Using ontologies in integrative tools for protozoan parasite research


Protozoan parasites such as those that cause malaria and toxoplasmosis remain major threats to global health, and a significant biodefense concern.  Current treatments are limited and sometimes compromised by acquired resistance. Solutions will come from the integration and mining of ongoing research. The need for data integration is common among research communities tackling complex topics such as the biology of eukaryotic pathogens, their interaction with hosts, and the search for druggable targets and vaccine candidates. Biomedical researchers have greatly benefited from the Gene Ontology (GO) that provides standardized terms for annotating protein function, location, and participation in processes. GO and other relevant ontologies have largely been developed to support human and model organism biology with only limited representation of protozoan parasite biology. In addition, the availability and use of standard terms is also very limited for the inputs and outputs of bioinformatic tools that are commonly used to analyze protozoan parasite datasets and is a barrier for linking these tools together. In the Integrative Tools for Protozoan Parasite Research (ITPPR) project, we have started addressing these areas by developing tools needed by the communities served by EuPathDB ( We are using ontology-based models as part of our process to build tools for collecting information on isolates, describing phenotypic outcomes of transgenic parasites, and for joining web services running sequence similarity and alignment analysis. Ontologies are drawn from the OBO Foundry and include the Infectious Disease Ontology (IDO) and OBI (Ontology for Biomedical Investigations). 


Chris Stoeckert is Research Professor of Genetics at the University of Pennsylvania and a core member of the Center for Bioinformatics. His research is in genomics and functional genomics data integration covering databases, standards and ontologies, and data modeling and analysis. He directs CBIL (Computational Biology and Informatics Lab) that has developed the GUS database system. He is a co-investigator of the EuPathDB Bioinformatics Resource Center ( that supports protozoan parasite research with sites like PlasmoDB ( He also leads the Beta Cell Genomics ( component of the Beta Cell Biology Consortium. He is president of the Functional Genomics Data Society (formerly known as MGED), led the effort to build the MGED Ontology (MO), and is an active developer of the Ontology for Biomedical Investigations (OBI). With David Roos and his group, he has developed OrthoMCL to generate groups of orthologous genes.