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MartLoader

MartLoader. Anthony Cros Joachim Baran. Overview. Motivation Creating ICGC marts Performance evaluation Improvization Current MartLoader implementation MartLoader in development Aims Architecture Front-end: configuration and mart planning

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MartLoader

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  1. MartLoader Anthony Cros Joachim Baran

  2. Overview • Motivation • Creating ICGC marts • Performance evaluation • Improvization • Current MartLoader implementation • MartLoader in development • Aims • Architecture • Front-end: configuration and mart planning • Back-end: parallelization and mart generation

  3. Creating ICGC Marts • Import data in line with the ICGC Submission Manual • Transform data values/ranges • for BioMart compatibility • for presentation through BioMart’s web-interface • Generate a mart database

  4. Comparison to MartBuilder • Similar workflows, but different requirements Not in 3NF. Decoding and Rewriting Schema Discovery Validation Builder Loader 3NF Denormalization Generic Transformation* *Currently focusing on ICGC only.

  5. current martloader Over to Anthony

  6. Performance Evaluation • Is the choice of the database system relevant? • PostgreSQL vs MySQL MyISAMvs MySQL InnoDB • Is using UNIX file based joins faster than database joins? • relational databases are optimized for joining data • file based joins require • sorting of the key columns of the input file • joining on the sorted key columns • importing the result into the database

  7. Performance Evaluation • PostgreSQL slightly outperforms MySQL • Database backend not of major importance though

  8. Performance Evaluation • UNIX file based sort + join + SQL import fastest

  9. Developing an Improved MartLoader • Rapid configuration with bespoken UI • Optimized mart generation and data loading • Being generic & flexible Exchangeable components: • Front-end • Abstract data model • Planning algorithm • Back-end • Parallelization • Mart generation Backend Interface File Abstract Data Model File Graphical User Interface Planning Algorithm File-Processing Mart Generation

  10. Versatile Use of Interfaces • Serve ICGC specific needs • interface elements reflecting ICGC Submission Manual parameters • consistency checking and verification of the data model .xls ICGC configuration • tailored interface • input assistanceand verification Backend Interface File Abstract Data Model File Graphical User Interface Planning Algorithm

  11. Versatile Use of Interfaces • Serve ICGC specific needs • interface elements reflecting ICGC Submission Manual parameters • consistency checking and verification of the data model • WormBase/ WormMart • ease the migration to 0.8 • demonstrate MartLoader’sgeneric interface to inspire other developers * .xls ICGC configuration WormBase • tailored interface • input assistanceand verification Backend Interface File Abstract Data Model File Graphical User Interface Planning Algorithm *AceDB:aC. elegansdatabase

  12. Versatile Use of Interfaces • Serve ICGC specific needs • interface elements reflecting ICGC Submission Manual parameters • consistency checking and verification of the data model • WormBase/ WormMart • ease the migration to 0.8 • demonstrate MartLoader’sgeneric interface to inspire other developers • MartBuilder • incorporate the advanced backend into MartBuilder * .xls ICGC configuration MartBuilder WormBase • tailored interface • input assistanceand verification Backend Interface File Abstract Data Model File Graphical User Interface Planning Algorithm *AceDB:aC. elegansdatabase

  13. Current Data Source and Mart Management

  14. MartLoader User Interface Mock Up

  15. MartLoader User Interface Mock Up

  16. MartLoader User Interface Mock Up

  17. Mart Planning Decoding and Rewriting Validation Transformation

  18. backend Over to Anthony

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