GeneCite: a stand-alone open source tool for high-throughput literature and pathway mining.
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.
Hammamieh
Rasha
R
Walter Reed Army Institute of Research, Molecular Pathology, Silver Spring, Maryland 20910, USA.
Chakraborty
Nabarun
N
Wang
Yan
Y
Laing
Mark
M
Liu
Zaigang
Z
Mulligan
John
J
Jett
Marti
M
D019295:Computational Biology; D003628:Database Management Systems; D016247:Information Storage and Retrieval / Q000379:methods*; D012984:Software; D014584:User-Computer Interface