Difference between revisions of "Trykipedia"

Trykipedia is a Wiki-based resource for the ontologies and other tools being created as a part of the NIH funded project, "The Semantics and Services enabled Problem Solving Environment for Trypanosoma cruzi." This project aims to utilize state-of-the-art semantic technologies for effective querying of multiple databases through creation of a suite of ontologies modeling multiple aspects of T. cruzi research domain. As a part of the project, two ontologies have been created, namely Ontology for Parasite Life Cycle (OPL) and Parasite Experiment Ontology (PEO). One of the objectives of the project was to create a platform for Life cycle and Experiment ontologies for T. cruzi that can later be extended for other human parasites with community collaborations. We are currently working with the Sanger Instiute (UK) to extend PLO with Plasmodium sp. and other human parasites.

• Trykipedia - Wiki based resource
• Parasite Experiment ontology - Ontology that models experimental conditions and results
• Ontology for Parasite Life Cycle - Ontology that models all the lifecycle stages of various kinetoplastids
• Provenir Ontology - Upper level provenance ontology
• Cuebee - Graphical semantic query interface
• AskCuebe - Facilitate making query with Natural language
• kino -An integrated tools to annotate and search documents such as scientific literature, academic articles and XML files.
• OPTIMA - An ontology alignment tool
• OntoCAT - Dynamic form creation through an ontology
• iExplore - Graphical interactive exploration tool

Parasitic Trypanosoma brucei surrounded by red blood cells in a smear of infected blood. (Copyright: Jürgen Berger and Dr. Peter Overath, Max Planck Institute for Developmental Biology, Tübingen.)

Trypanosoma cruzi is a protozoan parasite and a relative of other human pathogens that cause African sleeping sickness and leishmaniasis. Approximately 18 million people in Latin America are infected with this parasite, and as many as 40% of these are predicted to eventually suffer from Chagas disease, which is the leading cause of heart disease and sudden death in middle-aged adults in the region. Currently, there is a single manufactured drug for treatment of the infection; but this drug has severe side effects and is also carcinogenic. Diagnosis of the infection is poor and there are no vaccines for prevention of the infection. Moreover, T. cruzi presents a level of complexity that, though not unique, is substantial.

Research in many biological systems, particularly those involving infectious agents, continues to experience an enormous increase in information with the sequencing of genomes, the use of expression profiling, and the completion of proteomic analyses. For example, annotated genomes and comparative analyses of two T. cruzi related kinetoplastids, Trypanosoma brucei and Leishmania major, and a whole organism (all life-cycle stages) proteome analysis of T. cruzi have been published. Data from other sequencing projects in T. cruzi, including ESTs, preexisting and ongoing expression profiling (DNA microarray) and proteome analyses are also available. These dynamic datasets, addressing different but logically related aspects, are distributed over multiple databases that undergo frequent additions and curation. It is difficult to integrate these datasets manually from multiple sources. Therefore, we propose to use ontology-driven technology to integrate local and external datasets to answer biological questions at mulitple level of granularity. Project Page

• Parasite Experiment ontology - Ontology that models experimental conditions and results
• Ontology for Parasite Life Cycle - Ontology that models all the lifecycle stages of various kinetoplastids
• Provenir Ontology - Upper level provenance ontology
• Publications - conference and journal publications generated from this research
• People - people who are involved in this research
• Manuscript Details - A Semantic Problem Solving Environment for Integrative Parasite Research: Identification of Intervention Targets for Trypanosoma cruzi.

• Kno.e.sis Center, Wright State University
• Tarleton Research Group, Center for Tropical and Emerging Global Diseases(CTEGD), University of Georgia
• Intelligent Thought and Action Lab, THINC Lab, University of Georgia
• National Center for Biological Ontologies, NCBO, Stanford University
• The Wellcome Trust Sanger Institute, Cambridge, UK
• The Oswaldo Cruz Institute (Fiocruz), Brazil

We invite new members to collaborate with us in extending Parasite Life cycle Ontology (PLO) and/or Parasite Experiment Ontology (PEO).

• Cuebee
  • Manuscript Query 1 with Cuebee
  • Manuscript Query 2 with Cuebee
  • Manuscript Query 3 with Cuebee
• How to use iExplore
• kino Video Demonstration

This research is part of project: "Semantics and Services enabled Problem Solving Environment for Tcruzi," a collaborative R01 grant 1R01HL087795-01A1 funded by National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), 05/2008 - 03/2013. Principal Investigator : Amit Sheth Kno.e.sis Center, Wright State University.