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This article is part of the supplement: Proceedings of Ontologies in Biomedicine and Life Sciences (OBML 2011)

Open Access Proceedings

Towards an ontological representation of morbidity and mortality in Description Logics

Filipe Santana1*, Fred Freitas1, Roberta Fernandes1, Zulma Medeiros23 and Daniel Schober4*

Author Affiliations

1 Informatics Center, Federal University of Pernambuco (CIn/UFPE), Recife, Pernambuco, 50.740-560, Brazil

2 Parasitology Department, Aggeu Magalhães Research Center, Oswaldo Cruz Foundation, (CPqAM/Fiocruz), Recife, Pernambuco, 50.670-420, Brazil

3 Pathology Department, Institute of Biological Sciences, University of Pernambuco, Recife, Pernambuco, 50.100-130, Brazil

4 Institute of Medical Biometry and Medical Informatics (IMBI), University Medical Center, Freiburg, 79104, Germany

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Journal of Biomedical Semantics 2012, 3(Suppl 2):S7  doi:10.1186/2041-1480-3-S2-S7

Published: 21 September 2012

Abstract

Background

Despite the high coverage of biomedical ontologies, very few sound definitions of death can be found. Nevertheless, this concept has its relevance in epidemiology, such as for data integration within mortality notification systems. We here introduce an ontological representation of the complex biological qualities and processes that inhere in organisms transitioning from life to death. We further characterize them by causal processes and their temporal borders.

Results

Several representational difficulties were faced, mainly regarding kinds of processes with blurred or fiat borders that change their type in a continuous rather than discrete mode. Examples of such hard to grasp concepts are life, death and its relationships with injuries and diseases. We illustrate an iterative optimization of definitions within four versions of the ontology, so as to stress the typical problems encountered in representing complex biological processes. We point out possible solutions for representing concepts related to biological life cycles, preserving identity of participating individuals, i.e. for a patient in transition from life to death. This solution however required the use of extended description logics not yet supported by tools. We also focus on the interdependencies and need to change further parts if one part is changed.

Conclusion

The axiomatic definition of mortality we introduce allows the description of biologic processes related to the transition from healthy to diseased or injured, and up to a final death state. Exploiting such definitions embedded into descriptions of pathogen transmissions by arthropod vectors, the complete sequence of infection and disease processes can be described, starting from the inoculation of a pathogen by a vector, until the death of an individual, preserving the identity of the patient.