Metabolomics Standards Initiative MSI Ontology group OWG

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Metabolomics Standards Initiative (MSI)Ontology
group (OWG)
Susanna-Assunta Sansone MSI Ontology WG
Chair (The European Bioinformatics Institute
EBI) On behalf of the MSI OWG members http//msi-
workgroups.sf.net
OBI workshop, LIAI, Jan 29th Feb 2nd, 2007
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Established end of 2005

• Develops standards for data communications
• Minimal reporting requirements -gt Contributing to
  MIBBI project
• Format and ontology -gt Contributing to FuGE and
  OBI projects
• Stakeholders from academia, regulatory bodies and
  industries

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MSI OWG

• Current members and contributors
• Andy Tseng (Human Serum Metabolome Project, Un
  of Manchester)
• Chris Taylor (EBI and HUPO-PSI)
• Daniel Schober (EBI and HUPO-PSI) -gt BBSRC
  e-Science Grant (BB/D524283/1)
• Helen Atherton, Dennis Rubtsov (Un of Cambridge)
• Helen Jenkins (Un of Wales)
• John Lindon (Imperial College)
• Irena Spasic (MCISB, Manchester, UK)
• Larissa Soldatova (University of Wales)
• Lori Querengasser (Un of Alberta)
• Mark Viant (Un of Birmingham)
• Matej Oresic (VTT Technical Research Centre of
  Finland)
• Oliver Fiehn, Martin Scholz, Bertram Ludaescher
  (UCDavis Genome Center)
• Philippe Rocca-Serra (EBI and MGED Society) -gt
  NuGO (EU NoE 503630)
• Ricardo Pietrobon (Duke University)
• Susanna-Assunta Sansone (EBI, MGED Society and
  HUPO-PSI)
• Areas of interest and applications
• Clinical/plant/environmental/toxicology/nutrition
  metabolomics, systems biology

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MSI OWG Goals

• Provide descriptors for MSI Format and Minimal
  Requirements
• Reaching a consensus on a set of controlled
  vocabularies (CVs)
• - Leveraging on existing resources and efforts
• Developing a corresponding ontology
• Working under the Open Biomedical Ontology (OBO)
  umbrella, now part of the National Center for
  BioMedical Ontology (NCBiO)
• Achieve consistent semantic description across
  data resources
• Software and databases, both private and public
• Assist to model the experimental workflow
• Design of an investigation, the sample source and
  treatments, the instrumentation used, the data
  generated and the types of analyses performed on
  it

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CVs/Ontology Coverage

• Capitalize on synergies, where commonality exists

                                       
 
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OWG Activities

• Naming conventions for naming and annotating RUs
  within RAs
• For terms (in the CV) or classes (ontology)
• Endorsed also by with HUPO-PSI
• Metadata elements to tag both RUs within RAs
• Descriptive and administrative metadata
• Focus on instrument-dependent components
• First draft of the NMR ontology, importing OBI
  and BFO classes
• Taxonomy of 247 classes (OWL OBO format),
  posted under OBO
• gt Terms for methods, instruments and parameters
• gt Normalized according to the naming convention
  and metadata docs
• Work in progress with HUPO-PSI for MS and
  chromatography
• Text mining approaches to enrich the ontology
• Populate the CVs and refine the ontology
• Direct contribution to OBI
• Work in progress on Investigation Design and
  Data Pre-Processing