Yongqun He

ORCID

Publication Activity (10 Years)

Years Active: 2005-2024
Publications (10 Years): 94

Top Venues

Publications

Jie Zheng, Xingxian Li, Anna Maria Masci, Hayleigh Kahn, Anthony Huffman, Eliyas Asfaw, Yuanyi Pan, Jinjing Guo, Virginia He, Justin Song, Andrey I. Seleznev, Asiyah Yu Lin, Yongqun He
Empowering standardization of cancer vaccines through ontology: enhanced modeling and data analysis. J. Biomed. Semant. 15 (1) (2024)
Hasin Rehana, Benu Bansal, Nur Bengisu Çam, Jie Zheng, Yongqun He, Arzucan Özgür, Junguk Hur
Nested Named Entity Recognition using Multilayer BERT-based Model. CLEF (Working Notes) (2024)
Anthony Huffman, Xumeng Zhang, Meghana Lanka, Jie Zheng, Anna Maria Masci, Yongqun He
Ontological representation, modeling, and analysis of parasite vaccines. J. Biomed. Semant. 15 (1) (2024)
John Beverley, Robin McGill, Sam Smith, Jie Zheng, Giacomo De Colle, Finn Wilson, Matthew Diller, William D. Duncan, William R. Hogan, Yongqun He
Credentials in the Occupation Ontology. CoRR (2024)
Michael Rabenberg, Carter Benson, Federico Donato, Yongqun He, Anthony Huffman, Shane Babcock, John Beverley
Grounding Realizable Entities. CoRR (2024)
Jianfu Li, Yiming Li, Yuanyi Pan, Jinjing Guo, Zenan Sun, Fang Li, Yongqun He, Cui Tao
Mapping vaccine names in clinical trials to vaccine ontology using cascaded fine-tuned domain-specific language models. J. Biomed. Semant. 15 (1) (2024)
Ling Zheng, Yehoshua Perl, Yongqun He
Big knowledge visualization of the COVID-19 CIDO ontology evolution. BMC Medical Informatics Decis. Mak. 23 (1) (2023)
Anthony Huffman, Edison Ong, Timothy Brunson, Nasim Sanati, Jie Zheng, Anna Maria Masci, Guanming Wu, Yongqun He
Ontology-based Representation and Analysis of Conditional Vaccine Immune Responses Using Omics Data. ICBO (2023)
Sijia Liu, Andrew Wen, Liwei Wang, Huan He, Sunyang Fu, Robert T. Miller, Andrew E. Williams, Daniel R. Harris, Ramakanth Kavuluru, Mei Liu, Noor Abu-El-Rub, Dalton Schutte, Rui Zhang, Masoud Rouhizadeh, John D. Osborne, Yongqun He, Umit Topaloglu, Stephanie S. Hong, Joel H. Saltz, Thomas Schaffter, Emily R. Pfaff, Christopher G. Chute, Tim Duong, Melissa A. Haendel, Rafael Fuentes, Peter Szolovits, Hua Xu, Hongfang Liu
An open natural language processing (NLP) framework for EHR-based clinical research: a case demonstration using the National COVID Cohort Collaborative (N3C). J. Am. Medical Informatics Assoc. 30 (12) (2023)
Hasin Rehana, Nur Bengisu Çam, Mert Basmaci, Yongqun He, Arzucan Özgür, Junguk Hur
Evaluation of GPT and BERT-based models on identifying protein-protein interactions in biomedical text. CoRR (2023)
John Beverley, Sam Smith, Matthew Diller, William D. Duncan, Jie Zheng, John W. Judkins, William R. Hogan, Robin McGill, Damion M. Dooley, Yongqun He
The Occupation Ontology (OccO): Building a Bridge between Global Occupational Standards. JOWO (2023)
Anthony Huffman, Edison Ong, Junguk Hur, Adonis D'mello, Hervé Tettelin, Yongqun He
COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning. Briefings Bioinform. 23 (4) (2022)
Nor Raihan Mohammad Shabani, Che Muhammad Khairul Hisyam Ismail, Amy Amilda Anthony, Chiuan Herng Leow, Candy Chuah, Abu Bakar Abdul Majeed, Norazmi Mohd Nor, Yongqun He, Kirnpal Kaur Banga Singh, Chiuan Yee Leow
immunogenic candidates. Comput. Biol. Medicine 148 (2022)
Yongqun He, Samuel Smith, Damion M. Dooley
Foundational Development of an Occupation Ontology. JOWO (2022)
Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-Hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng, Anna Maria Masci, Liwei Wang, Hongfang Liu, Fatima Zohra Smaili, Robert Hoehndorf, Zoë May Pendlington, Paola Roncaglia, Xianwei Ye, Jiangan Xie, Yi-Wei Tang, Xiaolin Yang, Suyuan Peng, Luxia Zhang, Luonan Chen, Junguk Hur, Gilbert S. Omenn, Brian D. Athey, Barry Smith
A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology. J. Biomed. Semant. 13 (1) (2022)
Warren Manuel, Rashmie Abeysinghe, Yongqun He, Cui Tao, Licong Cui
Identification of missing hierarchical relations in the vaccine ontology using acquired term pairs. J. Biomed. Semant. 13 (1) (2022)
Asiyah Yu Lin, Yuki Yamagata, William D. Duncan, Leigh C. Carmody, Tatsuya Kushida, Hiroshi Masuya, John Beverley, Biswanath Dutta, Michael DeBellis, Zoë May Pendlington, Paola Roncaglia, Yongqun He
A Community Effort for COVID-19 Ontology Harmonization. ICBO (2021)
Ling Zheng, Yehoshua Perl, Yongqun He, Christopher Ochs, James Geller, Hao Liu, Vipina Kuttichi Keloth
Visual comprehension and orientation into the COVID-19 CIDO ontology. J. Biomed. Informatics 120 (2021)
Sebastian Köhler, Michael A. Gargano, Nicolas Matentzoglu, Leigh Carmody, David Lewis-Smith, Nicole A. Vasilevsky, Daniel Danis, Ganna Balagura, Gareth Baynam, Amy M. Brower, Tiffany J. Callahan, Christopher G. Chute, Johanna L. Est, Peter D. Galer, Shiva Ganesan, Matthias Griese, Matthias Haimel, Julia Pazmandi, Marc Hanauer, Nomi L. Harris, Michael Hartnett, Maximilian Hastreiter, Fabian Hauck, Yongqun He, Tim Jeske, Hugh Kearney, Gerhard Kindle, Christoph Klein, Katrin Knoflach, Roland Krause, David Lagorce, Julie A. McMurry, Jillian A. Miller, Monica C. Munoz-Torres, Rebecca L. Peters, Christina K. Rapp, Ana Rath, Shahmir A. Rind, Avi Z. Rosenberg, Michael M. Segal, Markus G. Seidel, Damian Smedley, Tomer Talmy, Yarlalu Thomas, Samuel A. Wiafe, Julie Xian, Zafer Yüksel, Ingo Helbig, Christopher J. Mungall, Melissa A. Haendel, Peter N. Robinson
The Human Phenotype Ontology in 2021. Nucleic Acids Res. 49 (Database-Issue) (2021)
Randi Vita, Jie Zheng, Rebecca C. Jackson, Damion M. Dooley, James A. Overton, Mark A. Miller, Daniel C. Berrios, Richard H. Scheuermann, Yongqun He, Hande Küçük-McGinty, Mathias Brochhausen, Aisyah Yu Lin, Sagar B. Jain, Marcus C. Chibucos, John Judkins, Michelle G. Giglio, Irene Y. Feng, Gully Burns, Matthew H. Brush, Bjoern Peters, Christian J. Stoeckert Jr.
Standardization of assay representation in the Ontology for Biomedical Investigations. Database J. Biol. Databases Curation 2021 (2021)
Easheta Shah, Roshan Desai, Suyuan Peng, Luxia Zhang, Yongqun He
Ontology Modeling and Analysis of COVID-19-associated Acute Kidney Injury and Its Underlying Molecular Mechanisms. ICBO (2021)
Yingtong Liu, Wenjun Ju, Becky Steck, Sanjay Jain, Matthias Kretzler, Yongqun He
Ontology-based Modeling, Representation, and Analysis of Biomarkers in Healthy and Disease Kidney Tissue. ICBO (2021)
Guirui Huang, Suyuan Peng, Luxia Zhang, Yongqun He
Identification and Ontology Term Enrichment Analysis of Genes Associated with COVID-19 and Acute Kidney Disease. ICBO (2021)
Edison Ong, Michael F. Cooke, Anthony Huffman, Zuoshuang Xiang, Mei U. Wong, Haihe Wang, Meenakshi Seetharaman, Ninotchka Valdez, Yongqun He
Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning. Nucleic Acids Res. 49 (Webserver-Issue) (2021)
Anthony Huffman, Anna Maria Masci, Jie Zheng, Nasim Sanati, Timothy Brunson, Guanming Wu, Yongqun He
CIDO ontology updates and secondary analysis of host responses to COVID-19 infection based on ImmPort reports and literature. J. Biomed. Semant. 12 (1) (2021)
Sijia Liu, Andrew Wen, Liwei Wang, Huan He, Sunyang Fu, Robert T. Miller, Andrew E. Williams, Daniel R. Harris, Ramakanth Kavuluru, Mei Liu, Noor Abu-El-Rub, Rui Zhang, John D. Osborne, Masoud Rouhizadeh, Yongqun He, Emily R. Pfaff, Christopher G. Chute, Tim Duong, Melissa A. Haendel, Rafael Fuentes, Peter Szolovits, Hua Xu, Hongfang Liu
An Open Natural Language Processing Development Framework for EHR-based Clinical Research: A case demonstration using the National COVID Cohort Collaborative (N3C). CoRR (2021)
Ling Wan, Justin Song, Virginia He, Jennifer Roman, Grace Whah, Suyuan Peng, Luxia Zhang, Yongqun He
Development of the International Classification of Diseases Ontology (ICDO) and its application for COVID-19 diagnostic data analysis. BMC Bioinform. (6) (2021)
Edison Ong, Haihe Wang, Mei U. Wong, Meenakshi Seetharaman, Ninotchka Valdez, Yongqun He
Vaxign-ML: supervised machine learning reverse vaccinology model for improved prediction of bacterial protective antigens. Bioinform. 36 (10) (2020)
Fang Li, Jingcheng Du, Yongqun He, Hsing-yi Song, Mohcine Madkour, Guozheng Rao, Yang Xiang, Yi Luo, Henry W. Chen, Sijia Liu, Liwei Wang, Hongfang Liu, Hua Xu, Cui Tao
Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events. J. Am. Medical Informatics Assoc. 27 (7) (2020)
Yongqun He, Hong Yu, Edison Ong, Yang Wang, Yingtong Liu, Anthony Huffman, Hsin-Hui Huang, John Beverley, Asiyah Yu Lin, William D. Duncan, Sivaram Arabandi, Jiangan Xie, Junguk Hur, Xiaolin Yang, Luonan Chen, Gilbert S. Omenn, Brian D. Athey, Barry Smith
CIDO: The Community-Based Coronavirus Infectious Disease Ontology. ICBO/ODLS (2020)
Ying Yang, Michael Wybrow, Yuan-Fang Li, Tobias Czauderna, Yongqun He
OntoPlot: A Novel Visualisation for Non-hierarchical Associations in Large Ontologies. IEEE Trans. Vis. Comput. Graph. 26 (1) (2020)
Anthony Huffman, Yongqun He
OGG-CoV: Ontology Representation and Analysis of Genes and Genomes of Coronaviruses (short paper). ICBO/ODLS (2020)
Hongjie Pan, Xiaocui Bian, Sheng Yang, Yongqun He, Xiaolin Yang, Yuqin Liu
The cell line ontology-based representation, integration and analysis of cell lines used in China. BMC Bioinform. (5) (2019)
Edison Ong, Peter Sun, Kimberly Berke, Jie Zheng, Guanming Wu, Yongqun He
VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions. BMC Bioinform. (21) (2019)
Kaiyong Liu, Yongqun He
Ontological Derivation of Mendeleev's Periodic Table of Chemical Elements. ICBO (2019)
Samantha Sayers, Li Li, Edison Ong, Shunzhou Deng, Guanghua Fu, Yu Lin, Brian Yang, Shelley Zhang, Zhenzong Fa, Bin Zhao, Zuoshuang Xiang, Yongqing Li, Xing-Ming Zhao, Michal Olszewski, Luonan Chen, Yongqun He
Victors: a web-based knowledge base of virulence factors in human and animal pathogens. Nucleic Acids Res. 47 (Database-Issue) (2019)
Junguk Hur, Cui Tao, Yongqun He
A 2018 workshop: vaccine and drug ontology studies (VDOS 2018). BMC Bioinform. (21) (2019)
Hong Yu, Solomiya Nysak, Noemi Garg, Edison Ong, Xianwei Ye, Xiangyan Zhang, Yongqun He
ODAE: Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions. BMC Bioinform. (7) (2019)
Muhammad Amith, Frank J. Manion, Chen Liang, Marcelline R. Harris, Dennis Wang, Yongqun He, Cui Tao
Architecture and usability of OntoKeeper, an ontology evaluation tool. BMC Medical Informatics Decis. Mak. (4) (2019)
Hsin-Hui Huang, Meng Liu, Yongqun He
Ontological Modeling of Two-Component Regulatory Systems. ICBO (2019)
Yongqun He, Jie Zheng, Anna Maria Masci, Jihad S. Obeid
Alignment of the Ontology of Host-Microbiome Interactions (OHMI) High Level Terms with Existing OBO Ontologies. ICBO (2019)
Yongqun He, Haihe Wang, Jie Zheng, Daniel P. Beiting, Anna Maria Masci, Hong Yu, Kaiyong Liu, Jianmin Wu, Jeffrey L. Curtis, Barry Smith, Alexander V. Alekseyenko, Jihad S. Obeid
OHMI: the ontology of host-microbiome interactions. J. Biomed. Semant. 10 (1) (2019)
Edison Ong, Yongqun He
Ontolion: A Web-based Integrative Ontology Development Platform. ICBO (2019)
Meng Liu, Hong-Yu Ou, Yongqun He
ICEO: a Biological Ontology for Representing and Analyzing the Bacterial Integrative and Conjugative Element. ICBO (2019)
Yongqun He, William D. Duncan, Daniel J. Cooper, Jens Hansen, Ravi Iyengar, Edison Ong, Kendal Walker, Omar Tibi, Sam Smith, Lucas M. Serra, Jie Zheng, Sirarat Sarntivijai, Stephan C. Schürer, K. Sue O'Shea, Alexander D. Diehl
OSCI: standardized stem cell ontology representation and use cases for stem cell investigation. BMC Bioinform. (5) (2019)
Yongqun He, Edison Ong, Jennifer Schaub, Frederick Dowd, John F. O'Toole, Anastasios Siapos, Christian G. Reich, Sarah Seager, Ling Wang, Hong Yu, Jie Zheng, Christian J. Stoeckert Jr., Xiaolin Yang, Sheng Yang, Becky Steck, Christopher Park, Laura Barisoni, Matthias Kretzler, Jonathan Himmelfarb, Ravi Iyengar, Sean D. Mooney
OPMI: the Ontology of Precision Medicine and Investigation and its Support for Clinical Data and Metadata Representation and Analysis. ICBO (2019)
Mert Tiftikci, Arzucan Özgür, Yongqun He, Junguk Hur
Machine learning-based identification and rule-based normalization of adverse drug reactions in drug labels. BMC Bioinform. (21) (2019)
Ying Yang, Michael Wybrow, Yuan-Fang Li, Tobias Czauderna, Yongqun He
OntoPlot: A Novel Visualisation for Non-hierarchical Associations in Large Ontologies. CoRR (2019)
Sirarat Sarntivijai, Yongqun He, Alexander D. Diehl
Cells in ExperimentaL Life Sciences (CELLS-2018): capturing the knowledge of normal and diseased cells with ontologies. BMC Bioinform. (5) (2019)
Jian-Jian Ren, Tingni Sun, Yongqun He, Yuji Zhang
A statistical analysis of vaccine-adverse event data. BMC Medical Informatics Decis. Mak. 19 (1) (2019)
Ling Wan, Edison Ong, Yongqun He
ICDO: Ontological Representation of the International Classification of Diseases (ICD) and its Application in English and Chinese Healthy Data Standardization. ICBO (2019)
Meng Liu, Hong-Yu Ou, Yongqun He
OGG-Bac: Ontological Representation of Orthologous Bacterial Genes. ICBO (2019)
Jun Li, Cui Tai, Zixin Deng, Weihong Zhong, Yongqun He, Hong-Yu Ou
VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria. Briefings Bioinform. 19 (4) (2018)
Yongqun He, Becky Steck, Edison Ong, Laura Mariani, Chrysta Lienczewski, Ulysses J. Balis, Matthias Kretzler, Jonathan Himmelfarb, John F. Bertram, Evren U. Azeloglu, Ravi Iyengar, Deborah Hoshizaki, Sean D. Mooney
KTAO: A Kidney Tissue Atlas Ontology to Support Community-Based Kidney Knowledge Base Development and Data Integration. ICBO (2018)
Junguk Hur, Arzucan Özgür, Yongqun He
Ontology-based literature mining and class effect analysis of adverse drug reactions associated with neuropathy-inducing drugs. J. Biomed. Semant. 9 (1) (2018)
J. Neil Otte, Cooper Stansbury, Jonathan Vajda, Frank J. Manion, Elizabeth Umberfield, Yongqun He, Marcelline R. Harris, Jihad S. Obeid, Mathias Brochhausen, William D. Duncan, Cui Tao
Coordinated Evolution of Ontologies of Informed Consent. ICBO (2018)
Edison Ong, Yongqun He, Jie Zheng
eXtensible Ontology Development (XOD) using Web-based Ontoanimal Tools. ICBO (2018)
Yongqun He, Zuoshuang Xiang, Jie Zheng, Yu Lin, James A. Overton, Edison Ong
The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability. J. Biomed. Semant. 9 (1) (2018)
Muhammad Amith, Frank J. Manion, Chen Liang, Marcelline R. Harris, Dennis Wang, Yongqun He, Cui Tao
OntoKeeper: Semiotic-driven Ontology Evaluation Tool For Biomedical Ontologists. BIBM (2018)
Edison Ong, Sirarat Sarntivijai, Simon Jupp, Helen E. Parkinson, Yongqun He
Comparison, alignment, and synchronization of cell line information between CLO and EFO. BMC Bioinform. 18 (S-17) (2017)
Marcelline R. Harris, Frank J. Manion, Hsing-yi Song, Yongqun He, Muhamamd F. Amith, Cui Tao
From Scoping Review to Metadata: An Evidence-Based Approach to Identifying Informed Consent Metadata for Biorepositories. AMIA (2017)
Jie Zheng, Huan Li, Qingzhi Liu, Yongqun He
The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines. Quant. Biol. 5 (4) (2017)
Mert Tiftikci, Arzucan Özgür, Yongqun He, Junguk Hur
Extracting Adverse Drug Reactions using Deep Learning and Dictionary Based Approaches. TAC (2017)
Richard D. Boyce, Erica A. Voss, Vojtech Huser, Lee Evans, Christian G. Reich, Jon D. Duke, Nicholas P. Tatonetti, Tal Lorberbaum, Michel Dumontier, Manfred Hauben, Magnus Wallberg, Lili Peng, Sara Dempster, Yongqun He, Anthony G. Sena, Vassilis Koutkias, Pantelis Natsiavas, Patrick B. Ryan
Large-scale adverse effects related to treatment evidence standardization (LAERTES): an open scalable system for linking pharmacovigilance evidence sources with clinical data. J. Biomed. Semant. 8 (1) (2017)
Sirarat Sarntivijai, Alexander D. Diehl, Yongqun He
Cells in experimental life sciences - challenges and solution to the rapid evolution of knowledge. BMC Bioinform. 18 (S-17) (2017)
Edison Ong, Zuoshuang Xiang, Bin Zhao, Yue Liu, Yu Lin, Jie Zheng, Chris Mungall, Mélanie Courtot, Alan Ruttenberg, Yongqun He
Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration. Nucleic Acids Res. 45 (Database-Issue) (2017)
Edison Ong, Jiangan Xie, Zhaohui Ni, Qingping Liu, Sirarat Sarntivijai, Yu Lin, Daniel J. Cooper, Raymond Terryn, Vasileios Stathias, Caty Chung, Stephan C. Schürer, Yongqun He
Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses. BMC Bioinform. 18 (S-17) (2017)
Meiu Wong, Rebecca Racz, Edison Ong, Yongqun He
Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping and OAE-based representation and analysis of adverse events in patients treated with cancer drugs. AMIA (2017)
Edison Ong, Yongqun He
OLOBO: A New Ontology for Linking and Integrating Open Biological and Biomedical Ontologies. ICBO (2017)
Qingping Liu, Jiahao Wang, Yan Zhu, Yongqun He
Ontology-based systematic representation and analysis of traditional Chinese drugs against rheumatism. BMC Syst. Biol. 11 (S-7) (2017)
Junguk Hur, Arzucan Özgür, Yongqun He
Ontology-based literature mining of E. coli vaccine-associated gene interaction networks. J. Biomed. Semant. 8 (1) (2017)
Edison Ong, Jiangan Xie, Zhaohui Ni, Qingping Liu, Yu Lin, Vasileios Stathias, Caty Chung, Stephan C. Schürer, Yongqun He
The Cell Line Ontology Integration and Analysis of the Knowledge of LINCS Cell Lines. ICBO/BioCreative (2016)
Edison Ong, Zuoshuang Xiang, Jie Zheng, Barry Smith, Yongqun He
Ontobull and BFOConvert: Web-based Programs to Support Automatic Ontology Conversion. ICBO/BioCreative (2016)
Yu Lin, Jie Zheng, Yongqun He
VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms. J. Biomed. Semant. 7 (2016)
Yongqun He, Zhaohui S. Qin, Jie Zheng
EGO: A Biomedical Ontology for Integrative Epigenome Representation and Analysis. ICBO/BioCreative (2016)
Jingshan Huang, Karen Eilbeck, Barry Smith, Judith A. Blake, Dejing Dou, Weili Huang, Darren A. Natale, Alan Ruttenberg, Jun Huan, Michael T. Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison J. Strachan, Nisansa de Silva, Mohan Vamsi Kasukurthi, Vikash Kumar Jha, Yongqun He, Shaojie Zhang, Xiaowei Wang, Zixing Liu, Glen M. Borchert, Ming Tan
The development of non-coding RNA ontology. Int. J. Data Min. Bioinform. 15 (3) (2016)
Abra Guo, Rebecca Racz, Junguk Hur, Yu Lin, Zuoshuang Xiang, Lili Zhao, Jordan Rinder, Guoqian Jiang, Qian Zhu, Yongqun He
Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events. J. Biomed. Semant. 7 (2016)
Mei Li, Yuying Cao, Liwei Wang, Hongfang Liu, Yongqun He
Ontology-Based Analysis of Adverse Drug Reactions Associated with Anti-infection Drugs in China. AMIA (2016)
Cui Tao, Yongqun He, Sivaram Arabandi
Vaccine and Drug Ontology Studies (VDOS 2014). J. Biomed. Semant. 7 (2016)
Arzucan Özgür, Junguk Hur, Yongqun He
The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature. BioData Min. 9 (2016)
Alexander D. Diehl, Terrence F. Meehan, Yvonne M. Bradford, Matthew H. Brush, Wasila M. Dahdul, David S. Dougall, Yongqun He, David Osumi-Sutherland, Alan Ruttenberg, Sirarat Sarntivijai, Ceri E. Van Slyke, Nicole A. Vasilevsky, Melissa A. Haendel, Judith A. Blake, Christopher J. Mungall
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. J. Biomed. Semant. 7 (2016)
Arzucan Özgür, Junguk Hur, Zuoshuang Xiang, Edison Ong, Dragomir R. Radev, Yongqun He
Ignet: A Centrality and INO-based Web System for Analyzing and Visualizing Literature-mined Networks. ICBO/BioCreative (2016)
Jingshan Huang, Karen Eilbeck, Barry Smith, Judith A. Blake, Dejing Dou, Weili Huang, Darren A. Natale, Alan Ruttenberg, Jun Huan, Michael T. Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison J. Strachan, Yongqun He, Shaojie Zhang, Xiaowei Wang, Zixing Liu, Glen M. Borchert, Ming Tan
The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology. J. Biomed. Semant. 7 (2016)
Edison Ong, Yongqun He
Application of Ontobedia on Cell Line Ontology Development. AMIA (2016)
Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Yu Lin, Alfred O. Hero III, Barry Smith, Yongqun He
The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis. J. Biomed. Semant. 7 (2016)
Yongqun He, Guoqian Jiang
Bridging Vaccine Ontology and NCIt vaccine domain for cancer vaccine data integration and analysis. ICBO (2015)
Yu Lin, Zuoshuang Xiang, Yongqun He
Ontology-based representation and analysis of host-Brucella interactions. J. Biomed. Semant. 6 (2015)
Arzucan Özgür, Junguk Hur, Yongqun He
Extension of the Interaction Network Ontology for Literature Mining of Gene-gene Interaction Networks from Sentences with Multiple Interaction Keywords. BDM2I@ISWC (2015)
Jingshan Huang, Karen Eilbeck, Judith A. Blake, Dejing Dou, Darren A. Natale, Alan Ruttenberg, Barry Smith, Michael T. Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Yongqun He, Shaojie Zhang, Xiaowei Wang, He Zhang, Zixing Liu, Ming Tan
A domain ontology for the Non-Coding RNA field. BIBM (2015)
Yongqun He, Jie Zheng, Yu Lin
Ontoanimal tools for reusing ontologies, generating and editing ontology terms, and dereferencing ontology terms. ICBO (2015)
Edison Ong, Yongqun He
GOfox: Semantics-based simplified hierarchical classification and interactive visualization to support GO enrichment analysis. ICBO (2015)
Zuoshuang Xiang, Jie Zheng, Yu Lin, Yongqun He
Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns. J. Biomed. Semant. 6 (2015)
Yongqun He, Jie Zheng, Yu Lin
Ontorat: Automatic generation and editing of ontology terms. ICBO (2015)
Junguk Hur, Arzucan Özgür, Zuoshuang Xiang, Yongqun He
Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions. J. Biomed. Semant. 6 (2015)
Rebecca Racz, Xinna Li, Mukti Patel, Zuoshuang Xiang, Yongqun He
DNAVaxDB: the first web-based DNA vaccine database and its data analysis. BMC Bioinform. 15 (S-4) (2014)
Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Terrence F. Meehan, Alexander D. Diehl, Uma D. Vempati, Stephan C. Schürer, Chao Pang, James Malone, Helen E. Parkinson, Yue Liu, Terue Takatsuki, Kaoru Saijo, Hiroshi Masuya, Yukio Nakamura, Matthew H. Brush, Melissa A. Haendel, Jie Zheng, Christian J. Stoeckert Jr., Bjoern Peters, Christopher J. Mungall, Thomas E. Carey, David J. States, Brian D. Athey, Yongqun He
CLO: The cell line ontology. J. Biomed. Semant. 5 (2014)
Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Yu Lin, Alfred O. Hero III, Barry Smith, Yongqun He
OBCS: The Ontology of Biological and Clinical Statistics. ICBO (2014)
Frank J. Manion, Elizabeth Eisenhauer, Alla Karnovsky, Yongqun He, Yu Lin, Marcelline R. Harris
Analysis of Content Coverage for Informed Consent Concepts. AMIA (2014)
Yongqun He, Rebecca Racz, Samantha Sayers, Yu Lin, Thomas E. Todd, Junguk Hur, Xinna Li, Mukti Patel, Boyang Zhao, Monica Chung, Joseph Ostrow, Andrew Sylora, Priya Dungarani, Guerlain Ulysse, Kanika Kochhar, Boris Vidri, Kelsey Strait, George W. Jourdian, Zuoshuang Xiang
Updates on the web-based VIOLIN vaccine database and analysis system. Nucleic Acids Res. 42 (Database-Issue) (2014)
Jie Zheng, Zuoshuang Xiang, Christian J. Stoeckert Jr., Yongqun He
Ontodog: a web-based ontology community view generation tool. Bioinform. 30 (9) (2014)

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Publication Activity (10 Years)

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Yongqun He