Describing the breakbone fever: IDODEN, an ontology for dengue fever

Abstract

Background: Ontologies represent powerful tools in information technology because they enhance interoperability and facilitate, among other things, the construction of optimized search engines. To address the need to expand the toolbox available for the control and prevention of vector-borne diseases we embarked on the construction of specific ontologies. We present here IDODEN, an ontology that describes dengue fever, one of the globally most important diseases that are transmitted by mosquitoes.

Methodology/principal findings: We constructed IDODEN using open source software, and modeled it on IDOMAL, the malaria ontology developed previously. IDODEN covers all aspects of dengue fever, such as disease biology, epidemiology and clinical features. Moreover, it covers all facets of dengue entomology. IDODEN, which is freely available, can now be used for the annotation of dengue-related data and, in addition to its use for modeling, it can be utilized for the construction of other dedicated IT tools such as decision support systems.

Conclusions/significance: The availability of the dengue ontology will enable databases hosting dengue-associated data and decision-support systems for that disease to perform most efficiently and to link their own data to those stored in other independent repositories, in an architecture- and software-independent manner.

Figure 1. The “data item” hierarchy of terms in IDODEN.

Font colours indicate the different levels of the hierarchy while a small yellow box in front of a term shows that it has children. The minus sign indicates that all child terms are listed.

Figure 2. The “disposition” hierarchy of terms in IDODEN.

Font colours indicate the different levels of the hierarchy while a small yellow box in front of a term shows that it has children. The minus sign indicates that all child terms are listed while the plus sign indicates the presence of child terms that are not shown in the Figure.

Figure 3. The classes “process of dengue fever” (A) and “object aggregate” (B) in IDODEN.

Only terms relating to the diagnosis of dengue fever are shown. Font colours indicate the different levels of the hierarchy while a small yellow box in front of a term shows that it has children. The minus sign indicates that all child terms are listed while the plus sign indicates the presence of children terms that are not shown in the Figure.

Figure 4. The complete class “role” in IDODEN.

All terms shown are children of “role”. With the exception of the terms that are not preceded by a small yellow box all have children that are not shown. The arrow denotes that the terms in the right column follow those in the left one.

Figure 5. The class “vaccine” in IDODEN.

Given the different relations linking the terms, we have used a non-hierarchical way of showing the vaccine calls and its children/related terms. The colours of the arrows indicate different relations.

Figure 6. Ontological model of miRNA-mediated regulation of Dengue virus infection.

The arrows show the different relations linking the ontology terms; the colours indicate different relations as listed above the model. Ontologies and terms in italics show classes that have been imported from ontologies other than IDODEN. Several terms have been omitted from the model.

Figure 7. Ontological model of a dengue fever infection.

The arrows show the different relations linking the ontology terms; the colours indicate different relations as listed at the upper right corner of the model. Ontologies and terms in italics show classes that have been imported from ontologies other than IDODEN. Several terms have been omitted from the model.

Figure 8. Ontological model of the 1927–1928 dengue fever epidemic in Athens.

The arrows show the different relations linking the ontology terms; the colours indicate different relations as listed at the lower right corner of the model. Ontologies and terms in italics show classes that have been imported from ontologies other than IDODEN. The dashed green line denotes an “exact synonym relationship” between Aedes aegypti and Stegomyia fasciata, the term used for the former species in 1928. Several terms have been omitted from the model.