v129 released!

November 30, 2022 —

Announcing v129 release of the ENCODE portal, highlighted by the following updates:

  • Schema changes
    • Updated File output_type and Analysis Step input_file_types and output_file_types  with the following mapping:
      • “topologically associated domains” changed to “contact domains” 
      • “mapping quality thresholded chromatin interactions” changed to “mapping quality thresholded contact matrix”
      • “chromatin interactions” changed to “contact matrix”
      • “DNA accessibility raw signal” changed to “nuclease cleavage frequency”
      • “long range chromatin interactions” changed to “loops”
      • “nested topologically associated domains” changed to “nested contact domains”
      • “allele-specific chromatin interactions” changed to “allele-specific contact matrix”
      • “variants chromatin interactions” changed to “variants contact matrix”
      • “haplotype-specific chromatin interactions” changed to “haplotype-specific contact matrix”
      • “haplotype-specific DNA accessibility raw signal” changed to “haplotype-specific nuclease cleavage frequency”
      • “haplotype-specific DNA accessibility corrected signal” changed to “haplotype-specific nuclease cleavage corrected frequency”
    • Added the following enums to File output_type and to Analysis Step input_file_types and output_file_types
      • depth normalized signals matrix
      • z scores matrix
      • TF peaks matrix
      • enhancer-gene links
      • thresholded links
      • cell type data
    • Updated Analysis Step analysis_step_type enum of “topologically associated domain identification” to “contact domain identification”
    •  Updated Annotation annotation_type enum of “long-range chromatin interactions” to “loops”
    • Added the following enums to Annotation annotation_type
      • cell type annotation
      • regulatory elements signal matrix
  • UI changes
    • Added Protein Knockdown (Degron) Matrix page, highlighting datasets investigating protein knockdowns
    • Adjusted search result titles for Series objects to display age units
    • Adjusted association graph code to support graphs for Aggregate Series
    • Improved Mouse Development Matrix:
      • Fixed bug affecting display of ChIP-seq datasets
      • Changed button formatting and layout and added “Jump to tissue” buttons
      • Changed design to single column layout
    • Added facet for Award RFA to Human Donor Matrix page
    • Fixed bug causing incorrect file counts in the file filters panel on dataset summary pages
    • Adjusted links to Functional Characterization search in the toolbar menu and front page card
  • Other changes
    • Updated audit details for processed data of Hi-C and ChIA-PET datasets in accordance with File output_type changes
    • Updated audits to no longer apply to data belonging to File Sets or Series
    • Updated assay_slims for long read single cell RNA-seq to include “transcription”
    • Increased maximum allowed attachment size
    • Updated calculation of assay_title for Hi-C related experiments
    • Fixed issue with calculation of biosample_summary for Functional Characterization Series
    • Added column for azure_uri in downloaded metadata tables
    • Fixed bug that prevented adding datasets to your cart from another user’s cart

 v129 software version: https://github.com/ENCODE-DCC/encoded/releases/tag/v129.0

All of the source code used for the portal website is open source and available through our repository hosted at GitHub (www.github.com/ENCODE-DCC/)