title: Extraction of biological interaction networks from scientific literature.
abstract: Biology can be regarded as a science of networks: interactions between various biological entities (eg genes, proteins, metabolites) on different levels (eg gene regulation, cell signalling) can be represented as graphs and, thus, analysis of such networks might shed new light on the function of biological systems. Such biological networks can be obtained from different sources. The extraction of networks from text is an important technique that requires the integration of several different computational disciplines. This paper summarises the most important steps in network extraction and reviews common approaches and solutions for the extraction of biological networks from scientific literature.
authors.affiliation: NRW International Graduate School in Bioinformatics and Genome Research, Bielefeld University, Postfach 10 01 31, D-33501 Bielefeld, Germany. askusa@cebitec.uni-bielefeld.de
authors.forename: Andre
authors.initials: A
authors.lastname: Skusa
authors.forename: Alexander
authors.initials: A
authors.lastname: Rüegg
authors.forename: Jacob
authors.initials: J
authors.lastname: Köhler
mesh_terms: D000043:Abstracting and Indexing / Q000379:methods; D000818:Animals; D001185:Artificial Intelligence; D001695:Biology / Q000379:methods; D002468:Cell Physiological Phenomena; D003628:Database Management Systems; D016206:Databases, Bibliographic; D004282:Documentation / Q000379:methods*; D005786:Gene Expression Regulation / Q000502:physiology*; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D008954:Models, Biological; D009323:Natural Language Processing; D010363:Pattern Recognition, Automated / Q000379:methods; D010506:Periodicals as Topic; D012586:Science / Q000379:methods; D015398:Signal Transduction / Q000502:physiology*; D009626:Terminology as Topic