We propose research on data-representation and integration tools to advance understanding of protozoan parasite genome biology. Many of these tools will also be useful for other pathogens and some will be useful for providing links to the host. In this proposal, we build on previous accomplishments with apicomplexan and functional genomic databases to attack critical problems that can be addressed through data integration and enhanced data processing. In order to make data integration possible for pathogen genome databases, algorithms and tools, we will develop the necessary semantics (ontologies) in the context of the Open Biomedical Ontologies (OBO) Foundry. We will also further develop WebProtigi to facilitate collaborative ontology building and integration of ontologies. Taking advantage of these semantics, we will develop new tools to facilitate research on protozoan and links to hosts (human, mouse and other vertebrates), by building upon Web services and the Galaxy open source platform to enable large-scale data analysis without dedicated software development.
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 proposed research will provide new frameworks and tools to facilitate data integration and computational mining of genomic-scale datasets.
| Bandrowski, Anita; Brinkman, Ryan; Brochhausen, Mathias et al. (2016) The Ontology for Biomedical Investigations. PLoS One 11:e0154556 |
| Zheng, Jie; Harris, Marcelline R; Masci, Anna Maria et al. (2016) The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis. J Biomed Semantics 7:53 |
| Zheng, Jie; Xiang, Zuoshuang; Stoeckert Jr, Christian J et al. (2014) Ontodog: a web-based ontology community view generation tool. Bioinformatics 30:1340-2 |
| Dugan, Vivien G; Emrich, Scott J; Giraldo-Calderón, Gloria I et al. (2014) Standardized metadata for human pathogen/vector genomic sequences. PLoS One 9:e99979 |
