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Browsing by Subject "Information storage and retrieval"
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Item Annotation and Information Extraction of Consumer-Friendly Health Articles for Enhancing Laboratory Test Reporting(American Medical Informatics Association, 2024-01-11) He, Zhe; Tian, Shubo; Erdengasileng, Arslan; Hanna, Karim; Gong, Yang; Zhang, Zhan; Luo, Xiao; Lustria, Mia Liza A.; Engineering Technology, Purdue School of Engineering and TechnologyViewing laboratory test results is patients' most frequent activity when accessing patient portals, but lab results can be very confusing for patients. Previous research has explored various ways to present lab results, but few have attempted to provide tailored information support based on individual patient's medical context. In this study, we collected and annotated interpretations of textual lab result in 251 health articles about laboratory tests from AHealthyMe.com. Then we evaluated transformer-based language models including BioBERT, ClinicalBERT, RoBERTa, and PubMedBERT for recognizing key terms and their types. Using BioPortal's term search API, we mapped the annotated terms to concepts in major controlled terminologies. Results showed that PubMedBERT achieved the best F1 on both strict and lenient matching criteria. SNOMED CT had the best coverage of the terms, followed by LOINC and ICD-10-CM. This work lays the foundation for enhancing the presentation of lab results in patient portals by providing patients with contextualized interpretations of their lab results and individualized question prompts that they can, in turn, refer to during physician consults.Item Metrics Toolkit: an online evidence-based resource for navigating the research metrics landscape(Medical Library Association, 2018-10) Champieux, Robin; Coates, Heather L.; Konkiel, Stacy; Gutzman, Karen; University LibraryWhile research metrics may seem well established in the scholarly landscape, it can be challenging to understand how they should be used and how they are calculated. The Metrics Toolkit is an online evidence-based resource for researchers, librarians, evaluators, and administrators in their work to demonstrate or assess the impact of research.Item Preparing a collection of radiology examinations for distribution and retrieval(Oxford University Press, 2016-03) Demner-Fushman, Dina; Kohli, Marc D.; Rosenman, Marc B.; Shooshan, Sonya E.; Rodriguez, Laritza; Antani, Sameer; Thoma, George R.; McDonald, Clement J.; Department of Radiology and Imaging Sciences, IU School of MedicineOBJECTIVE: Clinical documents made available for secondary use play an increasingly important role in discovery of clinical knowledge, development of research methods, and education. An important step in facilitating secondary use of clinical document collections is easy access to descriptions and samples that represent the content of the collections. This paper presents an approach to developing a collection of radiology examinations, including both the images and radiologist narrative reports, and making them publicly available in a searchable database. MATERIALS AND METHODS: The authors collected 3996 radiology reports from the Indiana Network for Patient Care and 8121 associated images from the hospitals' picture archiving systems. The images and reports were de-identified automatically and then the automatic de-identification was manually verified. The authors coded the key findings of the reports and empirically assessed the benefits of manual coding on retrieval. RESULTS: The automatic de-identification of the narrative was aggressive and achieved 100% precision at the cost of rendering a few findings uninterpretable. Automatic de-identification of images was not quite as perfect. Images for two of 3996 patients (0.05%) showed protected health information. Manual encoding of findings improved retrieval precision. CONCLUSION: Stringent de-identification methods can remove all identifiers from text radiology reports. DICOM de-identification of images does not remove all identifying information and needs special attention to images scanned from film. Adding manual coding to the radiologist narrative reports significantly improved relevancy of the retrieved clinical documents. The de-identified Indiana chest X-ray collection is available for searching and downloading from the National Library of Medicine (http://openi.nlm.nih.gov/).