v123 released!

Announcing v123 release of the ENCODE portal, highlighted by the following updates: 

• Schema changes
  • Updated “gkmSVM-model” enum of Annotation annotation_type to “gkm-SVM model”
  • Added “TF binding prediction model,” “enhancer prediction model,” “promoter prediction model,” “filtered reads,” “archr project,” “genome subcompartments,” and “chromatin stripes” enums to File output_type and Analysis Step input_file_types and output_file_types
  • Added “mex” enum to File file_format_type
  • Fixed schema link in “supersedes” property of Single Cell Unit to point to Single Cell Units
  • Added new object schemas for scATAC Alignment Quality Metric, scATAC Read Quality Metric, scATAC Multiplet Quality Metric, scATAC Library Complexity Quality Metric, scATAC Analysis Quality Metric, and Collection
  • Added treatment_type_details property to Treatments with enums “agonist” and “antagonist”
  • Added “control” and “labeling” enums to Treatment purpose
  • Added datapoint property to Functional Characterization Experiment and Functional Characterization Series
  • Upgraded encyclopedia_version numbering of Annotations
  • Added “current” enum to Annotation encyclopedia_version
  • Modified calculation of biosample_summary property of Experiment, Functional Characterization Experiment, Biosample, and Series
  • Added “chromatin states,” “histone modifications,” and “synthetic elements” enums to Reference elements_selection_method
  • Upgraded “ATAC-seq,” “DNase-seq,” “transcription factors,” and “GRO-cap” enums of Reference elements_selection_method to “accessible genome regions,” “DNase hypersensitive sites,” “TF binding sites,” and “transcription start sites” respectively, and upgraded both “point mutations” and “single nucleotide polymorphisms” enums of Reference elements_selection_method to “sequence variants”
• UI updates
  • Updated Encyclopedia landing page
  • Added facet groupings to Functional Characterization Experiment, Functional Characterization Series, and Transgenic Enhancer Experiment search pages
  • Added table of Reference data to Functional Characterization Experiment and Functional Characterization Series pages
  • Removed Life Stage and Run Type facets from Functional Characterization Experiment and Functional Characterization Series search pages, and removed Life Stage from Transgenic Enhancer Experiment search page
  • Updated result titles on Functional Characterization Experiment search page
  • Updated Valis genome browser to display Batch information on tracks
  • Added italicization to organism scientific names in various tables
  • Added feature to add all experiments in a series to a Cart
  • Added biological replicate facet to Cart page

v123 software version: https://github.com/ENCODE-DCC/encoded/releases/tag/v123.0

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/)