title: GeneCite: a stand-alone open source tool for high-throughput literature and pathway mining.
abstract: Systematic extraction of relevant biological facts from available massive scientific knowledge source is emerging as a significant task for the science community. Its success depends on several key factors, including the precision of a given search, the time of its accomplishment, and the communicative prowess of the mined information to the users. GeneCite - a stand-alone Java-based high-throughput data mining tool - is designed to carry out these tasks for several important knowledge sources simultaneously, allowing the users to integrate the results and interpret biological significance in a time-efficient manner. GeneCite provides an integrated high-throughput search platform serving as an information retrieval (IR) tool for probing online literature database (PubMed) and the sequence-tagged sites' database (UniSTS), respectively. It also operates as a data retrieval (DR) tool to mine an archive of biological pathways integrated into the software itself. Furthermore, GeneCite supports a retrieved data management system (DMS) showcasing the final output in a spread-sheet format. Each cell of the output file holds a real-time connection (hyperlink) to the given online archive reachable at the users' convenience. The software is free and currently available online www.bioinformatics.org; www.wrair.army.mil/Resources.
authors.affiliation: Walter Reed Army Institute of Research, Molecular Pathology, Silver Spring, Maryland 20910, USA.
authors.forename: Rasha
authors.initials: R
authors.lastname: Hammamieh
authors.forename: Nabarun
authors.initials: N
authors.lastname: Chakraborty
authors.forename: Yan
authors.initials: Y
authors.lastname: Wang
authors.forename: Mark
authors.initials: M
authors.lastname: Laing
authors.forename: Zaigang
authors.initials: Z
authors.lastname: Liu
authors.forename: John
authors.initials: J
authors.lastname: Mulligan
authors.forename: Marti
authors.initials: M
authors.lastname: Jett
mesh_terms: D019295:Computational Biology; D003628:Database Management Systems; D016247:Information Storage and Retrieval / Q000379:methods*; D012984:Software; D014584:User-Computer Interface