Rao Aditya, Yeleswarapu Sri Jyothsna, Raghavendra Gudladona, Srinivasan Rajgopal, Bulusu Gopalakrishnan
Life Sciences Division, Tata Consultancy Services Ltd, Hyderabad 500081, India.
In Silico Biol. 2009;9(4):195-202.
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.
恶性疟原虫是导致90%以上疟疾死亡病例的寄生虫。对“组学”（基因组学、蛋白质组学、转录组学、相互作用组学）数据的整理和挖掘能够增进我们对恶性疟原虫生物学的理解，并有助于抗击疟疾。PlasmoID（疟原虫信息发现）是一款为动态探索疟原虫的“组学”格局而开发的工具。PlasmoID数据库包含了多种经过计算和整理的恶性疟原虫蛋白质-蛋白质相互作用数据集，以及涉及蛋白质-小分子实体的二元关系、从已发表文献中人工整理的蛋白质-蛋白质关系和基于代谢途径的蛋白质-蛋白质相互作用。其图形用户界面被设计为开源网络可视化工具Cytoscape的一个插件。该插件的重要功能包括对画布上加载的任何网络进行同步表格展示、在数据库中找到一对节点之间的最短路径、在数据库中搜索和扩展实体，以及通过该界面将新实体添加到数据库的能力。疟疾研究人员现在可以无缝查询异构的“组学”数据集，并添加专有数据来生成和可视化恶性疟原虫的代谢途径和细胞过程网络模型。PlasmoID可从http://pfalciparum.atc.tcs.com/PlasmoID下载。
