ArticleJournal of the American Medical Informatics Association : JAMIA2017
Improving a full-text search engine: the importance of negation detection and family history context to identify cases in a biomedical data warehouse.
Article in Journal of the American Medical Informatics Association : JAMIA, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Integrating Health Care Data in an Informatics for Integrating Biology & the Bedside (i2b2) Model Persisted Through Elasticsearch: Design, Implementation, and Evaluation in a French University Hospital.JMIR medical informatics · 2025Article
- Navigating disruption in the PID landscape: embracing opportunities and anticipating threats in the next ten years.Frontiers in immunology · 2025Review
- Identification of Child Survivors of Sex Trafficking From Electronic Health Records: An Artificial Intelligence Guided Approach.Child maltreatment · 2024Article
- Validation of large language models for detecting pathologic complete response in breast cancer using population-based pathology reports.BMC medical informatics and decision making · 2024Article
- Clinical Information Retrieval: A Literature Review.Journal of healthcare informatics research · 2024Article
- Applying Natural Language Processing to Textual Data From Clinical Data Warehouses: Systematic Review.JMIR medical informatics · 2023Review
- "Unhappy triad" of the trauma elbow in children: Diagnosis, classification, and mid-term outcomes.Journal of children's orthopaedics · 2023Article
- CovAID: Identification of factors associated with severe COVID-19 in patients with inflammatory rheumatism or autoimmune diseases.Frontiers in medicine · 2023Article
- Evaluation of Doc'EDS: a French semantic search tool to query health documents from a clinical data warehouse.BMC medical informatics and decision making · 2022Article
- The prediction of hospital length of stay using unstructured data.BMC medical informatics and decision making · 2021Observational
- Common Arterial Trunk Associated with Functionally Univentricular Heart: Anatomical Study and Review of the Literature.Journal of cardiovascular development and disease · 2021Article
- Contextual property detection in Dutch diagnosis descriptions for uncertainty, laterality and temporality.BMC medical informatics and decision making · 2021Article
- Family History Extraction From Synthetic Clinical Narratives Using Natural Language Processing: Overview and Evaluation of a Challenge Data Set and Solutions for the 2019 National NLP Clinical Challenges (n2c2)/Open Health Natural Language Processing (OHNLP) Competition.JMIR medical informatics · 2021Article
- Natural Language Processing for Rapid Response to Emergent Diseases: Case Study of Calcium Channel Blockers and Hypertension in the COVID-19 Pandemic.Journal of medical Internet research · 2020Article
- The "salt and pepper" pattern on renal ultrasound in a group of children with molecular-proven diagnosis of ciliopathy-related renal diseases.Pediatric nephrology (Berlin, Germany) · 2020Article
- Natural Language Processing of Clinical Notes on Chronic Diseases: Systematic Review.JMIR medical informatics · 2019Review
- Replicating medication trend studies using ad hoc information extraction in a clinical data warehouse.BMC medical informatics and decision making · 2019Article
- Expanding the Diversity of Texts and Applications: Findings from the Section on Clinical Natural Language Processing of the International Medical Informatics Association Yearbook.Yearbook of medical informatics · 2018Review
- Next generation phenotyping using narrative reports in a rare disease clinical data warehouse.Orphanet journal of rare diseases · 2018Article
- Ad Hoc Information Extraction for Clinical Data Warehouses.Methods of information in medicine · 2018Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
objectiveThe repurposing of electronic health records (EHRs) can improve clinical and genetic research for rare diseases. However, significant information in rare disease EHRs is embedded in the narrative reports, which contain many negated clinical signs and family medical history. This paper presents a method to detect family history and negation in narrative reports and evaluates its impact on selecting populations from a clinical data warehouse (CDW). MATERIALS AND
methodsWe developed a pipeline to process 1.6 million reports from multiple sources. This pipeline is part of the load process of the Necker Hospital CDW.
resultsWe identified patients with "Lupus and diarrhea," "Crohn's and diabetes," and "NPHP1" from the CDW. The overall precision, recall, specificity, and F-measure were 0.85, 0.98, 0.93, and 0.91, respectively.
conclusionThe proposed method generates a highly accurate identification of cases from a CDW of rare disease EHRs.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.