OHNLP Publications

From Open Health Natural Language Processing (OHNLP) Consortium
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When using a pipeline or annotator from OHNLP, please cite the appropriate publication(s):

Contents

medKAT/P

Automatically extracting cancer disease characteristics from pathology reports into a Disease Knowledge Representation Model.
Anni Coden, Guergana Savova, Igor Sominsky, Michael Tanenblatt, James Masanz, Karin Schuler, James Cooper, Wei Guan and Piet C. de Groen. 2009.
Journal of Biomedical Informatics 2009;42:937-49.
Interactive Exploration of Model-based Automatically Extracted Data.
Anni Coden, Igor Sominsky, Michael Tanenblatt.
ICDM'08. Pisa, Italy.
Text Analysis Integrated into a Medical Information Retrieval System: Challenges related to Word Sense Disambiguation.
AR Coden, GK Savova, JD Buntrock, IL Sominsky, PV Ogren, CG Chute, and PC de Groen.
MEDINFO, 2007.
Word sense disambiguation across two domains: Biomedical literature and clinical notes.
Guergana K. Savova, Anni R. Coden, Igor L. Sominsky, Rie Johnson, Philip V. Ogren, Piet C. de Groen and Christopher G. Chute.
Journal of Biomedical Informatics, March 4, 2008.
CFE - a system for testing, evaluation and machine learning of UIMA based applications.
Igor Sominsky, Anni Coden, Michael Tanenblatt.
LREC 2008. Marrakech, Morocco.
JANUS - A system for annotating, vetting and testing natural language processing systems.
Michael Tanenblatt, Anni Coden, Igor Sominsky.
Rocky08 - Sixth Annual Rocky Mountain Bioinformatics Conference, December 2008.

MedCoref

Coreference analysis in clinical notes: a multi-pass sieve with alternate anaphora resolution modules.
Jonnalagadda SR, Li D, Sohn S, Wu ST, Wagholikar K, Torii M, Liu H.
J Am Med Inform Assoc. 2012 Sep-Oct;19(5):867-74. doi: 10.1136/amiajnl-2011-000766. Epub 2012 Jun 16.

MedTagger

Using machine learning for concept extraction on clinical documents from multiple data sources.
Torii M, Wagholikar K, Liu H.
J Am Med Inform Assoc. 2011 Sep-Oct;18(5):580-7. doi: 10.1136/amiajnl-2011-000155. Epub 2011 Jun 27.
Integrated cTAKES for concept mention detection and normalization.
Liu H, Wagholikar K, Jonnalagadda SR, Sohn S.
CLEF 2013 Share/eHealth challenges September 23-26, 2013.

MedTime

Comprehensive temporal information detection from clinical text: medical events, time, and TLINK identification.
Sohn S, Wagholikar KB, Jonnalagadda SR, Tao C, Komandur RE, Liu H.
J Am Med Inform Assoc. 2013 Sep-Oct;20(5):836-42. doi: 10.1136/amiajnl-2013-001622. Epub 2013 Apr 4.

cTAKES

Refer to Apache cTAKES publications.

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