IDOMAL: the malaria ontology revisited

Abstract

BackgroundWith about half a billion cases, of which nearly one million fatal ones, malaria constitutes one of the major infectious diseases worldwide. A recently revived effort to eliminate the disease also focuses on IT resources for its efficient control, which prominently includes the control of the mosquito vectors that transmit the Plasmodium pathogens. As part of this effort, IDOMAL has been developed and it is continually being updated.FindingsIn addition to the improvement of IDOMAL’s structure and the correction of some inaccuracies, there were some major subdomain additions such as a section on natural products and remedies, and the import, from other, higher order ontologies, of several terms, which were merged with IDOMAL terms. Effort was put on rendering IDOMAL fully compatible as an extension of IDO, the Infectious Disease Ontology. The reason for the difficulties in fully reaching that target were the inherent differences between vector-borne diseases and “classical” infectious diseases, which make it necessary to specifically adjust the ontology’s architecture in order to comprise vectors and their populations.ConclusionsIn addition to a higher coverage of domain-specific terms and optimizing its usage by databases and decision-support systems, the new version of IDOMAL described here allows for more cross-talk between it and other ontologies, and in particular IDO. The malaria ontology is available for downloading at the OBO Foundry (http://www.obofoundry.org/cgi-bin/detail.cgi?id=malaria_ontology) and the NCBO BioPortal (http://bioportal.bioontology.org/ontologies/1311).

VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases

“…Our most recent additions are (i) a new ontology describing dengue fever (IDODEN – Infectious Disease Ontology DENgue) (Mitraka et al. , submitted), (ii) and update of the malaria ontology (IDOMAL - Infectious Disease Ontology MALaria) ( 19 , 20 ) and (iii) an ontology describing the domain of microRNAs (MiRNAO – MicroRNA Ontology). All VectorBase ontologies follow the rules established by the OBO (Open Biomedical Ontologies) Foundry ( 21 ), and can be browsed either at VectorBase ( https://www.vectorbase.org/ontology-browser ) or the NCBO (National Center for Biomedical Ontology) Bioportal ( http://bioportal.bioontology.org ).…”

DMTO: a realistic ontology for standard diabetes mellitus treatment

“…Regarding medical domains other than diabetes , ontologies have modelled the semantics of many diseases, such as malaria (IDOMAL [ 41 ]), cancer (NanoParticle [ 42 ]), periodontitis (PeriO [ 43 ]), and rehabilitation of knee conditions (TRAK [ 44 ]). The following are some examples of ontology-based CDSS systems.…”

De Novo Assembly and Transcriptome Analysis of the Mediterranean Fruit Fly Ceratitis capitata Early Embryos

“…The cost- and time-effectiveness of Next Generation Sequencing technologies [35] , [36] and the development of new reverse genetics tools (RNAi, TALENs and CRISPR-Cas9) allow many insect species to become model organisms in evolutionary and developmental studies as well as substrates for biotechnological applications [37] – [43] . Integrated international initiatives recently started to focus on comparative genomics studies in insects, which eventually will be very useful to develop alternative control strategies for pest species or disease vectors as well as to improve the existing ones [26] , [44] – [49] .…”