Bioinformatics Vol. 19 no. 3 2003
Pages 402-407
© 2003 Oxford University Press
Identification of key concepts in biomedical literature using a modified Markov heuristic
1 The Institute for Genomic Research, Rockville,
MD, 20850, USA
2 Human Genome Sciences, Rockville,
MD, 20850, USA
3 Howard Hughes Medical Institute, Berkeley,
CA, 94720, USa
Received on June 27, 2002
; revised on September 26, 2002
; accepted on September 29, 2002
Motivation: The recent explosion of interest in mining the biomedical literature for associations between defined entities such as genes, diseases and drugs has made apparent the need for robust methods of identifying occurrences of these entities in biomedical text. Such concept-based indexing is strongly dependent on the availability of a comprehensive ontology or lexicon of biomedical terms. However, such ontologies are very difficult and expensive to construct, and often require extensive manual curation to render them suitable for use by automatic indexing programs. Furthermore, the use of statistically salient noun phrases as surrogates for curated terminology is not without difficulties, due to the lack of high-quality part-of-speech taggers specific to medical nomenclature.
Results: We describe a method of improving the quality of automatically extracted noun phrases by employing prior knowledge during the HMM training procedure for the tagger. This enhancement, when combined with appropriate training data, can greatly improve the quality and relevance of the extracted phrases, thereby enabling greater accuracy in downstream literature mining tasks.
Contact: bmajoros{at}tigr.org