A democracy of reportingstandards for omics studiesKees van BochoveNBIC BioAssist taskforce leadermetabolomics and study firstname.lastname@example.org
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
Central question: How do I turn study descriptions andmetadata tables into a persistent, queryable database? Database Query
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…
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
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!
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