Biomedical Ontologies for Parasite Research

TitleBiomedical Ontologies for Parasite Research
Publication TypeConference Paper
Year of Publication2010
AuthorsVinh Nguyen, Satya S. Sahoo, Priti Parikh, Todd Minning, D. Brent Weatherly, Flora Logan, Amit Sheth, Rick Tarleton
Conference NameIntelligent System for Molecular Biology (ISMB)
PublisherIntelligent System for Molecular Biology (ISMB)
Conference LocationBoston, MA
KeywordsOntology and Parasite
Abstract

Trypanosoma cruzi is a protozoan parasite that causes Chagas disease or American trypanosomiasis,which is the leading cause of death in Latin America. The primary objective of this study is to create an ontology-driven information infrastructure to support parasite researchers in identifying gene knockout, vaccination, or drug targets for T. cruzi. This involves querying across multiple datasets from diverse sources, such as proteome, pathway, internal lab data, etc. that are often represented in heterogeneous formats. To address this, a multi-ontology parasite knowledge repository (PKR) is being created with an intuitive graphical query interface called Cuebee. The PKR is underpinned by the Parasite Lifecycle Ontology (PLO) and Parasite Experiment Ontology (PEO) that has been released for public use through National Center for Biomedical Ontology (NCBO). The PLO models lifecycle stages of T. cruzi and two related kintoplastids, T. brucei and Leishmania major. It also describes the host, parasitic, and vector organisms, and anatomical location corresponding to each stage. On the other hand, the PEO models gene knockout, strain creation, proteomics, and microarray data. All the entities in PLO and PEO are linked to each other by explicitly modeled named relationships; for example, 'Trypanosoma_cruzi->has_vector_organism->triatominae.' Both PLO and PEO are used as schema to semantically annotate the experimental data and transform them into semantic web Resource Description Framework (RDF) format. PLO and PEO along with Cuebee interface will allow biologists to formulate queries over multiple data sources to find gene knockout, vaccination, or drug targets for T. cruzi and related parasites

Full Text

Vinh Nguyen, Satya Sahoo, Priti Parikh, Todd Minning, Brent Weatherly, Flora Logan, Amit Sheth, Rick Tarleton, 'Biomedical Ontologies for Parasite Research', ISMB, Boston, 11-13 July 2010.
project: Tcruzi
year: 2010
related resource url: http://knoesis.wright.edu/library/download/ISMB_Abstract_Final.pdf
venue name: Intelligent System for Molecular Biology (ISMB)
hasURL: http://knoesis.wright.edu/library/download/ismb_2010_Vinh.pdf

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