IDOMAL: an ontology for malaria

Abstract

Background: Ontologies are rapidly becoming a necessity for the design of efficient information technology tools, especially databases, because they permit the organization of stored data using logical rules and defined terms that are understood by both humans and machines. This has as consequence both an enhanced usage and interoperability of databases and related resources. It is hoped that IDOMAL, the ontology of malaria will prove a valuable instrument when implemented in both malaria research and control measures.

Methods: The OBOEdit2 software was used for the construction of the ontology. IDOMAL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium.

Results: The first version of the malaria ontology covers both clinical and epidemiological aspects of the disease, as well as disease and vector biology. IDOMAL is meant to later become the nucleation site for a much larger ontology of vector borne diseases, which will itself be an extension of a large ontology of infectious diseases (IDO). The latter is currently being developed in the frame of a large international collaborative effort.

Conclusions: IDOMAL, already freely available in its first version, will form part of a suite of ontologies that will be used to drive IT tools and databases specifically constructed to help control malaria and, later, other vector-borne diseases. This suite already consists of the ontology described here as well as the one on insecticide resistance that has been available for some time. Additional components are being developed and introduced into IDOMAL.

Figure 1

The position of chloroquine in IDOMAL. The figure shows the positions of chloroquine in the IDOMAL ontology tree. A: the is_a path from chloroquine to the top-level object class; B: three different paths leading from chloroquine and converging to process of malaria (an is_a child of the top-level class process) linking parent-children terms with different relations; C: the third path of chloroquine leading to the top-level class role through two different relations. The different relations are indicated by different signs and colours: grey box = is_a, blue circle = part_of, yellow box = has_role, green box = agent_in.

Figure 2

The class process in IDOMAL. The upper-most terms within the class process are indicated here. Most relations shown are is_a relations (grey box) with two exceptions in which part_of relations (blue circles) are indicated. The small boxes containing a plus sign signify that the term contains a number of children terms, while the boxes with a minus sign show a "terminal" term that has no children in the ontology.

Figure 3

The TRAP protein in IDOMAL. The two different paths in which the protein TRAP (enclosed in a red and white rectangle) is found are shown here. In B, the is_a path leads to the upper class object, while in A the position of TRAP in the clade leading to the class process is shown. In addition to is_a (grey rectangle) and part_of (blue circle), two additional relations are used for the correct setting of the term: participates_in (grey rectangle) and preceded_by (orange rectangle).