v130 released!

March 24, 2023 —

Announcing v130 release of the ENCODE portal, highlighted by the following updates:

  • Schema changes
    • Added the following enums to File output_type and to Analysis Step input_file_types and output_file_types
      • normalized observed signal profile
      • normalized predicted signal profile
      • normalized predicted bias profile
      • normalized observed signal profile (plus strand)
      • normalized observed signal profile (minus strand)
      • normalized predicted signal profile (plus strand)
      • normalized predicted signal profile (minus strand)
      • selected regions for predicted signal and sequence contribution scores
      • representative IDR thresholded peaks
    • Updated File output_type and Analysis Step input_file_types and output_file_types with the following mapping:
      • “predicted profile” changed to “predicted signal profile”
      • “bias model” changed to “bias models”
    • Added the following enums to Annotation annotation_types
    • Updated internal_tags of all Dataset subclasses with the following mapping:
      • ENCYCLOPEDIAv3 changed to ENCYCLOPEDIAv0.3
      • ENCYCLOPEDIAv4 changed to ENCYCLOPEDIAv1
      • ENCYCLOPEDIAv5 changed to ENCYCLOPEDIAv2
      • ENCYCLOPEDIAv6 changed to ENCYCLOPEDIAv3
    • Added the following enums to Annotation and Experiment internal_tags:
      • RegulomeDB_2_2
      • RegulomeDB_2_3
      • RegulomeDB_3_0
      • RegulomeDB_3_1
    • Added “seqFISH” enum to Pipeline assay_term_names
  • UI changes
    • Added publication citation on ENTEx matrix page
    • Added links to BPNet models on pages of related Experiments
    • Revamped Stem Cell matrix page
    • Added Functional Characterization Experiment matrix page
    • Added Disease Series to the Series Search page
    • Updated Rush Alzheimer’s Disease matrix page to use new terminology
    • Fixed bug where Experiments with Analyses of mixed genome annotations would result in page crashes
    • Fixed bug on Organism Development Series pages affecting worm or fly series missing synchronization
  • Other changes
    • Updated Cart to adjust which files are automatically selected when “Show Default Data Only” option is checked
    • Removed the Walkme feature from the Portal
    • Updated Valis genome browser to display the most recent release of cell-type agnostic cCREs
    • Updated summaries for organoid biosamples
    • Fixed bug causing certain CRISPR screen related files to not visualize correctly in Valis genome browser

v130 software version: https://github.com/ENCODE-DCC/encoded/releases/tag/v130.0

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/)