v125 released!

Announcing v125 release of the ENCODE portal, highlighted by the following updates: 

• Schema changes
  • Genetic Modification updates
    • Added cas_organism property, to be specified only on CRISPR genetic modifications
    • Upgraded genetic modifications of Category “transgene insertion” to “insertion”
    • Upgraded CRISPR genetic modifications of Category “activation” to “CRISPRa”
    • Upgraded characterization CRISPR genetic modifications of Category “disruption” or “deletion” to “CRISPR cutting”
    • Upgraded CRISPR genetic modifications of Category “binding” to “CRISPR dCas”
    • Upgraded characterization CRISPR genetic modifications of Category “interference” to “CRISPRi”
  • Upgraded assay_term_name of “transgenic enhancer assay” to “enhancer reporter assay”
  • Upgraded assay_term_name property of Functional Characterization Experiments based on examined_loci.expression_measurement_method metadata as follows:

    • examined_loci.expression_measurement_method	New assay_term_name
      None	Proliferation CRISPR screen
      HCR-FlowFISH	Flow-FISH CRISPR screen
      PrimeFlow	Flow-FISH CRISPR screen
      antibody Sort-seq	FACS CRISPR screen
      endogenous protein Sort-seq	FACS CRISPR screen
      Magnetic separation Sort-seq	FACS CRISPR screen
      Fluorescence activated cell sorting	FACS CRISPR screen
      qPCR	FACS CRISPR screen

  • Adjusted assay slims of Functional Characterization Experiments as follows:

    • assay_term_name	assay_slim
      Control CRISPR screen FACS CRISPR screen Flow-FISH CRISPR screen Proliferation CRISPR screen	CRISPR screen
      Control MPRA Control STARR-seq MPRA STARR-seq	Massively parallel reporter assay
      Pooled clone sequencing	Library preparation
      Perturbation followed by snATAC-seq Perturbation followed by scRNA-seq	Single cell

• UI changes
  • Moved RNAget page to new endpoint
• Other changes
  • Updated ontology file to add organ and cell slims for several immune cell related Biosample Types, and add new ontology terms for additional immune cell types.
  • Added audit to flag Functional Characterization Experiments with mismatched readouts
  • Added audit to flag CRISPR screen Functional Characterization Experiments that are not in Series

v125 software version: https://github.com/ENCODE-DCC/encoded/releases/tag/v125.0

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/)