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- Title
FindZebra online search delving into rare disease case reports using natural language processing.
- Authors
Liévin, Valentin; Hansen, Jonas Meinertz; Lund, Allan; Elstein, Deborah; Matthiesen, Mads Emil; Elomaa, Kaisa; Zarakowska, Kaja; Himmelhan, Iris; Botha, Jaco; Borgeskov, Hanne; Winther, Ole
- Abstract
Early diagnosis is crucial for well-being and life quality of the rare disease patient. Access to the most complete knowledge about diseases through intelligent user interfaces can play an important role in supporting the physician reaching the correct diagnosis. Case reports may offer information about heterogeneous phenotypes which often further complicate rare disease diagnosis. The rare disease search engine FindZebra.com is extended to also access case report abstracts extracted from PubMed for several diseases. A search index for each disease is built in Apache Solr adding age, sex and clinical features extracted using text segmentation to enhance the specificity of search. Clinical experts performed retrospective validation of the search engine, utilising real-world Outcomes Survey data on Gaucher and Fabry patients. Medical experts evaluated the search results as being clinically relevant for the Fabry patients and less clinically relevant for the Gaucher patients. The shortcomings for Gaucher patients mainly reflect a mismatch between the current understanding and treatment of the disease and how it is reported in PubMed, notably in the older case reports. In response to this observation, a filter for the publication date was added in the final version of the tool available from deep.findzebra.com/<disease> with <disease> = gaucher, fabry, hae (Hereditary angioedema). Author summary: Rare diseases affect a substantial part of the population. However, they are especially challenging to diagnose. Because of their rarity, physicians often ignore rare diseases in the differential diagnosis. When confronted with hard-to-diagnose patients, physicians often turn to online resources like Google or PubMed, which index both general disease information as well as case reports. Case reports are a unique asset in helping the diagnosis of rare diseases because they often present with a varied and complex phenotype, which might not appear in the general literature. Nonetheless, searching for patient-relevant case reports is challenging. A tool dedicated to searching case reports assisting diagnosis is still missing because general-purpose search engines, like PubMed search, are primarily set up for literature search and because advanced search tools like FindZebra do not handle case reports. In this study, we present a novel online search tool https://deep.findzebra.com/ dedicated to searching PubMed case reports based on a patient description (age, sex, symptoms, negative findings, etc.). Two medical experts evaluated the tool on forty challenging cases (twenty Fabry and twenty Gaucher). To our knowledge, this is the first specialized search tool for case reports that is built to assist diagnosis. This study provides a clear recipe for building and validating modern medical information retrieval systems to index and search complex and heterogeneous data.
- Subjects
ONLINE information services; INTERNET; NATURAL language processing; SEARCH engines; CASE studies; RESEARCH funding; MEDLINE; RARE diseases
- Publication
PLoS Digital Health, 2023, Vol 1, Issue 6, p1
- ISSN
2767-3170
- Publication type
Article
- DOI
10.1371/journal.pdig.0000269