Abstract
BackgroundCardiovascular disease (CVD) has become the leading cause of death in China, and most of the cases can be prevented by controlling risk factors. The goal of this study was to build a corpus of CVD risk factor annotations based on Chinese electronic medical records (CEMRs). This corpus is intended to be used to develop a risk factor information extraction system that, in turn, can be applied as a foundation for the further study of the progress of risk factors and CVD.ResultsWe designed a light annotation task to capture CVD risk factors with indicators, temporal attributes and assertions that were explicitly or implicitly displayed in the records. The task included: 1) preparing data; 2) creating guidelines for capturing annotations (these were created with the help of clinicians); 3) proposing an annotation method including building the guidelines draft, training the annotators and updating the guidelines, and corpus construction. Meanwhile, we proposed some creative annotation guidelines: (1) the under-threshold medical examination values were annotated for our purpose of studying the progress of risk factors and CVD; (2) possible and negative risk factors were concerned for the same reason, and we created assertions for annotations; (3) we added four temporal attributes to CVD risk factors in CEMRs for constructing long term variations. Then, a risk factor annotated corpus based on de-identified discharge summaries and progress notes from 600 patients was developed. Built with the help of clinicians, this corpus has an inter-annotator agreement (IAA) F1-measure of 0.968, indicating a high reliability.ConclusionTo the best of our knowledge, this is the first annotated corpus concerning CVD risk factors in CEMRs and the guidelines for capturing CVD risk factor annotations from CEMRs were proposed. The obtained document-level annotations can be applied in future studies to monitor risk factors and CVD over the long term.
Highlights
Cardiovascular disease (CVD) has become the leading cause of death in China, and most of the cases can be prevented by controlling risk factors
We adopted some technologies from that task, and made some adjustments: (1) we proposed annotation guidelines of 12 CVD risk factors for the free text in Chinese electronic medical records (CEMRs) on the advices of medical experts; (2) positive, possible, negative information and under-threshold examination values form a part of one’s health condition and can be used to develop a long term supervision system, so these information were appended for our annotations; (3) for a long term monitoring, time information is critical, so we created temporal attributes for marking the occurrence time of risk factors in CEMRs
In consideration of building an information extraction (IE) system for automatically monitoring risk factors to avoid CVD, we developed a corpus of CVD risk factor annotations including indicators, temporal attributes and assertions based on CEMRs
Summary
Cardiovascular disease (CVD) has become the leading cause of death in China, and most of the cases can be prevented by controlling risk factors. The goal of this study was to build a corpus of CVD risk factor annotations based on Chinese electronic medical records (CEMRs). This corpus is intended to be used to develop a risk factor information extraction system that, in turn, can be applied as a foundation for the further study of the progress of risk factors and CVD. In 2010, the ministry of health in China published the basic norms of medical records writing [8] and the basic norms of electronic medical records [9], making these data more normative Together, these characteristics make CEMR an effective medium for studies that involve extracting CVD risk factors. We designed a task to extract CVD risk factors from CEMRs
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