Metware

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My ten minute contribution to the International Metabolomics Workshop @ EBI/Hinxton/UK.

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Metware

  1. 1. MetWare Aiding metabolite identification (and more) Egon Willighagen et al. Uppsala University (formerly Plant Research International / Biometris, Wageningen University) 20089-01-27/28, UU
  2. 2. International Collaboration MetWare development is Open Steffen Neumann, Leibniz-Institut f¨r Pflanzenbiochemie, u Halle, Germany http://www.ipb-halle.de/ BioAssist/NMC, Utrecht/Leiden/Wageningen/NL http://www.metabolomicscentre.nl/ Plant Research International http://www.pri.wur.nl/ Pharmaceutical Biosciences, Uppsala/SE http://www.farmbio.uu.se/ 20089-01-27/28, UU
  3. 3. Our Solution: MetWare + MetFlow 20089-01-27/28, UU
  4. 4. MetWare: the building blocks The Design backed up with an ontology conform standards like ArMet Interfaces ... ... towards humans: website (JSF-based) ... towards databases: SQL ... towards softare: Java Beans ... towards workflows: BioMart + webservices ... towards statistics software: BioMart ... towards other databases: Life Science ID 20089-01-27/28, UU
  5. 5. MetWare Design: Modules MetRAW storage facility for RAW metabolomics data MetMETA metadata about DoE, genotypes, illness, conditions, ... MetOBSERV observed metabolites, characterized by RT, mass spectrum, NMR, ... MetID know metabolites MetCHAR (putative) identity assignments http://apbioinf001.wurnet.nl/ABWiki/MetWare http://metware.wiki.sourceforge.net/ 20089-01-27/28, UU
  6. 6. MetWare Ontology Extends the ArMet Ontology <skos:Concept rdf:about=quot;Emailquot;> <skos:prefLabel>e-mail</skos:prefLabel> <skos:definition>The email address of the user.</skos:definition> <skos:broader rdf:resource=quot;Peoplequot;/> <skos:broader rdf:resource=quot;&armet;Emailquot;/> </skos:Concept> (No, it does not have to be XML; N3 is fine too. It’s RDF, that’s important.) 20089-01-27/28, UU
  7. 7. Autogeneration of a Java API and unit tests Why? hides the SKOS/XML hides the SQL Advantages of autogeneration always synchronized to the ontology and the SQL automatically generation of unit tests who said our group didn’t do unit tests ?!?! Where are these Java beans used? the web GUI: JavaServer Faces ... 20089-01-27/28, UU
  8. 8. JavaServer Faces: split layout from data model 20089-01-27/28, UU
  9. 9. Conclusions... Provides the tools to automate data analysis Provides storage for your metabolomics data Decreases information loss http://www.metware.org/ 20089-01-27/28, UU

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