1. Fred Freitas
Informatics Center - Federal University of Pernambuco, Brazil
KR & KM group - University of Mannheim, Germany
Stefan Schulz
Institut für Medizinische Biometrie und Medizinische Informatik Universitätsklinikum Freiburg, Germany
Zulma Medeiros
Aggeu Magalhães Research Center, Oswaldo Cruz Foundation (CPqAM/FIOCRUZ), Recife, Pernambuco, Brazil
Neglected tropical diseases - A challenge to biomedical ontology engineering

2. summary Domain description Use cases envisaged
Diseases, actions, institutions involved
Use cases envisaged
Ontologies and their connections
Challenges

3. neglected tropical diseases (NTDs)
They have been hardly heard of in richer countries …
… but cause severe disability in the world's poorest regions in over 1 billion people [WHO]
Lymphatic filariasis,
Onchocerciasis,
Schistosomiasis,
Leishmaniasis
Chagas disease(American trypanosomiasis)
Trachoma
Dengue
Malaria …

4. Common features of these diseases
In most (if not all) of them, biological organisms play these different roles:
Pathogens: complicated organisms with different relevant lifecycles that cause disabilities in humans
Vectors: transmit the pathogens, if their habitat is comfortable for them to reproduce
Hosts: are also a means of transmission (e.g. dogs)
These organisms exhibit complicated lifecycles
They cause diseases with diverse sets of manifestations and symptoms
NTDs require different kinds of actions
prophylaxis, detection and treatment

5. An example: Schistosomiasis

6. ACTIONS against NTDs In Brazil
Prophylaxis: To prevent their transmission
Improvement of basic sanitation (long term)
Educational programs
Field operations
In the environment, by avoiding a comfortable habitat for the organisms
E.g. cover river parts with small polystyrene balls
Against vectors, to reduce heir population
E.g., a chemical smoke to kill dengue’s mosquitoes
Detection: To check individuals’ and populations’ prevalence
Treatments

7. Involved institutions
Municipalities, Federal and State Universities
Actions, treatment, registration
Federal States
Inter-municipality action coordination, policies and guidelines definitions, database analysis
Federal Government
State coordination of the actions, policy and guidelines definitions, database analysis
Oswaldo Cruz Foundation’s instances
Study, research on the disease as well as its actions, campaign planning and creation of treatment and diagnosis new methods

8. summary Domain description Use cases envisaged
Diseases, actions, institutions involved
Use cases envisaged
Ontologies and their connections
Challenges

9. Intended Use cases for the ontologies I
Decision support systems (DSS) for neglected diseases
Stakeholders: governments on the 3 levels
Phase 1: ontology-based information integration that allows querying heterogeneous NTDs-related databases from different governmental sources (county, state and country).
Integration with OTICSSS [Bissolotti & Silva 2009], an emerging health information integration initiative in Brazil.
Phase 2: Diagnoses of the situation
Phase 3: Assessment of actions’ effectiveness

10. Intended Use cases for the ontologies Ii
A document search engine for NTDs
Morphosemantic indexing developed by Freiburg partners
Ontology-enhanced text processing
take advantage not only of keywords, but also of the ontology structure
Intelligent agents/decision support systems that
assist on diagnosis and prognosis of neglected diseases in potential and actual patients.
serve as a basis for eLearning artifacts
1-The ontology labels are mostly in English (only partially extended by Spanish and Portuguese labels available from multilingual terminologies), whereas many resources are only available in Portuguese. The solution is here to re-use and adapt an existing cross-language indexing system. 
2-This can be a breakthrough in the project, a good usage testbed for the definitions being built. This type of system will probably be the last one to be implemented, given that the others have still somewhat started.

11. summary Domain description Use cases envisaged
Diseases, actions, institutions involved
Use cases envisaged
Ontologies and their connections
Challenges

12. EXTERNAL ONTOLOGIES TO BE USED
BioTop
Core ontology for biomedicine
SNOMED
Procedures, treatments, pharmacological products, diseases, social context, body structure, event,…
OBO, GO
Malaria [Ceusters & Smith 2009]: guideline
Issue: how to integrate

13. Biotop Basic Formal Ontology Middle downwards: Top:
BFO is based on four principles:
Realism
Fallibilism
Perspectivism
Adequatism

14. MODELING PRINCIPLES Modeling with good ontological engagement Reuse
Temporal aspects are sometimes needed [Ceusters & Smith 2009]
If possible, adopting OWL DL, or its temporal variations [Artale & Franconi 1998, Lutz 2002]
Reuse
Since diseases share common features…
Pathogens, hosts, habitat type and locations, disease, exams
…a core ontology(ies) about them facilitates reuse
Issue: a new core ontology vs extending BioTop
Modularization

15. Environment/ Hosts / Vectors
Prophylactic actions
ONTOLOGIES
Managementactions
Pathogens
Detection
Biologicla part
Treatment
Diseases

16. ONTOLOGY BRIDGING A new NTD extend the core ontology on NTDs
Vectors\pathogens\diseases: connects to Biotop and may reuse some vocabulary \ definitions from external sources (GO, SNOMED,…)
Actions connect to BFO and the core ontology to be defined
guidelinesReuse is crux – MODIFY
EVERYBODY USES BFO
Malaria from smith is a starting point

17. TEMPORAL ASPECTS
On time t1, there was x1 new instances of the disease detected by exams in a population p and a certain prophylactic action pa1 was taken
On time t9, the rate of the new instances x9 is falling down (x1>x9) for the same number of new exams in the same conditions
If ok, this is due to pai
The same for treatments
guidelinesReuse is crux – MODIFY
EVERYBODY USES BFO
Malaria from smith is a starting point 17

18. summary Domain description Use cases envisaged
Diseases, actions, institutions involved
Use cases envisaged
Ontologies and their connections
Challenges

19. political x vectors’ habitats
Administrative regions are arbitrarily delineated, but endemies don’t respect such divisions
They depend upon natural sources of the vectors/hosts, mostly geographical accidents
Actions can only be well succeeded / assessed if they focus to the endemic spaces
They vary according to the disease
Schistosomiasis: hydrographic basins
Dengue/Malaria/Filariasis: sources of still water
Bubonic plague: mountains, hills …
Intemunicipality/state coordination

20. Modeling challenges Different granularities
individual disease vs. affected populations
Linking very different entity types (e.g., socioeconomic factors, housing, mobility,…)
Public health authorities and their roles in the process
Temporal management of data, according to what is defined in the ontology (phases, stages, action sequences, …)
Complicated organisms with different relevant lifecycles
Broad spectrum of disease manifestations
Benefit: the different standpoints (health researchers, managers, workers) hopefully can live in harmony
treatment and prevention both related to individuals and populations

21. Thank you for your attention!
Questions , remarks?

22. references
Bissolotti, k. ; Tavares, J. L. . Integração de Tecnologias de Informação e Conhecimento no Projeto OTICSSS. In: XVII Encontro de Jovens Pesquisadores, 2009, Caxias do Sul. XVII Encontro de Jovens Pesquisadores, 2009.
Elena Beißwanger, Stefan Schulz, Holger Stenzhorn and Udo Hahn BioTop: An Upper Domain Ontology for the Life Sciences - A Description of its Current Structure, Contents, and Interfaces to OBO Ontologies in Applied Ontology, Volume 3, Issue 4, Pages , IOS Press, Amsterdam, Netherlands, December 2008
Freitas, F. ; Schulz, S. ; Moraes, E. . Survey of current terminologies and ontologies in biology and medicine. RECIIS. Electronic Journal of Communication, Information and Innovation in Health (English edition. Online), v. 3, p. 1-13, 2009
Alessandro Artale, Enrico Franconi. A Temporal Description Logic for Reasoning about Actions and Plans, Journal of Articial Intelligence Research 9 (1998) /98
Lutz, C. The Complexity of Description Logics with Concrete Domains, PhD Thesis.
Werner Ceusters, Barry Smith, Malaria Diagnosis and the Plasmodium Life Cycle: the BFO Perspective, Nature, Nov 2009.

23. Modeling challenges Modularization of the big life science ontologies
BioTop, SNOMED,…
In order to guarantee more
Control, management
Better visualization
Reasoning performance
treatment and prevention both related to individuals and populations 23