IDO 2008IDO 2008

Dengue Ontology,Dengue Ontology,

User-Developer perspectiveUser-Developer perspective

OverviewOverview

Biology Current system A decision support system as a solution What is Dengue?What is Dengue? Really, what is Dengue?Really, what is Dengue? The DDSSThe DDSS Control Vocabulary Control Vocabulary Dengue OntologyDengue Ontology

Disease and Mosquito Cycle

1 Main mosquito vector1 Main disease target3 Disease manifestations4 Virus serotypes9 Day from egg to adult*14 day to become infectious*

* Temperature dependenthttp://www.entm.purdue.edu/publichealth/images/downloads/lifecycle-mosquito.jpg

http://en.wikipedia.org/wiki/Denguehttp://www.who.int/mediacentre/factsheets/fs117/en/

Merida

500 000 (estimated) DHF cases require hospitalization each year 2.5% of those affected die 2.5 billion people at risk

Urban Area of Merida

Because of the interaction of three semi-independent components the vector borne

disease behave differently from communicable diseases.Total

casesin 2007

Merida

Potential for rapid outbreak response based on clinical syndromic surveillance

What is Dengue?What is Dengue? DisambiguationDisambiguation

Dengue Virus is_a PathogenDengue Virus is_a Pathogen Dengue Fever is_a DiseaseDengue Fever is_a Disease Dengue Fever is_a DiagnosisDengue Fever is_a Diagnosis Dengue Fever Clasic is_a ManifestationDengue Fever Clasic is_a Manifestation Dengue Case instance_of Dengue Fever?Dengue Case instance_of Dengue Fever?

What is Dengue?What is Dengue? WHOWHO

Dengue fever and dengue hemorrhagic fever Dengue fever and dengue hemorrhagic fever (DHF) are acute febrile diseases, found in the (DHF) are acute febrile diseases, found in the tropics and Africa, and caused by four closely tropics and Africa, and caused by four closely related virus serotypes of the genus Flavivirus, related virus serotypes of the genus Flavivirus, family Flaviviridae.family Flaviviridae.

(Some) Health Departments(Some) Health Departments What WHO Says but, it is not Dengue until it was What WHO Says but, it is not Dengue until it was

been confirmed by the laboratory.been confirmed by the laboratory.

What is Dengue?What is Dengue? Most dengue cases are usually clinically Most dengue cases are usually clinically

diagnosediagnose No Pathognomonic symptomNo Pathognomonic symptom The list includes more than 50The list includes more than 50 They can drastically vary by subject and by outbreak.They can drastically vary by subject and by outbreak.

There are 3 WHO recognized There are 3 WHO recognized diagnosisdiagnosis (manifestations)(manifestations) Dengue Fever a.k.a Classic DengueDengue Fever a.k.a Classic Dengue Dengue Hemorrhagic Fever (Thrombocytopenia <1x 10Dengue Hemorrhagic Fever (Thrombocytopenia <1x 1055

platelets/mm³ platelets/mm³ Dengue Shock syndromeDengue Shock syndrome Dengue Fever with hemorrhagic manifestationsDengue Fever with hemorrhagic manifestations

What is Dengue?What is Dengue? What is Diagnosis?What is Diagnosis? What is Disease?What is Disease?

Disease Ontology Workshop

The Ontology of Diagnosis(to be quoted as work in progress)

Baltimore, MD, USA. November 7, 2006

Juan PerezJuan Perez

DengueDengue

was was diagnoseddiagnosed

byby

PCRPCR

Diagnosing

Person

Disease

method

instance-of at t1

inst-of at t2

Pedro JuarezPedro Juarez

DHFDHF

was was diagnoseddiagnosed

by by

PCRPCR

instance-of at t1

instance-of at t1

instance-of at t1

inst-of at t2

inst-of at t2

inst-of at t2

Juan PerezJuan PerezDengueDenguewas was

diagnoseddiagnosedbybyPCRPCR

Diagnosing

Person

Disease

method

instance-of at t1

inst-of at t2

Pedro JuarezPedro JuarezDHFDHFwas was

diagnoseddiagnosedby by PCRPCR

Person Dengue Fever Dengue Virus

Symptoms

depend_on

caused_by

depend_on

Juan’s headache

Juan’s mialgya

Juan’s bleedinggums

Juan’s head

Juan’s muscles

Juan’s gums

Person

Symptoms

has_location

has_location

has_location

Head

gum

has_part

has_part

instance-of at t

instance-of at t

depens_on

A well-formed diagnosis of dengue?

Dengue Fever

caused_by

is_a?

Disease

Juan’s DengueJuan’s portion

of viruses

instance-of at t

A well-formed diagnosis of dengue?

Dengue Fevercaused_by

Disease

Juan’s Dengue

instance-of at t

AsymptomaticDengue Fever

Dengue Fever HemorrhagicDengue Fever

Hem. Manif.Dengue Fever

Shock syndromeDengue

is_a

Dengue virus

Realization_of

Diagnosis

is_ahas_symptom

Headache Epistaxis

has_symptom

Juan PerezJuan Perez

DengueDengue

was foundwas found

inin

320 South320 Southstreet #456street #456

Finding

Person

Disease

Place

instance-of at t1

inst-of at t2

Pedro JuarezPedro Juarez

DHFDHF

was foundwas found

in in

12 North12 Northstreet #123street #123

instance-of at t1

instance-of at t1

instance-of at t1

inst-of at t2

inst-of at t2

inst-of at t2

Dengue Fevercaused_by

Disease

Juan’s DengueJuan’s Dengue

instance-of at t

is_a

Dengue virus

located_in

320 South320 Southstreet #456street #456

Premiseinstance-of at t

Block MX1235Block MX1235

located_in

Blockinstance-of at t

MeridaMerida

located_in

Populated placeinstance-of at t

Problems of using EnglishProblems of using English

Street Street Ni▄os Caj¬¯nNi▄os Caj¬¯n and and Ninos CajonNinos Cajon and and Nignos CajonNignos Cajon are not Niños Cajón are not Niños Cajón Add all the characters of all the lenguajesAdd all the characters of all the lenguajes Is not just annotation. Wrong characters Is not just annotation. Wrong characters

renders the terms useless.renders the terms useless. Jorgue Guachintón Jorgue Guachintón located_inlocated_in

Guayomin Guayomin located_inlocated_in Yunited EstatesYunited Estates is is not George Washington…. not George Washington….

Juan PerezJuan Perez

DengueDengue

was was diagnoseddiagnosed

byby

symptoms …symptoms …

Diagnosing

Person

Disease

symptoms

instance-of at t1

inst-of at t2

Pedro JuarezPedro Juarez

DHFDHF

was was diagnoseddiagnosed

by by

symptoms ..symptoms ..

instance-of at t1

instance-of at t1

instance-of at t1

inst-of at t2

inst-of at t2

inst-of at t2

A well-formed diagnosis of dengue?

Juan’s Dengue

instance-of at tx

AsymptomaticDengue Fever

Dengue Fever HemorrhagicDengue Fever

Hem. Manif.Dengue Fever

Shock syndromeDengue

has_symptom

Headacheonset

Epistaxis

has_symptom

t

Juan goes to the doctor

Juan is hospitalized

Low bloodpressure

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

Data Analysis

Management tool, GIS software,

Statistical packages,Modeling

Data Storage

SQL data warehouse

Data Entry

Data format,

Data entry screens

Data Collection

Sampling schemes

Dengue Decision Support System

Data Retrieval

Manage-ment tool

Data Display

XHTML files,Text files,

GIS software,Google Earth,

Outputs: Charts, Graphs, Maps, Tables

Management Decisions

Program Strategy

& Methodology

FEEDBACK TOPROGRAM

STRATEGY & METHODOLOGY

Interpretation (comparison with local historical data, relation to critical thresholds etc)

DDSS (1): System flow

scheme

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

http://www.entm.purdue.edu/publichealth/images/downloads/lifecycle-mosquito.jpg

Infected Count --

Case Reports

•Surveillance

• Counts and ndexes

• Breeding Sites

Case Reports

•Control Activities

• ULV Insecticide spray

• Immature Control

• Breeding site control

•Control Activities(Reactive)

•Control Activities(Reactive) -

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

GUI: MS Visual Basic

Database: Access or SQL Server Express

2–tier system (GUI – Database)

Present

2–tier system (GUI – Database)

GUI: MS Visual Basic

Database: PostgreSQLwith PostGISextension

Future

3–tier system (GUI – Business Logic - Database)

Java

VB-Java

PostgreSQL with PostGIS

extension

IDOIDONeed LogoNeed Logo

ZedGraph

PostgreSQL

R Stats Pack

PlottingLibrary

Reporting

Google Earth

DDSS (5): Use of open source software

Thank youThank you