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

98−

01−

01

99−

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01

00−

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01

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01

0

100

200

0

100

200

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

2/9

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)

3/9

Data in many shapes and sizes

4/9

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

5/9

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

9/9

Next Steps