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6th International Disaster and Risk Conference IDRC 2016 Integrative Risk Management - Towards Resilient Cities. 28 August - 01 September 2016 in Davos, Switzerland
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6th International Disaster and Risk Conference IDRC 2016 Integrative Risk Management - Towards Resilient Cities. 28 August - 01 September 2016 in Davos, Switzerland
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6th International Disaster and Risk Conference IDRC 2016 Integrative Risk Management - Towards Resilient Cities. 28 August - 01 September 2016 in Davos, Switzerland
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6th International Disaster and Risk Conference IDRC 2016 Integrative Risk Management - Towards Resilient Cities. 28 August - 01 September 2016 in Davos, Switzerland
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6th International Disaster and Risk Conference IDRC 2016 Integrative Risk Management - Towards Resilient Cities. 28 August - 01 September 2016 in Davos, Switzerland
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6th International Disaster and Risk Conference IDRC 2016 Integrative Risk Management - Towards Resilient Cities. 28 August - 01 September 2016 in Davos, Switzerland
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EID2 Database: New Tools for One Health Research and Policy Development
1. 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
2. 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
3. What is a pathogen (1)
Causes of disease
Pathogens
Micro-organisms
Claire Risley clr25@aber.ac.uk
6. What is a pathogen (2)
Claire Risley clr25@aber.ac.uk
7. 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
8. 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
13. Extent of EID2
• 762,361 organisms (~250,000 species)
• 276,426 country interactions (all countries
represented)
• 122,524 organism interactions (~25,000 host-
pathogen species interactions)
• 31,953 organism interactions in countries
Claire Risley clr25@aber.ac.uk
14. 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
15. Quality of country matching
(nucleotide data)
Correct
91.11%
Water
1.46%
Incorrect
5.95%
Irrelevant
0.91% Unidentifi
able
0.56%
Country
Correct
99.81%
Water
Bodies
0.19%
Incorrect
0.0019%
2012 country level disambiguation 2012 Sub country level disambiguation
e.g.
Yugoslavia,
USSR
Claire Risley clr25@aber.ac.uk
16. Quality of organism matching
(nucleotide data)
29%
16%
26%
26%
3%
Unidentifyable
Unidentified
Correct to species level
Correct to genus level
Incorrect
Claire Risley clr25@aber.ac.uk
27. 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.
28. 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
29. 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 open-
access 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