Automatically extracting information needs from complex clinical questions

J Biomed Inform. 2010 Dec;43(6):962-71. doi: 10.1016/j.jbi.2010.07.007. Epub 2010 Jul 27.


Objective: Clinicians pose complex clinical questions when seeing patients, and identifying the answers to those questions in a timely manner helps improve the quality of patient care. We report here on two natural language processing models, namely, automatic topic assignment and keyword identification, that together automatically and effectively extract information needs from ad hoc clinical questions. Our study is motivated in the context of developing the larger clinical question answering system AskHERMES (Help clinicians to Extract and aRrticulate Multimedia information for answering clinical quEstionS).

Design and measurements: We developed supervised machine-learning systems to automatically assign predefined general categories (e.g. etiology, procedure, and diagnosis) to a question. We also explored both supervised and unsupervised systems to automatically identify keywords that capture the main content of the question.

Results: We evaluated our systems on 4654 annotated clinical questions that were collected in practice. We achieved an F1 score of 76.0% for the task of general topic classification and 58.0% for keyword extraction. Our systems have been implemented into the larger question answering system AskHERMES. Our error analyses suggested that inconsistent annotation in our training data have hurt both question analysis tasks.

Conclusion: Our systems, available at, can automatically extract information needs from both short (the number of word tokens <20) and long questions (the number of word tokens >20), and from both well-structured and ill-formed questions. We speculate that the performance of general topic classification and keyword extraction can be further improved if consistently annotated data are made available.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms*
  • Artificial Intelligence
  • Databases, Factual
  • Information Storage and Retrieval / methods*
  • Natural Language Processing