v119 released!

July 9, 2021 —

Announcing v119 release of the ENCODE portal, highlighted by the following updates: 

  • Added alpha release of Encyclopedia landing page
  • Modified Experiment and Annotation track info of Valis genome browser to display Target
  • Exposed RNA-Get API and updated RNA-Get page UI
  • Fixed calculation of visualizable files in Cart’s genome browser and filtered files belonging to non-released analyses when “Show default data only” is checked
  • Added Target facet to Cart page
  • Added simple_summary property to Biosample and simple_biosample_summary property to Experiment, Functional Characterization Experiment, and Single Cell Unit
  • Updated Valis genome browser to display simple_biosample_summary info for each track
  • Updated Functional Characterization Series tables to display biosample summary and expression readout percentage/percentile information
  • Added filter_type and filter_value properties to File
  • Allowed submission of .txt files for sequence barcodes Files
  • Added “fluorescence activated cell sorting” and “CRISPRi-FlowFISH” enums to Functional Characterization Experiment examined_loci.expression_measurement_method
  • Added “merging” enum to Analysis Step analysis_step_types
  • Changed assay slimming of long read scRNA-seq to Single Cell
  • Excluded long read scRNA-seq from missing RNA fragment size audit
  • Adjusted biosample characterization audit to consider parent biosamples
  • Added “DHS” enum to Annotation annotation_subtype, and restricted modification of annotation_subtype to admins only
  • Added documents embedding to Annotation
  • Embedded elements_reference on Functional Characterization Series and modified UI to display elements_reference
  • Added elements_selection_method property to References to support Functional Characterization Experiments
  • Updated Disease Series UI to split disease and no disease datasets
  • Replaced Description column of tables on Series pages with Biosample summary
  • Added file association graph to Functional Characterization Series
  • Updated titles of Analyses displayed in File details tab of Series pages
  • Increased file upload token expiration time to 36 hours
  • Added Biosamples to set_status_up list for Transgenic Enhancer Experiments

v119 software version: https://github.com/ENCODE-DCC/encoded/releases/tag/v119.0

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/)