Data Portal Release Notes

Version	Date
v2.0.0	February 8, 2024
v1.30.4	May 11, 2023
v1.30.0	July 8, 2022
v1.29.0	August 23, 2021
v1.28.0	May 17, 2021
v1.25.1	August 14, 2020
v1.25.0	July 2, 2020
v1.24.1	March 10, 2020
v1.23.1	December 10, 2019
v1.23.0	November 6, 2019
v1.22.0	July 31, 2019
v1.21.0	June 5, 2019
v1.20.0	April 17, 2019
v1.19.0	February 20, 2019
v1.18.0	December 18, 2018
v1.17.0	November 7, 2018
v1.16.0	September 27, 2018
v1.15.0	August 23, 2018
v1.14.0	June 13, 2018
v1.13.0	May 21, 2018
v1.12.0	February 15, 2018
v1.11.0	December 21, 2017
v1.10.0	November 16, 2017
v1.9.0	October 24, 2017
v1.8.0	August 22, 2017
v1.6.0	June 29, 2017
v1.5.2	May 9, 2017
v1.4.1	October 31, 2016
v1.3.0	September 7, 2016
v1.2.0	August 9th, 2016
v1.1.0	June 1st, 2016
v1.0.1	May 18, 2016

Release 2.0.0

GDC Product: GDC Data Portal
Release Date: February 8, 2024

New Features and Changes

GDC 2.0 is a major update to the original GDC Data Portal introduced in 2016. This latest version adopts a "cohort-centric" workflow, in which users build custom sets of cases to analyze, and introduces several new analysis tools. New features of GDC 2.0 include:

A cohort-centric workflow in which a cohort is first built and then analyzed using tools on the Data Portal. All of these functionalities can be reached from the Analysis Center.
- This includes a toolbar, that can be used to view or modify an existing cohort while using any analysis tool.
Core tools that compose the main functionalities of the GDC Data Portal:
- Cohort Builder: Build a cohort of cases using clinical and biospecimen properties
- Repository: Download files based on a specific cohort
- Projects: Browse, filter, and create cohorts based on GDC projects
Analysis tools that analyze specific cohorts:
- Mutation Frequency: Analyze somatic mutations that were called in the WXS and Targeted Sequencing pipelines and their associated genes
- Clinical Data Analysis: Analyze and visualize clinical data associated with your cohort
- Cohort Comparison: Analyze the properties of multiple cohorts
- Set Operations: Display a Venn diagram and compare/contrast cohorts or gene/mutation sets
- BAM Slicing Download: Download a specific region of a BAM file created by the GDC
- ProteinPaint: Visualize somatic mutations on a specific linear gene or chromosomal region
- Gene Expression Clustering: Visualizes gene expression clustering for a specific cohort
- Sequence Reads: Visualize the reads within a specific BAM file
- OncoMatrix: Visualize the most commonly mutated genes across a cohort

Bugs Fixed Since Last Release

Not applicable as this is the initial release of GDC 2.0.

Known Issues and Workarounds

Section 508 Accessibility:
- There are known Section 508 accessibility issues that the GDC plans to address in subsequent releases. If a user encounters a Section 508 barrier, please contact GDC Support (support@nci-gdc.datacommons.io) for assistance. Known Section 508 issues are identified below.
  - There are keyboard focus and navigation issues in analysis tools that use popup windows/overlays for custom user selections. Impacted analysis tools include BAM Slicing, Sequence Reads, Gene Expression Clustering, OncoMatrix, and ProteinPaint.
  - Heatmaps within the Sequence Reads tool do not contain concise alternative text or equivalent alternatives. Additionally, equivalent alternatives to the Box plots, QQ plots, Venn diagrams, and the body plot on the home page are not available.
  - In the Gene Expression Clustering tool and OncoMatrix, there are no headers for genes, clusters, and/or cases in the heatmap.
  - In the Gene Expression Clustering tool, color is used to convey gene expression values but there are no patterns to convey the same information as color. Color is also used in ProteinPaint and the Sequence Reads tool to convey consequence type but there are no distinguishing patterns.
  - Some text can be difficult to read on a small screen at a 200% zoom level.
  - Keyboard focus is not returned to the triggering element when modals are closed.
  - Assistive technologies may not behave correctly with some controls due to incorrect, missing, or redundant labels, attributes, or roles.
Cohorts:
- Cohorts are under active development and their behavior may change in the first several months after the release of GDC Portal 2.0. As this process may result in the loss of saved cohorts on the portal, we highly recommend exporting cohorts locally.
- Cohorts created based on CNV losses or gains may not have the correct composition when filtered by additional mutated genes. As a workaround, first filter by the mutated genes before creating cohorts based on CNV losses and gains.
- Cohorts filtered by mutated genes and SSMs not in those genes may unexpectedly result in 0 cases.
- When saving a cohort, the confirmation notification may be automatically dismissed before the saving dialog has closed.
- Using "Save As" to replace a cohort with itself will result in an error notification despite the replacement being successful.
- Cohorts containing FM-AD cases may not update correctly when users with dbGaP access to FM-AD (phs001179) log in or out. As a workaround, logging in before creating cohorts with FM-AD cases is recommended.
- If removing gene/mutation filters from a cohort temporarily results in 0 cases, cohorts may not display data in Mutation Frequency, Cohort Builder, and the summary charts. As a workaround, remove the gene and mutation filters, then add them back.
Survival Plot:
- The survival plot in Cohort Comparison does not display text indicating that there is insufficient survival data to plot.
- The survival plot in Mutation Frequency may flicker when the cohort has 0 cases.
- In Mutation Frequency, the downloaded image may display a survival curve when none is plotted within the portal.
- When the survival plot is zoomed in and an image is downloaded, the curves within the image may extend beyond the y-axis.
Cart:
- Spinners on the Download Cart and Download Associated Data buttons may be displayed longer than expected. This is a visual issue and does not affect the use of these buttons.
- More than 5 GB of files in total may be downloaded at a time via the browser if the user first attempts to download controlled access data without being logged in, then logs in via the information dialog displayed before continuing with the download.
- Using multiple browser tabs with the portal when adding or removing files from the cart may result in the cart not being updated as expected.
Mutation Frequency:
- Gene/mutation sets created from the tables in Mutation Frequency may contain 0 genes/mutations if the cohort has Available Data filters or Biospecimen filters.
- Attempting to download a TSV of all the mutations in the GDC may result in an error due to the length of time needed to generate the TSV. As a workaround, limit the number of mutations downloaded to 1.5 million.
Main Toolbar:
- Attempting to download the Clinical/Biospecimen TSV or JSON before the cohort has fully loaded may result in an error.
- The TSV of the cases table may not contain the expected tabs.
OncoMatrix:
- Manually deleting all genes will result in an error message "Error: Cannot read properties of undefined (reading 'lst')". The user can close and re-open OncoMatrix for use.
- Dragging genes only works once. After one gene is dragged to a new position, no genes can be dragged to new positions.
- In OncoMatrix, the cases may not get re-sorted as expected after a certain sequence of actions
ProteinPaint:
- A nested filter may be constructed for a Lollipop subtrack, e.g. sex=male AND ( primarysite=aa OR disease=bb ), but cannot be translated into GDC cohort filters. The translation code has a preliminary implementation that only works for "flat" filters without nesting.
- Cohorts cannot be created using the Create Cohort button in ProteinPaint for a single sample
- In ProteinPaint, the total number of samples in a category breakdown and the total number of samples in the sunburst ring are not based on a user's current cohort
- In ProteinPaint, when clicking on a sunburst ring, the sample table is not showing up
- In ProteinPaint, a Disco plot launched from the sunburst ring can show "undefined" in the plot header
- A ProteinPaint plot launched from OncoMatrix and Gene Expression Clustering does not observe the current cohort and displays mutated cases for all GDC
In the Gene Expression Clustering tool, if any part of the dendrogram is selected and the current cohort is modified, then the new dendrogram will render with scattered subtrees selected.
The "A" in the Allele Summary text is cut off in the Sequence Reads tool.
Quick Search may not display results if the the same search input is applied twice quickly. As a workaround, temporarily change the input before reentering the intended search.
Filters related to numeric values may display a smaller number than what the user entered within the Cohort Builder. This is a visual issue and does not affect the filters applied to the cohort.
When the Cohort Comparison tool is loading, the loading spinner may be displayed above the other areas of the Analysis Center.
The Repository tool may display an incorrect file size total of 0 bytes when filtering is applied within the tool and the active cohort contains Available Data filters.
The Slide Image Viewer will display a black image temporarily if a user zooms in on a slide then switches to another slide.
In Set Operations, the saving of gene and mutation sets may be unsuccessful if the saving dialog is manually dismissed after the Save button is clicked.
Clicking the X button on the Unexpected Error dialog box does not dismiss it. The workaround is to click the OK button.

Release 1.30.4

GDC Product: GDC Data Portal
Release Date: May 11, 2023

New Features and Changes

The GDC Legacy Archive has officially been retired.
- The Legacy Archive Portal can no longer be reached.
- Any API call to query files from the Legacy Archive will no longer work.
- Downloads for files from the Legacy Archive will work normally with manifests that were generated previously.

Bugs Fixed Since Last Release

The Clinical TSV download in the case entity page and cart now contain TSVs for pathology detail, follow up, and molecular test entities.
Fixed bug in which demographic information would not download as a TSV when diagnosis information was not available.

Known Issues and Workarounds

Pre-release Data Portal login is not supported on Internet Explorer or the last version of Edge (42). Edge 41 does login successfully.
Custom Facet Filters
- Some definitions are missing from the property list when adding custom facet file or case filters.
Visualizations
- Negative numbers may be displayed for the Missing value category in the Treatment node within a Clinical Analysis. This occurs with projects that have multiple treatment nodes per case. All other values should be accurate.
- SIFT and PolyPhen annotations are missing from the export JSON of the mutation table. They are present in the export TSV.
- Data Portal graphs cannot be exported as PNG images in Internet Explorer. Graphs can be exported in PNG or SVG format from Chrome or Firefox browsers . Internet Explorer does not display chart legend and title when re-opening previously downloaded SVG files, the recommendation is to open downloaded SVG files with another program.
Repository and Cart
- The annotation count in File table of Repository and Cart does not link to the Annotations page anymore. The user can navigate to the annotations through the annotation count in Repository - Case table.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release 1.30.0

GDC Product: GDC Data Portal
Release Date: July 8, 2022

New Features and Changes

None

Bugs Fixed Since Last Release

Fixed error in which the manifest could not be downloaded directly from the GDC Data Portal in certain instances.

Known Issues and Workarounds

Pre-release Data Portal login is not supported on Internet Explorer or the last version of Edge (42). Edge 41 does login successfully.
Custom Facet Filters
- Some definitions are missing from the property list when adding custom facet file or case filters.
Visualizations
- Negative numbers may be displayed for the Missing value category in the Treatment node within a Clinical Analysis. This occurs with projects that have multiple treatment nodes per case. All other values should be accurate.
- SIFT and PolyPhen annotations are missing from the export JSON of the mutation table. They are present in the export TSV.
- Data Portal graphs cannot be exported as PNG images in Internet Explorer. Graphs can be exported in PNG or SVG format from Chrome or Firefox browsers . Internet Explorer does not display chart legend and title when re-opening previously downloaded SVG files, the recommendation is to open downloaded SVG files with another program.
Repository and Cart
- The annotation count in File table of Repository and Cart does not link to the Annotations page anymore. The user can navigate to the annotations through the annotation count in Repository - Case table.
Legacy Archive
- The footer says version 1.9, but it is actually 1.13
- Filtering by vital_status does not function in the Legacy Archive due to updates in how this property has been indexed. A workaround is to perform the case level filtering in the GDC Data Portal and copy the filter string for use in the Legacy Archive or the legacy API.
- Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.
- Exporting the Cart table in JSON will export the GDC Archive file table instead of exporting the files in the Cart only.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release 1.29.0

GDC Product: GDC Data Portal
Release Date: August 23, 2021

New Features and Changes

None

Bugs Fixed Since Last Release

Fixed error in which the data summaries in the clinical analysis and cart pages were only partially displayed when viewed in Chrome v.91.0.4472.

Known Issues and Workarounds

Pre-release Data Portal login is not supported on Internet Explorer or the last version of Edge (42). Edge 41 does login successfully.
Custom Facet Filters
- Some definitions are missing from the property list when adding custom facet file or case filters.
Visualizations
- Negative numbers may be displayed for the Missing value category in the Treatment node within a Clinical Analysis. This occurs with projects that have multiple treatment nodes per case. All other values should be accurate.
- SIFT and PolyPhen annotations are missing from the export JSON of the mutation table. They are present in the export TSV.
- Data Portal graphs cannot be exported as PNG images in Internet Explorer. Graphs can be exported in PNG or SVG format from Chrome or Firefox browsers . Internet Explorer does not display chart legend and title when re-opening previously downloaded SVG files, the recommendation is to open downloaded SVG files with another program.
Repository and Cart
- The annotation count in File table of Repository and Cart does not link to the Annotations page anymore. The user can navigate to the annotations through the annotation count in Repository - Case table.
Legacy Archive
- The footer says version 1.9, but it is actually 1.13
- Filtering by vital_status does not function in the Legacy Archive due to updates in how this property has been indexed. A workaround is to perform the case level filtering in the GDC Data Portal and copy the filter string for use in the Legacy Archive or the legacy API.
- Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.
- Exporting the Cart table in JSON will export the GDC Archive file table instead of exporting the files in the Cart only.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release 1.28.0

GDC Product: GDC Data Portal
Release Date: May 17, 2021

New Features and Changes

New columns were added to the "molecular test" table at the bottom of the case entity page to display additional molecular test fields.

Bugs Fixed Since Last Release

None

Known Issues and Workarounds

When accessing the data portal with Chrome v.91.0.4472, users may experience some display errors. This includes the data summary in the clinical analysis and cart pages being only partially displayed.
Pre-release Data Portal login is not supported on Internet Explorer or the last version of Edge (42). Edge 41 does login successfully.
Custom Facet Filters
- Some definitions are missing from the property list when adding custom facet file or case filters.
Visualizations
- Negative numbers may be displayed for the Missing value category in the Treatment node within a Clinical Analysis. This occurs with projects that have multiple treatment nodes per case. All other values should be accurate.
- SIFT and PolyPhen annotations are missing from the export JSON of the mutation table. They are present in the export TSV.
- Data Portal graphs cannot be exported as PNG images in Internet Explorer. Graphs can be exported in PNG or SVG format from Chrome or Firefox browsers . Internet Explorer does not display chart legend and title when re-opening previously downloaded SVG files, the recommendation is to open downloaded SVG files with another program.
Repository and Cart
- The annotation count in File table of Repository and Cart does not link to the Annotations page anymore. The user can navigate to the annotations through the annotation count in Repository - Case table.
Legacy Archive
- The footer says version 1.9, but it is actually 1.13
- Filtering by vital_status does not function in the Legacy Archive due to updates in how this property has been indexed. A workaround is to perform the case level filtering in the GDC Data Portal and copy the filter string for use in the Legacy Archive or the legacy API.
- Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.
- Exporting the Cart table in JSON will export the GDC Archive file table instead of exporting the files in the Cart only.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release 1.25.1

GDC Product: GDC Data Portal
Release Date: August 14, 2020

New Features and Changes

API improvements were made to increase portal performance.

Bugs Fixed Since Last Release

None

Known Issues and Workarounds

Pre-release Data Portal login is not supported on Internet Explorer or the last version of Edge (42). Edge 41 does login successfully.
Custom Facet Filters
- Some definitions are missing from the property list when adding custom facet file or case filters.
Visualizations
- Negative numbers may be displayed for the Missing value category in the Treatment node within a Clinical Analysis. This occurs with projects that have multiple treatment nodes per case. All other values should be accurate.
- SIFT and PolyPhen annotations are missing from the export JSON of the mutation table. They are present in the export TSV.
- Data Portal graphs cannot be exported as PNG images in Internet Explorer. Graphs can be exported in PNG or SVG format from Chrome or Firefox browsers . Internet Explorer does not display chart legend and title when re-opening previously downloaded SVG files, the recommendation is to open downloaded SVG files with another program.
Repository and Cart
- The annotation count in File table of Repository and Cart does not link to the Annotations page anymore. The user can navigate to the annotations through the annotation count in Repository - Case table.
Legacy Archive
- The footer says version 1.9, but it is actually 1.13
- Filtering by vital_status does not function in the Legacy Archive due to updates in how this property has been indexed. A workaround is to perform the case level filtering in the GDC Data Portal and copy the filter string for use in the Legacy Archive or the legacy API.
- Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.
- Exporting the Cart table in JSON will export the GDC Archive file table instead of exporting the files in the Cart only.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release 1.25.0

GDC Product: GDC Data Portal
Release Date: July 2, 2020

New Features and Changes

Suppressed Experimental Strategy filter on the Exploration page as this currently filters for files with a particular strategy, not for cases. This may cause confusion amongst users. The filter will be re-instated in a future release once the logic is available to filter more appropriately for cases tied to a specific strategy.
Updated the filter control panel styling across the Portal to have clearer titles (e.g. "Search Cases" instead of "Cases" in the quick search box).
Made minor updates to the styling of the filter query display at the top of the Exploration page (spacing, borders).
Added an expand/collapse control to the quick search bar of Clinical tab on the Exploration page, to be consistent with other Exploration tabs.
Added a clear title above the counts in each filter control panel across the Portal (e.g. "# Cases", "# Genes", etc.).
Moved various action buttons above the results table on the Repository Page to more accessible locations.
Improved load time of the initial custom filter list on the Repository Page, when clicking "Add a Filter Filter" or "Add a Case/Biospecimen Filter".

Bugs Fixed Since Last Release

Fixed a bug in the Age at Diagnosis table on the Cohort Comparison page, where the # of cases in the table was not consistent with the # of cases shown when clicking the link to the Exploration page.
Fixed minor positional accuracy issue of the lollipop data points on the Protein Viewer.
Fixed bug on the Protein Viewer where, if clicking to switch between different lollipop data points, details of the previous lollipop was not closing.
Fixed bug where the quick search bar on the Exploratin Page's Genes filter tab was not expanding/collapsing properly.
Fixed bug in the pop-up warning message when adding or removing items from the Cart, where long filenames were spilling outside the border of the pop-up.
Fixed typo in the "View Cases in Exploration" button on the Repository page.
Fixed typo in the pop-up user consent message when downloading controlled files from the Cart.

Known Issues and Workarounds

Pre-release Data Portal login is not supported on Internet Explorer or the last version of Edge (42). Edge 41 does login successfully.
Custom Facet Filters
- Some definitions are missing from the property list when adding custom facet file or case filters.
Visualizations
- Negative numbers may be displayed for the Missing value category in the Treatment node within a Clinical Analysis. This occurs with projects that have multiple treatment nodes per case. All other values should be accurate.
- SIFT and PolyPhen annotations are missing from the export JSON of the mutation table. They are present in the export TSV.
- Data Portal graphs cannot be exported as PNG images in Internet Explorer. Graphs can be exported in PNG or SVG format from Chrome or Firefox browsers . Internet Explorer does not display chart legend and title when re-opening previously downloaded SVG files, the recommendation is to open downloaded SVG files with another program.
Repository and Cart
- The annotation count in File table of Repository and Cart does not link to the Annotations page anymore. The user can navigate to the annotations through the annotation count in Repository - Case table.
Legacy Archive
- The footer says version 1.9, but it is actually 1.13
- Filtering by vital_status does not function in the Legacy Archive due to updates in how this property has been indexed. A workaround is to perform the case level filtering in the GDC Data Portal and copy the filter string for use in the Legacy Archive or the legacy API.
- Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.
- Exporting the Cart table in JSON will export the GDC Archive file table instead of exporting the files in the Cart only.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release 1.24.1

GDC Product: GDC Data Portal
Release Date: March 10, 2020

New Features and Changes

Removed unnecessary comma and y-axis value from title of the mutation details pop-up in the Protein Viewer.
Added Tobacco Smoking Status field to the Exposures tab on the Case entity page.
Added a link to the Cart where users can access instructions for downloading the GDC Genome Build reference files.
Added logic to prevent duplicate fetching of data for Clinical Analysis survival plots and optimize rendering.
Added a button to clear searches for certain Portal search controls that were previously missing this ability.
Reduced whitespace between Oncogrid and its control panel to optimize spacing and layout.
Made entire Clinical Analysis results page responsive (card columns now scale & stack in response to the size of the browser window).
Replaced Clinical Analysis function for printing clinical cards to a single PDF file, with more flexible functionality to instead download all the cards in SVG and/or PNG format.
Added message to notify users when they try to access the Portal using Microsoft Internet Explorer, indicating which browsers are officially supported.
Added arrow icon to sortable columns across the Portal to indicate the current sort direction.

Bugs Fixed Since Last Release

Fixed bug where clicking a primary site on the Human Body Image was not re-directing to the Exploration page.
Fixed layout issue where long Annotation Notes were exceeding the border of the text box.
Fixed layout issue where the Repository header and action buttons were scaling and wrapping incorrectly if the browser window is shrunk beyond a certain threshold.
Fixed layout issue where the responsive Clinical Analysis Cards were clipping improperly as the browser window is shrunk beyond a certain threshold.
Fixed bug where the Clinical Tab on the Exploration page was crashing when entering a custom range of Years for the Age at Diagnosis facet.
Fixed various minor cosmetic and color issues in PNG, SVG downloads of the Clinical Analysis survival plots.
Fixed bug where the x-axis in PNG, SVG downloads of histograms across the Portal was being bolded incorrectly.
Fixed bug where the expand/collapse symbols in the UI were incorrectly being exported in the TSV download of the Projects table.
Fixed bug where Oncogrid's modal for customizing colors could not be scrolled below the fold if it was shrunk beyond a certain threshold.
Fixed incorrect DTT hyperlink in the GDC Apps menu.
Fixed bug where the "dbSNP rs ID" facet could not be minimized in the Exploration page's Mutations facet tab.
Fixed layout issue where the Portal's header incorrectly overlaps some content when a notification banner is displayed.
Fixed some minor layout & styling issues in the Exploration page's facets panel.
Fixed bug where the Case ID on the Exploration page's Cases facet tab was not searchable in certain scenarios.
Fixed bug where the Expand/Collapse button state was not changing properly when being used in the Biospecimen section of the Case entity page.
Fixed incorrect capitalization of "dbGaP" in the Summary section of the Project entity page.
Fixed layout issue where the Advanced Search query box on the Repository page could expanded beyond the margins of the box's border.

Known Issues and Workarounds

Pre-release Data Portal login is not supported on Internet Explorer or the last version of Edge (42). Edge 41 does login successfully.
Custom Facet Filters
- Some definitions are missing from the property list when adding custom facet file or case filters.
Visualizations
- Negative numbers may be displayed for the Missing value category in the Treatment node within a Clinical Analysis. This occurs with projects that have multiple treatment nodes per case. All other values should be accurate.
- SIFT and PolyPhen annotations are missing from the export JSON of the mutation table. They are present in the export TSV.
- Data Portal graphs cannot be exported as PNG images in Internet Explorer. Graphs can be exported in PNG or SVG format from Chrome or Firefox browsers . Internet Explorer does not display chart legend and title when re-opening previously downloaded SVG files, the recommendation is to open downloaded SVG files with another program.
Repository and Cart
- The annotation count in File table of Repository and Cart does not link to the Annotations page anymore. The user can navigate to the annotations through the annotation count in Repository - Case table.
Legacy Archive
- The footer says version 1.9, but it is actually 1.13
- Filtering by vital_status does not function in the Legacy Archive due to updates in how this property has been indexed. A workaround is to perform the case level filtering in the GDC Data Portal and copy the filter string for use in the Legacy Archive or the legacy API.
- Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.
- Exporting the Cart table in JSON will export the GDC Archive file table instead of exporting the files in the Cart only.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release 1.23.1

GDC Product: GDC Data Portal
Release Date: December 10, 2019

New Features and Changes

Updated display of x-axis units on the homepage Human Body chart to more easily display increased case counts for newly-added projects

Bugs Fixed Since Last Release

None

Known Issues and Workarounds

Pre-release Data Portal login is not supported on Internet Explorer or the last version of Edge (42). Edge 41 does login successfully.
Custom Facet Filters
- Some definitions are missing from the property list when adding custom facet file or case filters.
Visualizations
- Negative numbers may be displayed for the Missing value category in the Treatment node within a Clinical Analysis. This occurs with projects that have multiple treatment nodes per case. All other values should be accurate.
- SIFT and PolyPhen annotations are missing from the export JSON of the mutation table. They are present in the export TSV.
- Data Portal graphs cannot be exported as PNG images in Internet Explorer. Graphs can be exported in PNG or SVG format from Chrome or Firefox browsers . Internet Explorer does not display chart legend and title when re-opening previously downloaded SVG files, the recommendation is to open downloaded SVG files with another program.
Repository and Cart
- The annotation count in File table of Repository and Cart does not link to the Annotations page anymore. The user can navigate to the annotations through the annotation count in Repository - Case table.
Legacy Archive
- The footer says version 1.9, but it is actually 1.13
- Filtering by vital_status does not function in the Legacy Archive due to updates in how this property has been indexed. A workaround is to perform the case level filtering in the GDC Data Portal and copy the filter string for use in the Legacy Archive or the legacy API.
- Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.
- Exporting the Cart table in JSON will export the GDC Archive file table instead of exporting the files in the Cart only.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release 1.23.0

GDC Product: GDC Data Portal
Release Date: November 6, 2019

New Features and Changes

Added Clinical Data Analysis feature that allows Users to:
- Explore clinical data via the new Clinical Tab on the Exploration page.
- Build custom Case sets based on that clinical data for later analysis.
- Create an analysis to examine the clinical variables in a Case set, using various tools including histograms, survival plots, box plots, QQ plots, and custom binning.
- Download the data (as TSV, JSON) and plots (as PNG, SVG) of each clinical variable in an anlysis.
- Save an analysis to local storage to resume later (as long as storage is not cleared).
Added links to CIViC annotations on the Gene and Mutation entity pages.
Updated the default Top Mutated Genes histogram on the Exploration page to display only COSMIC Genes by default.
Added Follow-Ups tab and nested Molecular Tests to Case entity page.
Added text to BAM slicing modal to instruct Users how to access unmapped reads.

Bugs Fixed Since Last Release

Fixed font in exported PNGs, SVGs to be consistent with the Portal UI.
Made custom Case and File filters in the Repository page case insensitive.
Fixed bug where pfam domains in Protein Viewer could not be clicked in Firefox.
Fixed bug where TSV download button could not be clicked in MS Edge.
Fixed controlled access alert pop-up in the Cart so that the modal disappears correctly once the User has successfully logged in and initiated the download.

Known Issues and Workarounds

Pre-release Data Portal login is not supported on Internet Explorer or the last version of Edge (42). Edge 41 does login successfully.
Custom Facet Filters
- Some definitions are missing from the property list when adding custom facet file or case filters.
Visualizations
- Negative numbers may be displayed for the Missing value category in the Treatment node within a Clinical Analysis. This occurs with projects that have multiple treatment nodes per case. All other values should be accurate.
- SIFT and PolyPhen annotations are missing from the export JSON of the mutation table. They are present in the export TSV.
- Data Portal graphs cannot be exported as PNG images in Internet Explorer. Graphs can be exported in PNG or SVG format from Chrome or Firefox browsers . Internet Explorer does not display chart legend and title when re-opening previously downloaded SVG files, the recommendation is to open downloaded SVG files with another program.
Repository and Cart
- The annotation count in File table of Repository and Cart does not link to the Annotations page anymore. The user can navigate to the annotations through the annotation count in Repository - Case table.
Legacy Archive
- The footer says version 1.9, but it is actually 1.13
- Filtering by vital_status does not function in the Legacy Archive due to updates in how this property has been indexed. A workaround is to perform the case level filtering in the GDC Data Portal and copy the filter string for use in the Legacy Archive or the legacy API.
- Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.
- Exporting the Cart table in JSON will export the GDC Archive file table instead of exporting the files in the Cart only.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release 1.22.0

GDC Product: GDC Data Portal
Release Date: July 31, 2019

New Features and Changes

Replaced existing Clinical, Biospecimen columns on the Projects page with 4 columns: Clinical, Clinical Supplement, Biospecimen, Biospecimen Supplement. The Clinical and Biospecimen columns now link directly to the project page, and their counts indicate the total cases in the project. The Clinical Supplement and Biospecimen Supplement columns work the same as the old Clinical and Biospecimen columns - They link to the Repository page with Files filtered based on the Project and Data Category (Clinical or Biospecimen).
Added a new icon to the GDC Apps menu, which links to the GDC Publications website page.
Added the Synchronous Malignancy field to the Diagnoses / Treatments tab on the Case entity page.
Added the Pack Years Smoked field to the Exposures tab on the Case entity page.
Increased length of x-axis labels on histograms to 10 characters so that projects with names that are typically standard 10 chars will display fully (e.g. most TCGA projects like TCGA-BRCA).

Bugs Fixed Since Last Release

Fixed bug where the PNG, SVG files for the Overall Survival Plot could not be downloaded.

Known Issues and Workarounds

Pre-release Data Portal login is not supported on Internet Explorer or the last version of Edge (42). Edge 41 does login successfully.
Custom Facet Filters
- Some definitions are missing from the property list when adding custom facet file or case filters.
Visualizations
- SIFT and PolyPhen annotations are missing from the export JSON of the mutation table. They are present in the export TSV.
- Data Portal graphs cannot be exported as PNG images in Internet Explorer. Graphs can be exported in PNG or SVG format from Chrome or Firefox browsers . Internet Explorer does not display chart legend and title when re-opening previously downloaded SVG files, the recommendation is to open downloaded SVG files with another program.
Repository and Cart
- The annotation count in File table of Repository and Cart does not link to the Annotations page anymore. The user can navigate to the annotations through the annotation count in Repository - Case table.
Legacy Archive
- Filtering by vital_status does not function in the Legacy Archive due to updates in how this property has been indexed. A workaround is to perform the case level filtering in the GDC Data Portal and copy the filter string for use in the Legacy Archive or the legacy API.
- Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.
- Exporting the Cart table in JSON will export the GDC Archive file table instead of exporting the files in the Cart only.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release 1.21.0

GDC Product: GDC Data Portal
Release Date: June 5, 2019

New Features and Changes

Changed all Survival Plots to display the Duration (x-axis) in years instead of days.
Updated data references to clinical properties throughout the Portal to match the underlying changes in the GDC data dictionary.

Bugs Fixed Since Last Release

Fixed bug where X-axis labels in histograms were cut off when displayed.
Renamed the 'Experimental Strategies' facet on the Projects page to singular form.
Fixed bug where columns with a % value of infinity (due to division by zero) show as 'NaN%'. Replaced instead with a label of '--'.
Fixed bug where the download button in the cart access banner was still disabled after a user logged in from the banner. Instead, the experience is now improved so that after login, the banner is closed and the user must explicitly click 'Download' again.
Fixed bug where if a new user logs into the Portal and views their profile, the app crashes if the user has no projects assigned yet.
Fixed bug where Survival Rate numbers in the Survival Plot plot y-axis did not scale properly and overlapped into the axis lines.

Known Issues and Workarounds

Pre-release Data Portal login is not supported on Internet Explorer or the last version of Edge (42). Edge 41 does login successfully.
Custom Facet Filters
- Some definitions are missing from the property list when adding custom facet file or case filters.
Visualizations
- SIFT and PolyPhen annotations are missing from the export JSON of the mutation table. They are present in the export TSV.
- Data Portal graphs cannot be exported as PNG images in Internet Explorer. Graphs can be exported in PNG or SVG format from Chrome or Firefox browsers . Internet Explorer does not display chart legend and title when re-opening previously downloaded SVG files, the recommendation is to open downloaded SVG files with another program.
Repository and Cart
- The annotation count in File table of Repository and Cart does not link to the Annotations page anymore. The user can navigate to the annotations through the annotation count in Repository - Case table.
Legacy Archive
- Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.
- Exporting the Cart table in JSON will export the GDC Archive file table instead of exporting the files in the Cart only.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release 1.20.0

GDC Product: GDC Data Portal
Release Date: April 17, 2019

New Features and Changes

Upgraded the Portal to use the latest React Javascript library (version 16.8)

Bugs Fixed Since Last Release

None

Known Issues and Workarounds

Pre-release Data Portal login is not supported on Internet Explorer or the last version of Edge (42). Edge 41 does login successfully.
Custom Facet Filters
- Some definitions are missing from the property list when adding custom facet file or case filters.
Visualizations
- SIFT and PolyPhen annotations are missing from the export JSON of the mutation table. They are present in the export TSV.
- Data Portal graphs cannot be exported as PNG images in Internet Explorer. Graphs can be exported in PNG or SVG format from Chrome or Firefox browsers . Internet Explorer does not display chart legend and title when re-opening previously downloaded SVG files, the recommendation is to open downloaded SVG files with another program.
Repository and Cart
- The annotation count in File table of Repository and Cart does not link to the Annotations page anymore. The user can navigate to the annotations through the annotation count in Repository - Case table.
Legacy Archive
- Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.
- Exporting the Cart table in JSON will export the GDC Archive file table instead of exporting the files in the Cart only.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release 1.19.0

GDC Product: GDC Data Portal
Release Date: February 20, 2019

New Features and Changes

Added support for viewing of controlled-access mutations in the Data Portal
Added a new data access notification to remind logged-in users with access to controlled data that they need to follow their data use agreement. The message is fixed at the top of the Portal.
Added the ability to search for previous versions of files. If the user enters the UUID of a previous version that cannot be found, the Portal returns the UUID of the latest version available.
Renamed the Data Category for "Raw Sequencing Data" to "Sequencing Reads" throughout the portal where this appears, to be consistent with the Data Dictionary.
Added a link in the Portal footer to the GDC support page.

Bugs Fixed Since Last Release

Fixed bug where Survival Plot button never stops loading if plotting mutated vs. non-mutated cases for a single Gene.
Fixed inconsistent button styling when downloading controlled Downstream Analyses Files from File Entity page.
Removed unnecessary Survival column from Arrange Columns button on Case Entity, Gene Entity pages.
Removed unnecessary whitespace from pie charts on Repository page.
Added missing File Size unit to Clinical Supplement File, Biospecimen Supplement File tables on Case Entity page.
Fixed bug where clicking on Case Counts in Projects Graph tab was going to the Repository Files tab instead of the Cases tab.
Fixed bug where the counts shown beside customer filters on the Repository Cases tab were not updating when filtering on other facets.
Fixed bug where clicking the # of Affected Cases denominator on the Gene page's Most Frequent Somatic Mutations table displayed an incorrect number of Cases.

Known Issues and Workarounds

Pre-release Data Portal login is not supported on Internet Explorer or the last version of Edge (42). Edge 41 does login successfully.
Custom Facet Filters
- Some definitions are missing from the property list when adding custom facet file or case filters.
Visualizations
- SIFT and PolyPhen annotations are missing from the export JSON of the mutation table. They are present in the export TSV.
- Data Portal graphs cannot be exported as PNG images in Internet Explorer. Graphs can be exported in PNG or SVG format from Chrome or Firefox browsers . Internet Explorer does not display chart legend and title when re-opening previously downloaded SVG files, the recommendation is to open downloaded SVG files with another program.
Repository and Cart
- The annotation count in File table of Repository and Cart does not link to the Annotations page anymore. The user can navigate to the annotations through the annotation count in Repository - Case table.
Legacy Archive
- Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.
- Exporting the Cart table in JSON will export the GDC Archive file table instead of exporting the files in the Cart only.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release 1.18.0

GDC Product: GDC Data Portal
Release Date: December 18, 2018

New Features and Changes

A new data access message has been added when downloading controlled data. Users must agree to abide by data access control policies when downloading controlled data.
In the Mutation free-text search in Exploration, mutation display now includes the UUID, genomic location, and matched search term for easier mutation searching.
The ability to sort on ranked columns has been made available.

Bugs Fixed Since Last Release

In some cases, text was being cut off on the Project page visualization tab. Text is no longer cut off.
HGNC link on Gene page broke as the source format url changed; The format was updated and the link is now functional
In the biospecimen details on the Case page, the cart icon would disappear once clicked. It now is always visible.

Known Issues and Workarounds

Pre-release Data Portal login is not supported on Internet Explorer or the last version of Edge (42). Edge 41 does login successfully.
Custom Facet Filters
- Some definitions are missing from the property list when adding custom facet file or case filters.
Visualizations
- SIFT and PolyPhen annotations are missing from the export JSON of the mutation table. They are present in the export TSV.
- Data Portal graphs cannot be exported as PNG images in Internet Explorer. Graphs can be exported in PNG or SVG format from Chrome or Firefox browsers . Internet Explorer does not display chart legend and title when re-opening previously downloaded SVG files, the recommendation is to open downloaded SVG files with another program.
Repository and Cart
- The annotation count in File table of Repository and Cart does not link to the Annotations page anymore. The user can navigate to the annotations through the annotation count in Repository - Case table.
Legacy Archive
- Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.
- Exporting the Cart table in JSON will export the GDC Archive file table instead of exporting the files in the Cart only.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release 1.17.0

GDC Product: GDC Data Portal
Release Date: November 7, 2018

New Features and Changes

Copy Number Variation (CNV) data derived from GISTIC results are now available in the portal:
- View number of CNV events on a gene in a cohort in the Explore Gene table tab
- Explore CNVs associated with a gene on the Gene Entity Page
- Explore CNVs concurrently with mutations on the Oncogrid with new visualization

Bugs Fixed Since Last Release

None

Known Issues and Workarounds

Custom Facet Filters
- Some definitions are missing from the property list when adding custom facet file or case filters.
Visualizations
- SIFT and PolyPhen annotations are missing from the export JSON of the mutation table. They are present in the export TSV.
- Data Portal graphs cannot be exported as PNG images in Internet Explorer. Graphs can be exported in PNG or SVG format from Chrome or Firefox browsers . Internet Explorer does not display chart legend and title when re-opening previously downloaded SVG files, the recommendation is to open downloaded SVG files with another program.
Repository and Cart
- The annotation count in File table of Repository and Cart does not link to the Annotations page anymore. The user can navigate to the annotations through the annotation count in Repository - Case table.
Legacy Archive
- Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.
- Exporting the Cart table in JSON will export the GDC Archive file table instead of exporting the files in the Cart only.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release 1.16.0

GDC Product: GDC Data Portal
Release Date: September 27, 2018

New Features and Changes

Updated Human Body Image to aggregate all current primary sites to available Major Primary Sites

Bugs Fixed Since Last Release

Fixed link on cart download error popup
Updated Cancer Distribution table to have dropdown menus for primary_site and disease_type
Updated Y-axis label on Top Mutated Cancer Genes in Selected Projects Graph
Updated Set Operation Image to remove stray text

Known Issues and Workarounds

Advanced Search
- For advanced search and custom file facet filtering there are some properties that will appear as options that are no longer supported (e.g. file_state).
Custom facet filters
- Some definitions are missing from the property list when adding custom facet file or case filters.
Visualizations
- SIFT and PolyPhen annotations are missing from the Export JSON of the mutation table. They are present in the export TSV.
- Data Portal graphs cannot be exported as PNG images in Internet Explorer. Graphs can be exported in PNG or SVG format from Chrome or Firefox browsers . Internet Explorer does not display chart legend and title when re-opening previously downloaded SVG files, the recommendation is to open downloaded SVG files with another program.
Repository and Cart
- The annotation count in File table of Repository and Cart does not link to the Annotations page anymore. The user can navigate to the annotations through the annotation count in Repository - Case table.
Legacy Archive
- Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.
- Exporting the Cart table in JSON will export the GDC Archive file table instead of exporting the files in the Cart only.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release 1.15.0

GDC Product: GDC Data Portal
Release Date: August 23, 2018

New Features and Changes

File Versions are now visible in the "File Versions" section on the File Entity Page.
"View Files in Repository" and "View Cases in Repository" button methods were updated to work faster.

Bugs Fixed Since Last Release

Fixed warning messages that prompted users to login even when already logged in. Error warnings now correctly prompt users to reference dbGAP for data access if already signed in.
Fixed error where you could click Go on Case ID wildcard facet before inputting any data.
Fixed cart header to be a consistent color for the whole table.
Fixed error where you could save a set with no name or items, which resulted in an infinite spinner.
Fixed table width issue when FM-AD was selected as a filter.
Updated broken help link on Advanced Query.

Known Issues and Workarounds

Advanced Search
- For advanced search and custom file facet filtering there are some properties that will appear as options that are no longer supported (e.g. file_state).
Custom facet filters
- Some definitions are missing from the property list when adding custom facet file or case filters.
Visualizations
- SIFT and PolyPhen annotations are missing from the Export JSON of the mutation table. They are present in the export TSV.
- Data Portal graphs cannot be exported as PNG images in Internet Explorer. Graphs can be exported in PNG or SVG format from Chrome or Firefox browsers . Internet Explorer does not display chart legend and title when re-opening previously downloaded SVG files, the recommendation is to open downloaded SVG files with another program.
Repository and Cart
- The annotation count in File table of Repository and Cart does not link to the Annotations page anymore. The user can navigate to the annotations through the annotation count in Repository - Case table.
Legacy Archive
- Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.
- Exporting the Cart table in JSON will export the GDC Archive file table instead of exporting the files in the Cart only.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release 1.14.0

GDC Product: GDC Data Portal
Release Date: June 13, 2018

New Features and Changes

Added new Experimental Strategies Diagnostic Slide Image, Bisulfite-Seq, ChIP-Seq, and ATAC-Seq to Case and Project entity pages.

Bugs Fixed Since Last Release

Fixed download of clinical and biospecimen data from the Repository when Case table rows are selected.

Known Issues and Workarounds

Custom facet filters
- Some definitions are missing from the property list when adding custom facet file or case filters.
Visualizations
- SIFT and PolyPhen annotations are missing from the Export JSON of the mutation table. They are present in the export TSV.
- Data Portal graphs cannot be exported as PNG images in Internet Explorer. Graphs can be exported in PNG or SVG format from Chrome or Firefox browsers . Internet Explorer does not display chart legend and title when re-opening previously downloaded SVG files, the recommendation is to open downloaded SVG files with another program.
Repository and Cart
- When user is logged in and try to download a controlled file he does not have access to, he's prompted to log in. He should be promted to request access.
- The annotation count in File table of Repository and Cart does not link to the Annotations page anymore. The user can navigate to the annotations through the annotation count in Repository - Case table.
Legacy Archive
- Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.
- Exporting the Cart table in JSON will export the GDC Archive file table instead of exporting the files in the Cart only.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release details are maintained in the GDC Data Portal Change Log.

Release 1.13.0

GDC Product: GDC Data Portal
Release Date: May 21, 2018

New Features and Changes

Added new image viewer functionality for viewing tissue slide images

Bugs Fixed Since Last Release

Updated gene reference labels on gene entity page to adhere to preferred usage
Fixed issue with user profile displaying all projects twice

Known Issues and Workarounds

Custom facet filters
- Some definitions are missing from the property list when adding custom facet file or case filters.
Visualizations
- SIFT and PolyPhen annotations are missing from the Export JSON of the mutation table. They are present in the export TSV.
- Data Portal graphs cannot be exported as PNG images in Internet Explorer. Graphs can be exported in PNG or SVG format from Chrome or Firefox browsers . Internet Explorer does not display chart legend and title when re-opening previously downloaded SVG files, the recommendation is to open downloaded SVG files with another program.
Repository and Cart
- When user is logged in and try to download a controlled file he does not have access to, he's prompted to log in. He should be promted to request access.
- The annotation count in File table of Repository and Cart does not link to the Annotations page anymore. The user can navigate to the annotations through the annotation count in Repository - Case table.
Legacy Archive
- Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.
- Exporting the Cart table in JSON will export the GDC Archive file table instead of exporting the files in the Cart only.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release details are maintained in the GDC Data Portal Change Log.

Release 1.12.0

GDC Product: GDC Data Portal
Release Date: February 15, 2018

New Features and Changes

Provided the ability to export clinical and biospecimen data in a TSV format from the Case, Project, Exploration, Repository and Cart pages.
Removed from the Project entity page the sections about mutated genes, somatic mutations and affected Cases and replaced with a button "Explore data" that will open the Exploration page filtered on the project. Indeed the Exploration page provides the same information. Added a breakdown of cases per primary site for a Project entity page with multiple primary sites (e.g. FM-AD).
Added display of coding DNA change and impacts for all the transcripts (instead of canonical transcript only) in the Mutation entity page - Consequences section. In the mutation table (e.g. in Repository), the impacts and consequences are displayed for the canonical transcript only.

Bugs Fixed Since Last Release

Replaced the suggested set name when saving a set with selected items, e.g. for case set the suggested name is now "Custom Case selection".
Fixed the protein viewer to indicate when there are overlapping mutations. Mousing over the dot showing multiple mutations will open a right panel with the list of all the corresponding mutations.
Fixed Mutation entity page - Consequences table: the "Coding DNA Change" column is now populated for all the transcripts.
Fixed download clinical and download biospecimen actions from TCGA-BRCA project.
Fixed facet behavior that did not reset back to showing all options after pressing reset-arrow.
Fixed error when user was trying to save a set with no value in the textbox "Save top:".
Removed somatic mutation section from Case entity page for cases with no open-access mutation data (e.g. FM-AD or TARGET cases).
Fixed error where a blank page appears after unselecting Cancer Gene Census mutation facet.
Fixed duplicated date in sample sheet name (e.g. gdc_sample_sheet_YYYY-MM-DD_HH-MM.tsv.YYYY-MM-DD_HH-MM.tsv).
Fixed error when annotations were not downloaded along with the file (in File entity page and Cart).

Known Issues and Workarounds

Custom facet filters
- Some definitions are missing from the property list when adding custom facet file or case filters.
Visualizations
- SIFT and PolyPhen annotations are missing from the Export JSON of the mutation table. They are present in the export TSV.
- Data Portal graphs cannot be exported as PNG images in Internet Explorer. Graphs can be exported in PNG or SVG format from Chrome or Firefox browsers . Internet Explorer does not display chart legend and title when re-opening previously downloaded SVG files, the recommendation is to open downloaded SVG files with another program.
Repository and Cart
- When user is logged in and try to download a controlled file he does not have access to, he's prompted to log in. He should be promted to request access.
- The annotation count in File table of Repository and Cart does not link to the Annotations page anymore. The user can navigate to the annotations through the annotation count in Repository - Case table.
Legacy Archive
- Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.
- Exporting the Cart table in JSON will export the GDC Archive file table instead of exporting the files in the Cart only.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release details are maintained in the GDC Data Portal Change Log.

Release 1.11.0

GDC Product: GDC Data Portal
Release Date: December 21, 2017

New Features and Changes

Updated UI to support SIFT and Polyphen annotations
A Sample Sheet can now be created which allows easy association between file names and the case and sample submitter_id
Updated Advanced Search page to include options to Add All Files to Cart, Download Manifest, and View X Cases in Exploration
Provide clear message rather than blank screen if survival plots cannot be calculated for particular cohort comparison
Display sample_type on associated entities section on file page
Allows for special characters in case, gene, and mutation set upload (-, :, >, .)

Bugs Fixed Since Last Release

Fixed error when trying to download large number of files from the Legacy Archive cart
Fixed number of annotations displayed in Legacy Archive for particular entities
Replaced missing bars to indicate proportion of applicable files and cases on project entity page in Cases and File Counts by Data Category table
Fixed project page display when projects are selected that contain no mutation data in the facet panel
Fixed error where exporting case sets as TSV included fewer cases than the total
Fixed error in exploration section when adding custom facets. Previously selecting 'Only show fields with values' did not result in the expected behavior
Fixed error where number of associated entities for a file was showing an incorrect number

Known Issues and Workarounds

Sample sheet will download with a file name including the date duplicated (e.g. gdc_sample_sheet_YYYY-MM-DD_HH-MM.tsv.YYYY-MM-DD_HH-MM.tsv)
Custom facet filters
- Definitions are missing from the property list when adding custom facet file or case filters
Visualizations
- Data Portal graphs cannot be exported as PNG images in Internet Explorer. Graphs can be exported in PNG or SVG format from Chrome or Firefox browsers . Internet Explorer does not display chart legend and title when re-opening previously downloaded SVG files, the recommendation is to open downloaded SVG files with another program.
- In the protein viewer there may be overlapping mutations. In this case mousing over a point will just show a single mutation and the other mutations at this location will not be apparent.
Entity page
- On the mutation entity page, in the Consequences Table, the "Coding DNA Change" column is not populated for rows that do not correspond to the canonical mutation.
Repository and Cart
- The annotation count in File table of Repository and Cart does not link to the Annotations page anymore. The user can navigate to the annotations through the annotation count in Repository - Case table.
Legacy Archive
- Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.
- Exporting the Cart table in JSON will export the GDC Archive file table instead of exporting the files in the Cart only.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release details are maintained in the GDC Data Portal Change Log.

Release 1.10.0

GDC Product: GDC Data Portal
Release Date: November 16, 2017

New Features and Changes

Support for uploading Case and Mutation sets in Exploration page
Support for saving, editing, removing Case, Gene and Mutation sets in the Exploration page
Added a Managed Sets menu where the user can see their saved sets
Added an Analysis menu with two analyses: Set Operation and Cohort Comparison
Added a User Profile page that shows all the projects and permissions assigned to the user: available in the username dropdown after the user logs in

Bugs Fixed Since Last Release

Project page
- On the project page, the Summary Case Count link should open the case tab on the Repository page - instead it opens the file page

Known Issues and Workarounds

Custom facet filters
- Definitions are missing from the property list when adding custom facet file or case filters
- Selecting 'Only show fields with values' will show some fields without values in the Repository section. This works correctly under the Exploration section.
Visualizations
- Data Portal graphs cannot be exported as PNG images in Internet Explorer. Graphs can be exported in PNG or SVG format from Chrome or Firefox browsers . Internet Explorer does not display chart legend and title when re-opening previously downloaded SVG files, the recommendation is to open downloaded SVG files with another program.
- In the protein viewer there may be overlapping mutations. In this case mousing over a point will just show a single mutation and the other mutations at this location will not be apparent.
Entity page
- On the mutation entity page, in the Consequences Table, the "Coding DNA Change" column is not populated for rows that do not correspond to the canonical mutation.
Repository and Cart
- The annotation count in File table of Repository and Cart does not link to the Annotations page anymore. The user can navigate to the annotations through the annotation count in Repository - Case table.
Legacy Archive
- Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.
- Exporting the Cart table in JSON will export the GDC Archive file table instead of exporting the files in the Cart only.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release details are maintained in the GDC Data Portal Change Log.

Release 1.9.0

GDC Product: GDC Data Portal
Release Date: October 24, 2017

New Features and Changes

Support for projects with multiple primary sites per project
Support for slides that are linked to sample rather than portion

Bugs Fixed Since Last Release

None

Known Issues and Workarounds

Visualizations
- Data Portal graphs cannot be exported as PNG images in Internet Explorer. Graphs can be exported in PNG or SVG format from Chrome or Firefox browsers . Internet Explorer does not display chart legend and title when re-opening previously downloaded SVG files, the recommendation is to open downloaded SVG files with another program.
- In the protein viewer there may be overlapping mutations. In this case mousing over a point will just show a single mutation and the other mutations at this location will not be apparent.
Project page
- On the project page, the Summary Case Count link should open the case tab on the Repository page - instead it opens the file page
Entity page
- On the mutation entity page, in the Consequences Table, the "Coding DNA Change" column is not populated for rows that do not correspond to the canonical mutation.
Repository and Cart
- The annotation count in File table of Repository and Cart does not link to the Annotations page anymore. The user can navigate to the annotations through the annotation count in Repository - Case table.
Legacy Archive
- Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.
- Exporting the Cart table in JSON will export the GDC Archive file table instead of exporting the files in the Cart only.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release details are maintained in the GDC Data Portal Change Log.

Release 1.8.0

GDC Product: GDC Data Portal
Release Date: August 22, 2017

New Features and Changes

Major features/changes:

A feature that links the exploration and repository pages was added. For example:
- In the exploration page, cases with a specific mutation could be selected. This set could then be linked to the repository page to download the data files associated with these cases.
- In the repository menu, the user can select cases associated with specific files. The set could then be linked to exploration page to view the variants associated with this set of cases.
Users can now upload a custom gene list to the exploration page and leverage the GDC search and visualization features for cases and variants associated with the gene set.
Filters added for the gene entity page. For example:
- Clicking on a mutated gene from the project page will display mutations associated with the gene that are present in this project (filtered protein viewer, etc.).
- Clicking on a mutated gene from the exploration page will display the mutations associated with the gene filtered by additional search criteria, such as "primary site is Kidney and mutation impact is high".
UUIDs are now hidden from tables and charts to simplify readability. The UUIDs can still be exported and viewed in the tables using the "arrange columns" feature. In the mutation table, UUIDs are automatically exported.
Mutation entity page - one consequence per transcript is shown (10 rows by default) in the consequence table. The user should display all rows before exporting the table.

Bugs Fixed Since Last Release

Exploration
- Combining "Variant Caller" mutation filter with a case filter will display incorrect counts in the mutation facet. The number of mutations in the resulting mutation table is correct.
- Mutation table: it is difficult to click on the denominator in "#Affected Cases in Cohort" column displayed to the left side of the bar. The user should click at a specific position at the top of the number to be able to go to the corresponding link.

Known Issues and Workarounds

Visualizations
- Data Portal graphs cannot be exported as PNG images in Internet Explorer. Graphs can be exported in PNG or SVG format from Chrome or Firefox browsers . Internet Explorer does not display chart legend and title when re-opening previously downloaded SVG files, the recommendation is to open downloaded SVG files with another program.
- In the protein viewer there may be overlapping mutations. In this case mousing over a point will just show a single mutation and the other mutations at this location will not be apparent.
Project page
- On the project page, the Summary Case Count link should open the case tab on the Repository page - instead it opens the file page
Entity page
- On the mutation entity page, in the Consequences Table, the "Coding DNA Change" column is not populated for rows that do not correspond to the canonical mutation.
Repository and Cart
- The annotation count in File table of Repository and Cart does not link to the Annotations page anymore. The user can navigate to the annotations through the annotation count in Repository - Case table.
Legacy Archive
- Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.
- Exporting the Cart table in JSON will export the GDC Archive file table instead of exporting the files in the Cart only.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release details are maintained in the GDC Data Portal Change Log.

Release 1.6.0

GDC Product: GDC Data Portal
Release Date: June 29, 2017

New Features and Changes

There was a major new release of the GDC Data Portal focused on Data Analysis, Visualization, and Exploration (DAVE). Some important new features include the following:

New visual for the Homepage: a human body provides the number of Cases per Primary Site with a link to an advanced Cancer Projects search
The Projects menu provides the Top 20 Cancer Genes across the GDC Projects and the Case Distribution per Project
A new menu "Exploration" is an advanced Cancer Projects search which provides the ability to apply Case, Gene, and Mutation filters to look for:
- List of Cases with the largest number of Somatic Mutations
- The most frequently mutated Genes
- The most frequent Variants
- Oncogrid view of mutation frequency
Visualizations are provided across the Project, Case, Gene and Mutation entity pages:
- List of most frequently mutated genes and most frequent variants
- Survival plots for patients with or without specific variants
- Survival plots for patients with or without variants in specific genes
- Lollipop plots of mutation frequency across protein domains
Links to external databases (COSMIC, dbSNP, Uniprot, Ensembl, OMIM, HGNC)
Quick Search for Gene and Mutation entity pages
The ability to export the current view of a table in TSV
Retired GDC cBioPortal

For detailed updates please review the Data Portal User Guide.

Bugs Fixed Since Last Release

BAM Slicing dialog box does not disappear automatically upon executing the BAM slicing function. The box can be closed manually.
Very long URLs will produce a 400 error. Users may encounter this after clicking on "source files" on a file page where the target file is derived from hundreds of other files such as for MAF files.
If bam slicing produces an error pop-up message it will be obscured behind the original dialog box.
- Internet Explorer users are not able to use the "Only show fields with no values" when adding custom facets
- Exporting large tables in the Data Portal may produce a 500 error. Filtering this list to include fewer cases or files should eliminate the error

Known Issues and Workarounds

New Visualizations
- Cannot export Data Portal graphs in PNG in Internet Explorer. Graphs can be exported to PNG or SVG from Chrome or Firefox browsers . Internet would not display chart legend and title when re-opening previously downloaded SVG files, recommendation is to open downloaded SVG files with another software.
- In the protein viewer there may be overlapping mutations. In this case mousing over a point will just show a single mutation and the other mutations at this location will not be apparent.
Exploration
- Combining "Variant Caller" mutation filter with a case filter will display wrong counts in the mutation facet. The number of mutations in the result mutation table is correct.
- Mutation table: it is difficult to click on the denominator in "#Affected Cases in Cohort" column displayed to the left side of the bar. The user should click at a specific position at the top of the number to be able to go to the corresponding link.
Entity page
- On the mutation entity page, in the Consequences Table, the "Coding DNA Change" column is not populated for rows that do not correspond to the canonical mutation.
Repository and Cart
- The annotation count in File table of Repository and Cart does not link to the Annotations page anymore. The user can navigate to the annotations through the annotation count in Repository - Case table.
Legacy Archive
- Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.
- Exporting the Cart table in JSON will export the GDC Archive file table instead of exporting the files in the Cart only.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release details are maintained in the GDC Data Portal Change Log.

Release 1.5.2

GDC Product: GDC Data Portal
Release Date: May 9, 2017

New Features and Changes

Removed link to Data Download Statistics Report
Updated version numbers of API, GDC Data Portal, and Data Release

Bugs Fixed Since Last Release

None

Known Issues and Workarounds

General
- Exporting large tables in the Data Portal may produce a 500 error. Filtering this list to include fewer cases or files should eliminate the error
- After successful authentication, the authentication popup does not close for Internet Explorer users running in "Compatibility View". Workaround is to uncheck "Display Intranet sites in Compatibility View" in Internet Explorer options. Alternatively, refreshing the portal will correctly display authentication status.
- BAM Slicing dialog box does not disappear automatically upon executing the BAM slicing function. The box can be closed manually.
- Due to preceding issue, If bam slicing produces an error pop-up message it will be obscured behind the original dialog box.
- Very long URLs will produce a 400 error. Users may encounter this after clicking on "source files" on a file page where the target file is derived from hundreds of other files such as for MAF files. To produce a list of source files an API call can be used with the search parameter "fields=analysis.input_files.file_name".
  - Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.

Example

https://api.gdc.cancer.gov/files/455e26f7-03f2-46f7-9e7a-9c51ac322461?pretty=true&fields=analysis.input_files.file_name

Cart
- Counts displayed in the top right of the screen, next to the Cart icon, may become inconsistent if files are removed from the server.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- Internet Explorer users are not able to use the "Only show fields with no values" when adding custom facets
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release details are maintained in the GDC Data Portal Change Log.

Release 1.4.1

GDC Product: GDC Data Portal
Release Date: October 31, 2016

New Features and Changes

Added a search feature to help users select values of interest in certain facets that have many values.
Added support for annotation ID queries in quick search.
Added a warning when a value greater than 90 is entered in the "Age at Diagnosis" facet.
Added Sample Type column to file entity page.
Authentication tokens are refreshed every time they are downloaded from the GDC Data Portal.
Buttons are inactive when an action is in progress.
Improved navigation features in the overview chart on portal homepage.
Removed State/Status from File and Case entity pages
Removed the "My Projects" feature.
Removed "Created" and "Updated" dates from clinical and biospecimen entities.

Bugs Fixed Since Last Release

Advanced search did not accept negative values for integer fields.
Moving from facet search to advanced search resulted in an incorrect advanced search query.
Some facets were cut off in Internet Explorer and Firefox.

Known Issues and Workarounds

General
- Exporting large tables in the Data Portal may produce a 500 error. Filtering this list to include fewer cases or files should eliminate the error
- After successful authentication, the authentication popup does not close for Internet Explorer users running in "Compatibility View". Workaround is to uncheck "Display Intranet sites in Compatibility View" in Internet Explorer options. Alternatively, refreshing the portal will correctly display authentication status.
- BAM Slicing dialog box does not disappear automatically upon executing the BAM slicing function. The box can be closed manually.
- Due to preceding issue, If bam slicing produces an error pop-up message it will be obscured behind the original dialog box.
- Very long URLs will produce a 400 error. Users may encounter this after clicking on "source files" on a file page where the target file is derived from hundreds of other files such as for MAF files. To produce a list of source files an API call can be used with the search parameter "fields=analysis.input_files.file_name".
  - Downloading a token in the GDC Legacy Archive does not refresh it. If a user downloads a token in the GDC Data Portal and then attempts to download a token in the GDC Legacy Archive, an old token may be provided. Reloading the Legacy Archive view will allow the user to download the updated token.

Example

https://api.gdc.cancer.gov/files/455e26f7-03f2-46f7-9e7a-9c51ac322461?pretty=true&fields=analysis.input_files.file_name

Cart
- Counts displayed in the top right of the screen, next to the Cart icon, may become inconsistent if files are removed from the server.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- Internet Explorer users are not able to use the "Only show fields with no values" when adding custom facets
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release details are maintained in the GDC Data Portal Change Log.

Release 1.3.0

GDC Product: GDC Data Portal
Release Date: September 7, 2016

New Features and Changes

A new "Metadata" button on the cart page to download merged clinical, biospecimen, and file metadata in a single consolidated JSON file. May require clearing browser cache
Added a banner on the Data Portal to help users find data
Added support for "Enter" key on login button
On the Data page, the browser will remember which facet tab was selected when hitting the "Back" button
In file entity page, if there is a link to one single file, redirect to this file's entity page instead of a list page.

Bugs Fixed Since Last Release

Adding a mix of open and controlled files to the cart from any Case entity pages was creating authorization issues
Opening multiple browser tabs and adding files in those browser tabs was not refreshing the cart in other tabs.
When user logs in from the advanced search page, the login popup does not automatically close
When removing a file from the cart and clicking undo, GDC loses track of permission status of the user towards this file and will ask for the user to log-in again.
Download File Metadata button produces incomplete JSON output omitting such fields as file_name and submitter_id. The current workaround includes using the API to return file metadata.
Annotations notes do not wrap to the next line at the beginning or the end of a word, some words might be split in two lines
Sorting annotations by Case UUID causes error

Known Issues and Workarounds

General
- When no filters are engaged in the Legacy Archive or Data Portal, clicking the Download Manifest button may produce a 500 error and the message "We are currently experiencing issues. Please try again later.". To avoid this error the user can first filter by files or cases to reduce the number files added to the manifest.
- After successful authentication, the authentication popup does not close for Internet Explorer users running in "Compatibility View". Workaround is to uncheck "Display Intranet sites in Compatibility View" in Internet Explorer options. Alternatively, refreshing the portal will correctly display authentication status.
- BAM Slicing dialog box does not disappear automatically upon executing the BAM slicing function. The box can be closed manually.
- Due to preceding issue, If bam slicing produces an error pop-up message it will be obscured behind the original dialog box.
- Very long URLs will produce a 400 error. Users may encounter this after clicking on "source files" on a file page where the target file is derived from hundreds of other files such as for MAF files. To produce a list of source files an API call can be used with the search parameter "fields=analysis.input_files.file_name".
- On the Legacy Archive, searches for "Case Submitter ID Prefix" containing special characters are not displayed correctly above the result list. The result list is correct, however.

Example

https://api.gdc.cancer.gov/files/455e26f7-03f2-46f7-9e7a-9c51ac322461?pretty=true&fields=analysis.input_files.file_name

Cart
- Counts displayed in the top right of the screen, next to the Cart icon, may become inconsistent if files are removed from the server.
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- Internet Explorer users are not able to use the "Only show fields with no values" when adding custom facets
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode.

Release details are maintained in the GDC Data Portal Change Log.

Release 1.2.0

GDC Product: GDC Data Portal
Release Date: August 9th, 2016

New Features and Changes

Added a retry (1x) mechanism for API calls
Added support for ID fields in custom facets
Added Case Submitter ID to the Annotation entity page
Added a link to Biospeciment in the Case entity page

Bugs Fixed Since Last Release

General.
- Not possible to use the browser's back button after hitting a 404 page
- 404 page missing from Legacy Archive Portal
- Table widget icon and export JSON icon should be different
- Download SRA XML files from the legacy archive portal might not be possible in some context
Data and facets
- Default values for age at diagnosis is showing 0 to 89 instead of 0 to 90
- Biospecimen search in the case entity page does not highlight (but does bold and filter) results in yellow when title case is not followed
- Table sorting icon does not include numbers
- '--' symbol is missing on empty fields (blank instead), additional missing fields identified since last release.

Known Issues and Workarounds

General
- When no filters are engaged in the Legacy Archive or Data Portal, clicking the Download Manifest button may produce a 500 error and the message "We are currently experiencing issues. Please try again later.". To avoid this error the user can first filter by files or cases to reduce the number files added to the manifest.
- After successful authentication, the authentication popup does not close for Internet Explorer users running in "Compatibility View". This only impact users at the NIH. Workaround is to uncheck "Display Intranet sites in Compatibility View" in Internet Explorer options. Alternatively, refreshing the portal will correctly display authentication status.
- When user login from the advanced search page, the login popup does not automatically close
Cart
- When removing a file from the cart and clicking undo, GDC looses track of permission status of the user towards this file and will ask for the user to log-in again.
- Counts displayed in the top right of the screen, next to the Cart icon, might get inconsistent if files are removed from the server.
- Download File Metadata button produces incomplete JSON output omitting such fields as file_name and submitter_id. The current workaround includes using the API to return file metadata.
Annotations
- Annotations notes do not wrap to the next line at the beginning or the end of a word, some words might be split in two lines
- Sorting annotations by Case UUID causes error
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- Internet Explorer users are not able to use the "Only show fields with no values" when adding custom facets
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibilty mode

Release details are maintained in the GDC Data Portal Change Log.

Release 1.1.0

GDC Product: GDC Data Portal
Release Date: June 1st, 2016

New Features and Changes

This is a bug-fixing release, no new features were added.

Bugs Fixed Since Last Release

General
- Fixed 508 compliance issues.
- Disabled download manifest action on projects without files.
- Updated the portal to indicate to the user that his session expired when he tries to download the authentication token.
- Unselected "My project" filter after user logs-in.
- Fixed missing padding when query includes "My Projects".
- Enforced "Add to cart" limitation to 10,000 files everywhere on the Data Portal.
Tables
- Improved usability of the "Sort" feature
- Updated the "Add all files to cart" button to add all files corresponding to the current query (and not only displayed files).
- Fixed an issue where Platform would show "0" when selected platform is "Affymetrix SNP 6.0".
Data
- Corrected default values populated when adding a custom range facet.
- Fixed an issue preventing the user to sort by File Submitter ID in data tables.
File Entity Page
- Improved "Associated Cases/Biospecimen" table for files associated to a lot of cases.
- Fixed an error when performing BAM Slicing.

Known Issues and Workarounds

General.
- After successful authentication, the authentication popup does not close for Internet Explorer users running in "Compatibility View". This only impact users at the NIH. Workaround is to uncheck "Display Intranet sites in Compatibility View" in Internet Explorer options. Alternatively, refreshing the portal will correctly display authentication status.
- Download SRA XML files from the legacy archive portal might not be possible in some context
- Not possible to use the browser's back button after hitting a 404 page
- 404 page missing from Legacy Archive Portal
- Table widget icon and export JSON icon should be different
Data and facets
- Default values for age at diagnosis is showing 0 to 89 instead of 0 to 90
- Biospecimen search in the case entity page does not highlight (but does bold and filter) results in yellow when title case is not followed
- Table sorting icon does not include numbers
- '--' symbol is missing on empty fields (blank instead), additional missing fields identified since last release.
Cart
- When removing a file from the cart and clicking undo, GDC looses track of permission status of the user towards this file and will ask for the user to log-in again.
- Counts displayed in the top right of the screen, next to the Cart icon, might get inconsistent if files are removed from the server.
Annotations
- Annotations notes do not wrap to the next line at the beginning or the end of a word, some words might be split in two lines
Web Browsers
- Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.
- Internet Explorer users are not able to use the "Only show fields with no values" when adding custom facets
- The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibilty mode

Release details are maintained in the GDC Data Portal Change Log.

Release 1.0.1

GDC Product: GDC Data Portal
Release Date: May 18, 2016

New Features and Changes

This is a bug-fixing release, no new features were added.

Bugs Fixed Since Last Release

Tables and Export
- Restore default table column arrangement does not restore to the default but it restores to the previous state
Cart and Download
- Make the cart limit warning message more explanatory
- In some situations, adding filtered files to the cart might fail
Layout, Browser specific and Accessibility
- When disabling CSS, footer elements are displayed out of order
- If javascript is disabled html tags are displayed in the warning message
- Layout issues when using the browser zoom in function on tables
- Cart download spinner not showing at the proper place
- Not all facets are expanded by default when loading the app

Known Issues and Workarounds

General
- If a user has previously logged into the Portal and left a session without logging out, if the user returns to the Portal after the user's sessionID expires, it looks as if the user is still authenticated. The user cannot download the token and gets an error message that would not close. The user should clear the cache to properly log out.
- '--' symbol is missing on empty fields (blank instead)
- Download manifest button is available for TARGET projects with 0 files, resulting in error if user clic on button
- After successful authentication, the authentication popup does not close for Internet Explorer users running in "Compatibility View". This only impact users at the NIH. Workaround is to uncheck "Display Intranet sites in Compatibility View" in Internet Explorer options. Alternatively, refreshing the portal will correctly display authentication status.
Data
- When adding a custom range facet, default values are incorrectly populated
- The portal might return incorrect match between cases and files when using field cases.samples.portions.created_datetime (custom facet or advanced search). Note: this is not a UI issue.
- Sorting File Submitter ID option on the file tab result in a Data Portal Error
Tables and Export
- Table sorting icon does not include numbers
Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on GDC Website.

Release details are maintained in the GDC Data Portal Change Log.