Design and evaluation of an ontology based information extraction system for radiological reports. - Ergin Soysal; Ilyas Cicekli; Nazife Baykal (Comput. Biol. Medicine, 2010)

Ontology based information extraction on free text radiological reports using natural language processing approach ; Serbest metin radyoloji raporlarından, doğal dil işleme yaklaşımları kullanılarak ontoloji temelli enformasyon çıkarımı. - Ergin Soysal (2010)

Security Standards for Electronic Health Records. - Öznur Esra Par; Ergin Soysal (ASONAM, 2012)

Identifying Metastases from Pathology Reports in Lung Cancer Patients. - Ergin Soysal; Jeremy L. Warner; Joshua C. Denny; Hua Xu 001 (AMIA, 2014)

Clinical Language Annotation, Modeling, and Processing Toolkit (CLAMP) - a user-centric NLP system. - Ergin Soysal; Jingqi Wang; Min Jiang 007; Yonghui Wu; Hua Xu 001 (AMIA, 2015)

UTH-CCB: The Participation of the SemEval 2015 Challenge - Task 14. - Jun Xu 007; Yaoyun Zhang; Jingqi Wang; Yonghui Wu; Min Jiang 007; Ergin Soysal; Hua Xu 001 (SemEval@NAACL-HLT, 2015)

A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case. - Liang-Chin Huang; Ergin Soysal; W. Jim Zheng; Zhongming Zhao; Hua Xu 001; Jingchun Sun (BMC Syst. Biol., 2015)

A Scalable Dataset Indexing Infrastructure for the bioCADDIE Data Discovery System. - Jeffrey S. Grethe; Ibrahim Burak Özyurt; Hua Xu 001; Xiaoling Chen; Ruiling Liu; Ergin Soysal; Anupama E. Gururaj; Hyeon-Eui Kim; Trevor Cohen; Todd R. Johnson; Mandana Salimi; Saeid Pournejati; et al. (AMIA, 2016)

Development of DataMed, a Data Discovery Index Prototype by bioCADDIE: Laying the Groundwork for Biomedical Data Discovery. - Hua Xu 001; Jeffrey S. Grethe; Xiaoling Chen; Ruiling Liu; Ergin Soysal; Anupama E. Gururaj; Yueling Li; Ibrahim Burak Özyurt; Hyeon-Eui Kim; Trevor Cohen; Todd R. Johnson; Mandana Salimi; et al. (AMIA, 2016)

Leveraging syntactic and semantic graph kernels to extract pharmacokinetic drug drug interactions from biomedical literature. - Yaoyun Zhang; Heng-Yi Wu; Jun Xu 007; Jingqi Wang; Ergin Soysal; Lang Li 001; Hua Xu 001 (BMC Syst. Biol., 2016)

CLAMP - A User-Centric Clinical Natural Language Processing Toolkit. - Hua Xu 001; Ergin Soysal; Jingqi Wang; Min Jiang 007; Yonghui Wu (AMIA, 2017)

Identifying Metastases related Information from Pathology Reports of Lung Cancer Patients. - Ergin Soysal; Jeremy L. Warner; Joshua C. Denny; Hua Xu 001 (CRI, 2017)

A long journey to short abbreviations: developing an open-source framework for clinical abbreviation recognition and disambiguation (CARD). - Yonghui Wu; Joshua C. Denny; S. Trent Rosenbloom; Randolph A. Miller; Dario A. Giuse; Lulu Wang; Carmelo Blanquicett; Ergin Soysal; Jun Xu 007; Hua Xu 001 (J. Am. Medical Informatics Assoc., 2017)

DataMed - an open source discovery index for finding biomedical datasets. - Xiaoling Chen; Anupama E. Gururaj; Ibrahim Burak Özyurt; Ruiling Liu; Ergin Soysal; Trevor Cohen; Firat Tiryaki; Yueling Li; Nansu Zong; Min Jiang 007; Deevakar Rogith; Mandana Salimi; et al. (J. Am. Medical Informatics Assoc., 2018)

CLAMP - a toolkit for efficiently building customized clinical natural language processing pipelines. - Ergin Soysal; Jingqi Wang; Min Jiang 007; Yonghui Wu; Serguei Pakhomov; Hongfang Liu; Hua Xu 001 (J. Am. Medical Informatics Assoc., 2018)

Developing Customizable Cancer Information Extraction Modules for Pathology Reports Using CLAMP. - Ergin Soysal; Jeremy L. Warner; Jingqi Wang; Min Jiang 007; Krysten Harvey; Sandeep Kumar Jain; Xiao Dong; Hsing-yi Song; Harish Siddhanamatha; Liwei Wang 010; Qi Dai; Qingxia Chen; et al. (MedInfo, 2019)

Cohort selection for clinical trials: n2c2 2018 shared task track 1. - Amber Stubbs; Michele Filannino; Ergin Soysal; Samuel Henry 001; Özlem Uzuner (J. Am. Medical Informatics Assoc., 2019)