrans-Omics for Precision Medicine (TOPMed)
Sponsored by the National Institutes of Health's National Heart, Lung, and Blood Institute (NHLBI), TOPMed is a program to generate scientific resources to enhance our understanding of fundamental biological processes that underlie heart, lung, blood, and sleep disorders (HLBS).
Nurses Health Study (NHS)
The Nurses' Health Study and Nurses' Health Study II are among the largest investigations into the risk factors for major chronic diseases in women.
Human Cell Atlas (HCA)
The Human Cell Atlas is made up of comprehensive reference maps of all human cells — the fundamental units of life — as a basis for understanding fundamental human biological processes and diagnosing, monitoring, and treating disease.
The Encyclopedia Of DNA Elements (ENCODE)
The ENCODE project aims to delineate all functional elements encoded in the human genome. To this end, ENCODE has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification.
The Cancer Genome Atlas (TCGA) is a dataset comprised of over two petabytes of genomic data, produced in a collaboration between the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI).
Using a Data Explorer
If you have permission to view a dataset, clicking browse data will open a data explorer. Here you can create your own subset of data (cohort) by choosing criteria relevant to your research. When you export the subset to your workspace, it will appear as a Cohort table in the Data tab.
In the clip above, we create a unique cohort by filtering for patients with a few types of cancers, and then limiting the cohort by gender.
Clicking Export > Send reveals an import data screen where you can select the workspace to send your custom cohort.
For step-by-step instructions on on how to use custom cohorts with SQL and BigQuery, see Accessing and analyzing custom cohorts with Data Explorer.
Showcase and Tutorials Library
One of the best ways to get started in Terra is to explore the curated Showcase Workspaces in the Library (access from the dropdown in the main navigation menu at the top left). These workspaces span a variety of use cases to show how peers design similar experiments. They are standardized for completeness and ease of use.
Classes of Showcase Workspaces
- Tutorial workspaces
- Specific analysis tools (i.e., WDLs, Jupyter Notebooks, Hail, Bioconductor)
- Experimental strategies (i.e., GWAS, Exome analysis, RNA-seq)
- Scientific domains (Cancer, infectious diseases, single-cell, immunology)
They're great as templates or to help reproduce instructive results and learn established methodologies - and you don't have to be logged into Terra to see them (though you will have to log in to make your own copy so you can work in it!).
Using Showcase workspaces as templates
You should find enough detail in the workspace description to analyze the included sample data. Or, if you prefer, cost and time estimates give you the confidence to run on your own data.
Code and Workflows Library
The Code and Workflows Library contains GATK Best Practices workflows and links to both Dockstore and the Broad Methods Repository (look in the right column). You'll find workflow components to run individually or to string together in these workflow repositories.
How to import workflows to your workspace
- See Finding the workflow you need (and its JSON) in the Methods Repository
- See How to import a workflow and its parameter file from Dockstore into Terra
All workflows in Terra use Workflow Description Language (WDL)