- Article -
| In Silico Biology 9, 0016 (2009); ©2009, Bioinformation Systems e.V. |
PlasmoID: A P. falciparum protein information discovery tool
Aditya Rao*, Sri Jyothsna Yeleswarapu, Gudladona Raghavendra, Rajgopal Srinivasan and Gopalakrishnan Bulusu*
Life Sciences Division, TCS Innovation Labs Hyderabad, Tata Consultancy Services Ltd, 1 Software Units Layout, Madhapur, Hyderabad 500081, India
* Corresponding authors
Email: aditya@atc.tcs.com, gopal@atc.tcs.com
Edited by E. Wingender; received December 16, 2008; revised February 23 and April 13, 2009; accepted April 13, 2009; published July 12, 2009
Abstract
Plasmodium falciparum is the parasite responsible for more than 90% of deaths that occur due to malaria. Organization and mining of 'omic' (genomic, proteomic, transcriptomic, interactomic) data can improve our understanding of P. falciparum biology and help in the fight against malaria. PlasmoID (Plasmodium Information Discovery) is a tool developed for the dynamic exploration of the parasite's 'omic' landscape. Diverse computational and curated P. falciparum protein-protein interaction datasets, as well as binary relationships involving protein-small molecule entities, manually curated protein-protein relationships derived from the published literature and protein-protein interactions based on metabolic pathways are included in the PlasmoID database. The graphical user interface is designed as a plug-in to Cytoscape, an open-source network visualization tool. Important features of this plug-in include a synchronized tabular representation of any network loaded on the canvas, ability to find the shortest path between a pair of nodes in the database, search and expansion of entities from the database, and the ability to add new entities to the database through the interface. Malaria researchers can now seamlessly interrogate heterogeneous 'omic' datasets as well as add proprietary data to generate and visualize P. falciparum pathway and cell process network models. PlasmoID can be downloaded from http://pfalciparum.atc.tcs.com/PlasmoID.
Keywords: P. falciparum, malaria, systems biology, PlasmoID, interactome