OHNLP Publications


Desiderata for delivering NLP to accelerate healthcare AI advancement and a Mayo Clinic NLP-as-a-service implementation

Andrew Wen, Sunyang Fu, Sungrim Moon, Mohamed El Wazir, Andrew Rosenbaum, Vinod C. Kaggal, Sijia Liu, Sunghwan Sohn, Hongfang Liu & Jungwei Fan

NPJ digital medicine 2 (1), 1-7


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.


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.


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.


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.


MedTator: a serverless annotation tool for corpus development

Huan He, Sunyang Fu, Liwei Wang, Sijia Liu, Andrew Wen, Hongfang Liu

Bioinformatics, Volume 38, Issue 6, 15 March 2022, Pages 1776-1778.

Towards User-centered Corpus Development: Lessons Learnt from Designing and Developing MedTator

Huan He, Sunyang Fu, Liwei Wang, Liwei Wang, Andrew Wen, Sijia Liu, Sungrim Moon, Kurt Miller, Hongfang Liu

AMIA 2022 Annual Symposium, Nov 5 - 9, 2022.

Visual Text Analysis for NLP System Evaluation and Development

Huan He, Sunyang Fu, Liwei Wang, Liwei Wang, Andrew Wen, Sijia Liu, Sungrim Moon, Kurt Miller, Hongfang Liu

The 13th Workshop on Visual Analytics in Healthcare (VAHC 2022), AMIA 2022 Annual Symposium, Nov 5, 2022.

Visualization of Text Annotations for Corpus Development

Huan He, Sunyang Fu, Liwei Wang, Liwei Wang, Andrew Wen, Sijia Liu, Sungrim Moon, Kurt Miller, Hongfang Liu

IEEE VIS 2022 Poster, Oct 16 - 21, 2022.

MedTator: A Lightweight Interactive Multi-Document Annotation Tool.

Huan He, Sunyang Fu, Liwei Wang, Andrew Wen, Sijia Liu, Hongfang Liu

AMIA Informatics Summit 2022 System Demonstration, Chicago, IL, USA, March 21 - 24, 2022.

2022 IEEE 10th International Conference on Healthcare Informatics (ICHI) Poster, Rochester, MN, USA, June 11 - 14, 2022.


Refer to Apache cTAKES publications.