Presentatie nbic2011templates

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Presentatie nbic2011templates

  1. 1. A democracy of reportingstandards for omics studiesKees van BochoveNBIC BioAssist taskforce leadermetabolomics and study capturekees@thehyve.nl
  2. 2. Origin of the question: consortiaNutritional Phenotype Data Support Platform (DSP)Database Project (dbNP)http://dbnp.org http://www.nmcdsp.orgTheir aims:  Get an overview over studies of all partners  Share study data  Standardization of bioinformatics
  3. 3. Central question: How do I turn study descriptions andmetadata tables into a persistent, queryable database? Database Query
  4. 4. We studied many available open source solutions…and finally decided to create our own•  Pedro•  OpenBIS•  WikiLIMS•  ISACreator Open formats: XML formats: MAGE-ML,•  SysMO-DB FuGE, LabKey etc.•  Annotare Tab-delimited formats:•  LabKey MAGETAB, ISATAB, XGAP•  MOLGENIS RDF •  i3Cube•  And more…
  5. 5. GSCF: Generic Study Capture Framework•  Open source web application, developed in•  Grails = Groovy on Rails•  Groovy is an extension of the Java language, it compiles to Java bytecode (can be run on any Java VM)•  Development started October/November 2009, on average 4 fulltime programmers since then•  Current version is 0.8.0•  Info: http://dbnp.org•  Test it: http://demo.dbnp.org•  Source code: http://trac.nbic.nl/gscf
  6. 6. GSCF homepage
  7. 7. Chris Taylor (MIBBI) about data standards “Coverage of experimental design in current bioinformatics standards is meagre at best”
  8. 8. Study design
  9. 9. GSCF study design wizard
  10. 10. GSCF study design wizard
  11. 11. Use of ontologies: users don’t like long term lists
  12. 12. Study design overview
  13. 13. Machiel Jansen about Knowledge Representation “The representation of knowledge will always depend on its use”
  14. 14. Study overview – which columns should be there?
  15. 15. Different ‘data levels’ in a study•  Study (meta level)•  Subject (source organism, e.g. humans, mice, plants, cell lines)•  Event (e.g. treatment, compound, diet)•  Sampling Event (e.g. DNA isolation, liver sampling)•  Sample (e.g. blood sample, urine sample)•  Assay (e.g. transcriptomics, metabolomics, sequencing)•  Lines up mostly with both ISATAB and MIBBI Foundry
  16. 16. GSCF template editor – Subject level
  17. 17. GSCF template editor – Event level
  18. 18. Barend Mons about structured data “Everyone wants structured data, but no one wants to fill out the forms”
  19. 19. Importer – upload Excel file
  20. 20. Importer – map your Excel file unto templates
  21. 21. Jildau Bouwman about study capturing “If we really want to do personalized health research, we have to capture everything that might affect our measurements!”
  22. 22. DbNP data model REST protocol
  23. 23. Transcriptomics module
  24. 24. Metabolomics module
  25. 25. Next Generation Sequencing module
  26. 26. Query composer
  27. 27. Query results on Study level
  28. 28. Query results on Sample level
  29. 29. Query results on Assay level
  30. 30. Next steps•  Within the NMC DSP project, we will create a ‘GSCF data fetch’ functionality in Galaxy, enabling the execution of workflows on specific data-slices from the database•  Connect to Semantic Web efforts (OpenPHACTS project) – we also have a pilot with TNO and UvA on using a triple store to enrich GSCF assay results•  Align with other projects: e.g. Hackathon result gscf4molgenis•  Employ the NBIC philosophy – these tools are also available to you!
  31. 31. Hackathon results – GSCF – MOLGENIS adapterhttp://hackathon.nmcdsp.org | http://trac.nbic.nl/gscf4molgenis
  32. 32. AcknowledgementsTjeerd Abma Barend MonsAdem Bilican Ben van OmmenJildau Bouwman Linette PellisChristine Chichester Janneke van der PloegSudeshna Das Marijana RadonjicMarjan van Erk Theo ReijmersChris Evelo Erik RoosPrasad Gajula Marco RoosRoeland van Ham Frans Paul RuziusThomas Hankemeier Jahn SaitoMargriet Hendriks Susanna SansoneGuido Hooiveld Siemen SikkemaRobert Horlings Rob StierumPeter Horvatovich Eugene van SomerenRob Hooft Morris SwertzMachiel Jansen Chris TaylorJim Kaput Michael van VlietKostas Karasavvas Jeroen WesbeekBart Keijser Katy WolstencroftMatthew Lange Suzan WopereisScott Marshall Gooitzen Zwanenburg

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