CONAN: An integrative system for biomedical literature mining

Abstract

The amount of information about the genome, transcriptome and proteome, forms a problem for the scientific community: how to find the right information in a reasonable amount of time. Most research aiming to solve this problem, however, concentrate on a certain organism or a very limited dataset. Complementary to those algorithms, we developed CONAN, a system which provides a full-scale approach, tailored to experimentalists, designed to combine several information extraction methods and connect the outcome of these methods to gather novel information. Its methods include tagging of gene/protein names, finding interaction and mutation data, tagging of biological concepts, linking to MeSH and Gene Ontology terms, which can all be found back by querying the system. We present a full-scale approach that will ultimately cover all of PubMed/MEDLINE. We show that this universality has no effect on quality: our system performs as well as existing systems. © Springer-Verlag Berlin Heidelberg 2005.