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Developing a RadLex-Based Named Entity Recognition Tool for Mining Textual Radiology Reports: Development and
Shintaro Tsuji1,2, Andrew Wen1, Naoki Takahashi3
1Department of Health Sciences Research, Department of Radiology, Rochester, MN, United States.
Background:
Named entity recognition (NER) plays an important role in extracting the features of descriptions such as the name and location of a disease for mining free-text radiology reports. However, the performance of existing NER tools is limited because the number of entities that can be extracted depends on the dictionary lookup. In particular, the recognition of compound terms is very complicated because of the variety of patterns.
Objective:
The aim of this study is to develop and evaluate an NER tool concerned with compound terms using RadLex for mining free-text radiology reports.
Methods:
We leveraged the clinical Text Analysis and Knowledge Extraction System (cTAKES) to develop customized pipelines using both RadLex and SentiWordNet (a general purpose dictionary). We manually annotated 400 radiology reports for compound terms in noun phrases and used them as the gold standard for performance evaluation (precision, recall, and F-measure). In addition, we created a compound terms-enhanced dictionary (CtED) by analyzing false negatives and false positives and applied it to another 100 radiology reports for validation. We also evaluated the stem terms of compound terms by defining two measures: occurrence ratio (OR) and matching ratio (MR).
Results:
The F-measure of cTAKES+RadLex+general purpose dictionary was 30.9% (precision 73.3% and recall 19.6%) and that of the combined CtED was 63.1% (precision 82.8% and recall 51%). The OR indicated that the stem terms of effusion, node, tube, and disease were used frequently, but it still lacks capturing compound terms. The MR showed that 71.85% (9411/13,098) of the stem terms matched with that of the ontologies, and RadLex improved approximately 22% of the MR from the cTAKES default dictionary. The OR and MR revealed that the characteristics of stem terms would have the potential to help generate synonymous phrases using the ontologies.
Conclusions:
We developed a RadLex-based customized pipeline for parsing radiology reports and demonstrated that CtED and stem term analysis has the potential to improve dictionary-based NER performance with regard to expanding vocabularies.
