Dataset Information

Meta-generalis: A novel method for structuring information from radiology reports.

ABSTRACT:

Background

A structured report for imaging exams aims at increasing the precision in information retrieval and communication between physicians. However, it is more concise than free text and may limit specialists' descriptions of important findings not covered by pre-defined structures. A computational ontological structure derived from free texts designed by specialists may be a solution for this problem. Therefore, the goal of our study was to develop a methodology for structuring information in radiology reports covering specifications required for the Brazilian Portuguese language, including the terminology to be used.

Methods

We gathered 1,701 radiological reports of magnetic resonance imaging (MRI) studies of the lumbosacral spine from three different institutions. Techniques of text mining and ontological conceptualization of lexical units extracted were used to structure information. Ten radiologists, specialists in lumbosacral MRI, evaluated the textual superstructure and terminology extracted using an electronic questionnaire.

Results

The established methodology consists of six steps: 1) collection of radiology reports of a specific MRI examination; 2) textual decomposition; 3) normalization of lexical units; 4) identification of textual superstructures; 5) conceptualization of candidate-terms; and 6) evaluation of superstructures and extracted terminology by experts using an electronic questionnaire. Three different textual superstructures were identified, with terminological variations in the names of their textual categories. The number of candidate-terms conceptualized was 4,183, yielding 727 concepts. There were a total of 13,963 relationships between candidate-terms and concepts and 789 relationships among concepts.

Conclusions

The proposed methodology allowed structuring information in a more intuitive and practical way. Indications of three textual superstructures, extraction of lexicon units and the normalization and ontologically conceptualization were achieved while maintaining references to their respective categories and free text radiology reports.

SUBMITTER: Barbosa F

PROVIDER: S-EPMC5052551 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature

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Publications

Meta-generalis: A novel method for structuring information from radiology reports.

Barbosa Flavio F Traina Agma Jucci AJ Muglia Valdair Francisco VF

Applied clinical informatics 20160824 3

<h4>Background</h4>A structured report for imaging exams aims at increasing the precision in information retrieval and communication between physicians. However, it is more concise than free text and may limit specialists' descriptions of important findings not covered by pre-defined structures. A computational ontological structure derived from free texts designed by specialists may be a solution for this problem. Therefore, the goal of our study was to develop a methodology for structuring inf ...[more]

PMID: 27580980

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Project description:ObjectivesTo provide insights for on-site development of transformer-based structuring of free-text report databases by investigating different labeling and pre-training strategies.MethodsA total of 93,368 German chest X-ray reports from 20,912 intensive care unit (ICU) patients were included. Two labeling strategies were investigated to tag six findings of the attending radiologist. First, a system based on human-defined rules was applied for annotation of all reports (termed "silver labels"). Second, 18,000 reports were manually annotated in 197 h (termed "gold labels") of which 10% were used for testing. An on-site pre-trained model (Tmlm) using masked-language modeling (MLM) was compared to a public, medically pre-trained model (Tmed). Both models were fine-tuned on silver labels only, gold labels only, and first with silver and then gold labels (hybrid training) for text classification, using varying numbers (N: 500, 1000, 2000, 3500, 7000, 14,580) of gold labels. Macro-averaged F1-scores (MAF1) in percent were calculated with 95% confidence intervals (CI).ResultsTmlm,gold (95.5 [94.5-96.3]) showed significantly higher MAF1 than Tmed,silver (75.0 [73.4-76.5]) and Tmlm,silver (75.2 [73.6-76.7]), but not significantly higher MAF1 than Tmed,gold (94.7 [93.6-95.6]), Tmed,hybrid (94.9 [93.9-95.8]), and Tmlm,hybrid (95.2 [94.3-96.0]). When using 7000 or less gold-labeled reports, Tmlm,gold (N: 7000, 94.7 [93.5-95.7]) showed significantly higher MAF1 than Tmed,gold (N: 7000, 91.5 [90.0-92.8]). With at least 2000 gold-labeled reports, utilizing silver labels did not lead to significant improvement of Tmlm,hybrid (N: 2000, 91.8 [90.4-93.2]) over Tmlm,gold (N: 2000, 91.4 [89.9-92.8]).ConclusionsCustom pre-training of transformers and fine-tuning on manual annotations promises to be an efficient strategy to unlock report databases for data-driven medicine.Key points• On-site development of natural language processing methods that retrospectively unlock free-text databases of radiology clinics for data-driven medicine is of great interest. • For clinics seeking to develop methods on-site for retrospective structuring of a report database of a certain department, it remains unclear which of previously proposed strategies for labeling reports and pre-training models is the most appropriate in context of, e.g., available annotator time. • Using a custom pre-trained transformer model, along with a little annotation effort, promises to be an efficient way to retrospectively structure radiological databases, even if not millions of reports are available for pre-training.

Project description:Traditional radiology reports are narrative texts that include a description of imaging findings. Recent implementation of advanced reporting software allows for incorporation of annotated key images and hyperlinks directly into text reports, but these tools usually do not substitute in-person consultations with radiologists, especially in challenging cases. Use of on-demand audio/visual reports with screen capture software is an emerging technology, providing a more engaged imaging service. Our study evaluates a video reporting tool that utilizes PACS integrated screen capture software for musculoskeletal imaging studies in the emergency department. Our hypothesis is that referring orthopedic surgeons would find that recorded audio/video reports add value to conventional reports, may increase engagement with radiology staff, and also facilitate understanding of imaging findings from urgent musculoskeletal cases. Seven radiologists prepared a total of 47 audiovisual reports for 9 attending orthopedic surgeons from the emergency department. We applied two surveys to evaluate the experience of the referring physicians using audio/visual reports as a complementary material from the conventional text report. Positive responses were statistically significant in most questions including: if the clinical suspicion was answered in the video; willingness to use such technology in other cases; if the audiovisual report made the imaging findings more understandable than the traditional report; and if the audiovisual report is faster to understand than the traditional text report. Use of audiovisual reports in emergency musculoskeletal cases is a new approach to evaluate potentially challenging cases. These results support the potential of this technology to re-establish the radiologist's role as an essential member of patient care and also provide more engaging, precise, and personalized reports. Further studies could streamline these methods in order to minimize work redundancy with traditional text reporting or even evaluate acceptance of using only audiovisual radiology reports. Additionally, widespread adoption would require integration with the entire radiology workflow including non-urgent cases and other medical specialties.

Dataset Information

Meta-generalis: A novel method for structuring information from radiology reports.

Background

Methods

Results

Conclusions

Publications

Meta-generalis: A novel method for structuring information from radiology reports.

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