MetWare
Aiding 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
Jan van Haarst (JSF pages)
Joost de Groot (ProtoRAW)
Mark Fiers (BioMoby services, MetWare integration)
Velitchka Mihaleva (RT/RI prediction modeling)
Egon Willighagen (SKOS, integration of data preprocessing)
Roeland van Ham (group leader)
http://www.ab.wur.nl/
2008-05-08, AB@PRI

The Setting
Metabolite identity
accurate mass, retention time
isotope pattern
full mass spectrum
Systems Biology
if we change this, what happens to the metabolome?
Where, this :=
genotype, mutations
transcription
growing conditions
geographical location
...
2008-05-08, AB@PRI

The Problems
Biochemical
biological variation
detection limits
rough chemical characterization
Bio- and Chemoinformatics
No uniform access
Many manual steps involved
Data sizes
Diversity of standards and formats
Information loss!
2008-05-08, AB@PRI

The Solutions
Biochemical
wait for next generation devices (not)
know your errors
maximize information extraction
Bio- and Chemoinformatics
improve data extraction
standardized programming interfaces
standardized ontologies
standardized data exchange formats
(did you spot the pattern?)
2008-05-08, AB@PRI

Our Solution: MetWare + MetFlow
2008-05-08, AB@PRI

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
2008-05-08, AB@PRI

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/
2008-05-08, AB@PRI

MetWare Design: Graphical...
2008-05-08, AB@PRI

MetMETA: annotating the wet side
2008-05-08, AB@PRI

MetOBSERV: annotating the dry side
2008-05-08, AB@PRI

MetWare Ontology
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’s
important.)
2008-05-08, AB@PRI

Resource Description Framework
triple
the subject is a resource
the object might be a resource
depending on that, two types of predicates
resource predicate resource
resource predicate literal
See also wp:Resource Description Framework
2008-05-08, AB@PRI

Simple Knowledge Organisation System
XML for ontology definition
based on RDF and the Web Ontology Language (OWL)
unlike OWL it has loose relations (no is a)
skos:broader
skos:narrower
skos:related
has a few basic resource-predicate-literal relations
skos:prefLabel
skos:definition
See also wp:SKOS
2008-05-08, AB@PRI

SPARQL Protocol and RDF Query Language
See also wp:SPARQL
2008-05-08, AB@PRI

Query Results...
See Sesame (http://www.OpenRDF.org)
2008-05-08, AB@PRI

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
...
2008-05-08, AB@PRI

JavaServer Faces: split layout from data model
2008-05-08, AB@PRI

JavaServer Faces: the source
2008-05-08, AB@PRI

MetWare Interface 2: BioMart
Integration: Taverna, R
http://www.biomart.org/, EBI/CSHL
2008-05-08, AB@PRI

ProtoRAW: the RAW data storage
Joost can tell you all about this...
2008-05-08, AB@PRI

Collaboration
MetWare development
Steffen Neumann, Leibniz-Institut f¨r Pflanzenbiochemie,
u
Halle, Germany
our MetWare co-founder in September 2007
http://www.ipb-halle.de/
BioAssist/NMC, Utrecht/Leiden and Mark/Wageningen
joined in April 2008
will focus on clinical data
spectral trees
integration with workflow environments
http://www.metabolomicscentre.nl/
2008-05-08, AB@PRI

Conclusions...
Provides the tools to automate data analysis
Provides storage for your metabolomics data
Decreases information loss
http://metware.sf.net/
2008-05-08, AB@PRI