v4.5.0

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

• PyCellBase:
  http://docs.opencb.org/display/cellbase/REST+Clients
  http://docs.opencb.org/display/cellbase/Python+client+library
• CellBaseR
  https://bioconductor.org/packages/release/bioc/html/cellbaseR.html
• Reimplemented Java client; provided within the CellBase code, cellbase-client module
• New JavaScript client

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

CellBase v4.5.0-rc development release

new development version 4.5.0-rc

v4.5.0-beta

Beta release of 4.5.0

CellBase v4.0.0 Stable Release

• Data:
  • upgraded to ENSEMBL 82
  • new sources: HPO, GERP++, Gene Expression Atlas, GoNL, EXaC, UK10K, 1kG phase 3, ESP
• Completely new Java DB Adaptor API
• REST API:
  • Improvements over available methods and new end points
  • Comprehensively documented. API specification available through the Swagger interface
• Much more (and better) documentation at the GitHub wiki
• Major tests improvements
• New Variant data model used to store and handle ENSEMBL variation data - standardizes variant handling within OpenCB
• Major improvements on variant annotation:
  • Complete refactoring of the variant annotation code
  • New Variant Annotation data model
  • New annotation data: GERP++, CADD, UniProt, InterPro, population frequencies from GoNL, EXaC, UK10K, 1kG phase 3, ESP
• Many performance improvements, bug fixes and code clean ups

v4.0.0-rc

New release candidate v4.0.0-rc

CellBase v3.2.0 Stable Release

New stable CellBase v3.2.0. Many changes have been made and many tests and bugs need to be fixed. Major changes include:

• Many new queries and web services implemented
• New data sources and functionality added such as Gene Expression Atlas (EBI), InterPro or DGIdb among others
• Variant Annotation:
  • data model improvements
  • variants are now annotated with Uniprot, InterPro, gene expression and gene drug interactions
• New CellBase server installed at University of Cambridge at bioinfo.hpc.cam.ac.uk/cellbase, beta available at bioinfodev.hpc.cam.ac.uk/cellbase
• Swagger, README and documentation have been significantly improved
• Performance improvements all across CellBase, many bugs fixed and code clean ups

Some issues solved:

https://github.com/opencb/cellbase/issues?q=milestone%3Av3.2.0

CellBase v3.1.0 Stable Release

New stable CellBase v3.1.0. Many changes have been made and many tests and bugs need to be fixed. Major changes include:

• New cellbase-app CLI using JCommander, this allows to download, build and load automatically CellBase
• New Variant Annotator developed, it has been tested and benchmarked against Ensembl VEP
• Swagger, README and documentation has been improved
• New data sources and functionality added. Human GRCh38 supported
• New data installation at University of Cambridge at bioinfo.hpc.cam.ac.uk/cellbase
• License changed to Apache License 2.0
• Performance improvements all across CellBase, many bugs fixed and code clean ups

Some issues developed:

https://github.com/opencb/cellbase/issues?q=milestone%3Av3.1.0

CellBase v3.1.0-RC.1

Second release candidate of CellBase v3.1.0. Many changes have been made and many tests and bugs need to be fixed. Major changes include:

• New cellbase-app CLI has been finished and tested
• New Variant Annotator has been tested and benchmarked against Ensembl VEP
• Some new web services developed
• Swagger, README and documentation has been improved
• Some new data sources and functionality added
• performance improvements, many bugs fixed and code clean ups

CellBase v3.1.0-RC

This is the first release candidate of CellBase v3.1.0. Many changes have been made and many tests and bugs need to be fixed. Major changes include:

• New cellbase-app replace old cellbase-build and there is a new data downloader and build
• A new Variant Annotator has been developed
• New CLI using JCommander has been developed
• Swagger, README and documentation has been improved
• Some new data sources and functionality

v3.0.0

The main features of this release are:

• migrate the storage engine from MySQL to MongoDB database to provide a higher performance and scalability
• cellbase-build has been improved, now the building is faster and more automatic
• CellBase now uses maven modules organization
• data models have been migrated to biodata repository
• new database such as UniProt and IntAct have been added
• swagger has been integrated