Reference

Note: Please cite the publication below in study manuscripts using CLAMP. Please inform us of your publication for our reference.

2017

Ergin Soysal, Jingqi Wang, Min Jiang, Yonghui Wu, Serguei Pakhomov, Hongfang Liu, Hua Xu. CLAMP – a toolkit for efficiently building customized clinical natural language processing pipelines. JAMIA, Doi: 10.1093/jamia/ocx132 Full text link

Awards & Publications

CLAMP is built on award-winning methods. Our team has participated in a number of clinical NLP challenges and top ranked for various tasks (see below). Now we have integrated such proven methods into CLAMP and make them available to the community.

Relevant Publications

2017

Ergin Soysal, Jingqi Wang, Min Jiang, Yonghui Wu, Serguei Pakhomov, Hongfang Liu, Hua Xu. CLAMP – a toolkit for efficiently building customized clinical natural language processing pipelines. JAMIA, Doi: 10.1093/jamia/ Full text link

2016

Lee H, Zhang Y, Xu J, Moon S, Wang J, Wu Y, and Xu H, UTHealth at SemEval-2016 Task 12: an End-to-End System for Temporal Information Extraction from Clinical Notes. Proceedings of the 10th International Workshop on Semantic Evaluation (SemEval-2016), 1292-1297, San Diego, California, June, 2016. Full text link Xu J, Wu Y, Zhang Y, Wang J, Lee H-J, Xu H. CD-REST: a system for extracting chemical-induced disease relation in literature. Database: The Journal of Biological Databases and Curation. 2016;2016:baw036. doi:10.1093/database/baw036. Full text link Zhang Y, Xu J, Chen H, Wang J, Wu Y, Manu P, Xu H. Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning.Database (Oxford). 2016. doi: 10.1093/database/baw049. Full text link

2015

Xu J, Zhang Y, Wang J, Wu Y, Jiang M, Soysal E, and Xu H. UTH-CCB: The Participation of the SemEval 2015 Challenge – Task 14. Proceedings of the 9th International Workshop on Semantic Evaluation (SemEval 2015). Denver, Colorado. 2015:311-314. Full text link Xu J, Wu Y, Zhang Y, Wang J, Liu R, Wei Q, and Xu H. UTH-CCB@BioCreative V CDR Task: Identifying Chemical-induced Disease Relations in Biomedical Text. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 2015:254-259. Full text link Zhang Y, Xu J, Wang J, Wu Y, Parkasam M and Xu H. UTH-CCB@BioCreative V Track 2: Recognizing Chemical Entities in Patents. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, 2015:147-148 Full text link

2014

Zhang Y, Wang J, Tang B, Wu Y, Jiang M, Chen Y, Xu H. UTH_CCB: A Report for SemEval 2014 – Task 7 Analysis of Clinical Text. SemEval 2014, 802–806, Dublin, Ireland, August 23-24, 2014. Full text link

2013

Tang B, Wu Y, Jiang M, and Xu H. A Machine Learning based System for Disorder Concept Extraction. 2013. Proceedings of CLEF 2013 Evaluation Labs and Workshop. Full text link Wu Y, Tang B, Jiang M, Moon S, Denny JC, Xu H. Clinical Acronym/Abbreviation Normalization using a Hybrid Approach. 2013. Proceedings of CLEF 2013 Evaluation Labs and Workshop. Full text link Tang B, Wu Y, Jiang M, Chen Y, Denny JC, Xu H. A hybrid system for temporal information extraction from clinical text. J Am Med Inform Assoc. 2013. Full text link

2011

Jiang M Chen Y Liu Met al. A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries. J Am Med Inform Assoc  2011;18:601–6. Full text link Jiang M Chen Y Liu Met al. A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries. J Am Med Inform Assoc  2011;18:601–6. Full text link

2010

Doan S Bastarache L Klimkowski Set al. Integrating existing natural language processing tools for medication extraction from discharge summaries. J Am Med Inform Assoc  2010;17:528–31. Full text link

Contact Us

Center for Computational Biomedicine

School of Biomedical Informatics

The University of Texas Health Science Center at Houston

7000 Fannin St, Houston, TX 77030

Research Coordinator

Anupama E. Gururaj, PhD

anupama.e.gururaj@uth.tmc.edu

713-500-3619

Technical Support

Jingqi Wang, MS - Analyst Programmer

jingqi.wang@uth.tmc.edu

713-500-3620

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