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@javild javild released this 25 Sep 16:26
· 2413 commits to develop since this release
v4.5.0
f43b0db

Variant annotation

  • Copy Number Variants and Structural Variants are now annotated: CNVs, INS, DEL, INV, DUP, TANDEM-DUP, BND
  • Variant Annotator handles imprecise definition of variant limits
  • Variant annotator can also provide consequence type prediction for not decomposed MNVs
  • Exon overlap added to returned variant annotation
  • Cytobands added to returned variant annotation
  • New annotation sources:
    • The Database of Genomics Variants
    • TRF simple repeats
    • WindowMasker
    • Genomic super duplications
  • Population frequencies from reference projects, PASS and non-PASS variants are now provided
  • Returned list of SO terms refined to improve VEP comparison result; 99.999% coincidence against VEP e83
  • Data model changes to the VariantAnnotation object
    • Deprecated field
      union { null, VariantTraitAssociation } variantTraitAssociation
      New traitAssociation field must be used instead:
      union { null, array<EvidenceEntry> } traitAssociation
    • Field
      union { null, int } exonNumber;
      present in previos 4.5.0-rc* releases is no longer available. This field was not present in stable 4.0.* releases. New Field:
      union { null, array<ExonOverlap> } exonOverlap
      is used instead.
    • Other additional fields:
union { null, array<Cytoband> } cytoband;
union { null, array<Repeat> } repeat;

Clinical functionality

  • WARNING: previous feature/clinical/* REST endpoints have been deprecated and will no longer supported
  • New "clinical" category
  • Re-implementation of all clinical variants functionality
    • Homogenization of data models: all clinical variant sources are integrated into Variant objects
    • New web services added
  • New IARCTP53 data source integrated

New CellBase client libraries

ENSEMBL e89 GRCh38 data ready

  • Code adapted to be compatible with e89 GRCh38 data.

Additional Web Service improvements

  • Transcripts within genes can now be filtered by annotation flag, e.g. "basic"
  • "search" method added to transcript category
  • New meta/about web service returns server code version and commit
  • New genomic/region//repeat web service to search for repeated regions
  • Gene expression searches improved

Created new documentation site

http://docs.opencb.org/display/cellbase/CellBase+Home

Improved logs

  • WS now log every query; facilitates diagnosis of server side problems
  • sl4j is now used for logging; date, time and thread are recorded for each log entry
    Configuration
  • Support for several Neo4j databases
  • Number of mongo connections per host can now be customized at the configuration file
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