Transcript IDO 2008 - Buffalo Ontology Site

IDO 2008
Dengue Ontology,
User-Developer perspective
Overview
Biology
 Current system
 A decision support system as a solution
 What is Dengue?
 Really, what is Dengue?
 The DDSS
 Control Vocabulary
 Dengue Ontology
Disease and Mosquito Cycle
1 Main mosquito vector
1 Main disease target
3 Disease manifestations
4 Virus serotypes
9 Day from egg to adult*
14 day to become infectious*
* Temperature dependent
http://www.entm.purdue.edu/publichealth/images/downloads/lifecycle-mosquito.jpg
Merida
500 000 (estimated) DHF cases
require hospitalization each year
2.5% of those affected die
2.5 billion people at risk
http://en.wikipedia.org/wiki/Dengue
http://www.who.int/mediacentre/factsheets/fs117/en/
Urban Area of Merida
Because of the interaction of three semi-independent
components the vector borne disease behave
differently from communicable diseases.
Total
cases
in
2007
Merida
Potential for rapid outbreak response based on clinical syndromic surveillance
What is Dengue?

Disambiguation
Dengue Virus is_a Pathogen
 Dengue Fever is_a Disease
 Dengue Fever is_a Diagnosis
 Dengue Fever Clasic is_a Manifestation
 Dengue Case instance_of Dengue Fever?

What is Dengue?

WHO


Dengue fever and dengue hemorrhagic fever (DHF) are acute
febrile diseases, found in the tropics and Africa, and caused by four
closely related virus serotypes of the genus Flavivirus, family
Flaviviridae.
(Some) Health Departments

What WHO Says but, it is not Dengue until it was been confirmed
by the laboratory.
What is Dengue?

Most dengue cases are usually clinically diagnose




No Pathognomonic symptom
The list includes more than 50
They can drastically vary by subject and by outbreak.
There are 3 WHO recognized diagnosis
(manifestations)




Dengue Fever a.k.a Classic Dengue
Dengue Hemorrhagic Fever (Thrombocytopenia <1x 105 platelets/mm³
Dengue Shock syndrome
Dengue Fever with hemorrhagic manifestations
What is Dengue?


What is Diagnosis?
What is Disease?
Disease Ontology Workshop
The Ontology of Diagnosis
(to be quoted as work in progress)
Baltimore, MD, USA. November 7, 2006
Juan Perez
Dengue
was diagnosed
instance-of
at t1
instance-of
at t1
instance-of
at t1
Person
Disease
Diagnosing
inst-of
at t2
inst-of
at t2
inst-of
at t2
DHF
was diagnosed
by
by
PCR
Pedro Juarez
instance-of
at t1
method
inst-of
at t2
PCR
Person
depend_on
Dengue Fever
depend_on
Dengue Virus
caused_by
Symptoms
Juan Perez instance-of
at t1
Dengue
was diagnosed
by
PCR
Person
Disease
Diagnosing
method
inst-of
at t2
Pedro Juarez
DHF
was diagnosed
by
PCR
Person
has_part
depens_on
Head
has_part
Symptoms
gum
instance-of
at t
instance-of
at t
Juan’s headache
has_location
Juan’s head
Juan’s mialgya
has_location
Juan’s muscles
Juan’s bleeding
gums
has_location
Juan’s gums
A well-formed diagnosis of dengue?
Disease
is_a?
Dengue Fever
instance-of
at t
Juan’s portion
of viruses
caused_by
Juan’s Dengue
A well-formed diagnosis of dengue?
Disease
is_a
Dengue virus
caused_by
instance-of
at t
Dengue Fever
Juan’s Dengue
Realization_of
Asymptomatic
Dengue Fever
Dengue Fever
has_symptom
Headache
Hem. Manif.
Dengue Fever
Hemorrhagic
Dengue Fever
has_symptom
Epistaxis
Shock syndrome
Dengue
is_a
Diagnosis
Juan Perez
Dengue
was found
instance-of
at t1
instance-of
at t1
instance-of
at t1
Person
Disease
Finding
inst-of
at t2
inst-of
at t2
inst-of
at t2
in
320 South
street #456
Pedro Juarez
DHF
was found
in
instance-of
at t1
Place
inst-of
at t2
12 North
street #123
Disease
is_a
Dengue virus
caused_by
Dengue Fever
instance-of
at t
Juan’s Dengue
located_in
320 South
street #456
instance-of
at t
Premise
instance-of
at t
Block
located_in
Block MX1235
located_in
Merida
instance-of
at t
Populated place
Problems of using English

Street Ni▄os Caj¬¯n and Ninos Cajon and Nignos
Cajon are not Niños Cajón
Add all the characters of all the lenguajes
 Is not just annotation. Wrong characters renders the
terms useless.


Jorgue Guachintón located_in Guayomin located_in
Yunited Estates is not George Washington….
Juan Perez
Dengue
was diagnosed
instance-of
at t1
instance-of
at t1
instance-of
at t1
Person
Disease
Diagnosing
inst-of
at t2
inst-of
at t2
inst-of
at t2
DHF
was diagnosed
by
by
symptoms …
Pedro Juarez
instance-of
at t1
symptoms
inst-of
at t2
symptoms ..
A well-formed diagnosis of dengue?
Juan’s Dengue
instance-of
at tx
Headache
onset
has_symptom
has_symptom
Asymptomatic
Dengue Fever
Dengue Fever
Low blood
pressure
Epistaxis
Hem. Manif.
Dengue Fever
Hemorrhagic
Dengue Fever
Shock syndrome
Dengue
t
Juan goes to the
doctor
Juan is
hospitalized
DDSS (1): System flow scheme
Functional definition of Decision Support System: An interactive and
adaptable system that aids the process of gathering and analyzing information,
gaining new insights, generating alternatives, and making decisions
Dengue Decision Support System
Program
Strategy
&
Methodology
Data
Collection
Sampling
schemes
Data
Entry
Data
format,
Data entry
screens
Data
Storage
Data
Retrieval
SQL data
warehouse
Management tool
Data
Analysis
Data
Display
Management tool,
GIS software,
Statistical packages,
Modeling
XHTML files,
Text files,
GIS software,
Google Earth,
Outputs: Charts, Graphs, Maps, Tables
FEEDBACK TO
PROGRAM
STRATEGY &
METHODOLOGY
Interpretation
(comparison with local historical data, relation to critical thresholds etc)
Management Decisions
DDSS (2): Essential DDSS characteristics
 Integrates into existing vector/dengue control programs at local/regional
levels (single DDSS) or national levels (DDSS network).
 DDSS application packages will be made accessible in English and Spanish
language versions.
 Self-application concept provides potential for rapid world-wide implementation.
 Flexible DDSS implementation to fit a wide range of resource environments.
 Minimum capital investment for implementation of a basic DDSS is estimated
at $1,500 per location (low-end computer, basic GPS unit and software).
 User-friendly; designed for use by regular vector control personnel.
 Standardized data entry formats to facilitate compilation of data from
multiple locally operated DDSS for national level analysis.
DDSS
(3)
DDSS
(5)
Disease and Vector control/surveillance activities
Case Reports
•Control Activities
•Control Activities
(Reactive)
• ULV Insecticide spray
• Immature Control
• Breeding site control
Infected Count --
•Surveillance
• Counts and ndexes
•Control Activities
(Reactive) Case Reports
http://www.entm.purdue.edu/publichealth/images/downloads/lifecycle-mosquito.jpg
• Breeding Sites
DDSS (7): Selected outputs from DDSS-1
 Documentation to support operational logistics:
- Workload and cost related to different program activities.
- Spatial coverage of surveillance and control activities.
- Insecticide types and quantities used.

Entomological data display outputs showing:
- Seasonal and spatial patterns of vector abundance.
- Contribution of different container types to vector production.
- Effect of implemented control strategies on vector abundance.

Epidemiological data display outputs showing:
- Distribution of DF and DHF cases by sex and age group.
- Seasonal and spatial patterns of occurrence of DF and DHF cases.
- Seasonal and spatial patterns of DF and DHF incidence (if population census
data are available).
- Effect of implemented vector control strategies on DF and DHF incidence
(based on passively collected data).

Priority Area classification for vector control.

GIS-backbone to support vector/dengue control (and build public health
capacity).
DDSS (8): Expected outcomes from DDSS-1
 Evidence-based decision making and use of locally appropriate
vector/dengue control program strategies and methodologies.
 Improved capacity for data entry, storage, retrieval, analysis and display.
 Better use of available resources through improved understanding of the
relative costs and benefits of different surveillance and control approaches.
 Better targeting of limited resources for vector control to high risk areas.
 Improved capacity for effective emergency vector control response through
more rapid flow of information between public health institutions and
vector/dengue control programs.
DDSS (4): Evolution of DDSS system design
Past
Present
Future
2–tier system
(GUI – Database)
2–tier system
(GUI – Database)
3–tier system
(GUI – Business Logic - Database)
GUI:
MS Visual Basic
GUI:
MS Visual Basic
Database:
Access
or
SQL Server
Express
Database:
PostgreSQL
with PostGIS
extension
VB-Java
Java
PostgreSQL with
PostGIS extension
DDSS (5): Use of open source software
Google
Earth
PostgreSQL
R Stats Pack
IDO
Need Logo
ZedGraph
Plotting
Library
Reporting
Thank you