ArticleJournal of the American Medical Informatics Association : JAMIA2019
Development and application of a high throughput natural language processing architecture to convert all clinical documents in a clinical data warehouse into standardized medical vocabularies.
Article in Journal of the American Medical Informatics Association : JAMIA, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
18 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Natural language processing algorithms for mapping clinical text fragments onto ontology concepts: a systematic review and recommendations for future studies.Journal of biomedical semantics · 2020Pooled it
- Methodological innovations to advance substance use disorder research: Proceedings of a NIDA workshop on target trial emulation and translational testing of digital health tools.Journal of substance use and addiction treatment · 2026Article
- Dynamic taxonomy generation for future skills identification using a named entity recognition and relation extraction pipeline.Frontiers in artificial intelligence · 2025Article
- Automated stratification of trauma injury severity across multiple body regions using multi-modal, multi-class machine learning models.Journal of the American Medical Informatics Association : JAMIA · 2024Article
- Clinical Data Warehousing: A Scoping Review.Journal of the Society for Clinical Data Management · 2024Article
- Applying Natural Language Processing to Textual Data From Clinical Data Warehouses: Systematic Review.JMIR medical informatics · 2023Review
- Article
- [Application of Medical Record Quality Control System Based on Artificial Intelligence].Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition · 2023Article
- The SMART Text2FHIR Pipeline.medRxiv : the preprint server for health sciences · 2023Article
- The SMART Text2FHIR Pipeline.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2023Article
- Enhancing an enterprise data warehouse for research with data extracted using natural language processing.Journal of clinical and translational science · 2023Article
- Translational NLP: A New Paradigm and General Principles for Natural Language Processing Research.Proceedings of the conference. Association for Computational Linguistics. North American Chapter. Meeting · 2021Article
- External validation of an opioid misuse machine learning classifier in hospitalized adult patients.Addiction science & clinical practice · 2021Observational
- Prediction of severe chest injury using natural language processing from the electronic health record.Injury · 2021Article
- Validation of an alcohol misuse classifier in hospitalized patients.Alcohol (Fayetteville, N.Y.) · 2020Article
- Publicly available machine learning models for identifying opioid misuse from the clinical notes of hospitalized patients.BMC medical informatics and decision making · 2020Observational
- Desiderata for delivering NLP to accelerate healthcare AI advancement and a Mayo Clinic NLP-as-a-service implementation.NPJ digital medicine · 2019Review
- Epidemiological challenges in pandemic coronavirus disease (COVID-19): Role of artificial intelligence.Wiley interdisciplinary reviews. Data mining and knowledge discoveryReview
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
Abstract
objectiveNatural language processing (NLP) engines such as the clinical Text Analysis and Knowledge Extraction System are a solution for processing notes for research, but optimizing their performance for a clinical data warehouse remains a challenge. We aim to develop a high throughput NLP architecture using the clinical Text Analysis and Knowledge Extraction System and present a predictive model use case. MATERIALS AND
methodsThe CDW was comprised of 1 103 038 patients across 10 years. The architecture was constructed using the Hadoop data repository for source data and 3 large-scale symmetric processing servers for NLP. Each named entity mention in a clinical document was mapped to the Unified Medical Language System concept unique identifier (CUI).
resultsThe NLP architecture processed 83 867 802 clinical documents in 13.33 days and produced 37 721 886 606 CUIs across 8 standardized medical vocabularies. Performance of the architecture exceeded 500 000 documents per hour across 30 parallel instances of the clinical Text Analysis and Knowledge Extraction System including 10 instances dedicated to documents greater than 20 000 bytes. In a use-case example for predicting 30-day hospital readmission, a CUI-based model had similar discrimination to n-grams with an area under the curve receiver operating characteristic of 0.75 (95% CI, 0.74-0.76). DISCUSSION AND
conclusionOur health system's high throughput NLP architecture may serve as a benchmark for large-scale clinical research using a CUI-based approach.
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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.