GoPubMed: ontologybased literature search applied to Gene Ontology and PubMed

Abstract. The biomedical literature grows at a tremendous rate, so that find-ing the relevant literature is becoming more and more difficult. To address this problem we introduce ontology-based literature search, which structures search results thorugh the categories of an ontology. We develop and implement GoP-ubMed, which submits keywords to PubMed, extracts GeneOntology-terms from the retrieved abstracts, and presents the relevant sub-ontology for browsing. For GoPubMed we develop a novel term extraction algorithm and evaluate its perfor-mance. GoPubMed is available at www.gopubmed.or