v122 released!

September 14, 2021 —

Announcing v122 release of the ENCODE portal, highlighted by the following updates: 

  • Schema changes
    • Added “gkmSVM-model” enum to Annotation annotation_type
    • Added “regulatory elements prediction model” enum to File output_type and Analysis_Step input_file_types and output_file_types
    • Added new property crispr_screen_tiling property to Reference
    • Added new property origin_batch to Biosample
    • Added “Deeply Profiled” enum to internal_tags of Datasets
    • Modified regex patterns for lot_id and product_id of Antibody Lot, Biosample, Library, and Treatment
    • Added “cell barcode” and “element barcode” enums to File read_structure.sequence_element
    • Added “mEGFP” enum to Genetic Modification introduced_tags
    • Added “selection” and “perturbation” enums to Treatment purpose
    • Added biological_replicates, bio_replicate_count, and tech_replicate_count properties to Experiment and Functional Characterization Experiment
    • Adjusted calculation of Biosample perturbed property to be true only if the Biosample has a Treatment with no purpose or “perturbation” purpose
  • UI updates
    • Modified biosample summaries to display metadata on inserted or deleted gene names from associated Genetic Modifications
    • Removed the following facets from the Functional Characterization Experiment search page: RFA, Expression measurement method, Library fragment size (nt), Mapped read length (nt), Read length (nt)
    • Updated facets on Functional Characterization Series search and adjusted calculation of Functional Characterization Series assay_slims and assay_title
    • Disabled visualize button on Mouse Development Matrix
    • Fixed bug in which Files displayed in a Cart’s file view were not removed from the file view after the File’s Dataset was removed from the Cart
    • Fixed bug where links to disease based searches from Rush AD brain matrix page were incorrect
    • Adjusted titles of Analyses to handle cases where the Analysis has no assembly property
  • Other changes
    • Added audit for Files without specification of read_structure
    • Added audit for Treatments without specification of purpose
    • Updated ontology

v122 software version: https://github.com/ENCODE-DCC/encoded/releases/tag/v122.0

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/)