Integrative Tools for Protozoan Parasite Research (ITPPR)

Christian Stoeckert, Dept. of Genetics, University of Pennsylvania, School of Medicine

Protozoan parasites such as those causing malaria and toxoplasmosis remain major threats to global health and significant biological defense concerns. Current treatments are limited and compromised by acquired resistance. There is tremendous potential to accelerate progress through integration of ongoing research efforts and data mining. The Integrated Tools for Protozoan Parasite Research (ITPPR) project will facilitate data integration for protozoan parasite research through use of standardized terms and their application in tools.  The value of this approach has been demonstrated in human and model organism biology, but there has been only limited representation of protozoan parasite biology. The ITPPR project will provide pathogen researchers with enhanced ability to perform computational mining of genomic-scale datasets in existing resources (in particular the EuPathDB suite of Web sites) and provide bioinformatics researchers with improved tools for developing ontologies and process-based workflows.  This will maximize impact with targeted users of the tools while allowing the ontologies and tools to be developed for general use in the parasite research field.

Ontology development for protozoan parasite research
Efficient, automated comparison of results from different studies is hindered by inconsistent and incomplete descriptions (e.g. source of pathogen isolates and associated phenotypes).  The Infectious Disease Ontology (IDO) project seeks to provide a common semantic description for phenotypes and annotations associated with pathogen biology and diversity. The ITPPR project will join IDO development by providing coverage for a range of protozoan parasites, complementing ongoing efforts on pathogens (viral, bacterial, and fungal), and vectors. The protozoan parasite IDO should facilitate data integration and improve the ability of Web sites and databases to support queries related to host-pathogen interactions.  A growing number of applications and resources (e.g., BLAST, KEGG Pathways) are directly accessible to computers through Web services, however use of the output of one service as input to another has proved difficult.  We will expand ontologies currently under development within the OBO Foundry to specify the missing components (e.g., Sequence Ontology, Ontology for Biomedical Investigations).

Analysis and mining tools for protozoan parasite research
Researchers have an increasing need to perform large or repetitive computational search and analysis tasks. The ITPPR project will create a Web-based graphical environment by modifying available open source software (Galaxy) to provide the tools most often needed by eukaryotic pathogen researchers in the form of Web services. This enhancement will allow access to all vertebrate genomes and associated data maintained in the UCSC Genome Browser, including several parasite hosts such as human, mouse and cow.  It will also empower researchers to automate large and/or repetitive search and analysis tasks via the Internet with no programming required.