Nutritional Genomics:

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Nutritional Genomics Evidence Based Nutritional
Science
Philippe Rocca-Serra EMBL-EBI and NutriGenomics
Organization (NuGO) OBI workshop San Diego, Jan
30th-Feb 3rd 2007
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Reporting Structure for Biological Investigations
Nutrigenomics, Environmental Genomics,
Toxicogenomics

• Communities where efforts are underway to
  promote data standards and to develop databases
  for storing biological investigations employing
  multiple OMICS technologies
• Activities and Supported Projects
• Building a reporting structure for biological
  investigations - MIBBI (MIcheck)
• Adding semantics to the reporting structure
  OBI
• Adding syntax to the reporting structure - FuGE
• Weaving the threads - Omics and Beyond
• Transcriptomics (MGED), Proteomics (PSI),
  Metabolomics (MSI)
• Genomics (GCS) and regulatory-driven efforts
• Leading Groups
• EMBL - The European Bioinformatics Institute
  (NET Project) -gt Susanna Sansone
• European Nutrigenomics Organisation (NuGO)-gt
  Philippe Rocca-Serra
• FDAs National Center for Toxicological Research
  (NCTR)-gt Weida Tong
• NERC Environmental Bioinformatics Centre
  (NEBC)-gt Norman Morrison
• NIEHS National Center for Toxicogenomics (NCT)-gt
  Jennifer Fostel

Sansone SA, Rocca-Serra P, Tong W, Fostel J,
Morrison N, Jones A. OMICS 2006, 2(10)164-171
www.mged.org/Workgroups/rsbi
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The Challenge - Defining the Marker of Health

• What is a healthy phenotype? Which gene
  expression patterns are healthy?
• What do physiological effect markers say about
  health?
• Which physiological effect markers are most
  useful?
• Can specific gene expression changes be
  interpreted what is a risk and what is a
  benefit?
• Are functional genomic techniques sufficiently
  sensitive to detect important early changes at a
  low level chronic exposure?

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The tools - Multi-Assays Investigations
INVESTIGATION
ASSAYS and DATA
STUDY(1)
Diet X treatment

• Conventional assays e.g.
• Physical parameters
• Clinical Chemistry
• Histopathology

Euthanasia
Target organ, tissue
Transcriptomics
RNA
Proteins
Proteomics
STUDY(2)
Fluids, Tissues, Cells

• Conventional assays e.g.
• Physical parameters
• Clinical Chemistry
• Histopathology

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The Ontology Activities and Use

• Investigation/Study/Assay descriptors
• Study Designs descriptors and classifiers
• Assays and end-points descriptors
• Including clinical trials
• Methods, SOPs, Protocols, Equipment descriptors
• BioMolecule descriptors
• Gene, protein, metabolites (leverage on OBO
  resources)
• Food and dietary components descriptors
• Annotation, integration and text mining
• Describe the experimental context uniformly
• - Data entry and query tools
• Integrate different investigations
• - From different biological and technological
  domains
• Search and annotate the literature
• - Text-mining applications

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We Need OBI to Describe Multi-Omics
Investigations

• Need to support multi-omics investigations from
  several collaborators
• NutriGenomics Organization (NuGO, EU NoE)
• Network of 24 European research institutes
  working in nutritigenomics
• Committed to place data in the public domain -
  fulfil grants requirements
• CarcinoGenomics (EU IP)
• Network of 20 European research institutes
  working in toxicogenomics
• Committed to place data in the public domain -
  fulfil grants requirements
• NERC Bioinformatics Center (NEBC)
• - Supports environmental genomics research
  programmes
• - Committed to place data in the public domain
  - fulfil NEBC data policy
• Develop BioMAP infrastructure to collect these
  investigations uniformly
• Leverage on existing public repositories at EBI
• - Develop an unified submission and query
  interface
• Ensure compliance to standards, where these
  exists
• - Active involvement in MGED, HUPO-PSI and MSI
  standards group
• - Contribution to MIBBI, FuGE and OBI

BioMAP at www.ebi.ac.uk/net-project