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Ontologies and the Environment

Ontologies and the Environment. Norman Morrison OBI, San Diego - January 2007. …and some (re)organisational thinking regarding standards. NEBC. R eporting S tructure for B iological I nvestigations. Nutrigenomics , Environmental Genomics , Toxicogenomics.

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Ontologies and the Environment

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  1. Ontologies and the Environment Norman Morrison OBI, San Diego - January 2007 …and some (re)organisational thinking regarding standards

  2. NEBC

  3. 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) -> Susanna Sansone • European Nutrigenomics Organisation (NuGO)-> Philippe Rocca-Serra • FDA’s National Center for Toxicological Research (NCTR)-> Weida Tong • NERC Environmental Bioinformatics Centre (NEBC)-> Norman Morrison • NIEHS National Center for Toxicogenomics (NCT)-> 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

  4. Genomicsdatabase Proteomicsdatabase Transcriptomicsdatabase AnnotatedSequences Abundance data MIAPEdocument Expression data MIAMEdocument Sample(s) and Treatment(s) One experiment: Multiple Databases Clinical Nutritional Environmental Toxicological Somethingelseical

  5. omixed

  6. Sample Process Acclimation Environment Sample Process Transportation Environment Sample Process Capture Environment Requirement Group - Environment • Field Environment • Geographic Location • Altitude/Depth • Habitat Type • Meteorological Conditions • Laboratory Environment • Terrestrial • Aquatic • Atmospheric • Biotic Environment

  7. Addressing a real need • Retrieve all the transcriptomics experiments carried out on organisms from: • deep-sea thermal vents • arctic ice cores • rainforest canopy • alpine melt zone • Retrieve all the transcriptomic data carried out on organisms sampled from: • hot and dry environments • cold and wet environments • a height above 5,000 meters • Retrieve all the omic data from soil organisms subject to moderate heavy metal contamination.

  8. Ecozones, Biomes, Habitats, Biospheres…

  9. A hot, dry environment with very little vegetation?

  10. Acknowledgements • Morrison N, Bearden D, Bundy J, Collette T, Currie F, Davey MP, Haigh NS, Hancock D, Jones OAH, Rochfort S, Sansone SA, Štys D, Teng Q, Field D, Viant MR: Standard Reporting Requirements for Biological Samples in Metabolomics Experiments: Environmental Context. Metabolomics. In review. • Field D, Garrity G, Gray T, Morrison N, et al: Towards a richer description of our complete collection of genomes and metagenomes: the “Minimum Information about a Genome Sequence” (MIGS) specification. Nat Biotech 2007. In consultaion. • Morrison N, Wood AJ, Hancock D, Shah S, Hakes L, Gray T, Tiwari B, Kille P, Cossins A, Hegarty M et al: Annotation of environmental OMICS data: application to the transcriptomics domain. Omics 2006, 10(2):172-178. • Morrison N, Cochrane G, Faruque N, Tatusova T, Tateno Y, Hancock D, Field D: Concept of sample in OMICS technology. Omics 2006, 10(2):127-137.

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