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Update on Cholera Database
Andrew AzmanwithElizabeth Lee, Heather McKay, Josh Kaminsky, Justin Lessler and many others
GTFCC Epi/Surveillance Working Group :: 15 April 2019
dynamicsJohns Hopkins Bloomberg School Public Healthof
cholerataxonomy ~ Burden ~ Mapping ~ Modeling
iddynamics.jhsph.edu/cholera
Describing Cholera
pemba
unguja
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0
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0
100
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week of admission
susp
ecte
d ch
oler
a ca
ses
per
wee
k
0 10 100
rainfall (mm/week)
0
1
2
3
4
0 20 40
week of year
rela
tive
chol
era
risk
0
5
50
Weekly Rainfall (median)
<0.01
0.1
1
10
100
1000
10000
Mean annualincidence (per 100K)
A
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Where can cholera data come from?
Ministries of Health (sitreps, linelists, DHIS, press releases etc)In-depth research studiesMediaRegional summariesReports from WHO, UNICEF and others (with MoHs)
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Data in many shapes and sizes
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Taxonomy Database Structure
Metadatadata source and access informationcase definitionscontextmolecular details (when available)
ObservationsLocation (enclosing polygon or point)Timing (allowing for censoring)Number of cases/deaths (censoring possible)DemographicsOther user defined fields
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Taxonomy Database Interface
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Taxonomy Database Interface
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Taxonomy Database Interface
Public-facing versionCountry summary pagesSpecial user access? (e.g., for countries with non-public data)API and R package refinementFurther development of methods to deal with these messy data
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Next Steps