Data-driven surveillance: Transforming data into ... · datadrivensurveillance.org - Parma summer...
Transcript of Data-driven surveillance: Transforming data into ... · datadrivensurveillance.org - Parma summer...
datadrivensurveillance.org - Parma summer school, One-Health, 9-10 June 2020
DATA-DRIVEN SURVEILLANCE: Transforming data into actionable information in the One-Health health context Fernanda Dórea
Swedish National Veterinary Institute
ORION – WP3 – data interoperability – www.datadrivensurveillance.org/ontology
Surveillance
datadrivensurveillance.org - Parma summer school, One-Health, 9-10 June 2020
Data Information Action
Epidemiological data collection is abouttechnology, but effective disease
surveillance is about people
People matter in animal disease surveillance: Challenges
and opportunities for the aquaculture sector
Cecile Brugere
Dennis Mark Onuigbo
Kenton Ll. Morgan
datadrivensurveillance.org - Parma summer school, One-Health, 9-10 June 2020
Data Information Action
context knowledge insight
datadrivensurveillance.org - Parma summer school, One-Health, 9-10 June 2020
Data Information Action
context knowledge insight
datadrivensurveillance.org - Parma summer school, One-Health, 9-10 June 2020
Data Information ActionActionable
information
context knowledge insight
3.5400 positive
samples
3.5%
samples
positive
Prevalence?
DATA vs. INFORMATION
context knowledge
Data analysis
(reproducible)
datadrivensurveillance.org - Parma summer school, One-Health, 9-10 June 2020
BIG DATA
Volume
Velocity
Variety
ORION – WP3 – data interoperability – www.datadrivensurveillance.org/ontology
Surveillance
ORION – WP3 – data interoperability – www.datadrivensurveillance.org/ontology
One-Health Surveillance
ORION – WP3 – data interoperability – www.datadrivensurveillance.org/ontology
One-Health Surveillance
Shar
eK
no
w-h
ow
K
NO
WLE
DG
E
DA
TA
inte
rop
erab
ilit
y
prevalence
cases outbreaks
www.datadrivensurveillance.org/ontology
Investigation
Surv.
system
Surv.
Activity
Outbreak
Sample
disease
host
legislation
Sampling
designReporting
practices
place
Contribut-
ory factors
Place of
exposureFood
vehicle
result assay
material
cases
date
gender
Country
acquisition
Context
Levels of
information
Think of one dataset
ORION – WP3 – data interoperability – www.datadrivensurveillance.org/ontology
Lab data
Lab B
Interoperable
Lab data
Lab A
Lab data
Lab A
Lab data
Lab A
Epi data
Weather
data
Population
registry
Lab data
Lab DLab data
Lab C Epi data
ANIMALS
Epi data
FOOD
ORION – WP3 – data interoperability – www.datadrivensurveillance.org/ontology
Syntatic interoperability(harmonize structure)
Terminologies, data standards, dictionaries
Symptom
Diarrhoea
Symptom
Diarréia
Symptom
Diarrea
Minimum information tables
Mappings, data models
Semantic interoperability(align meaning)
Meaning, context
Source
Fecal swab
Source
Farm A
Species
Broilers
Species
Chickens
Target
Campylobacteriosis
Target
Campylobacter
ORION – WP3 – data interoperability – www.datadrivensurveillance.org/ontology
Machine interpretable
Knowledge model of a domain
Interoperability
Among data sources
Evolving knowledge
Across domains = Reusability
Semantic interoperability - ONTOLOGIES
Organism
Bacterium
Campylobacter
Avium
Gallus gallus
Mammal
Homo sapiens
Disease
Campylobacterio
sis
Production
type
Meat producing
Broiler
Clinical sign
Age
ORION – WP3 – data interoperability – www.datadrivensurveillance.org/ontology
Diagnostic
pneumonia
Clinical sign
Short of
breath
Respiratory cases
datadrivensurveillance.org - Parma summer school, One-Health, 9-10 June 2020
datadrivensurveillance.org - Parma summer school, One-Health, 9-10 June 2020
One Health
context
knowledge
Federated queries
”Code to data”
models
”Future-proof”
ORION – WP3 – data interoperability – www.datadrivensurveillance.org/ontology
ORION – WP3 – data interoperability – www.datadrivensurveillance.org/ontology
Traditional data life cycle
Data
productionData USE Results Archive Reuse
ORION – WP3 – data interoperability – www.datadrivensurveillance.org/ontology
Linked data model
Data
production
Data user 1
Store
DATA +
SCHEMAData user 2
Results
Results
Results
ORION – WP3 – data interoperability – www.datadrivensurveillance.org/ontology
Linked data model ”Future-proof”
Reuse knowledge
Discover knowledge
Evolve knowledge
ORION – WP3 – data interoperability – www.datadrivensurveillance.org/ontology
Health Surveillance Ontology
The dataprinciple
Supporting OHS data interoperability,
integration & interpretation
Tools for Linked-Open-Data production and
use
HumansCan understand a dataset if columns
are properly labelled, and if they can
read and understand the concepts.
Semantic ambiguity must be solved
by collaboration, agreement and
documentation
The knowledge that allows humans to
understand concepts and semantic
meaning can be programmed into an
ontology to allow reading of the dataset by
machines
ORION – WP3 – data interoperability – www.datadrivensurveillance.org/ontology
Surveillance reportchapters
ORION – WP3 – data interoperability – www.datadrivensurveillance.org/ontology
Surveillance report chapters
ORION – WP3 – data interoperability – www.datadrivensurveillance.org/ontology
Separate data from information
Enrich data with CONTEXT,
not standards
Allow machines to handle
information using
KNOWLEDGE
Treat your data user
like you are used to
treat your computer
Treat your computer
like you are used to
treat your data
users
datadrivensurveillance.org - Parma summer school, One-Health, 9-10 June 2020
datadrivensurveillance.org - Parma summer school, One-Health, 9-10 June 2020
datadrivensurveillance.org