KID - an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information o

Background: The amount of available biological information is rapidly increasing and the focus of biological research has moved from single components to networks and even larger projects aiming at the analysis, modelling and simulation of biological networks as well as large scale comparison of cellular properties. It is therefore essential that biological knowledge is easily accessible. However, most information is contained in the written literature in an unstructured way, so that methods for the systematic extraction of knowledge directly from the primary literature have to be deployed. Description: Here we present a text mining algorithm for the extraction of kinetic information such as KM, Ki, kcat etc. as well as associated information such as enzyme names, EC numbers, ligands, organisms, localisations, pH and temperatures. Using this rule- and dictionary-based approach, it was possible to extract 514,394 kinetic parameters of 13 categories (KM, Ki, kcat, kcat/KM, Vmax, IC50, S...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Stephanie Heinen, Bernhard Thielen, Dietmar Schomburg
• Keywords: Available Biological Information, Biological, BMCBI 2010, Large Scale Comparison