Spring Boot vs Quarkus the ultimate battle - DevoxxUK
Metabolomics Society meeting 2011 - presentatie Kees
1. Three challenges for metabolomics study databases Kees van Bochove June 2011Metabolomics Society Meeting
2. Metabolomics database If you search for ‘metabolomics database’ you get 400K+ results, most of them recent By far the most of these databases are compound-centric, few have real study data Of the metabolomics study databases, most are GC-MS, many NMR, almost no LC-MS
5. DSP: Open Source strategy We are not the only consortium storing data! Reach sustainability by working together with active open source projects like dbNP and Galaxy Everyone can start their own database using the same open source technology, in fact we use this strategy internally
6. Challenge 1: Study metadata Without proper and comprehensive description of the biological context of the sample, a metabolomics results database is useless Especially for mammalian studies, study designs are often complex, involving multiple factors, timepoints, samples etc. NMC strategy: partner with database initiatives from neighbor projects: NuGO (nutrigenomics), NBIC (bioinformatics), NTC (toxicogenomics) etc.: dbNP initiative http://dbnp.org
7. Data levels in DSP Lineastudy, code 06-E6P, inclusion criteria.. Femalehuman, 46 yearsold, BMI 26.4 5ml blood was taken at 4w after start study Blood sample Metabolomics LC-MS lipidomicsassay { LPC17:0: RT 1,416 Area 5469406 , … }
13. How to implement preprocessing? We chose not to in the end Supplied mzMatch pipeline in earlier stage, but preprocessing is often too intertwined with measurement SOP Move from vendor specific software to general frameworks like XCMS, mzMatch, mzMine etc. would be beneficial for comparability of data, but in practice requires a lot of effort/tuning
14. How to implement metabolite identity? Consensus at standardization workshops: InChI key to identify structure Not always clear which structure(s) a peak represents, and with untargeted metabolomics we might have no clue So we store ‘features’, which are specific to measurement SOP and preprocessing SOP, and link those to metabolite identity records
15. How to implement quantification? At the moment, we store only peak area or intensity, and any Internal Standard and Quality Control sample data is stored along with the biological sample data We expect that preprocessing / quality control is done before data import Working now on adding more levels of quantification, i.e. concentration
18. Challenge 3: embedding of data Metabolomics is often not the only performed analysis on samples Important to cross-linked to other environmental and genetic data Thanks to our partners, NuGO, NBIC etc. there are also modules for next generation sequencing, transcriptomics, and clinical chemistry data All this data is cross-queryable
23. Next focus We have several tools developed within NMC, such as spectral tree analysis tool Reach sustainability by merging those tools in one analytical platform Use existing bioinformatics open source project: Galaxy Re-use existing projects from collaborators: MetaboAnalyst from Human Metabolome Project, Alberta, Canada – David Wishart
25. Distributeddeployment of NMC DSP Study owners host study metadata at own institution Metabolomics labs host metabolomics modules Data access is governed by study owners TNO studies DSM studies TNO clinical chemistry PRI studies Shared processing & evaluation toolbox WUR transcriptomics DCL metabolomics PRI metabolomics etc...
26. Conclusion Many compound databases, few databases with actual study data Very hard to represent LC-MS measurements in a meaningful way Storing study design and sample metadata is key to analysis Many benefits of open collaboration, as opposed to closed-source in-house solutions Test it: http://test.nmcdsp.org login withusername ‘nmc’ and password ‘noordwijkerhout’ Suggestions/remarks to kees@thehyve.nl
27. Acknowledgements TjeerdAbma Adem Bilican JildauBouwman Christine Chichester Sudeshna Das Marjan van Erk Chris Evelo PrasadGajula Roeland van Ham Thomas Hankemeier Margriet Hendriks Guido Hooiveld Robert Horlings Peter Horvatovich Rob Hooft Machiel Jansen Jim Kaput KostasKarasavvas Bart Keijser Matthew Lange ScottMarshall Barend Mons Ben van Ommen LinettePellis Janneke van der Ploeg MarijanaRadonjic Theo Reijmers Erik Roos Marco Roos Frans Paul Ruzius JahnSaito SusannaSansone SiemenSikkema Rob Stierum Eugene van Someren Morris Swertz Chris Taylor Michael van Vliet Jeroen Wesbeek KatyWolstencroft Suzan Wopereis Gooitzen Zwanenburg
