Nutritional Genomics: - PowerPoint PPT Presentation

1 / 7
About This Presentation
Title:

Nutritional Genomics:

Description:

NERC Environmental Bioinformatics Centre (NEBC)- Norman Morrison. NIEHS National Center for Toxicogenomics (NCT)- Jennifer Fostel ... – PowerPoint PPT presentation

Number of Views:303
Avg rating:3.0/5.0
Slides: 8
Provided by: internapD
Category:

less

Transcript and Presenter's Notes

Title: Nutritional Genomics:


1
Nutritional Genomics Evidence Based Nutritional
Science
Philippe Rocca-Serra EMBL-EBI and NutriGenomics
Organization (NuGO) OBI workshop San Diego, Jan
30th-Feb 3rd 2007
2
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
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?

5
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

6
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

7
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
Write a Comment
User Comments (0)
About PowerShow.com