LITSEEK: public health literature search by metadata enhancement with external knowledge bases

Abstract

Biomedical literature is an important source of information in any researcher's investigation of genes, risk factors, diseases and drugs. Often the information searched by public health researchers is distributed across multiple disparate sources that may include publications from PubMed, genomic, proteomic and pathway databases, gene expression and clinical resources and biomedical ontologies. The unstructured nature of this information makes it difficult to find relevant parts from it manually and comprehensive knowledge is further difficult to synthesize automatically. In this paper we report on LITSEEK (LITerature Search by metadata Enhancement with External Knowledgebases), a system we have developed for the benefit of researchers at the Centers for Disease Control (CDC) to enable them to search the HuGE (Human Genome for Epidemiology) database of PubMed articles, from a pharmacogenomic perspective. Besides analyzing text using TFIDF ranking and indexing of the important terms, the proposed system incorporates an automatic consultation with PharmGKB - a human-curated knowledge base about drugs, related diseases and genes, as well as with the Gene Ontology, a human-curated, well accepted ontology. We highlight the main components of our approach and illustrate how the search is enhanced by incorporating additional concepts in terms of genes/drugs/diseases (called metadata for ease of reference) from PharmGKB. Various measurements are reported with respect to the addition of these metadata terms. Preliminary results in terms of precision based on expert user feedback from CDC are encouraging. Further evaluation of the search procedure by actual researchers is under way.