EID2 Database: New Tools for One Health Research and Policy Development
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EID2 Database: New Tools for One Health Research and Policy Development

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GRF 2nd One Health Summit 2013: Presentation by RISLEY, Dr. Claire Louise, University of Liverpool

GRF 2nd One Health Summit 2013: Presentation by RISLEY, Dr. Claire Louise, University of Liverpool

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EID2 Database: New Tools for One Health Research and Policy Development EID2 Database: New Tools for One Health Research and Policy Development Presentation Transcript

  • EID2 Database: New tools for One Health research and policy development Claire Risley Maya Wardeh, K. Marie McIntyre, Christian Setzkorn, Alan Radford, Matthew Baylis University of Liverpool University of Aberystwyth: clr25@aber.ac.uk
  • Some One Health Questions • Which hosts are likely to transmit pathogens to my host of interest? • Where is my pathogen and all its hosts found? – Where has it been found – Where else is it likely to be found Claire Risley clr25@aber.ac.uk
  • What is a pathogen (1) Micro-organisms Causes of disease Claire Risley Pathogens clr25@aber.ac.uk
  • Pathogens Claire Risley Non-infectious causes of disease or death clr25@aber.ac.uk
  • Pathogens Claire Risley Biodiversity of microorganisms clr25@aber.ac.uk
  • What is a pathogen (2) Claire Risley clr25@aber.ac.uk
  • Organisms can be both pathogens and hosts • We use only a statement about interaction • There are only ‘cargoes’ & ‘carriers’ – Which is which? • Specified directly in nucleotide db • Hierarchy for identification in papers Claire Risley clr25@aber.ac.uk
  • How Can We Know Who infects What and Where? • Nucleotide & paper information – Uploaded metadata can be as important as sequence – Useable data also in paper titles, keywords etc. • Built on tree of life – Links pairs of organisms – Recursive; can get info on higher level taxa Claire Risley clr25@aber.ac.uk
  • Taxon hierarchy of organisms Host Geodata Climate Layers Location EID2 Disease heirarchy Maps Claire Risley Pathogen Info Niche Models Links clr25@aber.ac.uk
  • Claire Risley clr25@aber.ac.uk
  • Host Pathogen Location EID2 Claire Risley clr25@aber.ac.uk
  • Claire Risley clr25@aber.ac.uk
  • Extent of EID2 • 762,361 organisms (~250,000 species) • 276,426 country interactions (all countries represented) • 122,524 organism interactions (~25,000 hostpathogen species interactions) • 31,953 organism interactions in countries Claire Risley clr25@aber.ac.uk
  • Data have undergone rounds of “Disambiguation” Host ambiguity: /host=“Prostitute” /host=“German shepherd” /host=“24 year old male” Geolocation ambiguity: /country=“Middle east” /country=“UK:north sea” NCBI heirarchy ambiguities Wolbachia sp. Claire Risley clr25@aber.ac.uk
  • Quality of country matching (nucleotide data) Water Bodies 0.19% Incorrect 0.0019% Incorrect 5.95% Water 1.46% Country Correct 99.81% e.g. Yugoslavia, USSR 2012 country level disambiguation Claire Risley Irrelevant 0.91% Unidentifi able 0.56% Correct 91.11% 2012 Sub country level disambiguation clr25@aber.ac.uk
  • Quality of organism matching (nucleotide data) 3% 26% 29% Unidentifyable Unidentified Correct to species level Correct to genus level 26% Claire Risley 16% Incorrect clr25@aber.ac.uk
  • Claire Risley clr25@aber.ac.uk
  • Claire Risley clr25@aber.ac.uk
  • Claire Risley clr25@aber.ac.uk
  • Claire Risley clr25@aber.ac.uk
  • Claire Risley clr25@aber.ac.uk
  • Claire Risley clr25@aber.ac.uk
  • Borrelia burgdorferi: Evidence of presence Claire Risley clr25@aber.ac.uk
  • Borrelia burgdorferi: Distribution of Predicted niche Claire Risley clr25@aber.ac.uk
  • Pathogens with the broadest host range 100 90 80 70 60 50 40 30 20 10 0 bacillus subtilis carrierPerCargo Claire Risley 89 cucumb corynes wolbach fusarium rabies west nile bacillus pora bemisia bacillus er ia oxyspor mosaic virus virus pumilus cassiicol tabaci cereus pipientis um virus a 86 80 74 71 70 68 67 61 59 clr25@aber.ac.uk
  • (non human) hosts with the most pathogen entries 300 250 200 150 100 50 0 equus pinus bos picea sus ovis zea gallus capra felis caball sylvest taurus abies scrofa aries mays gallus hircus catus us ris CargosPerCarrier 265 Claire Risley 210 200 188 174 129 127 126 124 123 clr25@aber.ac.uk
  • Using EID2 • Investigate NCBI’s output – Radford et al. J Gen Virol. 2012 September; 93(Pt 9): 1853–1868. • Comparing predictors of pathogen sharing – Sandoval et al. (in prep) : Felid pathogens, relatedness and proximity • Large-scale comparisons of climate predictions • Etc.
  • EID2: a new, useful resource: • EID2 updated: – More records – Greater sensitivity and specificity for Enhance hosts – Improved sub-country level recognition • Now very useful to all researchers: – Host/Pathogen/Location Information easily available – Location and climatic niche maps available – Interesting for many types of studies e.g. network analyses Claire Risley clr25@aber.ac.uk
  • Further Information • Maya’s contact info to log in: Maya.Wardeh@liverpool.ac.uk • Database URL: http://zoonosis.ac.uk/eid2 • McIntyre KM, Setzkorn C, Wardeh M, Hepworth PJ, Radford AD, Baylis M (2013) Using openaccess taxonomic and spatial information to create a comprehensive database for the study of mammalian and avian livestock and pet infections. Preventive Veterinary Medicine (in press) Claire Risley clr25@aber.ac.uk