Send to

Choose Destination
See comment in PubMed Commons below
J Am Med Inform Assoc. 2011 Sep-Oct;18(5):574-9. doi: 10.1136/amiajnl-2011-000302. Epub 2011 Jul 7.

A knowledge discovery and reuse pipeline for information extraction in clinical notes.

Author information

School of IT, The University of Sydney, Sydney, Australia.



Information extraction and classification of clinical data are current challenges in natural language processing. This paper presents a cascaded method to deal with three different extractions and classifications in clinical data: concept annotation, assertion classification and relation classification.


A pipeline system was developed for clinical natural language processing that includes a proofreading process, with gold-standard reflexive validation and correction. The information extraction system is a combination of a machine learning approach and a rule-based approach. The outputs of this system are used for evaluation in all three tiers of the fourth i2b2/VA shared-task and workshop challenge.


Overall concept classification attained an F-score of 83.3% against a baseline of 77.0%, the optimal F-score for assertions about the concepts was 92.4% and relation classifier attained 72.6% for relationships between clinical concepts against a baseline of 71.0%. Micro-average results for the challenge test set were 81.79%, 91.90% and 70.18%, respectively.


The challenge in the multi-task test requires a distribution of time and work load for each individual task so that the overall performance evaluation on all three tasks would be more informative rather than treating each task assessment as independent. The simplicity of the model developed in this work should be contrasted with the very large feature space of other participants in the challenge who only achieved slightly better performance. There is a need to charge a penalty against the complexity of a model as defined in message minimalisation theory when comparing results.


A complete pipeline system for constructing language processing models that can be used to process multiple practical detection tasks of language structures of clinical records is presented.

[Indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Silverchair Information Systems Icon for PubMed Central
    Loading ...
    Support Center