European radiology · 2025
RADEX: a rule-based clinical and radiology data extraction tool demonstrated on thyroid ultrasound reports.
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Howell Lewis, Zarei Amir, Wah Tze Min, Chandler James H, Karthik Shishir, Court Zara, Ng Helen, McLaughlan James R
Аннотация
OBJECTIVES: Radiology reports contain valuable information for research and audits, but relevant details are often buried within free-text fields. This makes them challenging and time-consuming to extract for secondary analyses, including training artificial intelligence (AI) models.
MATERIALS AND METHODS: This study presents a rule-based RAdiology Data EXtraction tool (RADEX) to enable biomedical researchers and healthcare professionals to automate information extraction from clinical documents. RADEX simplifies the translation of domain expertise into regular-expression models, enabling context-dependent searching without specialist expertise in Natural Language Processing. Its utility was demonstrated in the multi-label classification of fourteen clinical features in a large retrospective dataset (n = 16,246) of thyroid ultrasound reports from five hospitals in the United Kingdom (UK). A tuning subset (n = 200) was used to iteratively develop the search strategy, and a holdout test subset (n = 202) was used to evaluate the performance against reference-standard labels.
RESULTS: The dataset cardinality was 3.06, and the label density was 0.34. Cohen's Kappa was 0.94 for rater 1 and 0.95 for rater 2. For RADEX, micro-average sensitivity, specificity, and F1-score were 0.97, 0.96, and 0.94, respectively. The processing time was 12.3 milliseconds per report, enabling fast and reliable information extraction.
CONCLUSION: RADEX is a versatile tool for bespoke research and audit applications, where access to labelled data or computing infrastructure is limited, or explainability and reproducibility are priorities. This offers a time-saving and freely available option to accelerate structured data collection, enabling new insights and improved patient care.
KEY POINTS: Question Radiology reports contain vital information that is buried in unstructured free-text fields. Can we extract this information effectively for research and audit applications? Findings A rule-based RAdiology Data Extraction tool (RADEX) is described and used to classify fourteen key findings from thyroid ultrasound reports with sensitivity and specificity > 0.95. Clinical relevance RADEX offers clinicians and researchers a time-saving tool to accelerate structured data collection. This practical approach prioritises transparency, repeatability, and usability, enabling new insights into improved patient care.
MATERIALS AND METHODS: This study presents a rule-based RAdiology Data EXtraction tool (RADEX) to enable biomedical researchers and healthcare professionals to automate information extraction from clinical documents. RADEX simplifies the translation of domain expertise into regular-expression models, enabling context-dependent searching without specialist expertise in Natural Language Processing. Its utility was demonstrated in the multi-label classification of fourteen clinical features in a large retrospective dataset (n = 16,246) of thyroid ultrasound reports from five hospitals in the United Kingdom (UK). A tuning subset (n = 200) was used to iteratively develop the search strategy, and a holdout test subset (n = 202) was used to evaluate the performance against reference-standard labels.
RESULTS: The dataset cardinality was 3.06, and the label density was 0.34. Cohen's Kappa was 0.94 for rater 1 and 0.95 for rater 2. For RADEX, micro-average sensitivity, specificity, and F1-score were 0.97, 0.96, and 0.94, respectively. The processing time was 12.3 milliseconds per report, enabling fast and reliable information extraction.
CONCLUSION: RADEX is a versatile tool for bespoke research and audit applications, where access to labelled data or computing infrastructure is limited, or explainability and reproducibility are priorities. This offers a time-saving and freely available option to accelerate structured data collection, enabling new insights and improved patient care.
KEY POINTS: Question Radiology reports contain vital information that is buried in unstructured free-text fields. Can we extract this information effectively for research and audit applications? Findings A rule-based RAdiology Data Extraction tool (RADEX) is described and used to classify fourteen key findings from thyroid ultrasound reports with sensitivity and specificity > 0.95. Clinical relevance RADEX offers clinicians and researchers a time-saving tool to accelerate structured data collection. This practical approach prioritises transparency, repeatability, and usability, enabling new insights into improved patient care.