Semantics and Services enabled Problem Solving Environment for T. cruzi

Introduction

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. br/ br/ 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 ref 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. /ref and Leishmania major ref 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. /ref , and a whole organism (all life-cycle stages) proteome analysis of T. cruzi have been published ref Atwood, J.A., et al., The Trypanosoma cruzi Proteome, in Science 2005. p. 473 – 476. /ref . Data from other sequencing projects in T. cruzi, including ESTs ref 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. /ref , preexisting and ongoing expression profiling (DNA microarray ref 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. /ref ) 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. br/ br/ The Semantics and Services enabled Problem Solving Environment for T. cruzi 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. Trykipedia is a Wiki-based resource for the ontologies being created as part of this project: br/ br/

Provenance ontology for Transcriptome and Gene Knockout Experiment

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