MetWareAiding metabolite identification (and more)

Egon Willighagen et al.

Wageningen University – Plant Research International / Biometris

2008-05-08, AB@PRI

Who are we?

Applied Bioinformatics Group Plant Research International

I Jan van Haarst (JSF pages)

I Joost de Groot (ProtoRAW)

I Mark Fiers (BioMoby services, MetWare integration)

I Velitchka Mihaleva (RT/RI prediction modeling)

I Egon Willighagen (SKOS, integration of data preprocessing)

I Roeland van Ham (group leader)

http://www.ab.wur.nl/

2008-05-08, AB@PRI

The Setting

I Metabolite identityI accurate mass, retention timeI isotope patternI full mass spectrum

I Systems BiologyI if we change this, what happens to the metabolome?

I Where, this :=I genotype, mutationsI transcriptionI growing conditionsI geographical locationI ...

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The Problems

I BiochemicalI biological variationI detection limitsI rough chemical characterization

I Bio- and ChemoinformaticsI No uniform accessI Many manual steps involvedI Data sizesI Diversity of standards and formats

Information loss!

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The Solutions

I BiochemicalI wait for next generation devices (not)I know your errorsI maximize information extraction

I Bio- and ChemoinformaticsI improve data extractionI standardized programming interfacesI standardized ontologiesI standardized data exchange formatsI (did you spot the pattern?)

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Our Solution: MetWare + MetFlow

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MetWare: the building blocks

The Design

I backed up with an ontology

I conform standards like ArMet

Interfaces ...

I ... towards humans: website (JSF-based)

I ... towards databases: SQL

I ... towards softare: Java Beans

I ... towards workflows: BioMart + webservices

I ... towards statistics software: BioMart

I ... towards other databases: Life Science ID

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MetWare Design: Modules

I MetRAWI storage facility for RAW metabolomics data

I MetMETAI metadata about DoE, genotypes, illness, conditions, ...

I MetOBSERVI observed metabolites, characterized by RT, mass spectrum,

NMR, ...

I MetIDI know metabolites

I MetCHARI (putative) identity assignments

http://apbioinf001.wurnet.nl/ABWiki/MetWare

http://metware.wiki.sourceforge.net/

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MetWare Design: Graphical...

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MetMETA: annotating the wet side

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MetOBSERV: annotating the dry side

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MetWare Ontology

I Extends the ArMet Ontology

<skos:Concept rdf:about="Email">

<skos:prefLabel>e-mail</skos:prefLabel>

<skos:definition>The email address of the user.</skos:definition>

<skos:broader rdf:resource="People"/>

<skos:broader rdf:resource="&armet;Email"/>

</skos:Concept>

(No, it does not have to be XML; N3 is fine too. It’s RDF, that’simportant.)

2008-05-08, AB@PRI

Resource Description Framework

I triple

I the subject is a resource

I the object might be a resourceI depending on that, two types of predicates

I resource predicate resourceI resource predicate literal

See also wp:Resource Description Framework

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Simple Knowledge Organisation System

I XML for ontology definition

I based on RDF and the Web Ontology Language (OWL)I unlike OWL it has loose relations (no is a)

I skos:broaderI skos:narrowerI skos:related

I has a few basic resource-predicate-literal relationsI skos:prefLabelI skos:definition

See also wp:SKOS

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SPARQL Protocol and RDF Query Language

See also wp:SPARQL

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Query Results...

See Sesame (http://www.OpenRDF.org)

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Autogeneration of a Java API and unit tests

Why?

I hides the SKOS/XML

I hides the SQL

Advantages of autogeneration

I always synchronized to the ontology and the SQLI automatically generation of unit tests

I who said our group didn’t do unit tests ?!?!

Where are these Java beans used?

I the web GUI: JavaServer Faces

I ...

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JavaServer Faces: split layout from data model

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JavaServer Faces: the source

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MetWare Interface 2: BioMart

I Integration: Taverna, RI http://www.biomart.org/, EBI/CSHL

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ProtoRAW: the RAW data storage

Joost can tell you all about this...

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Collaboration

MetWare developmentI Steffen Neumann, Leibniz-Institut fur Pflanzenbiochemie,

Halle, GermanyI our MetWare co-founder in September 2007

http://www.ipb-halle.de/I BioAssist/NMC, Utrecht/Leiden and Mark/Wageningen

I joined in April 2008I will focus on clinical dataI spectral treesI integration with workflow environments

http://www.metabolomicscentre.nl/

2008-05-08, AB@PRI

Conclusions...

I Provides the tools to automate data analysis

I Provides storage for your metabolomics data

I Decreases information loss

http://metware.sf.net/

2008-05-08, AB@PRI