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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 LiverpoolUniversity of Aberystwyth: [email protected]
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 [email protected]
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 [email protected]
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 [email protected]
HostPathogen
Location
Niche Models
Maps InfoLinks
EID2
Taxon hierarchy of organisms
GeodataClimate Layers
DiseaseheirarchyClaire Risley [email protected]
Claire Risley [email protected]
Claire Risley [email protected]
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 [email protected]
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 ambiguitiesWolbachia sp.
Claire Risley [email protected]
Quality of country matching (nucleotide data)
Correct91.11%
Water1.46%
Incorrect5.95%
Irrelevant0.91% Unidentifiable
0.56%
Country Correct99.81%
Water Bodies0.19%
Incorrect0.0019%
2012 country level disambiguation 2012 Sub country level disambiguation
e.g. Yugoslavia, USSR
Claire Risley [email protected]
Quality of organism matching (nucleotide data)
29%
16%26%
26%
3%
UnidentifyableUnidentifiedCorrect to species levelCorrect to genus levelIncorrect
Claire Risley [email protected]
Claire Risley [email protected]
Claire Risley [email protected]
Claire Risley [email protected]
Claire Risley [email protected]
Claire Risley [email protected]
Claire Risley [email protected]
Pathogens with the broadest host range
bacillu
s subtilis
rabies viru
s
wolbachia pipientis
cucu
mber mosaic v
irus
west nile
virus
bacillu
s pumilu
s
corynesp
ora cassi
icola
bemisia
tabaci
fusarium oxys
porum
bacillus c
ereus
0
10
20
30
40
50
60
70
80
90
100
Claire Risley [email protected]
(non human) hosts with the most pathogen entries
bos tau
rus
picea a
bies
sus scro
fa
ovis ar
ies
equus c
aball
us
zea m
ays
gallu
s gall
us
pinus sylv
estris
capra
hircus
felis c
atus
0
50
100
150
200
250
300
Claire Risley [email protected]
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 [email protected]
Further Information
• Maya’s contact info to log in: [email protected]
• 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 [email protected]