Identification of key concepts in biomedical literature using a modified Markov heuristic.
BACKGROUND
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.
Majoros
W H
WH
The Institute for Genomic Research, Rockville, MD 20850, USA. bmajoros@tigr.org
Subramanian
G M
GM
Yandell
M D
MD
D000043:Abstracting and Indexing / Q000379:methods*; D000465:Algorithms; D003628:Database Management Systems; D016247:Information Storage and Retrieval / Q000379:methods*; D016239:MEDLINE; D008390:Markov Chains; D015233:Models, Statistical; D009323:Natural Language Processing; D010363:Pattern Recognition, Automated; D017432:Unified Medical Language System