v128 released!

August 10, 2022 —

 Announcing v128 release of the ENCODE portal, highlighted by the following updates:

  • Schema changes
    • Changed assay_title calculation for Hi-C experiments, dividing the experiments into intact Hi-C and in situ Hi-C
    • Added “ENCODE v4” and “ENCODE v5” enums for Annotation “encyclopedia_version” property
    • Added BPNetQualityMetric schema
    • Added the following enums to Analysis “analysis_step_types”:
      • contribution score calculation
      • model generation
      • sequence motif prediction
      • cell type annotation
      • element gene link prediction
      • selection 
    • Added the following enums to File “output_type” and to Analysis “input_file_types” and “output_file_types”
      • bias-corrected predicted signal profile
      • counts sequence contribution scores
      • model performance metrics
      • models
      • observed bias profile
      • observed control profile (minus strand)
      • observed control profile (plus strand)
      • observed signal profile
      • observed signal profile (minus strand)
      • observed signal profile (plus strand)
      • predicted bias profile
      • predicted profile
      • predicted signal profile (minus strand)
      • predicted signal profile (plus strand)
      • profile sequence contribution scores
      • selected regions for bias-corrected predicted signal profile
      • selected regions for count sequence contribution scores
      • selected regions for predicted signal profile
      • selected regions for predicted bias profile
      • selected regions for predicted signal profile (minus strand)
      • selected regions for predicted signal profile (plus strand)
      • selected regions for profile sequence contribution scores
      • sequence motifs
      • sequence motifs report
      • sequence motifs instances
      • training and test region
      • minus strand end position signal
      • minus strand normalized end position signal
      • plus strand end position signal
      • plus strand normalized end position signal
      • raw imaging signal
      • cell coordinates
      • cell type annotation
      • DNN-MPRA contribution scores
      • DNN-MPRA predicted signal
      • element gene links
      • thresholded element gene links
    • Added the following enums to Annotation “annotation_type”. “dsQTL” was removed from the enums.
      • element gene link predictions
      • ChromBPnet-model
      • BPnet-model
      • caQTL
      • genotyping
    • Added “high resolution slide image” enum to Document “document_type”
    • Added “seqFISH” enum to Experiment “assay_term_name”
    • Added “supersedes” property to Donor
    • Added “experimental_input” property to Reference
    • Changed “experimental_input” property in Annotation to be an array
    • Added “donor” property to Annotation 
    • Updated regex for “reagents” property in Genetic Modification
    • Added “altius” as namespace for aliases
    • Updated property definitions in the following objects:
      • AtacAlignmentEnrichmentQualityMetric
      • AtacAlignmentQualityMetric
      • AtacLibraryQualityMetric
      • AtacPeakEnrichmentQualityMetric
      • AtacReplicationQualityMetric
      • ChiaPetAlignmentQualityMetric
      • ChiaPetChrInteractionsQualityMetric
      • ChiaPetPeakEnrichmentQualityMetric
      • ChipAlignmentEnrichmentQualityMetric
      • ChipAlignmentQualityMetric
      • ChipLibraryQualityMetric
      • ChipPeakEnrichmentQualityMetric
      • ChipReplicationQualityMetric
      • ChipSeqFilterQualityMetric
      • DnaseFootprintingQualityMetric
      • GeneQuantificationQualityMetric
      • GeneTypeQuantificationQualityMetric
      • ​​HicQualityMetric
      • ScAtacAlignmentQualityMetric
      • ScAtacAnalysisQualityMetric
      • ScAtacCountsSummaryQualityMetric
      • ScAtacLibraryComplexityQualityMetric
      • ScAtacMultipletQualityMetric
      • ScAtacReadQualityMetric
      • ScrnaSeqCountsSummaryQualityMetric
      • StarSoloQualityMetric
  • UI changes
    • Added human and mouse body maps to Single Cell collection page
    • Updated links from home page cards
    • Disallowed queries with “limit=all” parameter from rendering on the frontend
    • Removed “View all” links from the interface
    • Fixed mislabeled organs on human body map diagrams
    • Updated default encyclopedia tracks displayed on Valis genome browser
  • Other changes
    • Updated ontology terms and term slimming
    • Adjusted invalid post_differentiation_time details audit to not trigger for Biosamples that are cell lines
    • Added quality standard audits applicable to Hi-C datasets
    • Fixed ChIP-seq related quality audits to exclude worm and fly datasets
    • Fixed bug causing malformed trackhubs for UCSC genome browser

v128 software version: https://github.com/ENCODE-DCC/encoded/releases/tag/v128.0

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/)