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## CFDE Portal Overview Video Outline

**INTRODUCTION**

*Showing CFDE homepage*

The Common Fund Data Ecosystem Portal is a metadata catalog containing data from Common Fund groups. 

The portal can be used to find data across Common Fund groups in one place and has the goal of making data more FAIR: findable, accessible, interoperable, and reusable.

*Scroll down to "Searchable Common Fund Data sets"*

The portal contains data from:

- 4D Nucleome Data Coordination and Integration Center
- Extracellular RNA Communication
- The Gabriella Miller Kids First Pediatric Research Program
- Genotype-Tissue Expression
- Glycosciences
- The Human BioMolecular Atlas Program
- The Human Microbiome Project
- Illuminating the Druggable Genome
- Library of Integrated Network-based Cellular Signatures
- Stimulating Peripheral Activity to Relieve Conditions
- University of California San Diego Metabolomics Workbench

**PREVIEW THE DATA**

*Scroll back up to "Preview the data"*

The information in the portal can be visualized with the "Preview the data" panel. The X and Y axis and data grouping can change the graph to give a snapshot of portal data, and a copy of this visualization can be downloaded.

*Pause speaking. Change graph axes and download graph images.*

**START YOUR SEARCH**

*Scroll to "Start your search" panel*

The "Start your search" panel also shows information about the data in the portal. The number of entries for each of these terms are displayed below each icon. For example, there are 334 anatomies in the portal at the time of recording.

Clicking a button will start a search with all entries of a selected type. These buttons are shortcuts to view all Anatomy, Assay, File, Biosample, Subject, Disease, Gene, or Compound entries.

*Click "Data Browser" tab*

You can find additional options under the "Data Browser" tab in bar at the top of the page. 

*Mouse to "Vocabulary" under "Data Browser" tab*

Clicking "Vocabulary" will display additional options.

**SEARCH FOR FILES**

*Click blank space to clear "Data Browser" drop down, then hover over "File" icon*

There are over 4.6 million files in the CFDE portal. This is a good place to start when searching for information. To start a search, click the "file" icon.

*Click on file to bring up filter page*

This page shows all of the files in the portal.

*Mouse over rows and columns*

Each row is a file in the portal. Each column contains additional information about the file. 

*Scroll horiztonally to show other columns, then scroll back*

Scrolling horizontally will display additional information categories, such as file format, data type, analysis type, and more.

**VIEW FILE DETAILS**

To view more information about a file, click "View details" on the left most column.

*Click "view details" for first file*

This will bring up a page with information about a file. The top of the page shows descriptive information for the file. 

*Scroll down to described biosample, subject, and collection*

Scrolling down shows the connections between this file in the portal. This shows the described biosample, subject, and collection associated with this file.

**FILTERING DATA**

*Scroll up, mouse over data browser, then select "FILE"*

Navigating back to the data browser and selecting "File" will again bring up all the files.

The panels under "Refine Search" on the left side of the screen are used for filtering data. Clicking a bar will expand it.

*Click on "Assay Type" and "Assay Type (Slim)"*

Some filters have a normal and slim version, which corresponds to the complexity of filter terms. For example, the "Assay Type" panel contains every assay used in the portal, while "Assay Type (slim)" contains a simplified list that may be useful for searching across Common Fund Data sets.

*Click on "Show More" at the bottom of "Assay Type"*

To view all of the possible filtering options, click "show more". You can scroll through pages of options 

*Scroll to bottom of page and click "Next at the bottom"*

or use a text search to find a term of interest. Check the box next to a filtered term of interest and hit submit to apply this filter.

*Type "electro*" into search bar. Select "Electron microscopy imaging assay" and hit "submit"*

**EXPORTING DATA**

Information about portal entries can be exported in a few ways. 

*Mouse over to Permalink*

The "Permalink" button will copy a URL to the current search filter. You can save this link or send it to a colleague to bring up this exact search.

*Mouse over to Export*

File information can be exported in BDBAG or NCPI file manifest formats. 

*Click clear all filters*

In order to find data that is accessible, navigate to the "Has Persistent ID" filter and select "Yes". These files will provide a URL or DRS ID that can be used to access a file.

*Copy and paste a URL into a browser*

**CONTENT REGISTRY**

A new feature of the portal is the content registry, which allows extra annotations on gene, anatomy, compound, and disease pages. To navigate to gene pages, use the "Data Browser" bar at the top of the page, mouse over "Vocabulary" and select "Gene".

*Mouse over Data Browser bar, mouse over "Vocabulary" and click "Gene"*

Select "View more" information about a gene to see information about it.

*Select "view more" for the first gene: DPM1, scroll to table*

On this page, you will see extra links and widgets. There is a table of external links at the top that is present on all gene pages.

The widgets below are only present on some gene pages, but will be expanded in the future. 

The first interactive widget shows gene expression information for each gene in different tissues through a GTEx API.

*Select "Specific sites only" and a few tissues*

The second widget shows the isoforms in a transcript list.

The third widget shows a context view of the gene through the UCSC Genome Browser.

**HOMEPAGE CONCLUSION**

*Scroll back up and hover over "log in"*

To get even more out of the portal, you can create an account. This will allow you to save favorite terms or create custom collections, and can facilitate access to controlled data sets.

To view an extended tour of our portal, you can watch a recording of a webinar on our training page.

*Show our URL of training page and webinar link*