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 Parasite Lifecycle Ontology (PLO) 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 latter 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.
- Kno.e.sis Center, Wright State University
- Tarleton Research Group, Center for Tropical and Emerging Global Diseases(CTEGD), University of Georgia
- Large Scale Distributed Information Systems, LSDIS 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).
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 muliple 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 Life cycle Ontology (PLO)
The PLO models the lifecycle stage details of T. cruzi and two related kinetoplastids, T. brucei and Leishmania major. In addition to lifecycle stages, the ontology also models necessary contextual details such as host information, vector information, strain and, anatomical location. We are currently working on extending PLO with other human parasites; such as Plasmodium, Schistosoma, and other kinetoplastids.
Parasite Experiment Ontology (PEO)
The PEO models the transcriptome and gene-knockout phases of T. cruzi experiment protocols. The ontology comprehensively models the processes, instruments, parameters, and sample details that will be used to annotate experimental results with “provenance” metadata (derivation history of results).
1. S. S. Sahoo, D.B. Weatherly, R. Mutharaju, P. Anantharam, A. Sheth, R.L. Tarleton, “Ontology-driven Provenance Management in eScience: an Application in Parasite Research”, The 8th International Conference on Ontologies, DataBases, and Applications of Semantics, (ODBASE 2009), Vilamoura, Algarve-Portugal, Nov 02 - 04, 2009.
2. S. S. Sahoo, A. Sheth, “Provenir ontology: Towards a Framework for eScience Provenance Management”, Microsoft eScience Workshop, Pittsburgh, PA Oct 15-17, 2009.
3. Prashant Doshi, Ravikanth Kolli, Christopher Thomas, Inexact matching of ontology graphs using expectation-maximization, Journal of Web Semantics: Science, Services and Agents on the World Wide Web, In Press 29 January 2009, ISSN 1570-8268, DOI: 10.1016/j.websem.2008.12.001.
4. Amit Sheth , Rick Tarleton , Prashant Doshi , Mark Musen , Natasha Noy , Satya S. Sahoo , D. B. Weatherly , Pablo N. Mendes, “Collaborative RO1 with NCBO Semantics and Services Enabled Problem Solving Environment For Trypanosoma Cruzi”, NCBC-AHM08, poster link
5. Satya S. Sahoo, Roger S. Barga, Jonathan Goldstein, Amit Sheth, "Provenance Algebra and Materialized View-based Provenance Management, Microsoft Research Technical Report, (MSR-TR-2008-170) November 2008 link
- Berriman M, G.E., Hertz-Fowler C, Blandin G, Renauld H, Bartholomeu DC, Lennard NJ, Caler E, Hamlin NE, Haas B, Bohme U, Hannick L, Aslett MA, Shallom J, Marcello L, Hou L, Wickstead B, Alsmark UC, Arrowsmith C, Atkin RJ, Barron AJ, Bringaud F, Brooks K, Carrington M, Cherevach I, Chillingworth TJ, Churcher C, Clark LN, Corton CH, Cronin A, Davies RM, Doggett J, Djikeng A, Feldblyum T, Field MC, Fraser A, Goodhead I, Hance Z, Harper D, Harris BR, Hauser H, Hostetler J, Ivens A, Jagels K, Johnson D, Johnson J, Jones K, Kerhornou AX, Koo H, Larke N, Landfear S, Larkin C, Leech V, Line A, Lord A, Macleod A, Mooney PJ, Moule S, Martin DM, Morgan GW, Mungall K, Norbertczak H, Ormond D, Pai G, Peacock CS, Peterson J, Quail MA, Rabbinowitsch E, Rajandream MA, Reitter C, Salzberg SL, Sanders M, Schobel S, Sharp S, Simmonds M, Simpson AJ, Tallon L, Turner CM, Tait A, Tivey AR, Van Aken S, Walker D, Wanless D, Wang S, White B, White O, Whitehead S, Woodward J, Wortman J, Adams MD, Embley TM, Gull K, Ullu E, Barry JD, Fairlamb AH, Opperdoes F, Barrell BG, Donelson JE, Hall N, Fraser CM, Melville SE, El-Sayed NM., The genome of the African trypanosome Trypanosoma brucei. Science, 2005 Jul 15. 309(5733): p. 416-22.
- Ivens AC, P.C., Worthey EA, Murphy L, Aggarwal G, Berriman M, Sisk E, Rajandream MA, Adlem E, Aert R, Anupama A, Apostolou Z, Attipoe P, Bason N, Bauser C, Beck A, Beverley SM, Bianchettin G, Borzym K, Bothe G, Bruschi CV, Collins M, Cadag E, Ciarloni L, Clayton C, Coulson RM, Cronin A, Cruz AK, Davies RM, De Gaudenzi J, Dobson DE, Duesterhoeft A, Fazelina G, Fosker N, Frasch AC, Fraser A, Fuchs M, Gabel C, Goble A, Goffeau A, Harris D, Hertz-Fowler C, Hilbert H, Horn D, Huang Y, Klages S, Knights A, Kube M, Larke N, Litvin L, Lord A, Louie T, Marra M, Masuy D, Matthews K, Michaeli S, Mottram JC, Muller-Auer S, Munden H, Nelson S, Norbertczak H, Oliver K, O'neil S, Pentony M, Pohl TM, Price C, Purnelle B, Quail MA, Rabbinowitsch E, Reinhardt R, Rieger M, Rinta J, Robben J, Robertson L, Ruiz JC, Rutter S, Saunders D, Schafer M, Schein J, Schwartz DC, Seeger K, Seyler A, Sharp S, Shin H, Sivam D, Squares R, Squares S, Tosato V, Vogt C, Volckaert G, Wambutt R, Warren T, Wedler H, Woodward J, Zhou S, Zimmermann W, Smith DF, Blackwell JM, Stuart KD, Barrell B, Myler PJ., The genome of the kinetoplastid parasite, Leishmania major. Science, 2005 Jul 15. 309(5733): p. 436-42.
- Atwood, J.A., et al., The Trypanosoma cruzi Proteome, in Science 2005. p. 473 – 476.
- Agüero F, Z.W., Weatherly DB, Mendes P, Kissinger JC, TcruziDB: an integrated, postgenomics community resource for Trypanosoma cruzi. Nucleic Acids Research, Jan 1 2006. 34(Database issue): p. D428-31.
- Minning TA, B.J., Garcia GA, McGraw RA, Tarleton RL, Microarray profiling of gene expression during trypomastigote to amastigote transition in Trypanosoma cruzi. Mol Biochem Parasitol., 2003 Sep. 131(1): p. 55-64.