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Practical sharing of environmental molecular data

This presentation by Bela Tiwari from the NERC Environmental Bioinformatics Centre highlights the vast amounts of molecular data available for environmental research, including entries in GenBank, EMBL, UniProt, and PubMed. It discusses the importance of structured data submission forms and the Env Initiative, aimed at developing community-based ontologies for describing environmental contexts of biological samples. The session emphasizes the significance of standardized data exchange formats and the impact of environmental research on critical areas like biodiversity, climate change, energy, health, and nutrition.

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Practical sharing of environmental molecular data

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  1. Practical sharing of environmental molecular data Bela Tiwari NERC Environmental Bioinformatics Centre

  2. CEH Oxford EBI Univ. Manchester Univ. Edinburgh

  3. A few numbers • 101,815,678 entries in Genbank (Rel 170 – Feb 15, 2009) • 158,001,051 entries in EMBL (Rel 99 – Feb 26, 2009) • 7754276 entries in Uniprot (Rel 14.9 – March 3, 2009) • 56217 structures in PDB (March 3, 2009) • 11448 experiments in GEO • 7723 experiments in ArrayExpress • 18702298 entries in PubMed (March 9, 2009) • 1762936 entries in PubMed Central (March 9, 2009)

  4. Structured web forms for (simple) sequence submissions

  5. Software for general sequence submissions

  6. NERC Environmental Bioinformatics Centre http://nebc.nox.ac.uk

  7. The 'Env' Initiative Representing environmental research in reporting requirements, data models, data exchange format, controlled vocabularies and ontologies. A community based ontology for describing the environment of an organism or biological sample • Impacts on data collected in the areas including: • Biodiversity • Climate Change • Energy • Health • Nutrition http://environmentontology.org/

  8. http://nebc.nox.ac.uk/envbase

  9. http://handlebar.sf.net

  10. Bio-Linux http://www.bio-linux.net

  11. http://www.mibbi.org

  12. Terminizer http://terminizer.org

  13. http://nebc.nox.ac.uk/envbase

  14. Bioinvestigation Index and ISAcreator http://www.ebi.ac.uk/bioinvindex

  15. Acknowledgements • NEBC • CEH Oxford • Dawn Field • Bela Tiwari • Tim Booth • Tim Booth • Jorge Soares • HannyNuhu • University of Manchester • Dave Hancock • Norman Morrison • EBI • Chris Taylor NERC Pamela Kempton Jason Snape Mark Thorley University of Manchester Giles Velarde EBI Susanna Sansone Philippe Rocca-Serra University of Manchester Mark Blaxter Many EG and PGP Researchers!

  16. The slides following this one were not in the presentation, but were kept in this file in case questions were asked where they would be useful.

  17. MICheckout: Supporting Users

  18. Data Management Software and Standards Development Bioinformatics Workstations NEBC Training and Support

  19. Data volumes have trends like this

  20. In practice… • Data policy • Standards • Software • Data management • Support

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