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Abstract Background 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. Results We 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. Conclusion To 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.

Web news provides a quick and convenient means to create collections of large documents. The creation of a web news corpus has typically required the construction of a set of HTML parsing rules to identify content text. In general, these parsing rules are written manually and treat different web pages differently. We address this issue and propose a news content recognition algorithm that is language and layout independent. Our method first scans a given HTML document and roughly localizes a set of candidate news areas. Next, we apply a designed scoring function to rank the best content. To validate this approach, we evaluate the systems performance using 1092 items of multilingual web news data covering 17 global regions and 11 distinct languages. We compare these data with nine published content extraction systems using standard settings. The results of this empirical study show that our method outperforms the second-best approach (Boilerpipe) by 6.04 and 10.79 % with regard to the relative micro and macro F-measures, respectively. We also apply our system to monitor online RSS news distribution. It collected 0.4 million news articles from 200 RSS channels in 20 days. This sample quality test shows that our method achieved 93 % extraction accuracy for large news streams. [ABSTRACT FROM AUTHOR]

The primary biomedical literature is being generated at an unprecedented rate, and researchers cannot keep abreast of new developments in their fields. Biomedical natural language processing is being developed to address this issue, but building reliable systems often requires many expert-hours. We present an approach for automatically developing collections of regular expressions to drive high-performance concept recognition systems with minimal human interaction. We applied our approach to develop MutationFinder, a system for automatically extracting mentions of point mutations from the text. MutationFinder achieves performance equivalent to or better than manually developed mutation recognition systems, but the generation of its 759 patterns has required only 5.5 expert-hours. We also discuss the development and evaluation of our recently published high-quality, human-annotated gold standard corpus, which contains 1,515 complete point mutation mentions annotated in 813 abstracts. Both MutationFinder and the complete corpus are publicly available at . [ABSTRACT FROM AUTHOR]