Software Release Notes
Release Notes for V4.0.9 (March 13, 2026)
Release Notes for V4.0.8 (February 23, 2026)
Release Notes for V4.0.7 (February 05, 2026)
Release Notes for V4.0.6 (January 22, 2026)
Release Notes for V4.0.5 (January 08, 2026)
Release Notes for V4.0.4 and V4.0.3 (November 20, 2025)
Release Notes for V4.0.2 (October 30, 2025)
Release Notes for V4.0.1 (September 25, 2025)
Release Notes for V4.0.0 (September 18, 2025)
Release Notes for V3.0.27 (June 27, 2025)
Release Notes for V3.0.26, V3.0.25, and V3.0.24 (June 11, 2025)
Release Notes for V3.0.23 (May 01, 2025)
Release Notes for V3.0.22, V3.0.21, V3.0.20, V.3.0.19.1 (April 17, 2025)
Release Notes for V3.0.19, V3.0.18, V.3.0.17, and V3.0.16 (February 18, 2025)
Release Notes for V3.0.15 (January 03, 2025)
Release Notes for V3.0.12 and V3.0.11 (October 17, 2024)
Release Notes for V3.0.10 and V3.0.9 (September 19, 2024)
Release Notes for V3.0.8 and V3.0.7 (August 16, 2024)
Release Notes for V3.0.6 and V3.0.5 (July 25, 2024)
Release Notes for V3.0.4.1 (July 16, 2024)
Release Notes for V3.0.4, V3.0.3 and V3.0.2 (July 2, 2024)
Release Notes for V3.0.1.1 (June 21, 2024)
Release Notes for V3.0.1 (May 30, 2024)
Release Notes for V2.0.2 and V2.0.1 (April 05, 2024)
Release Notes for V2.0.0 and V1.7.0 (March 12, 2024)
Release Notes for V1.6.13 and V1.6.12 (February 09, 2024)
Release Notes for V1.6.11, V1.6.10, and V1.6.9 (January 16, 2024)
Release Notes for V1.6.8, V1.6.7, V1.6.6, V1.6.5, and V1.6.4 (November 16, 2023)
Release Notes for V1.6.3, V1.6.2, and V1.6.1 (September 07, 2023)
Release Notes for V1.6.0 (July 28, 2023)
Release Notes for V1.5.6 (July 13, 2023)
Release Notes for V1.5.5, V1.5.4, and V1.5.3 (June 29, 2023)
Release Notes for V1.5.2 (May18, 2023)
Release Notes for V1.5.1, V1.5.0 and V1.4.12 (May 04, 2023)
Release Notes for V1.4.11 and V1.4.10 (March 23, 2023)
Release Notes for V1.4.9 and V1.4.8 (February 20, 2023)
Release Notes for V1.4.7, V1.4.6 and V1.4.5 (January 26, 2023)
Release Notes for V1.4.4 (December 1, 2022)
Release Notes for V1.4.2 and V1.4.3 (November 15, 2022)
Release Notes for V1.4.1(November 7, 2022)
Release Notes for V1.4.0 (October 06, 2022)
Release Notes for V1.3.14 (September 21, 2022)
Release Notes for V1.3.13 and V1.3.12 (September 07, 2022)
Release Notes for V1.3.11, V1.3.10, V1.3.9, and V1.3.8 (August 11, 2022)
Release Notes for V1.3.7 and V1.3.6 (June 16, 2022)
Release Notes for V1.3.5 and V1.3.4 (May 12, 2022)
Release Notes for V1.3.3, V1.3.2, and V1.3.1(April 15, 2022)
Release Notes for V1.3.0, V1.2.12, and V1.2.11(March 11, 2022)
Release Notes for V1.2.10, V1.2.9, and V1.2.8 (January 27, 2022)
Release Notes for V1.2.7 (December 3, 2021)
Release Notes for V1.2.6 (November 24, 2021)
Release Notes for V1.2.5 (October 28, 2021)
Release Notes for V1.2.4 (October 7, 2021)
Release Notes for V1.2.3 (September 24, 2021)
Release Notes for V1.2.2 (August 23, 2021)
Release Notes for V1.2.1 (August 11, 2021)
Release Notes for V1.2.0 (July 26, 2021)
Release Notes for V1.1.8 (June 24, 2021)
Release Notes for V1.1.7 (June 17, 2021)
Release Notes for V1.1.6 (June 4, 2021)
Release Notes for V1.1.5 (May 19, 2021)
Release Notes for V1.1.4 (May 6, 2021)
Release Notes for V1.1.3 (April 15, 2021)
Release Notes for V1.1.2 (March 19, 2021)
Release Notes for V1.1.1 (March 10, 2021)
Release Notes for V1.1.0 (February 18, 2021)
Release Notes for V1.0.24 (February 5, 2021)
Release Notes for V1.0.22 (January 5, 2021)
Release Notes for V1.0.21 (December 15, 2020)
Release Notes for V1.0.20 (December 2, 2020)
Release Notes for V1.0.19 (November 18, 2020)
Release Notes for V1.0.18 (November 12, 2020)
Release Notes for V1.0.17 (October 20, 2020)
Release Notes for V1.0.16 (October 2, 2020)
Release Notes for V1.0.15 (October 2, 2020)
Release Notes for V1.0.14 (September 11, 2020)
Release Notes for V1.0.13 (September 11, 2020)
Release Notes for V1.0.12 (August 13, 2020)
Release Notes for V1.0.11 (August 13, 2020):
Release Notes for V1.0.10 (July 8, 2020)
Release Notes for V1.0.9 (June 29, 2020)
Release Notes for V1.0.8 (June 16, 2020)
Release Notes for V1.0.7 (May 27, 2020)
Release Notes for V1.0.6 (May 13, 2020)
Release Notes for V1.0.4 (April 16, 2020)
Release Notes for V1.0.0 (March 23, 2020)
Improvements:
Fixes:
Known Issues:
Improvements:
Fixes:
Known Issues:
Improvements:
Fixes:
Known Issues:
Improvements:
Fixes:
Known Issues:
Improvements:
Fixes:
Corrected file count updates for Morphology and Site of Resection or Biopsy filters on Explore page (PDC-10460)
Updated external URL on https://pdc.cancer.gov/pdc/cloud-data-analysisin (PDC-10462)
Resolved Explore Page central table sorting that sometimes has invalid fields (PDC-10463)
Fixed sorting of Study Summary Biospecimen table on Explore page (PDC-10464)
Removed console.log and tokens to avoid display UI configuration (PDC-10523)
Updated image on the FAQ page (PDC-10437)
Known Issues:
Improvements:
Added "Follow-up" information under Clinical Data & Cohort Exploration" section and other updated to the PDC Documentation page (PDC-10409, PDC10404)
Fixes:
Set Proteogenomic data and resources for pan-cancer analysis, as the default first paper on the PanCancer page (PDC-10425).
Resolved performance issues with new Clinical queries in Gene Summary pages (PDC-10298)
Improved Study visualizer on Gene Summary page (PDC-10326)
Fixed duplicate publication issue (PDC-10286)
Updated Explore page filter to align General filters (PDC-10393)
Known Issues:
New Features:
PDC Documentation: The PDC Documentation Portal has been added to help the scientific community explore, submit, and export data more easily using the PDC Data Browser. The user interface includes content in Home, Usage, Tutorials, PDC Data Processes, and Data Submission sections. A side navigation menu has been added to help users quickly find information. (Epic-8919)
Improvements:
Fixes:
Fixed the issue with missing Protocol number for multiple Protocol studies on UI. (PDC-10272).
API page formatting issues are resolved (PDC-10331)
Issue of Data category -Raw Mass Spectra (Proprietary) files are shown on bottom of the list is resolved (PDC-10273)
Issue with Program filter does not function in Gene Summary page is resolved (PDC-10297)
Improvements:
o Added Analytical Fraction to General filters.
o Standardized filter value formatting.
o Streamlined Clear button behavior by removing redundant text.
o Linked Available Data Types heading to FAQ.
o Added hover underline to table headers to indicate hyperlinks.
o Refined megamenu behavior.
New Features:
PDC UI Redesign
The PDC user interface has undergone a major redesign to deliver a modern, intuitive, and consistent experience across the portal. The updates improve responsiveness, navigation, and usability through a clean, professional design. With simplified navigation, expanded filtering, and refreshed pages, users can explore proteomic and multi-omic datasets more easily and efficiently. (Epic: PDC-8919)
Homepage Redesign
Explore Page Redesign
o Consolidated into General, Clinical, and Gene groups with intuitive subcategories.
o Rarely used filters removed for a cleaner experience.
o Expanded clinical filters include demographics, diagnosis, treatment, exposure, and follow-up.
Study Summary Page Enhancements
Updated UI/UX and Backend framework
Framework migration to the Node.js 20, Angular 19 and PrimeNG 19, API Optimization, Scalability Improvements and Security Enhancements.
New Features:
Support for multiple protocols added to file views in the UI:
The specific protocol used in the generation of each file will be displayed in the protocol column Studies PDC000563 and PDC000564
Fixes
Fixed the issues with sorting the file table by protocol. (PDC-9811)
Known Issues
Some genes may have multiple records where there were multiple names previously for the same gene for example - 'INAVA'
Improvements
Improved Pan-Cancer page: Publications are now sorted by year for better chronological navigation (PDC-9746)
Case API refactored to improve efficiency and reduce latency (PDC-9808)
Fixes
Fixed issue of consistent file selection across Data Browser sections (PDC-9690)
GraphQL API updated to prevent 414 errors during gene searches with long query strings. For example- 'VCL (PDC-9697).
Updated experimentalMetadata API to retrieve instrument data from the SRM protocol (PDC-9698)
API documentation updated to align with changes in instrument data handling in experimentalMetadata (PDC-9757)
Fixed the issue related with using "Download Files" button on files shared with multiple studies repeatedly downloads (PDC -9846 and 9925)
Resolved caching issue affecting responses from the experimentalMetadata API (PDC-9801)
Known Issues
Some genes may have multiple records where there were multiple names previously for the same gene for example - 'INAVA'
Improvements
Added new acceptable value for Disease Type: "Neuroendocrine Neoplasms" (PDC-9664)
Fixes
Fixed PDC Data Browser vulnerabilities - Unpatched `path-to-regexp` ReDoS in 0.1 (PDC-9656)
Fixed process image visibility issues (PDC-9625)
Fixed the issue with PFB button for legacy files (PDC-9749)
Known Issues
The gene filter does not allow users to search by alias, for example - Gene A2M and alias 'S863-7'
Some older gene symbols which were previously searched may return errors indicating the gene is not present in PDC if searched via Gene filter for example - 'SEPT9'. These Gene symbols have slightly changed, for example 'SEPT9' to 'SEPTIN9'. These Genes can be searched via the search box on the upper right of the page.
Some genes may have multiple records where there were multiple names previously for the same gene for example - 'INAVA'
New Features:
Protein quantitation data processed and heatmaps are now available for the following studies:
Improvements
Add administrative banner to PDC Data Browser (PDC-9526, PDC-9561, PDC-9618, PDC-9562)
Updated News and Recent Release section on home page (PDC-9580)
Fixes
Fixed overlapping text on File page (PDC-9480)
Fixed Technology Advancement Studies banner size to align with other banners on the home page (PDC-9533)
Fixed the issue with file manifests pulled from Study Summary window (PDC-9626)
Fixed the issue with deployment pipelines (PDC-9529)
Known Issues
The gene filter does not allow users to search by alias, for example - Gene A2M and alias 'S863-7'
Some older gene symbols which were previously searched may return errors indicating the gene is not present in PDC if searched via Gene filter for example - 'SEPT9'. These Gene symbols have slightly changed, for example 'SEPT9' to 'SEPTIN9'. These Genes can be searched via the search box on the upper right of the page.
Some genes may have multiple records where there were multiple names previously for the same gene for example - 'INAVA'
Improvements
Aligned Gene full summary file functionality with Explore page selection behavior (PDC-9015)
Updated description for "experiment_type" (PDC-9191)
Restructured Public API Documentation: Workflow section now displays all Input Parameters (PDC-8259)
Fixes
Fixed 404 error for 'When was PDC launched?' link on the FAQ page (PDC-9194)
Fixed pagination issues on Study, Clinical, Biospecimen, Files, and Genes ( PDC-9136)
Fixed Access Denied error when downloading two lung cancer study files via manifest link ( PDC-9243)
Fixed partial display of selected rows number ( PDC-9310)
Known Issues
The gene filter does not allow users to search by alias, for example - Gene A2M and alias 'S863-7'
Some older gene symbols which were previously searched may return errors indicating the gene is not present in PDC if searched via Gene filter for example - 'SEPT9'. These Gene symbols have slightly changed, for example 'SEPT9' to 'SEPTIN9'. These Genes can be searched via the search box on the upper right of the page.
Some genes may have multiple records where there were multiple names previously for the same gene for example - 'INAVA'
Improvements
Upgraded cross-spawn to fix Regular Expression Denial of Service (ReDoS) (PDC-9222)
Known Issues
The gene filter does not allow users to search by alias, for example - Gene A2M and alias 'S863-7'
Some older gene symbols which were previously searched may return errors indicating the gene is not present in PDC if searched via Gene filter for example - 'SEPT9'. These Gene symbols have slightly changed, for example 'SEPT9' to 'SEPTIN9'. These Genes can be searched via the search box on the upper right of the page.
Some genes may have multiple records where there were multiple names previously for the same gene for example - 'INAVA'
Release Notes for V3.0.15, V3.0.14, and V3.0.13 (December 01, 2024)
Improvements
Updated PDC citation (PDC-9105)
"Protocol" is added to Study Summary Experimental Design view and export (PDC-8986)
Added protocol to fileMetadata and studyExperimentalDesign APIs (PDC-8988)
Restructured public API documentation ( Study and Quantitative section) to show all input parameters (PDC-8256 and PDC-8258)
API support for multiple protocol - fileMetadata API (PDC-9057 and PDC-8941)
Updated filesPerStudy API return all files, have optional limit and offset (PDC-9096)
Protocol column is added to Files view and export on Explore and Study summary page (PDC-9018)
Fixes
Fixed API support for multiple protocol - fileMetadata API (PDC-9057 and PDC-8941)
Updated PDC DD: Protocol -> dia_ims description (PDC-8997)
Fixed 508 Compliance issues (PDC-8915)
Fixed the issue of study record entry in Explore page should not be changed when filters are applied (PDC-9064 and PDC-9140)
Fixed the issue of all filters in Primary disease, Program, and Disease type to be aligned (PDC-9085)
Fixed API to get CF url for all sub-30GB files (PDC-9155)
Known Issues
The gene filter does not allow users to search by alias, for example - Gene A2M and alias 'S863-7'
Some older gene symbols which were previously searched may return errors indicating the gene is not present in PDC if searched via Gene filter for example - 'SEPT9'. These Gene symbols have slightly changed, for example 'SEPT9' to 'SEPTIN9'. These Genes can be searched via the search box on the upper right of the page.
Some genes may have multiple records where there were multiple names previously for the same gene for example - 'INAVA'
Improvements
Enhanced Protocol tab to accommodate future multiple protocols in Study summary dialogue (PDC-8255)
Fixes
Reviewed all high vulnerabilities on PDC Data Browser and mitigate those issues (PDC-8932)
Updated gene filter API query to make it case sensitive (PDC-8867)
Fixed the issue of files with spaces in the signed URL API (PDC-8898)
Fixed the issue of mismatch in row count when navigating pages after selecting all pages in Prebuilt Gene filter (PDC-8865)
Fixed Study API title (PDC-8911)
Fixed formatting and text issues on public API documentation page (PDC-8910)
Fixed the issue of inconsistent UI formatting across the Studies (PDC-8774)
Known Issues
The gene filter does not allow users to search by alias, for example - Gene A2M and alias 'S863-7'
Some older gene symbols which were previously searched may return errors indicating the gene is not present in PDC if searched via Gene filter for example - 'SEPT9'. These Gene symbols have slightly changed, for example 'SEPT9' to 'SEPTIN9'. These Genes can be searched via the search box on the upper right of the page.
Some genes may have multiple records where there were multiple names previously for the same gene for example - 'INAVA'
Improvements
Updated the News section (PDC-8916)
Improved Prebuilt Gene Lists to be case-sensitive and limit the results to human genes only (PDC-8764)
Fixes
Resolved known issues with API execution on the Swagger documentation page caused by configuration changes (PDC-8706)
Fixed the issue of inconsistent UI formatting across the Studies (PDC-8774)
Known Issues
The gene filter does not allow users to search by alias, for example - Gene A2M and alias 'S863-7'
Some older gene symbols which were previously searched may return errors indicating the gene is not present in PDC if searched via Gene filter for example - 'SEPT9'. These Gene symbols have slightly changed, for example 'SEPT9' to 'SEPTIN9'. These Genes can be searched via the search box on the upper right of the page.
Some genes may have multiple records where there were multiple names previously for the same gene for example - 'INAVA'
Improvements
Updated Out-of-date Version (MathJax) on UI (PDC-8688)
Fixes
Fixed the issue of top-right search bar links to wrong case-summary for samples and aliquots with identical case/sample/aliquot submitter IDs (PDC-8667)
Fixed getPaginatedGenes API Offset and Limit text (PDC-8715)
Fixed typo in Sample - tissue_collection_type in Data Dictionary is not fixed (PDC-8718)
Known Issues
Because of API document definition and configuration changes, several endpoints are currently experiencing issues, including - Syntax errors, Incorrect string values, Missing results, Incorrect responses, Null or empty responses, and Empty API tab display on UI.
The gene filter does not allow users to search by alias, for example - Gene A2M and alias 'S863-7'
Some older gene symbols which were previously searched may return errors indicating the gene is not present in PDC if searched via Gene filter for example - 'SEPT9'. These Gene symbols have slightly changed, for example 'SEPT9' to 'SEPTIN9'
Some genes may have multiple records where there were multiple names for the same gene previously for example - 'INAVA'
Improvements
Created public API endpoint for publications and updated public API documentation with new Publication API (PDC-8644, PDC-8597)
PDC gene reference table has been updated in accordance with Gencode v42. This update includes the following changes:
o Protein lists associated with each gene have been updated to include Ensemble protein identifiers and protein identifiers are searchable.
o A new field called Alias has been added. This field includes the original gene symbols for those whose names have been changed, along with other alternative names and symbols for genes.
o There is modification of gene-related APIs handling genes with aliases (PDC-8588, PDC-8563)
Fixes
Fixed mysql2 vulnerable to Prototype Pollution - PDCAPI and ChorusAPI (PDC-8583)
Reviewed npm audit and updated all required packages ( PDC-8587)
Fixed inconsistent file count behavior in Study manifests (PDC-8645)
Known Issues
Because of API document definition and configuration changes, several endpoints are currently experiencing issues, including - Syntax errors, Incorrect string values, Missing results, Incorrect responses, Null or empty responses, and Empty API tab display on UI.
The gene filter does not allow users to search by alias, for example - Gene A2M and alias 'S863-7'
Some older gene symbols which were previously searched may return errors indicating the gene is not present in PDC if searched via Gene filter for example - 'SEPT9'. These Gene symbols have slightly changed, for example 'SEPT9' to 'SEPTIN9'
Some genes may have multiple records where there were multiple names for the same gene previously for example - 'INAVA'
Fixes
Updated swagger-ui from 2.1.1 to 5.17.14 and handlebars in the public API documentation pages to mitigate vulnerabilities (PDC-8666)
Known Issues
Because of API document definition and configuration changes, several endpoints are currently experiencing issues, including - Syntax errors, Incorrect string values, Missing results, Incorrect responses, Null or empty responses, and Empty API tab display on UI.
Improvements
Added Panoply video link on 'Analyze PDC data in the cloud' page (PDC-8460)
Updated FAQ page how to download section with some additional details (PDC-8444)
Restructured public API documentation (Experimental section) to show all input parameters (PDC-8257)
Enhanced display for Treatment and Follow-Up on Case summary to accommodate future data for studies (PDC-8464)
Added Treatment entity to Case API documentation (PDC-8426)
Added Navigating PDC section of the FAQ (PDC-8546)
Added Treatment manifest info to How Do I download clinical and biospecimen data section of FAQ (PDC-8558)
Fixes
Fixed the issue of Experimental design and metadata API popup windows taking time to respond (PDC-8407)
Fixed misspelling of Case Submitter ID in clinical manifest (PDC-8509)
Output of clinical manifest export has been changed to have a .zip extension (PDC-8452)
Embargo date has been removed from Study APIs (PDC-8560)
Gene API Offset and Limit behavior has been corrected (PDC-8563)
Improvements
Updated handlebars.js to mitigate vulnerabilities (PDC-8555)
New Features:
Treatment tab is added to the Case Summary page to accommodate future Treatment data for Studies (PDC-83435)
Improvements
Restructured public API documentation (Disease section) to show all input parameters (PDC-8255)
Updated handlebars.js to mitigate vulnerabilities (PDC-8555)
Fixes
Fixed the issue of non-functional filters in Gene Summary pages (PDC-8342)
Fixed the mysql2 Remote Code Execution (RCE) via the readCodeFor function #277 on GraphQL (PDC-8360)
Fixed mysql2 Remote Code Execution (RCE) via the readCodeFor function #277 on PDC API and Chorus API (PDC-8361)
Mitigated directory listing vulnerability (PDC-8377)
Release Notes for V3.0.0 and V2.0.3 (May 02, 2024)
New Features:
Announcing a new feature in the PDC portal: the distribution of mass spectrometry-based Metabolomic and Lipidomic data generated by the CPTAC consortium! Things to know:
o This data includes raw mass spectrometry files, harmonized metadata, as well as any processed data submitted by data submitters as supplementary data.
o PDC does not perform bioinformatic analysis for metabolomics, so there won't be processed data from the PDC Common Data Analysis Pipeline (CDAP).
Improvements
The news and recent releases section on the home page
o Added PDC CRDC AACR paper (PDC-8266)
o Added link to CPTAC program survey (PDC-8393)
o Announce the release of CPTAC non-ccRCC studies (PDC-8393)
Announce the release of CPTAC non-ccRCC studies (PDC-8393)
Added instructions for how people can upload .d folders as zip and link to the toolkit (PDC-8265)
Restructured public API documentation (File section) to show all input parameters (PDC-8252)
Point file_submitter_id to original_file_name in API queries (PDC-8338)
Fixes
Added the missing Case example to pdcEntityReference API (PDC-8216)
Fixed the issue of the required value of Polarity to be consistent (PDC-8217)
Fixed the issue of UI and manifest header formatting for uniformity (PDC-8218)
Fixed nodemailer ReDoS when trying to send a specially crafted email #251 (PDC-8241)
Improvements
Performance tuning of slow queries collected from RDS logs (Epic -8013)
Improved performance of FileMetadata API (PDC- 8190)
Improved handling of Zero-Gene Scenarios in API Study/Genes Fetching (PDC-8165)
Optimize the Pan-Cancer page (PDC-8075)
Fixes
Fixed the issue of FileMetadata API crashing with large page size (PDC-8159)
Fixed the inactive Terra resource web link (PDC-8109)
Updated the caDSR link on the FAQ page (PDC-8110)
Fixed the issue of deselection of the individual study on Explore page and Gene full summary page (PDC-8153)
New Features
Updates have been made on API and UI changes to accommodate future metabolomic studies.
Updates have been made to the Data Dictionary documentation pages to add metabolomics specific properties.
Improvements
Updated Angular 15, PrimeNG 15, and Angular Dependencies (Epic- 6811)
Restructured public API documentation of Clinical, General, and Gene sections to show all input parameters (PDC-7971, 8047, 8048)
Fixes
Fixed the issues related to allCases, aliquotSpectralCount, and Protein APIs performance on Public API Documentation page (PDC-7965)
Email is updated on the PDC_clustergram page (PDC-8019)
Improvements
Improvements to Pan-Cancer page in Publication and Supplementary Information sections (PDC-8012)
Added 'biospecimen_laterality' value to getPaginatedUICase API (PDC-7899)
Public API documentation is restructured to show all input parameters for Case related APIs (PDC-7940)
Updated API documentation with file-related changes (PDC-7939)
UI changes are made to report message for genes that are not found in PDC studies (PDC-7786)
Only genes found in PDC studies are displayed under the gene tab and the count is synced with the actual number displayed (PDC-7896)
Added biospecimen_laterality' to the biospecimen manifest (PDC-7895)
Fixes
Fixed the issue of missing NCBI gene ID column in gene manifest files (PDC-7898)
Fixed the issue of the slow load of the PDC publication page (PDC-7957)
Fixed the issue of API changes to report errors for genes not used in studies (PDC-7785)
Improvements
Updated News and Recent Releases on the PDC Home page (PDC-7812)
Bundled Command Line and User Interface versions of the Download client into a single distribution (PDC-7593)
Restructured gene abundance and PTM APIs to improve performance (PDC-7688)
Enhanced getPaginatedUIGene to handle duplicate gene names (PDC-7629)
UI is changed to display ncbi_gene_id under gene tab (PDC-7635)
Fixes
Fixed the issue of Gene search discrepancy (PDC-7662)
Fixed the issue of fileMetadata API returning incorrect results (PDC-7770)
Known Issues
Gene manifests do not include NCBI gene IDs
Improvements
Replaced highcharts with D3 in PDC chart implementation (PDC-7278, 7454)
Added details about the file validation step on the "How to Submit Data" page ( PDC-7353)
"Plex Dataset Name" is redundant with the Run Metadata Id, hence removed from the Experimental design tab of the study summary page on the PDC Browser. The Data Dictionary page of Study Run Metadata has been updated to include a description of the Run Metadata Id (PDC-7315)
Updated the Gene filter on the Explore page to return an appropriate message if a gene is not found in PDC (PDC-7447)
Updated the documentation of the following APIs: studyExperimentDesign and protocolPerStudy (PDC-7439)
Reorganized APIs to sync up output in the public API documentation (PDC-7491, PDC-7559)
Subqueries are reorganized so that the same graphql object returns the same properties when used by different API subqueries (PDC-7493)
API changes to enforce submitter_id_name as the unique data source of study_name property (PDC-7463)
Added link to NIH data sharing policy and updated PDC data submission policies (PDC-7346)
Fixed semver vulnerable to Regular Expression Denial of Service #202 in PDC API, Chorus API, GraphQL API (PDC-7200)
Removed the Embargo Date from the Data Dictionary / Study page (PDC-7301)
Fixed vulnerability aiohttp.web.Application to HTTP request smuggling via IIhttp HTTP request parser #219 (PDC-7196)
Fixed duplicate D3 Charts occur on the UI when the Case URL is pasted in a new tab (PDC-7596)
Fixed the protocolPerStudy - PDC Study ID and Submitter ID examples on the API documentation page (PDC-7538)
Improvements
Updated News and Recent Releases on the PDC Home page (PDC-7314)
Upgraded dottie vulnerable to Prototype Pollution #192 - PDC API & Chorus API (PDC-7042)
Upgraded dottie vulnerable to Prototype Pollution #193 - GraphQL API (PDC-7041)
Updated tough-cookie Prototype Pollution vulnerability #198 - GraphQL API (PDC-7043)
Added 'Sample Type' to the heatmap default fields (PDC-7146)
Pan-cancer 'Resource' paper is displayed at the top of the list (PDC-7267)
Fixes
Fixed improper Input Validation in httpx #210 - PFB API (PDC-7154)
Fixed flask vulnerability to possible disclosure of permanent session cookie due to missing Vary: Cookie header #216 (PDC-7155)
Fixed high resource usage when parsing multipart form data with many fields #214 (PDC-7156)
Fixed catastrophic backtracking in URL authority parser when passed URL containing many @ characters #212 (PDC-7157)
Fixed removal of e-Tugra root certificate #220 (PDC-7195)
New Features
New Data Handoff Feature: Export PDC data directly into Broad Institute's FireCloud/Terra platform for analysis using the Portable Format for Bioinformatics (PFB). For more information, visit https://pdc.cancer.gov/pdc/cloud-data-analysis (PDC-7108)
Improvements
Improved row selection checkbox functionality on the Explore and Study Summary Pages (PDC-7012, 7109, 7127)
Minor updates to the content of the Common Data Analysis Pipeline (CDAP) page under the ANALYSIS menu (PDC-6981)
Improvements
Public API Query Results should be cached to avoid timeout (PDC-6930)
Mitigated sheetJS to fix Prototype Pollution issue (PDC-6799)
Fixes
Fixed the clinical dataset issue when exported from the Study Summary page of Pediatric Brain Tumor Atlas Studies (PDC-7031)
New Features
The Study Summary page has a new tab to export clinical and biospecimen data (PDC-6873)
Updates to the CPTAC Pan-Cancer data to present the open-access data (PDC-6931)
Improvements
Study summary pages should consistently show the total number of biospecimens independent of the filters applied on the explore page (PDC-6803)
Updated CaDSR and PSI: MS links in the Data Dictionary pages (PDC-6919)
Fixes
Removed Embargo information tooltip from the Publications, Supplementary Data, Technology Advancement Studies, and Study summary pages (PDC-6728)
Fixed the issue discrepancy between case numbers on the study summary and study browse pages (PDC-6794)
Fixed the typo of "Leukaemia" to "Leukemia" in the Data Dictionary (PDC-6795)
Improvements
Mitigated xml2js on PDC API and Chorus API (PDC-6719)
Updated 'Pancancer' to 'Pan-Cancer' (PDC-6790)
Fixes
Fixed issues related with the Submit button of the registration form (PDC-6665)
Fixed the issues related with the title of the PDC Workspace Data Submission Overview and the bottom of the page text gets covered by the table (PDC-6694)
New Features
Release of CPTAC Pan-Cancer analysis data: A new CPTAC Pan-Cancer Analysis Page has been set up to provide information on the data generated by the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC), which includes large-scale proteomic and genomic analysis of prevalent types of cancer to aid in cancer research. The page offers access to papers analyzing the data, links to the data itself, and supplementary materials from these publications. The page can be accessed from https://pdc.cancer.gov/pdc/cptac-pancancer (PDC-6514, PDC-6667, PDC-6681, PDC-6513, PDC-6575, PDC-6601, PDC-6680)
Updated the case summary page to display external reference information for cases that have complementary information available from other resources, provided the mapping information is submitted by the users (PDC-6543)
The Data Use page has been updated to include PDC citation (PDC-6676)
Improvements
Updated vulnerable OpenSSL included in cryptography wheels (PDC-6502)
Updated Sequelize package in GraphQL to fix critical issues (PDC-6500)
Updated Sequelize package in PDC and Chorus API (6495)
Updated Sequelize package in GraphQL to 7 (PDC-6553)
Fixes
Fixed PDC data download client rejects manifests older than one week (PDC-6538)
Removed the Embargo tooltip from the download button on the Explore page (PDC-6617)
New Features
"Protein quantitation data processed and heatmaps are now available for the following studies" (PDC-6591)
APOLLO LUAD - Phosphoproteome - FeNTA (PDC000436)
APOLLO LUAD - Phosphoproteome - TiO2 (PDC000435)
APOLLO LUAD - Proteome (PDC000434)
Improvements
API changed to get ptm data of numeric genes (PDC-6405)
The 'Case Summary' view shows the number of aliquots, next to 'Aliquots' (PDC-6398)
Fixes
Fixed the Gene Full Summary page issues for two Genes-1300017J02Rik and 4931406C07Rik (PDC-6361)
Fixed the issue of UI does not accommodate multiple samples corresponding to one diagnosis/clinical record (PDC-6397)
Fixed issues related to Clinical manifest export (PDC-6542)
Fixed the broken URL on the Public API Documentation page (PDC-6401)
Improvements
Mitigated jsonwebtoken vulnerability in PDC APIs (PDC-6250)
Mitigated vulnerability for qs in PDC API (PDC-6249)
Disabled introspection from apollo graphql playground (PDC-6344)
Updated display of Gene case-sensitive search results (PDC-6325)
Fixes
Removed the Embargo Date column from the Study, file, Technology Advancement Studies, Publications, and explore-quantitation-data file manifests (PDC-6308, PDC-6300)
Fixed the issue of inconsistent numbers of Cases on the Study Summary and Explore page (PDC-6357)
Fixed the issue of matrixFiles missing for Graphql server (PDC-6382)
Fixed the issue of the title of PDC Workspace Data Submission Overview gets covered by the table (PDC-6328)
New Features
New version of the PDC data submission tutorial videos are now available on the PDC How to Submit Data page (PDC-6301)
"Protein quantitation data processed and heatmaps are now available for the following studies" (PDC-5741)
PTRC TNBC - Proteome (PDC000408)
PTRC TNBC - Phosphoproteome (PDC000409)
PTRC TNBC PDX - Proteome (PDC000410)
Modifications have been made to the Data Dictionary documentation pages (PDC-6133, PDC-6194)
Case, Aliquot, Diagnosis, Demographic, Sample, Treatment, Follow-Up, Family History, and Exposure:
study_id has been removed as a unique key
Aliquot Run Metadata:
Missing property folder_name has been added
Gene Abundance:
Unique key: spectral_count_id has been replaced with gene_abundance_id
Missing properties aliquot_submitter_id and aliquot_id have been added
Aliquot_run_metadata:
Missing properties aliquot_submitter_id and aliquot_id have been added
Protocol:
column_inner_diameter: Data type has been corrected from cm to Number
File:
file_size: Data type has been corrected from String to Number
Study Run Metadata:
date: Data type has been corrected from String to Date (yyyy-MM-dd format)
replicate_number: Data Type has been corrected from String to Integer
Improvements
Removed Embargo feature from PDC as per NIH Data Sharing policy 2023.
o Updated API methods to ignore passed in acceptDua parameter (PDC-6137)
o Updated API documentation to explain acceptDua being optional (PDC-6138)
o Updated text on the portal to remove embargo feature (PDC-6136)
o Updated the PDC submission request form (PDC-6304)
Added a new enumeration "Non-Clear Cell Renal Cell Carcinoma" to disease_type of Case entity (PDC-6199)
Fixes
Fixed case insensitive search on filter values (PDC-6105)
Removed PDC Feedback Group links (PDC-6066)
Mitigated minimatch vulnerability in GraphQL APIs (PDC-5994)
Improvements
Added content to the How to Submit Data Page (PDC-5949)
Added age validation check with HIPPA guideline (PDC-5762)
Updated Data Dictionary: marked three Diagnosis properties as not required (PDC-5984)
Fixes
Removed the link to the discussion forum in the More menu on the home page (PDC-5972)
Improvements
Updated PDC UI to use Angular 7 (PDC-5413)
The APIs are checked for consistent data format (PDC-5647)
PDC UI is checked to ensure consistent data format (PDC-5648)
Updated API doc with the public API of reference (PDC-5934)
Merged publication API change into master (PDC-5935)
Updated Recent release (PDC-5956)
Fixes
Fixed CDAP dropdown on the Analysis button should open in a new tab (PDC-5831)
Fixed recent releases links should direct a user to the correct page (PDC-5832)
Fixed email should be updated to PDCHelpDesk@mail.nih.gov (PDC-5892)
Fixed NIH Federated Login creates a new username with user type id NIH which is not in the WS table (PDC-5894
Improvements
Fixes
Fixed the menu items issue that is not accessible on the How to Submit Page - NCI reported (PDC-5781)
Fixed display of the right version on the Study summary & Browse pages for studies that contain only version 2 (PDC-5936)
Improvements
Updated 'Recent updates' and 'News' section on the home page (PDC-5829)
Updated the login page and button for the new federated login from NIH (PDC -5119, PDC-5695)
Modified the News and Recent Releases section of the landing page to read JSON (PDC-5627, PDC-5628)
Updated the Data Download page to read JSON (PDC-5717, PDC-5718)
Updated How to Submit' page to add a link to the submission request form on the NCI request (PDC-5758)
Fixes
Fixed the incorrect File downloaded from PDC UI for PDC000410: reporterIon.correction.txt (PDC-5770)
Improvements
About page is updated on the NCI Request (PDC-5689)
Implement json parser of log files (PDC-5698)
Enhanced graphql logger to track base/sub queries (PDC-5630)
Improvements
Data Download Client User Interface documentation Improvement (PDC-5635)
Enhanced graphql logger to track questionable API calls (PDC-5037)
Checked Check AML_Ex_vivo heatmap data into github (PDC-5581)
Mitigate moment vulnerability in pdcapi and chorusapi (PDC-5576)
Mitigate XSS embedded in uploaded files for JBrowse (PDC-5651)
Mitigate XSS embedded in fileName for JBrowse (PDC-5653)
PDC-UI-Pipeline not updating view_heatmap.html (PDC-5596)
Some files unavailable through fileMetadata, but found using UIFile or filesPerStudy queries (PDC-5642)
Fixes
Fixed the PDC Study ID cannot be searched via the search box (PDC-5690)
Fixed some other metadata files that have a size of 0.000 MB in the UI (PDC-5603)
Fixed the site link update (PDC-5591)
New Features
Graphical user interface for PDC data download: Release of the first version of PDC Data Download Client User Interface v.1.0.0 to download data from PDC. More information can be found from the PDC data download documentation page available under the More menu on the PDC Data Bowser Homepage (PDC-5457, PDC-5489, PDC-5355)
Add new annotation information where diagnosis to sample references is shown (PDC-5414)
Add the associated sample id information for each diagnosis in related PUBLIC APIs (PDC-5329)
Improvements
Refactored filtered queries to avoid unexpected sql error (PDC-5429)
Upgraded graphql server to apollo-server-express 3.9.0 (PDC-5461)
Update 'unique keys' section of Exposure, Family History, Treatment and Follow-Up in Data Dictionary (PDC-5503)
Updated download documentation page (PDC-5408)
Updated public API documentation with tmt18 and tmt18-related fields (PDC-5398)
Updated public API documentation with sample-diagnosis association (PDC-5396)
Error message should be changed for incorrect username/password (PDC-5306)
Add 'annotation' to APIs that cover pdc.reference table (PDC-5412)
Reference related APIs may return annotation information (PDC-5312)
Modification of code to mitigate reflected cross-site scripting for heatmaps (PDC-4911, PDC-4909)
Modification to code to mitigate reflected cross-site scripting for the JBrowse app (PDC-4912)
Fixed Study name with special characters gets truncated (PDC-5428)
Fixed records in Clinical Manifest with no values for 'Annotation' off by one column (PDC-5519)
Fixed Case Summary shows 'Sample Annotation' in all entities, the position of values shifted when no annotation is present (PDC-5521)
Fixed spelling of parameters on the download documentation page (PDC-5365)
Fixed typos on the FAQ page (PDC-5400)
Fixed Case' API - Issues retrieving 'Case Submitter ID' from clinical entities (PDC-5257)
Fixed file download should process with any lambda error (PDC-5499)
Fixed AML Studies cannot be opened via the search box and search query issue (PDC-5515)
New Features
PDC data download client v1.0.0: Release of the first version of a command line tool to download data from PDC. More information can be found from the PDC data download documentation page available under the More menu on the PDC Data Bowser Homepage. (PDC-5351)
Diagnosis to sample mapping: For cases with multiple diagnoses, a mapping of each diagnosis record to a specific sample from the case is available in a new column named Related Entities in the clinical manifest. This information is also displayed in the clinical tab of the PDC Explore page and on the Case summary page (PDC-5206, PDC-5251)
Improvements
Enhance Diagnosis APIs to include auxlary_data (PDC-5205)
Update PDC data dictionary (PDC-5193)
Updates to FAQ page - NCI Request (PDC-5210)
Update link to OCCPR website for CPTAC data use agreement from PDC FAQ page - NCI request (PDC-5304)
Add the associated sample id information for each diagnosis in related APIs (PDC-5252)
Update API for additional columns that would be added to study_run_metadata for TMT16 and TMT18 (PDC-5290)
Fixes
Fixed misspelled property in the Biospecimen manifest: Pathilogy Report UUID (PDC-5174)
Fixed 'paginatedCasesSamplesAliquots' API does not filter Samples, Aliquots by study (PDC-5178)
Fixed Study Manifest files have zero value in columns (PDC-5245)
Fixed download issues of Technology Advancement Studies files (PDC-5240, PDC-5246)
Improvements
Updated paginated API calls in the UI to use the 'get All' parameter (PDC-5072)
Add dataStatsPerProgram to API documentation (PDC-5113)
Added new footers that are missing on some pages (PDC-5128)
Enhance getPaginatedUIPtm API to handle multiple genes (PDC-5053)
Gene filter should be hyperlinked and redirect users to Data Dictionary (PDC-4859)
The number of cases on the study summary page is wrong due to the additional diagnosis reports (PDC-5068)
Subject should be consistent with the PDC Help desk email (PDC-5123)
Update the 'How to Submit Data' page the rom updated Submission Primer (PDC-5127)
Fixes
Fixed misspelled property in the clinical manifest: 'Progession or Recurrence' (PDC-5057)
Fixed apply multiple direct study filters after applying any other filter (PDC-5086)
Fixed registering a new user dialog will not close automatically (PDC-5092)
Fixed Diagnosis: tumor_stage showing HTML code in the acceptable values (PDC-5103)
Fixed two links on the PDC Clustergram page that do not open (PDC-5124)
Fixed 'cases by disease type' section reflects diagnosis count rather than case count (PDC-5168)
New Features
Workspace Release Notes are added to the More dropdown menu (PDC-4967)
Two new PDC Footer links - the Disclaimer Policy and HHS Vulnerability Disclosure are added (PDC-4988)
Improvements
Remove the outdated Welcome page and redirect it to the home page (PDC-4898)
Set up review and promote Email Migration Utility to PDC 1.3.1 (PDC-4907)
Screenshots are updated with UI changes (PDC-4748)
Highlight a statement on the How to Submit data page (PDC-4975)
Updated links in the PDC browser to point to migrated documentation pages (PDC-4978)
Non-Raw files information and screenshots added to the PDC Workspace Data Submission Overview page (PDC-4861)
Convert the GET requests to the getPaginatedUIClinical API of the "Clinical" tab to POST (PDC-5045)
Created an API to provide file information per program (PDC-5048)
Update the link to the PDC data submission template (PDC-5064)
Renamed release notes in S3 (PDC-5102)
Enhance paginated APIs to validate cached results (PDC-4994)
Fixes
Fixed study filters in the sidebar that do not bubble to the top when Browse URL has preselected filters (PDC-4904)
Fixed the clear icon that works intermittently for Genes filter (PDC-4905)
Fixed the last row of Biospecimen and Clinical that is not getting selected when the user uses Select All Pages (PDC-4931)
Fixed alignment issues (PDC-4995)
Fixed password reset gives the error that the password link has expired (PDC-5028)
New Features
Updates to UI- UX - changes to the filter sidebar, tables, and tabs (PDC-4625, PDC-4626 PDC-4871, PDC-4817, PDC-4835)
Update the menu bar with wording and organization changes (PDC-4696)
Update homepage spotlight boxes per NCI approval (PDC-4697)
Add a link to cProSite under the ANALYSIS menu (PDC-4702)
Improvements
Update How to Submit page to remove a link to submission request form - NCI request (PDC-4814)
Add an optional parameter to UI-related APIs as a source indicator' (PDC-4724)
The source parameter is set in the UI calls to fetch details of a search result (PDC-4725)
Font size is increased in all tables per 508 compliances (PDC-4792)
Remove 'Cigarettes' from acceptable values for 'type_of_tobacco_used' (PDC-4754)
Log all API calls resulting from PDC portal search (PDC-4726)
Reformat log entries of the filtered query (PDC-4727)
Create bookmarks for FAQ (PDC-4692)
Doc change for fileMetadata API (PDC-4759)
Use filesPerStudy API to return signed URLs for multiple files (PDC-4781)
Implement wrappers for public APIs used by UI (PDC-4812)
Enhance the quantDataMatrix API error handling (PDC-4853)
Updated Screenshots with UI changes (PDC-4780)
Fix UI issues on Heatmaps page & filter stacking feature (PDC-4924)
Migrate PublicAPIDocumentation static page into PDC (PDC-4426)
Set up review and promote Email Utility to PDC 1.3.0 (PDC-4907)
UI change to call UI version of public APIs (PDC-4813)
Fixes
Fixed malfunction of named parameters in graphql API (PDC-4755)
Fixed a link on the Harmonization page that is not accessible to users (PDC-4617)
Fixed a link that should be redirected to the Prod environment (PDC-4682)
Update enums for 'therapeutic_agents' of Treatment entity in Data Dictionary & WS (PDC-4796)
Fixed one of the links of CPTAC forwarding has issues (PDC-4763)
Fixed domain name error during NIH Login and Update $PDCAPI_HOST on PROD to pdc.cancer.gov (PDC-4821, PDC-4900)
Fixed new Google account registration error (PDC-4906)
New Features
The clinical and biospecimen entities in the PDC data dictionaries are updated to synchronize with the latest publicly available GDC data dictionaries. The updates related to this activity are being rolled out in phases since release v1.2.5 and are concluded in this release (v1.2.10).
Details of all the Data Dictionary updates since v1.2.5
New properties added:
Case:
consent_type, days_to_consent
Analyte:
experimental_protocol_type, rna_integrity_number
Demographic:
country_of_residence_at_enrollment
Sample:
tissue_collection_type, sample_ordinal
Diagnosis:
adrenal_hormone, ann_arbor_b_symptoms_described, gleason_patterns_percent, margin_distance, satellite_nodule_present, who_cns_grade, sites_of_involvement, diagnosis_is_primary_disease, pregnant_at_diagnosis, tumor_depth, figo_staging_edition_year, margins_involved_site, gleason_grade_tertiary, eln_risk_classification, who_nte_grade
Exposure:
tobacco_use_per_day, age_at_onset, exposure_type, parent_with_radiation_exposure, smokeless_tobacco_quit_age, alcohol_type, marijuana_use_per_week, exposure_duration, secondhand_smoke_as_child, exposure_duration_years
Treatment:
treatment_effect_indicator, treatment_dose, treatment_dose_units, treatment_arm, number_of_cycles, route_of_administration, chemo_concurrent_to_radiation, treatment_frequency, reason_treatment_ended
Follow Up:
imaging_result,hormonal_contraceptive_use, hysterectomy_margins_involved, hysterectomy_type, body_surface_area, hormonal_contraceptive_type, imaging_type, haart_treatment_indicator, evidence_of_recurrence_type, recist_targeted_regions_number, days_to_imaging, eye_color, hiv_viral_load, history_of_tumor_type, cdc_hiv_risk_factors, pregnancy_outcome, cd4_count, undescended_testis_corrected_age, history_of_tumor, undescended_testis_history_laterality, undescended_testis_corrected, undescended_testis_corrected_laterality, procedures_performed, adverse_event_grade, recist_targeted_regions_sum, nadir_cd4_count, hormone_replacement_therapy_type, scan_tracer_used, aids_risk_factors, undescended_testis_history, undescended_testis_corrected_method, immunosuppressive_treatment_type
Properties with updated permissible value:
Analyte:
analyte_type, analyte_type_id
Case:
index_date
Diagnosis:
ajcc_clinical_stage, ajcc_pathologic_m, ajcc_pathologic_stage, classification_of_tumor, figo_stage, gleason_grade_group, metastasis_at_diagnosis_site, method_of_diagnosis, morphology, site_of_resection_or_biopsy, supratentorial_localization, tissue_or_organ_of_origin, tumor_grade
Exposure:
tobacco_smoking_status, type_of_tobacco_used
Follow Up:
comorbidity, risk_factor
Family History:
relationship_type, relationship_primary_diagnosis
Sample:
biospecimen_anatomic_site, composition, method_of_sample_procurement, sample_type, sample_type_id, tumor_descriptor
Treatment:
treatment_effect, treatment_intent_type, treatment_type
Redacted properties:
Sample:
is_ffpe, oct_embedded
Diagnosis:
mitotic_count, micropapillary_features
Exposure:
bmi, height, weight
Properties with modified acceptable data types:
Analyte:
260_a280_ratio, amount, analyte_quantity, analyte_volume, concentration, ribosomal_rna_28s_16s_ratio
Case:
days_to_lost_to_followup
Demographic:
weeks_gestation_at_birth
Diagnosis:
days_to_last_follow_up, days_to_last_known_disease_status, days_to_recurrence
Exposure:
alcohol_days_per_week, alcohol_drinks_per_day, cigarettes_per_day, pack_years_smoked, years_smoked
Family History:
relationship_age_at_diagnosis
Follow-Up:
bmi, dlco_ref_predictive_percent, fev1_ref_post_bronch_percent, fev1_ref_pre_bronch_percent, fev1_fvc_pre_bronch_percent, fev1_fvc_post_bronch_percent, height, weight
Portion:
weight
Sample:
intermediate_dimension, is_ffpe, longest_dimension, shortest_dimension, time_between_clamping_and_freezing, time_between_excision_and_freezing
The exported clinical data manifest archive (PDC_clinical_data_manifests_<timestamp>. tar.gz") is updated to include follow-up manifest. Three files are extracted from the tar.gz - clinical file manifest, exposure manifest, and follow-up manifest.
The Case summary page opens in a modal window which now contains six tabs: Demographics, Diagnosis, Exposure, Follow up, Sample, and Aliquot.
The following APIs are updated to return the new properties that are updated in this release -
case
paginatedCaseDemographicsPerStudy
paginatedCaseDiagnosesPerStudy
paginatedCasesSamplesAliquots
The following
APIs are updated to return the new entities and properties that are updated in
this release -
paginatedCaseExposuresPerStudy
paginatedCaseFollowUpsPerStudy
Improvements
Add two new Sample properties to the export manifest (PDC-4686)
Fixes
Improvements
Migrate data dictionary and harmonization static page into PDC (PDC-4424, PDC-4425)
Update APs with newly added columns (PDC-4391)
Fixes
Improvements
Fixes
New Features
● Update to clinical manifest to include new clinical data fields (PDC-4260)
● Update of Clinical data download from the portal:
To download clinical data from the PDC portal, identify the data of your interest by applying filters and then move to the 'Clinical' tab on the browse page. Select the checkbox to select a specific row, all rows on the age or all pages, and then click the export clinical manifest button in CSV or TSV format. Clinical data are organized into multiple files and are exported as a single tar.gz archive. The clinical manifest includes data for demographic and diagnosis, and the exposure manifest includes exposure-related data.
● Update public APIs and the API documentation to include the exposure node (PDC-4293):
case and clinicalPerStudy APIs updated to include exposure clinical data
Improvements
● The word "Disqualified" in the Export file has an HTML code (PDC-4286)
● Update 'recent updates' and 'news' section on home page (PDC-4307)
● Update FAQ page to include a question on how to download clinical data (PDC-4308)
● Update the data type of "pack_years_smoked" of Exposure to Float (PDC-4330)
● Synchronize the enums for DD attributes for the properties that are common with GDC (PDC-4243)
Fixes
● Fixed Gene Study count discrepancy in Browse and Full Summary page (PDC-4236)
● Fixed Data discrepancy for "Year of Death" (PDC-4283)
● Fixed set-value vulnerability in all APIs (PDC-4227)
● Fixed Feedback Survey page is inactive (PDC-4284)
● Fixed the Link Study Summary -DUA? to https://pdc.cancer.gov/pdc/data-use-guidelines (PDC-4238)
● Fixed Misspelled property in biospecimen manifests: 'Freexing Method' (PDC-4287)
● Fixed "Year of Death" = "0" in UI and Clinical manifest (PDC-4290)
● Fixed "Year of Death" is '0' in the Clinical manifest but it is 'Not Available" in UI (PDC-4292)
● Fixed PDC browser sporadically reports 'null' for 'Days-to-Birth' and 'Days-to-Death' in clinical manifest where there are values in UI (PDC-4318)
● Fixed "Year of Death" = "0" in UI and Clinical manifest (PDC-4290)
Fixes
● Fixed Data discrepancy for Year of Death (PDC-4283)
● Clustergram page should have a header, and all links should open in the new tab (PDC-4132)
Fixes
● Fixed when the user hovers over any box on the Explore Data dictionary page -the URL has https://pdc.esacinc.com (PDC-4068)
● Fixed the typo in Data Dictionary under Case (PDC-4127)
Improvements
● Study Summary: Place Data Category terms in a defined order instead of alphabetical or numerical (PDC-2552)
● Make all Quality Metrics Web files open in a new tab (PDC-3452)
● Make publication filters function like Browse filters (PDC-3646)
Fixes
● Fixed the label" Number of cases" disappearing with less than 90% (PDC-3393)
● Fixed issues with "Select this page" when sorting of the column is performed (PDC-4017)
● Fixed not all studies files get exported on the experimental Design tab (PDC-4060)
New Features
● Create a script to organize the downloaded files into folder structure (PDC-3986)
Improvements
● Handle redirect URL from cptac (PDC-4007)
● API updates to address CDA requests (PDC-3966)
● Doc change for new all Programs and programsProjectsStudies APIs (PDC-3987)
Fixes
● Fixed no links to download files in Export File Manifest for Version 1 Studies (PDC-3928)
● Fixed browse page/ Study filter has overlapping text for six studies (PDC-4003)
New Features
● Developed a new web page - TECHNOLOGY ADVANCEMENT STUDIES, to host data from CPTAC and their collaborators that do not conform to the PDC data model due to specialized experimental designs.
● Create UI and API for Technology Advancement Studies (PDC-3911, PDC-3929, PDC-3931, PDC-3935, PDC-3937, PDC-3969, PDC-3972, PDC-3973, PDC-3975, PDC-3985, PDC-4011)
● Update studyexperimentaldesign API and update the UI to accommodate the change in API (PDC-3847, PDC-3900)
● Develop backend study forwarding (PDC-3901)
● Doc change for new studyExperimentalDesign (PDC-3984)
● Include Publication Supplementary Material and Alternate Processing Pipeline file counts in column Metadata on Files tab on Browse page (PDC-3659)
● Update the front page to accommodate links to the new Technology Advancement Studies page replace the TOOLS & PIPELINES section with a new section TECHNOLOGY ADVANCEMENT STUDIES, relocate links in the original TOOLS & PIPLINES under ANALYSIS main menu item (PDC-4014)
Fixes
● Fixed PDC study version column is empty in files manifests opened from Files overlay windows (PDC-3984)
● Fixed Files issue that opens on the same browser page (PDC-3871)
New Features
● Make study filtering a primary filter tab (PDC-3776)
● Create studyCatalog API to return all versions of studies (PDC-3921, PDC-3922)
Improvements
● Investigate and implement the ability to only display the top ten filters in each category (PDC-3779)
● For large files generate an S3 signed URL instead of cloud front URL (PDC-3837)
● Public API change to handle study versioning (study APIs) (PDC-3839)
● Public API change to handle study versioning (clinbio APIs) (PDC-3840)
● Update the human body map to show the new AML study (PDC-3865)
● Update API documentation to announce support for versioning (PDC-3918)
Fixes
● Fixed 'S' symbol in Genes/ under checkbox of "Studies in Which the Gene Product Was Detected" (PDC-3765)
Improvements
● Implement deep linking to study filtering using PDC study ID (PDC-3778)
Fixes
Fixed the "Select all pages" issue on the Study Summary page (PDC-3748)
Removed PDC000121 from heatmap_data. json (PDC-3866)
New Features
● Develop APIs for returning legacy data files (PDC-3362)
● Remove the tooltip for the EXPORT button on the experimental design tab on the study summary page (PDC-3574)
● Upgrade libraries for vulnerability (PDC-3666, PDC-3732, PDC-3733)
● Input/output entity_id (uuid) in APIs (PDC-3668)
● API change to handle sort column on legacy studies (PDC-3637)
● API change to get files per publication (PDC-3671)
● Update the publication page to add a string field in the filters PubMed ID (PDC-3697, PDC-3698, PDC-3807)
● Add sorting to Heatmaps API (PDC-3723)
● Update Heatmaps page (PDC-3724)
● Separate files per publication for multiple publications belonging to the same study (PDC-3785)
● Include Disqualified annotation in Study Summary Experimental Design Table (PDC-3719)
● Add "(%)" symbol beside Normalized Collision Energy in the Protocol tab on UI (PDC-3720)
● Handle channels layout for TMT6 in PDC Browser - Study Summary - Run Metadata Page (PDC-3758)
Fixes
● Fixed filters cannot be canceled by 'x' on the button on the browse page. (PDC-3530)
● Fixed dialog to update user password when registering with existing email does not work (PDC-3569)
● Fixed Study Summary Files Popup: Unable to Sort File Name column (PDC-3643)
● Fixed existing issues with Checkbox handling on the "Browse" page (PDC-3700)
● Fixed loading PDC000109 and PDC000111 heatmaps by handling Label-Free experiment type heatmaps (PDC-3804)
● Fixed heatmap study API should only return studies of the current version (PDC-3810)
New Features
● Implementation: APIs for study heatmap management (PDC-597)
● Create and document a stats API per NCI Request (PDC-3640, PDC-3663)
Improvements
● Upgrade highcharts for vulnerability (PDC-3683)
● Updates to UI for Experimental Design tab for Study Run Metadata Submitter ID, Plex Dataset name, and TMTs channel ordering (PDC-3241)
● Increase the signed URL validity to 7 days (PDC-3535)
● API change to handle sort column on legacy studies (PDC-3637)
Fixes
● Fixed the "Select all pages" option issue (PDC-3667)
● Fixed correct case count of getPDCMetrics API (PDC-3754)
New Features
● Develop the APIs required for Publications screen (PDC-3446, PDC-3664)
● New publications page (PDC-3447, PDC-3572, PDC-3573, PDC-3578, PDC-3648)
● Create a new page - Explore quantitation Data (PDC-3521)
● Enhance case-related public APIs to handle multiple case queries (PDC-2980)
● Add DRS URL to files in the PFB manifest (PDC-3509)
Fixes
● Fixed duplicate emails should not be allowed for registration (PDC-3272)
● Fixed Files export manifest gets exported two times (PDC-3620)
● Fixed Query URLs include unescaped spaces (PDC-3645)
● Fixed the "Select all pages" option issue with Supplementary data files (PDC-3651)
New Features
● A new study version feature is introduced in this release:
○ What is a study version?
PDC studies can have multiple versions. Additional versions (updates) of a study are created when the underlying data changes substantially. This may involve changes to the raw data, processed data, and/or metadata. When a new version is created, it may fall out of sync with the original publication of this data. Use of the latest version is strongly encouraged, as it commonly represents an update directly from the submitter.
○ Features of the study versioning:
■ The portal and APIs always show/return the data for the latest version
■ The browse page study table shows a label of the latest version with the PDC study id
■ Previous versions can be accessed only through the study summary page of the latest/current version
■ A collapsible study version history panel on the study summary page provides links to older versions
■ No further navigation is possible from the older version study summary pages
(PDC-3404, PDC-3412, PDC-3474, PDC-3494, PDC-3528, PDC-3529)
Improvements
● Upgrade pug and pug-code-gen in pdcapi and chorusapi (PDC-3397)
● Handle files with spaces in the signed URL API (PDC-3414)
● Include Diagnosis property "tumor_largest_dimension_diameter" to the API (PDC-3428)
● Improve the visibility of the PDC Help email (PDC-3450)
● Improving Export manifest button design (PDC-3469)
● Update Swagger API documentation (PDC-3488)
Fixes
● Fix registration issue reported by user (PDC-3467)
● Fix TSV and CSV formats manifest different formatting (PDC-3484)
● Fix PDC000120 v1 and PDC000121 v1 are missing External References (PDC-3490)
● Fix Study Summary Files Popup checkbox on page 2 does not select files in the list (PDC-3532)
● Code change to support heatmap URL formulated with study id (PDC-3172)
● Change the datatype of "tumor_largest_dimension_diameter" of diagnosis to decimal (PDC-3386)
● Develop a simple maintenance page that looks like PDC Data Browser for downtime during new version deployment (PDC-3390)
● Roll back name change for fileMetadata API (PDC-3480)
Fixes
● Fix selection issue when export file manifest CSV and TSV buttons are clicked (PDC-3366)
● Fix values for property "label_free_quantitation" from WS not being displayed on UI (PDC-3367)
● Fix TSV Files and Studies manifests incorrect and manifests headers style (PDC-3482)
New Features
● Generate the manifests downloads in TSV format as well as CSV and allow format selection (PDC-3073, PDC-3074, PDC-3265, PDC-3331, PDC-3307)
Improvements
● API changes accommodating new ptm_abundance table structures (PDC-3171)
● Have "icd_10_code" and "synchronous_malignancy" property and value appear in Case Summary Diagnosis (PDC-3267)
Fixes
● Fix moving to next page is not working after sorting on 'Genomic & Imaging Data (PDC-2816)
● Fix Study Summary overlay window opens twice for studies whose embargo date is N/A (PDC-3174)
● Fix the sorting Issue on the Browse page on Clinical Table & Clinical under Study Summary (PDC-3198)
● Fix sorting Issues with File Type and File Size on the Browse page under the Files tab (PDC-3199)
New Features
● Develop Data Policy page (PDC-3251)
● APIs accept a new mandatory parameter - acceptDUA to ensure API users are aware of the PDC data use guidelines (PDC-3253)
Improvements
● Update API documentation with acceptDUA variable (PDC-3239)
● Include Diagnosis property "icd_10_code" and "synchronous_malignancy" in the API (PDC-3266)
● Log all API calls with source and arguments in graphql server log (PDC-3270)
● Add text about download limits in FAQ (PDC-3302)
Fixes
● Browse File selection check box in does not select all (PDC-3268)
● Create a new API returning case, sample, and aliquot mapping for a study (PDC-3022)
● Create a new page - Requesting Data Submission (PDC-3179)
● Limit multiple downloads of the same file from the same user within a 24-hour period to two downloads by updating GraphQL APIs to sign URLs using Cloudfront key (PDC-3170)
Improvements
● Troubleshooting: GraphQL APIs not reporting to google analytics (PDC-3050)
● Add project ID to Clinical tab on Browse page (PDC-3072)
● Update APIs for gene page to include study versions (PDC-3079)
● Update the PDC help email address to the new one provided by NIH (PDC-3166)
● Add a link to release notes and PDC discussion forum under the HELP panel on the home page (PDC-3181)
● Update 'recent updates' and 'news' section on home page (PDC-3186, PDC-3245)
● Add pancreas organs to human body image on the front page (PDC-3207)
● Add Not Reported as enumeration for property 'tumor stage' (PDC-3033)
● Generate a separate data release document and add links in the UI (PDC-3161, PDC-3164)
● Update text on how to submit page to reflect the new requesting data submission page (PDC-3180)
● Enhance paginated APIs to handle limit value of zero (PDC-3205)
● Add "Pancreatic Ductal Adenocarcinoma" to disease type (PDC-3210)
● Add publication for HNSCC study (PDC-3136)
● Lifting embargo date for CPTAC3 HNSCC studies and change to N/A for all expired studies (NCI request) (PDC-3202)
Fixes
● Fixed could not move from page to page on Genes tab on the Browse page (PDC-3032)
● Fixed all 'Related PDC Studies' names get changed to the name of the Study a user is on (PDC-3132)
● Fixed File Counts on Case Summary view for versioned studies (PDC-3188)
● Fixed export All Manifests hang when there are zero records for Genes (PDC-3204)
● Fixed downloading manifest even if there are zero records and file manifest downloading twice (PDC-3206)
● Fixed API did not return external study reference (PDC-3090)
● Fixed three typos on Clustergram page (PDC-3093)
● Fix GraphQL APIs vulnerabilities (PDC-3101, PDC-3133)
● Address issues with file_format categorization (PDC-3168)
Data Release
New Studies released:
● Program: International Cancer Proteogenome Consortium
○ Project: Oral Squamous Cell Carcinoma - Chang Gung University
○ Includes one new study -
■ Oral Squamous Cell Carcinoma Study Proteome
All of this includes ~3500 files and ~500 GB.
● Update UI browse APIs to add a version to query and get the latest version of a study by default (PDC-2968)
● Update UI filters APIs to use the latest version of the study (PDC-2969)
● Update search APIs to get the latest version of the study (PDC-2973)
● Update UI to use APIs for the file type to data category mapping (PDC-3010)
● Embargo Date of Study does not show as N/A when clicked from Related PDC Studies (PDC-2955)
● Embargo text/Download button on the File tab issue (PDC-2963)
● Studies with Embargo data as N/A are missing Embargo Note in Study Summary DUA tab (PDC-2970)
● Fix broken link in Help/API documentation/Clustergram Number 17 (PDC-2596)
Improvements
● Update Text on How to Submit Page (PDC-2883)
● Update clinical data for CPTAC 2 studies (PDC-2918)
● Update UI Study Summary API to include the study version in the query (PDC-2936)
● Update the Study Summary UI API to include the version number (PDC-2938)
● Update clinical-related public APIs to return external references (PDC-2978)
● Update case-related public APIs to return external references (PDC-2979)
● Create APIs to get a dynamic mapping of file data category to file type (PDC-3009)
Fixes
● Fixed register with Workspace dropdown has overlapping text (PDC-2940)
New Features
● Add download option for study table on gene summary page (PDC-2874)
Improvements
● FAQs Page improvements (PDC-2954)
● Update API to sign URLs to use the new Cloudfront key (PDC-2809)
● Add tooltips to Gene summary page column headers (PDC-2852)
● Reorganize FAQ page (PDC-2855)
● Add PDC Study ID to the study table on the gene summary page (PDC-2873)
● Add a hyperlink to the publication text on the study summary page (PDC-2906)
Fixes
● Fixed Data Harmonization page - all links should open in a new window (PDC-2841)
● Fixed empty embargo date should be replaced with N/A for Study Summary when searched through the Search box (PDC-2912)
● Fixed issue with opening Case Summary direct URL (PDC-2956)
New Features
● Add Embargo date to File tab on Browse page and file manifest in UI and API (PDC-2795, PDC-2815)
Improvements
● Gene/Protein Summary: Show N/A if Assay data is not available (PDC-2665)
● Update message for empty email when user clicks on Forgot password link (PDC-2676)
● Added a few new properties to Case Summary Sample and Aliquot views in UI and API (PDC-2691, PDC-2755)
● Update the public API documentation to include the new API of getPaginatedGenes (PDC-2776)
Fixes
● Fixed Data Table Alignment issue for Gene Summary Table w/ rows (PDC-2664)
● Fixed Add program not being populated when registering with Workspace (PDC-2764)
● Retool either heatmaps or body image tooltips to both works with the same library version (PDC-2794)
● Fixed spelling mistake in fraction number description (PDC-2756)
Data Release
New Studies released:
● Program: Clinical Proteomic Tumor Analysis Consortium
● Project: CPTAC2 Confirmatory
○ Includes six new studies -
■ Prospective Breast BI - Acetylome
■ Prospective Breast BI - CompRef Acetylome
■ Prospective Breast BI - CompRef Proteome
■ Prospective Breast BI - CompRef Phosphoproteome
■ Prospective Ovarian JHU Intact Glycoproteome
■ Prospective Ovarian JHU N-linked Glycosite-containing peptide
Updates to the previously released studies
● Program: Pediatric Brain Tumor Atlas - CBTTC
● Project: Proteogenomic Analysis of Pediatric Brain Cancer Tumors Pilot Study
○ Release of additional supplementary data for two studies -
■ Proteogenomic Analysis of Pediatric Brain Cancer Tumors Pilot Study - Proteome
■ Proteogenomic Analysis of Pediatric Brain Cancer Tumors Pilot Study - Phosphoproteome
All of this includes ~1400 files and ~350 GB.
New Features
● Develop a simple JMeter text to force cache of common gene summary (PDC-2732)
Improvements
● Create a gene API that returns the gene attributes (PDC-2690)
● Update stats on the front page (PDC-2799)
● Update recent updates and news sections on the front page (PDC-2800)
● Enhance pagination objects in APIs for better performance and clarity (PDC-2725)
● Update the Creative Commons version in Study DUA (PDC-2757)
● Allow the NCBI Gene Id field to contain non-numerical values (PDC-2766)
● Change tooltip text for the file download button to notify about the embargo (PDC-2796)
● Update the recent release section on the home page (PDC-2882)
Fixes
● Fixed case ids and sex fields that do not match the same case id on the Browse page (PDC-2544)
● Fixed multiple studies that had inactive links on the Study Summary page (PDC-2571)
● Fixed creating new account link did not work when the user got to login dialog via Submit Data menu (PDC-2675)
● Fixed data user agreement (DUA) popping up when embargo date is N/A (PDC-2744)
● Upgraded D3 library version to make heatmaps work again (PDC-2793)
New Features
● Update study summary screen to add contact details (PDC-2436)
Improvements
● Apply conditional formatting to the embargo date on the study summary pages (PDC-2598)
● Add embargo date to the study manifest on the browse page (PDC-2617)
● Address discrepancies in the public API Swagger (PDC-2637)
● Enhance public APIs to synchronize up with documentation (PDC-2642)
● Update Data Dictionary (PDC-2680)
● Update FAQs for setting up permissions to upload files from S3 to S3 (PDC-2639)
Fixes
● Fixed checkbox appears faded when clicking Metadata or Quality Metrics Count (PDC-2508)
● Fixed clinical tab in case summary does not show Program and Project (PDC-2610)
● Fixed the Graphql errors returned by APIs (PDC-2619)
● Fixed security vulnerability in GraphQL (PDC-2601, PDC-2602, PDC-2603, PDC-2604)
● Fixed Cases by Primary site bar charts do not get tooltips (PDC-2746)
Data Release
New Studies released:
● Program: Clinical Proteomic Tumor Analysis Consortium
● Project: CPTAC3 Discovery
○ Includes two new studies -
■ CPTAC GBM Discovery Study - Acetylome
■ CPTAC GBM Discovery Study - CompRef Acetylome
Updates to the previously released studies
● Program: Pediatric Brain Tumor Atlas - CBTTC
● Project: Proteogenomic Analysis of Pediatric Brain Cancer Tumors Pilot Study
● Release of additional supplementary data for two studies -
○ Proteogenomic Analysis of Pediatric Brain Cancer Tumors Pilot Study - Proteome
○ Proteogenomic Analysis of Pediatric Brain Cancer Tumors Pilot Study Phosphoproteome
All of this includes ~300 files and ~125 GB.
New Features
● Add Embargo date to the study API & update API documentation (PDC-2615, PDC-2616)
● Develop API to return contact details (PDC-2435)
Improvements
● Concatenate 'Not Reported' primary site at the end of the primary sites list on Browse page Studies table tab (PDC-2534)
● Add gene_id to geneSpectralCount API (PDC-2614)
● Enhancement of aliquotSpectralCount (PDC-2638)
● Show properties for Demography tab in Case Summary (PDC-2605)
Fixes
● Gene/Protein Summary missing Gene ID and Assays (PDC-2450)
● Browse/Primary filters/ URL does not get updated on the copied link (PDC-2520)
● Inactive links for three questions on the FAQ page with the same error (PDC-2595)
● Cases should not require a corresponding entry in the reference table (PDC-2606)
New Features
● Add highlighted Embargo date to FAQ, Study table, Study summaries, and other pages (PDC-2579, PDC-2580, PDC-2584, PDC-2591)
Improvements
● Get external_case_id and imaging_resource of Case from reference table (PDC-2335)
Fixes
● Update the FAQ page to use relative API link instead of hard code (PDC-2522)
● Fix highcharts vulnerability (PDC-2427)
Data Release
New Studies released:
● Program: Clinical Proteomic Tumor Analysis Consortium
● Project: CPTAC3 Discovery
○ Includes four new studies -
■ CPTAC LSCC Discovery Study - Proteome
■ CPTAC LSCC Discovery Study - Phosphoproteome
■ CPTAC LSCC Discovery Study - Acetylome
■ CPTAC LSCC Discovery Study - Ubiquitylome
Updates to the previously released studies
● Project: CPTAC3 Discovery
○ CPTAC UCEC Discovery Study - Proteome
○ CPTAC UCEC Discovery Study - Phosphoproteome
○ CPTAC UCEC Discovery Study - Acetylome
■ Additional plex added to proteome and phosphoproteome
■ Updated protein reports to include the newly added plex
■ Updated quantitation data for API access
■ added supplementary data
● Project: CPTAC3 Discovery
● Release of supplementary data
○ Proteogenomic Analysis of Pediatric Brain Cancer Tumors Pilot Study - Proteome
○ Proteogenomic Analysis of Pediatric Brain Cancer Tumors Pilot Study - Phosphoproteome
■ Release of supplementary data
All of this includes ~4000 files and ~1 TB.
Improvements
● Update Study Summary Overlay Window with changes to Diagnosis table columns (PDC-2535)
● Update text on the FAQ page (PDC-2507)
● Add a link to FAQ from the data block on study summary page (PDC-2506)
● Update API documentation to include aliquot_run_metadata_id (PDC-2490)
● Update UI for new files Data Category (PDC-2460)
● Update clinical manifest generation to include additional attributes (PDC-2397)
Fixes
● Fix typo on study summary page (PDC-2538)
● Fix the Graphql link across the portal and populate the page with the appropriate URL (PDC-2485)
New Features
● Add supplementary data to the study summary screen (PDC-2377, PDC-2378)
Improvements
● Rearrange the home page to match with original design (PDC-2288)
● Remove unused heatmap data folders (PDC-2309)
● Get fraction count from protocol (PDC-2336)
● Add aliquot_run_metadata_id to aliquot_run_metadata API entity (PDC-2366)
● Update biospecimen manifest generation to include new attributes (PDC-2396, PDC-2399)
● Update clinical manifest generation to include new attributes API update (PDC-2395)
● Open HeatMap in a separate tab (PDC-2234)
● Update the example for studyExperimentalDesign API in Swagger API Documentation (PDC-2342)
● Auto generates the PDC Data Dictionary from PDC YAMLs (PDC-2392)
● Remove unused fields from the diagnosis tab on Study Summary - API change (PDC-2417)
Fixes
● Fix dot-prop vulnerability for all APIs (PDC-2337)
● Fix pick filters & then reverse - Study count does not match Clinical tab on Browse page (PDC-2283)
● Fix Frequently Asked Questions under Help menu opens in the same tab (PDC-2352)
● Fix wrong spelling of "Analytical" on Study Summary (PDC-2363)
● Fix Study Run Metadata Submitter ID is outnumbered and out of order on Study summary page Experimental Design tab (PDC-2391)
Data Release
New Studies released:
● Program: Clinical Proteomic Tumor Analysis Consortium
Project: CPTAC3 Discovery
Includes two new studies -
CPTAC UCEC Discovery Study - Acetylome
CPTAC UCEC Discovery Study - Compref Acetylome
● Program: Georgetown Proteomics Research Program
Project: Georgetown Lung Cancer Proteomics Study
Includes one new study -
Georgetown Lung Cancer Proteomics Study (only raw data)
Updates to the previously released studies
● Program: Clinical Proteomic Tumor Analysis Consortium
Project: CPTAC3 Discovery
♦ Release of quantitation data through APIs and Updates to the protein assembly files.
CPTAC LUAD Discovery Study - Acetylome
CPTAC LUAD Discovery Study - Compref Acetylome
All of this includes ~500 files and ~110 GB.
Improvements
● Upgrade Apollo-server-express from 1.x to 2.x (PDC-2192)
● Update 'recent updates' and 'news' section on home page (PDC-2205, PDC-2253, PDC-2329)
● Update Statistics panel (PDC-2252, PDC-2222)
Fixes
● Data Dictionary-Project- Properties-Programs- (has no Acceptable Types/Values) (PDC-2246)
Improvements
● Add "6. Upload Clinical & Biospecimen Metadata" to the list in How to Submit Data (PDC-2209)
● No distinction between (highlighted) Liver and (unhighlighted) Kidney (PDC-2207)
● Add CRDC link on the about page (PDC-2239)
● Cases by Disease type: Not Reported should be grouped with Other (PDC-2282)
● Update Statistics panel (PDC-2204)
Fixes
● The liver or kidney on the human figure on the front page or the respective bar are not highlighted when the mouse hovers over them (PDC-2125)
● Home page / Cases by Primary Site has no information (PDC-2278)
● On the Browse page when picking filters & then reversing The study count does not match (PDC-2113)
● Study Summary: Wrong spelling of Strategy (PDC-2257)
Data Release
New studies released:
● Program: Clinical Proteomic Tumor Analysis Consortium
● Project: CPTAC3-Discovery
● Includes two new studies -
○ CPTAC LUAD Discovery Study Acetylome
○ CPTAC LUAD Discovery Study CompRef Acetylome
● All of this includes 491 files.
New Features
● New submission template with a version number on the 'How to Submit' page (PDC-2091, PDC-2092)
● Added search feature in Swagger API Documentation (PDC-2179)
Improvements
● Make API changes needed to distinguish user-submitted non-raw data (use the new data_source column) (PDC-2166)
● FAQ answer to the question "Is PDC launched?" is outdated and needs to be updated (PDC-2119)
● Update the Statistics panel with the data from the new studies (PDC-2204)
● Update 'recent updates' and 'news' section on home page (PDC-2223)
● Update the image of "Login to the PDC Workspace "on Home-Help-Data Submission (PDC-2133)
Fixes
● Fixed unstable Help drop-down menu which moved down the page when the user scrolled down the page and would change width occasionally (PDC-2135)
● Fixed when the user is on HeatMap page and wants to go back they must click the "Back" button twice to get back to the Browse page (PDC-2126)
● Fixed hyperlink of "sharing large-scale genomic data" on DUA widget has 404 error (PDC-2199)
Improvements
● Configure Sequelize to customize sequelize connection pool size takes care of queries timing out issues (PDC-2085)
● Change heatmaps to look for files by PDC study ID rather than name (PDC-2106)
● Update swagger to include all return parameters for the listed APIs (PDC-2088)
Fixes
● Case Submitter ID does not pull up all info if using the search window (PDC-1927)
● Fixed error with pulling Heat Maps when searching for Study ID the 2nd time from the top search bar (PDC-2089)
Improvements
● Search window dropdown list is updated to display results in sequential order (PDC-2013)
● The search bar annotation has been updated (PDC-2051)
● Updated Swagger Documentation to accommodate new API changes for PDC Study ID (PDC-2062)
● Updated the News section (PDC-2121)
● Updated the download help link on the File tab and added more content to the FAQ page (PDC-2101)
Fixes
● Fixed the spacing in between numbers for the Analytical Fractions chart of the Browse page (PDC-1731)
● Fixed spelling errors on the FAQ page (PDC-2090)
● Fixed an overlapping text in the home page/News section (PDC-2122)
New Features
● Start using major primary site on the human figure and bar chart on the front page (PDC-2020, PDC-2021)
Improvements
● File manifest download time improved (PDC-1940, PDC-1966)
● Data Dictionary pages are updated (PDC-1962)
● Sort the study table on the browse page by the PDC Study ID in descending order (PDC-2000)
● Update the default data use agreement text (PDC-2001)
● Update how to cite PDC on the FAQ page (PDC-2015)
● Show the PDC study name instead of the resource name in the internal reference table (PDC-1971, PDC-2018)
● Update clinical tab to use new external reference API (PDC-1987, PDC-2026)
● Update the API of quantDataMatrix to support the new PDC Study ID (PDC-2016)
● Add ajcc_staging_system_edition field to diagnosis section in case summary (PDC-2037)
Fixes
● Fixed spelling mistakes and typos on multiple pages (PDC-1906, PDC-1969, PDC-1970, PDC-2014)
● Fixed "Submission portal documentation" link not working under HELP section on the home page (PDC-2072)
● Get file metadata API on swagger - remove the label (PDC-1996)
Data Release
New Studies released:
● Program: International Cancer Proteogenomic Consortium
● Project: Academia Sinica Early-Stage Non-smoking Lung Adenocarcinoma
○ Includes two new studies:
■ Academia Sinica LUAD100-Phosphoproteome
■ Academia Sinica LUAD100-Proteome
● Program: CPTAC program Head and Neck Squamous Cell Carcinoma (HNSCC)
● Project: CPTAC3-Discovery
○ Includes two new studies:
■ CPTAC HNSCC Discovery Study - Phosphoproteome
■ CPTAC HNSCC Discovery Study - Proteome
New Features
● Enable search based on the external references (PDC-1931, PDC-1959)
● Round the Program Statistics numbers to the nearest Millions (PDC-1986)
● Annotate a CPTAC dataset in PRIDE SDRF format (PDC-1939)
● Update search to be able to search by new PDC ID (PDC-1875, PDC-1874, PDC-1873)
● Add external references to the study summary page (PDC-1883, PDC-1882, PDC-1881)
● Allow deep linking to the study summary page by PDC ID (PDC-1876)
● Implement search by partial PDC ID (PDC-1937)
Improvements
● Added Head and Neck organ on front page human body figure (PDC-1916)
● Add the new PDC id on the study table and in all the manifests (PDC-1930, PDC-1960)
● Improve multiple file downloads to show download status/progress on the browser (PDC-1932)
● Refine search functionality to return more results (PDC-1943)
● Style the clustergram help page to look like a regular PDC data browser page (PDC-1886)
● Add a direct link to the clustergram page from the API documentation page (PDC-1887)
● Standardize the IDs on the study summary and case summary pages (PDC-1888)
● Peptide Spectral Matches with Text file format are not considered in the count on Browse (PDC-1902)
● Add a release notes link to show release notes (PDC-1884)
● Update recent releases panel with newly added datasets (PDC-1893)
● Added heatmap and JSON data files for newly added datasets (PDC-1897)
Fixes
● Fixed File Type filter Proprietary on the Browse page Files filter tab, which could not be selected (PDC-1806)
● Fixed breadcrumbs filter info not working correctly when clearing filters (PDC-1804)
● Fixed jumping to the last pages on Browse page data tables when showing fifty results per page working very slow (PDC-1816)
● Fixed showing incorrect dialog when the user clicked on "Don't have an account" on the login window (PDC-1855)
● Fixed the vulnerable dependency in the PDC repository (PDC-1850)
Data Release
New Studies released:
Program: International Cancer Proteogenome Consortium
Project: Human Early-Onset Gastric Cancer - Korea University
Includes three new studies -
Proteogenomics of Gastric Cancer - Proteome
Proteogenomics of Gastric Cancer - Phosphoproteome
Proteogenomics of Gastric Cancer - Glycoproteome
All of this includes 10,943 files and ~8 TB of data.
New Features
● Added stomach (primary site) to bodymap figure on the front page (PDC-1857)
● Added study_id and study_submitter_id to study manifest (PDC-1789)
● Added 'Available Data Types and Files' to the HELP dropdown on the homepage (PDC-1726)
Improvements
● Improved SUBMIT DATA workspace login link text to show user status (PDC-1859)
● Updated content of How to Submit Data page (PDC-1827)
● Improved loading speed of Genes tab (PDC-1816)
● Added login notification when NIH/eRA option is used (PDC-1795)
● Added FAQ item on finding genomic and imaging mapping (PDC-1794)
● Added official logo on Submit Portal Documentation page (PDC-1787)
● Removed Proteomic Data Commons text from the image on about page (PDC-1786)
● Made the "How to Submit Data" page responsive (PDC-1779)
● Improved quantDataMatrixs loading speed (PDC-1772)
● Updated quantDataMatrix API documentation (PDC-1737)
● Linked the study and file tab table header to the file types on the FAQ page (PDC-1722)
● Updated the site URL to include just the domain name (PDC-1716)
Fixes
● Fixed News > www.asms.org link (PDC-1901)
● Fixed Dont have an account dialog (PDC-1855)
● Fixed Dont have an account dialog (PDC-1855)
● Fixed clinical table header resizing on the study summary page (PDC-1854)
● Fixed clinical table header text on the study summary page (PDC-1853)
● Fixed diagnosis->age at diagnosis text on case summary page (PDC-1852)
● Fixed quality metrics file count on study browses page (PDC-1851)
● Fixed file count on file browse page (PDC-1758)
● Fixed body map figure pop-up text, cases instead of studies (PDC-1815)
New Features
● Added a button on the Files tab on the browse page linking to the multiple download FAQs section (PDC-1702)
● Query URL bookmark option (merged branch PDC-1360-browse-query-bookmark)
Improvements
● Official logo everywhere (PDC-1588)
● All columns are now resizable in the clinical table (PDC-1660)
● An improved style for the search bar at the top right corner of the page (PDC-1708)
● Style external links with a special icon (PDC-1711)
● About page updated (PDC-1713)
● Style query URL bookmark (PDC-1445)
● Remove the icon from a login on the home page (PDC-1707)
● Added a dialog box asking the user if they want to register a new PDC account when the user tries to log in with an unregistered email (PDC-1661)
● When a user successfully registers a new account using Google sign-in option they are shown confirmation that the user is registered (PDC-1661)
Fixes
● Fixed spelling bugs on the Case Summary overlay window under the diagnosis tab (PDC-1679)
● Fixed highlighting incorrect search characters in the search bar (PDC-1659)
● Fixed an issue of changing a users name when the user updates their information in their PDC user account (PDC-1661)
● Keep users logged in after they refresh the PDC website page if the user was logged in earlier (PDC-1661)
● Fixed File type Text not included in file counts for studies (PDC-1703)
● Fixed workflow image staying on-screen on submit data help page (PDC-1747)
● Fixed gene filter not clearing when the filter is cleared issue with query URL bookmark feature (PDC-1782)
● Fixed spelling issues on the Submission Portal Documentation help page (PDC-1393)
● Fixed percentage not visible for some disease types on Browse page Donut graph (PDC-1657)
● Fixed inconsistent count between gene count and the actual number of genes in the gene tab on the Browse page (PDC-1668)