Literature DB >> 22195072

A cloud-based approach to medical NLP.

Kyle Chard1, Michael Russell, Yves A Lussier, Eneida A Mendonça, Jonathan C Silverstein.   

Abstract

Natural Language Processing (NLP) enables access to deep content embedded in medical texts. To date, NLP has not fulfilled its promise of enabling robust clinical encoding, clinical use, quality improvement, and research. We submit that this is in part due to poor accessibility, scalability, and flexibility of NLP systems. We describe here an approach and system which leverages cloud-based approaches such as virtual machines and Representational State Transfer (REST) to extract, process, synthesize, mine, compare/contrast, explore, and manage medical text data in a flexibly secure and scalable architecture. Available architectures in which our Smntx (pronounced as semantics) system can be deployed include: virtual machines in a HIPAA-protected hospital environment, brought up to run analysis over bulk data and destroyed in a local cloud; a commercial cloud for a large complex multi-institutional trial; and within other architectures such as caGrid, i2b2, or NHIN.

Mesh:

Year:  2011        PMID: 22195072      PMCID: PMC3243210     

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


  10 in total

1.  Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program.

Authors:  A R Aronson
Journal:  Proc AMIA Symp       Date:  2001

2.  Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications.

Authors:  Guergana K Savova; James J Masanz; Philip V Ogren; Jiaping Zheng; Sunghwan Sohn; Karin C Kipper-Schuler; Christopher G Chute
Journal:  J Am Med Inform Assoc       Date:  2010 Sep-Oct       Impact factor: 4.497

3.  caTIES: a grid based system for coding and retrieval of surgical pathology reports and tissue specimens in support of translational research.

Authors:  Rebecca S Crowley; Melissa Castine; Kevin Mitchell; Girish Chavan; Tara McSherry; Michael Feldman
Journal:  J Am Med Inform Assoc       Date:  2010 May-Jun       Impact factor: 4.497

4.  An overview of MetaMap: historical perspective and recent advances.

Authors:  Alan R Aronson; François-Michel Lang
Journal:  J Am Med Inform Assoc       Date:  2010 May-Jun       Impact factor: 4.497

5.  Integration of Hive and cell software in the i2b2 architecture.

Authors:  Michael Mendis; Nich Wattanasin; Rajesh Kuttan; Wensong Pan; Lori Philips; Kristel Hackett; Vivian Gainer; Henry C Chueh; Shawn Murphy
Journal:  AMIA Annu Symp Proc       Date:  2007-10-11

6.  caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid.

Authors:  Joel Saltz; Scott Oster; Shannon Hastings; Stephen Langella; Tahsin Kurc; William Sanchez; Manav Kher; Arumani Manisundaram; Krishnakant Shanbhag; Peter Covitz
Journal:  Bioinformatics       Date:  2006-06-09       Impact factor: 6.937

7.  Translational bioinformatics in the cloud: an affordable alternative.

Authors:  Joel T Dudley; Yannick Pouliot; Rong Chen; Alexander A Morgan; Atul J Butte
Journal:  Genome Med       Date:  2010-08-06       Impact factor: 11.117

8.  Word Sense Disambiguation by Selecting the Best Semantic Type Based on Journal Descriptor Indexing: Preliminary Experiment.

Authors:  Susanne M Humphrey; Willie J Rogers; Halil Kilicoglu; Dina Demner-Fushman; Thomas C Rindflesch
Journal:  J Am Soc Inf Sci Technol       Date:  2006-01-01

9.  Cloud computing for comparative genomics.

Authors:  Dennis P Wall; Parul Kudtarkar; Vincent A Fusaro; Rimma Pivovarov; Prasad Patil; Peter J Tonellato
Journal:  BMC Bioinformatics       Date:  2010-05-18       Impact factor: 3.169

10.  Taverna: a tool for building and running workflows of services.

Authors:  Duncan Hull; Katy Wolstencroft; Robert Stevens; Carole Goble; Mathew R Pocock; Peter Li; Tom Oinn
Journal:  Nucleic Acids Res       Date:  2006-07-01       Impact factor: 16.971

  10 in total
  4 in total

Review 1.  12 Plagues of AI in Healthcare: A Practical Guide to Current Issues With Using Machine Learning in a Medical Context.

Authors:  Stephane Doyen; Nicholas B Dadario
Journal:  Front Digit Health       Date:  2022-05-03

Review 2.  A scoping review of cloud computing in healthcare.

Authors:  Lena Griebel; Hans-Ulrich Prokosch; Felix Köpcke; Dennis Toddenroth; Jan Christoph; Ines Leb; Igor Engel; Martin Sedlmayr
Journal:  BMC Med Inform Decis Mak       Date:  2015-03-19       Impact factor: 2.796

3.  A Lightweight API-Based Approach for Building Flexible Clinical NLP Systems.

Authors:  Zhengru Shen; Hugo van Krimpen; Marco Spruit
Journal:  J Healthc Eng       Date:  2019-08-15       Impact factor: 2.682

4.  Efficient Reuse of Natural Language Processing Models for Phenotype-Mention Identification in Free-text Electronic Medical Records: A Phenotype Embedding Approach.

Authors:  Honghan Wu; Karen Hodgson; Sue Dyson; Katherine I Morley; Zina M Ibrahim; Ehtesham Iqbal; Robert Stewart; Richard Jb Dobson; Cathie Sudlow
Journal:  JMIR Med Inform       Date:  2019-12-17
  4 in total

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