IDO 2008 IDO 2008 Dengue Ontology, Dengue Ontology, User-Developer perspective User-Developer perspective
Dec 28, 2015
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