1. A democracy of reporting
standards for omics studies
Kees van Bochove
NBIC BioAssist taskforce leader
metabolomics and study capture
kees@thehyve.nl

2. Origin of the question: consortia
Nutritional Phenotype
Data Support Platform (DSP)
Database Project (dbNP)
http://dbnp.org http://www.nmcdsp.org
Their aims:
 Get an overview over studies of all partners
 Share study data
 Standardization of bioinformatics

3. Central question: How do I turn study descriptions and
metadata tables into a persistent, queryable database?
Database
Query

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. 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. GSCF homepage

7. Chris Taylor (MIBBI) about data standards
“Coverage of experimental design in current
bioinformatics standards is meagre at best”

8. Study design

9. GSCF study design wizard

10. GSCF study design wizard

11. Use of ontologies: users don’t like long term lists

12. Study design overview

13. Machiel Jansen about Knowledge Representation
“The representation of knowledge
will always depend on its use”

14. Study overview – which columns should be there?

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. GSCF template editor – Subject level

17. GSCF template editor – Event level

18. Barend Mons about structured data
“Everyone wants structured data,
but no one wants to fill out the forms”

19. Importer – upload Excel file

20. Importer – map your Excel file unto templates

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. DbNP data model
REST protocol

23. Transcriptomics module

24. Metabolomics module

25. Next Generation Sequencing module

26. Query composer

27. Query results on Study level

28. Query results on Sample level

29. Query results on Assay level

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. Hackathon results – GSCF – MOLGENIS adapter
http://hackathon.nmcdsp.org | http://trac.nbic.nl/gscf4molgenis

32. Acknowledgements
Tjeerd Abma Barend Mons
Adem Bilican Ben van Ommen
Jildau Bouwman Linette Pellis
Christine Chichester Janneke van der Ploeg
Sudeshna Das Marijana Radonjic
Marjan van Erk Theo Reijmers
Chris Evelo Erik Roos
Prasad Gajula Marco Roos
Roeland van Ham Frans Paul Ruzius
Thomas Hankemeier Jahn Saito
Margriet Hendriks Susanna Sansone
Guido Hooiveld Siemen Sikkema
Robert Horlings Rob Stierum
Peter Horvatovich Eugene van Someren
Rob Hooft Morris Swertz
Machiel Jansen Chris Taylor
Jim Kaput Michael van Vliet
Kostas Karasavvas Jeroen Wesbeek
Bart Keijser Katy Wolstencroft
Matthew Lange Suzan Wopereis
Scott Marshall Gooitzen Zwanenburg