Semantics and Services Enabled Problem Solving Environment for Trypanosoma cruzi

Amit Sheth, Satya Sahoo, Priti Parikh
Kno.e.sis Center, Wright State University


Link to Webinar recording:


The Trypanosoma Cruzi Semantic Problem Solving Environment (SPSE) is a collaborative bioinformatics research project involving researchers at the Kno.e.sis Center, Wright State University, the Tarleton Research Group at CTEGD, University of Georgia, and the National Center for Biomedical Ontologies (NCBO) at Stanford University. The primary objective of the project is to create an ontology-driven integrated environment to facilitate identification of vaccine, diagnostic, and chemotherapeutic targets in the human pathogen T.cruzi. T.cruzi is a protozoan parasite that causes American trypanosomiasis or Chagas disease, which is the leading cause of heart disease and sudden death in middle-aged adults in Latin America.. Approximately 18 million people in Latin America are infected with this parasite.

This presentation will cover the following subset of activities being carried out in the project:
1.    Creation of a Parasite Knowledge Repository (PKR):  The PKR aims to support complex biological queries related to T.cruzi vaccination or gene knockout targets over a variety of datasets including experiment data, structured data from external databases, and biomedical literature. The PKR is supported by two ontologies namely, (1) the Parasite Experiment ontology (PEO) that models gene knockout, strain creation, proteomics, and microarray experiment details, and (2) the Parasite Lifecycle ontology (PLO) to model the life cycle stages of T.cruzi, Trypanosoma Brucei, and Leishmania major. In addition, collaborations have been initiated with the Welcome Trust Sanger Institute (UK) and Oswaldo Cruz Institute (Fiocruz, Brazil) to model the lifecycle stages of Plasmodium, Schistosoma mansoni, and other kinetoplastids that have high significance to the parasite research community. The PKR is being populated with experiment datasets generated by our biology collaborators at the Tarleton Research Group (TRG) covering gene knockout, strain creation, proteomics, and microarray experiments.

2.    Trykipedia: Trykipedia is a Wiki-based discussion and dissemination platform for the parasite community and includes multi-media resource pages for each entities represented in the PKR that facilitates understanding and use by the parasite research community. Trykipedia includes descriptive texts along with images as part of the resource page for each entity.

3.    A Provenance Management Framework (PKR) for scientific data: Provenance is critical information in scientific applications to verify experiment process, validate data quality and associate trust values with scientific results. A coherent integration of the disparate datasets in T.cruzi SPSE requires the analysis of the associated provenance metadata. To achieve this objective a provenance management infrastructure called T.cruzi provenance system (TPS) is being implemented that addresses the (a) capture, (b) modeling, (c) storage, and (d) querying aspects of provenance management in T.cruzi SPSE. The TPS is an implementation of a generic framework for provenance that includes the provenir upper level provenance ontology, which facilitates provenance interoperability, a set of provenance query operators implemented in a query engine over a RDF database. Similar to the PKR, the TPS uses the PEO as a domain-specific provenance ontology. The presentation will include a brief discussion of provenance query execution over TRG laboratory datasets using the provenance query operator.