title: Computational construction of specialized biological networks.
abstract: Today we have access to more than 1500 molecular database systems inside the internet. Based on these databases and information systems, computer scientists developed and implemented different methods for the automatic integration and prediction of biological networks. The idea is to use such methods for the automatic prediction and expansion of rudimentary molecular knowledge. However, the inherent data deficiency problem concerning the properties of specialized network hampers the database- and text-mining-based network construction. This paper presents the concept concerning the computational network expansion, namely for the specific biological network-thiol-disulfide redox regulatory network. Besides, a network-contexted document retrieval system (ncDocReSy) is also introduced to assist the network reduction by providing indirectly relevant literature for user's manual curation. NcDocReSy combines literature search with biological network and ranks the retrieved literature according to the network topology. NcDocReSy is implemented as a Cytoscape plugin.
authors: Bioinformatics/Medical Informatics Department, Bielefeld University, Bielefeld 33615, Germany. hangmaolee@gmail.com
authors: Hang-Mao
authors: HM
authors: Lee
authors: Karl-Josef
authors: KJ
authors: Dietz
authors: Ralf
authors: R
authors: Hofestädt
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D057225:Data Mining / Q000379:methods*; D008954:Models, Biological; D009323:Natural Language Processing; D010506:Periodicals as Topic; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*
chemical_list: D020543:Proteome