Title: Nutritional Genomics:
1Nutritional Genomics Evidence Based Nutritional
Science
Philippe Rocca-Serra EMBL-EBI and NutriGenomics
Organization (NuGO) OBI workshop San Diego, Jan
30th-Feb 3rd 2007
2Reporting 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
3(No Transcript)
4 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?
5The 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
6The 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
7We 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