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.

Public Health Relevance

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.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM093132-03
Application #
8247691
Study Section
Biodata Management and Analysis Study Section (BDMA)
Program Officer
Brazhnik, Paul
Project Start
2010-04-01
Project End
2014-03-31
Budget Start
2012-04-01
Budget End
2014-03-31
Support Year
3
Fiscal Year
2012
Total Cost
$357,775
Indirect Cost
$47,806
Name
University of Pennsylvania
Department
Genetics
Type
Schools of Medicine
DUNS #
042250712
City
Philadelphia
State
PA
Country
United States
Zip Code
19104
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