Literature DB >> 26958189

Reviewing 741 patients records in two hours with FASTVISU.

Jean-Baptiste Escudié1, Anne-Sophie Jannot1, Eric Zapletal2, Sarah Cohen1, Georgia Malamut2, Anita Burgun1, Bastien Rance1.   

Abstract

The secondary use of electronic health records opens up new perspectives. They provide researchers with structured data and unstructured data, including free text reports. Many applications been developed to leverage knowledge from free-text reports, but manual review of documents is still a complex process. We developed FASTVISU a web-based application to assist clinicians in reviewing documents. We used FASTVISU to review a set of 6340 documents from 741 patients suffering from the celiac disease. A first automated selection pruned the original set to 847 documents from 276 patients' records. The records were reviewed by two trained physicians to identify the presence of 15 auto-immune diseases. It took respectively two hours and two hours and a half to evaluate the entire corpus. Inter-annotator agreement was high (Cohen's kappa at 0.89). FASTVISU is a user-friendly modular solution to validate entities extracted by NLP methods from free-text documents stored in clinical data warehouses.

Entities:  

Mesh:

Year:  2015        PMID: 26958189      PMCID: PMC4765586     

Source DB:  PubMed          Journal:  AMIA Annu Symp Proc        ISSN: 1559-4076


  23 in total

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3.  A simple algorithm for identifying negated findings and diseases in discharge summaries.

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Journal:  J Biomed Inform       Date:  2001-10       Impact factor: 6.317

4.  Pneumonia identification using statistical feature selection.

Authors:  Cosmin Adrian Bejan; Fei Xia; Lucy Vanderwende; Mark M Wurfel; Meliha Yetisgen-Yildiz
Journal:  J Am Med Inform Assoc       Date:  2012-04-26       Impact factor: 4.497

5.  Naïve Electronic Health Record phenotype identification for Rheumatoid arthritis.

Authors:  Robert J Carroll; Anne E Eyler; Joshua C Denny
Journal:  AMIA Annu Symp Proc       Date:  2011-10-22

6.  The clinical research data repository of the US National Institutes of Health.

Authors:  James J Cimino; Elaine J Ayres
Journal:  Stud Health Technol Inform       Date:  2010

7.  ConText: an algorithm for determining negation, experiencer, and temporal status from clinical reports.

Authors:  Henk Harkema; John N Dowling; Tyler Thornblade; Wendy W Chapman
Journal:  J Biomed Inform       Date:  2009-05-10       Impact factor: 6.317

8.  Secondary use of clinical data: the Vanderbilt approach.

Authors:  Ioana Danciu; James D Cowan; Melissa Basford; Xiaoming Wang; Alexander Saip; Susan Osgood; Jana Shirey-Rice; Jacqueline Kirby; Paul A Harris
Journal:  J Biomed Inform       Date:  2014-02-14       Impact factor: 6.317

Review 9.  A review of approaches to identifying patient phenotype cohorts using electronic health records.

Authors:  Chaitanya Shivade; Preethi Raghavan; Eric Fosler-Lussier; Peter J Embi; Noemie Elhadad; Stephen B Johnson; Albert M Lai
Journal:  J Am Med Inform Assoc       Date:  2013-11-07       Impact factor: 4.497

10.  Natural language processing of radiology reports for the detection of thromboembolic diseases and clinically relevant incidental findings.

Authors:  Anne-Dominique Pham; Aurélie Névéol; Thomas Lavergne; Daisuke Yasunaga; Olivier Clément; Guy Meyer; Rémy Morello; Anita Burgun
Journal:  BMC Bioinformatics       Date:  2014-08-07       Impact factor: 3.169

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  7 in total

1.  A novel data-driven workflow combining literature and electronic health records to estimate comorbidities burden for a specific disease: a case study on autoimmune comorbidities in patients with celiac disease.

Authors:  Jean-Baptiste Escudié; Bastien Rance; Georgia Malamut; Sherine Khater; Anita Burgun; Christophe Cellier; Anne-Sophie Jannot
Journal:  BMC Med Inform Decis Mak       Date:  2017-09-29       Impact factor: 2.796

2.  Improving a full-text search engine: the importance of negation detection and family history context to identify cases in a biomedical data warehouse.

Authors:  Nicolas Garcelon; Antoine Neuraz; Vincent Benoit; Rémi Salomon; Anita Burgun
Journal:  J Am Med Inform Assoc       Date:  2017-05-01       Impact factor: 4.497

3.  Integrating Heterogeneous Biomedical Data for Cancer Research: the CARPEM infrastructure.

Authors:  Bastien Rance; Vincent Canuel; Hector Countouris; Pierre Laurent-Puig; Anita Burgun
Journal:  Appl Clin Inform       Date:  2016-05-04       Impact factor: 2.342

4.  Next generation phenotyping using narrative reports in a rare disease clinical data warehouse.

Authors:  Nicolas Garcelon; Antoine Neuraz; Rémi Salomon; Nadia Bahi-Buisson; Jeanne Amiel; Capucine Picard; Nizar Mahlaoui; Vincent Benoit; Anita Burgun; Bastien Rance
Journal:  Orphanet J Rare Dis       Date:  2018-05-31       Impact factor: 4.123

5.  Deep Learning and Radiomics predict complete response after neo-adjuvant chemoradiation for locally advanced rectal cancer.

Authors:  Jean-Emmanuel Bibault; Philippe Giraud; Martin Housset; Catherine Durdux; Julien Taieb; Anne Berger; Romain Coriat; Stanislas Chaussade; Bertrand Dousset; Bernard Nordlinger; Anita Burgun
Journal:  Sci Rep       Date:  2018-08-22       Impact factor: 4.379

6.  Comparison of methods for early-readmission prediction in a high-dimensional heterogeneous covariates and time-to-event outcome framework.

Authors:  Simon Bussy; Raphaël Veil; Vincent Looten; Anita Burgun; Stéphane Gaïffas; Agathe Guilloux; Brigitte Ranque; Anne-Sophie Jannot
Journal:  BMC Med Res Methodol       Date:  2019-03-06       Impact factor: 4.615

7.  Hybrid Deep Learning for Medication-Related Information Extraction From Clinical Texts in French: MedExt Algorithm Development Study.

Authors:  Jordan Jouffroy; Sarah F Feldman; Ivan Lerner; Bastien Rance; Anita Burgun; Antoine Neuraz
Journal:  JMIR Med Inform       Date:  2021-03-16
  7 in total

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