Building a semantically annotated corpus of clinical texts

In this paper, we describe the construction of a semantically annotated corpus of clinical texts for use in the development and evaluation of systems for automatically extracting clinically significant information from the textual component of patient records. The paper details the sampling of textu...

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Bibliographic Details
Published in:Journal of biomedical informatics 2009-10, Vol.42 (5), p.950-966
Main Authors: Roberts, Angus, Gaizauskas, Robert, Hepple, Mark, Demetriou, George, Guo, Yikun, Roberts, Ian, Setzer, Andrea
Format: Article
Language:English
Subjects:
Abstracting and Indexing as Topic
Annotation guidelines
Biomedical Research
Clinical text
Corpora
Evaluation
Gold standards
Guidelines as Topic
Humans
Information extraction
Information Storage and Retrieval - methods
Internet
Medical Records
Models, Statistical
Natural Language Processing
Neoplasms
Semantic annotation
Semantics
Temporal annotation
Terminology as Topic
Text mining
User-Computer Interface
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Summary:In this paper, we describe the construction of a semantically annotated corpus of clinical texts for use in the development and evaluation of systems for automatically extracting clinically significant information from the textual component of patient records. The paper details the sampling of textual material from a collection of 20,000 cancer patient records, the development of a semantic annotation scheme, the annotation methodology, the distribution of annotations in the final corpus, and the use of the corpus for development of an adaptive information extraction system. The resulting corpus is the most richly semantically annotated resource for clinical text processing built to date, whose value has been demonstrated through its use in developing an effective information extraction system. The detailed presentation of our corpus construction and annotation methodology will be of value to others seeking to build high-quality semantically annotated corpora in biomedical domains.
ISSN:1532-0464
1532-0480
DOI:10.1016/j.jbi.2008.12.013