Yongqun He

159 papers Misc 5Journal 88Unranked 64
YearRankTypeTitle / Venue / Authors
2026 J jnl
AcuKG: a comprehensive knowledge graph for medical acupuncture.
J. Am. Medical Informatics Assoc.
Yiming Li, Xueqing Peng, Suyuan Peng, Jianfu Li, Donghong Pei, Qin Zhang, Yiwei Lu, Yan Hu, Fang Li, Li Zhou, Yongqun He, Cui Tao, Hua Xu, Na Hong
2025 J jnl
A Fourfold Pathogen Reference Ontology Suite.
CoRR
Shane Babcock, Carter Benson, Giacomo De Colle, Sydney Cohen, Alexander D. Diehl, Ram A. N. R. Challa, Ray Mavrovich, Joshua Billig, Anthony Huffman, Yongqun He, John Beverley
2025 J jnl
A fourfold pathogen reference ontology suite.
J. Biomed. Semant.
John Beverley, Shane Babcock, Carter Benson, Giacomo De Colle, Sydney Cohen, Alexander D. Diehl, Ram A. N. R. Challa, Ray Mavrovich, Joshua Billig, Anthony Huffman, Yongqun He
2025 J jnl
Cancer Vaccine Adjuvant Name Recognition from Biomedical Literature using Large Language Models.
CoRR
Hasin Rehana, Jie Zheng, Leo Yeh, Benu Bansal, Nur Bengisu Çam, Christianah Jemiyo, Brett A. McGregor, Arzucan Özgür, Yongqun He, Junguk Hur
2025 — conf
Exploring Blockchain Technology to Improve Vaccine Access in Low-Resource Countries.
MedInfo
Anirudh Babu, Matthew Dacso, Yongqun He, Muhammad Amith
2025 — conf
Modeling of Skills, Abilities, Competences, and Related Dispositions in the Occupation Ontology.
JOWO
Finn D. Wilson, Matthew Diller, Robin McGill, Sam Smith, Jie Zheng, Clarissa Savluchinske Feio Vieira, William D. Duncan, John Beverley, Yongqun He
2025 — conf
Towards Healthy Aging through Semantic Enrichment.
JOWO
John Beverley, Julie C. Bowker, Hollen N. Reischer, Rachel A. Mavrovich, Regina Hurley, Sean Kindya, Sam Smith, Jie Zheng, Yongqun He, Damayanthi Beera, William D. Duncan
2024 — conf
CellCards: Development of a Dynamic Ontology-Derived ETL Pipeline for Automatic Cell Information Extraction and Analysis.
ICBO
Mary Czelusniak, Emily Tran, Fatima Oudeif, Jie Zheng, William D. Duncan, Alexander D. Diehl, Yongqun He
2024 — conf
Credentials in the Occupation Ontology.
ICBO
John Beverley, Robin McGill, Sam Smith, Jie Zheng, Giacomo De Colle, Finn D. Wilson, Matthew Diller, William D. Duncan, William R. Hogan, Yongqun He
2024 J jnl
Credentials in the Occupation Ontology.
CoRR
John Beverley, Robin McGill, Sam Smith, Jie Zheng, Giacomo De Colle, Finn D. Wilson, Matthew Diller, William D. Duncan, William R. Hogan, Yongqun He
2024 — conf
Empowering Standardization of Cancer Vaccines Through Ontology: Enhanced Modeling and Data Analysis.
ICBO
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
2024 J jnl
Empowering standardization of cancer vaccines through ontology: enhanced modeling and data analysis.
J. Biomed. Semant.
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
2024 — conf
Enhancing Vaxign-DL for Vaccine Candidate Prediction with Added ESM-Generated Features.
ER (Workshops)
Yichao Chen, Yuhan Zhang, Yongqun He
2024 — conf
Grounding Realizable Entities.
ICBO
Michael Rabenberg, Carter Benson, Federico Donato, Yongqun He, Anthony Huffman, Shane Babcock, John Beverley
2024 J jnl
Grounding Realizable Entities.
CoRR
Michael Rabenberg, Carter Benson, Federico Donato, Yongqun He, Anthony Huffman, Shane Babcock, John Beverley
2024 — conf
Integrative Ontology of Bipolar Disorder (OBD): Advancing Bipolar Disorder Research Through an Interoperable Ontological Framework.
ER (Workshops)
Yujia Tian, Yongqun He, Rachel L. Richesson, Melvin G. McInnis
2024 J jnl
Mapping vaccine names in clinical trials to vaccine ontology using cascaded fine-tuned domain-specific language models.
J. Biomed. Semant.
Jianfu Li, Yiming Li, Yuanyi Pan, Jinjing Guo, Zenan Sun, Fang Li, Yongqun He, Cui Tao
2024 — conf
Nested Named Entity Recognition using Multilayer BERT-based Model.
CLEF (Working Notes)
Hasin Rehana, Benu Bansal, Nur Bengisu Çam, Jie Zheng, Yongqun He, Arzucan Özgür, Junguk Hur
2024 J jnl
Ontological representation, modeling, and analysis of parasite vaccines.
J. Biomed. Semant.
Anthony Huffman, Xumeng Zhang, Meghana Lanka, Jie Zheng, Anna Maria Masci, Yongqun He
2023 J jnl
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.
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
2023 J jnl
Big knowledge visualization of the COVID-19 CIDO ontology evolution.
BMC Medical Informatics Decis. Mak.
Ling Zheng, Yehoshua Perl, Yongqun He
2023 J jnl
Evaluation of GPT and BERT-based models on identifying protein-protein interactions in biomedical text.
CoRR
Hasin Rehana, Nur Bengisu Çam, Mert Basmaci, Yongqun He, Arzucan Özgür, Junguk Hur
2023 — conf
Ontology-based Representation and Analysis of Conditional Vaccine Immune Responses Using Omics Data.
ICBO
Anthony Huffman, Edison Ong, Timothy Brunson, Nasim Sanati, Jie Zheng, Anna Maria Masci, Guanming Wu, Yongqun He
2023 — conf
The Occupation Ontology (OccO): Building a Bridge between Global Occupational Standards.
JOWO
John Beverley, Sam Smith, Matthew Diller, William D. Duncan, Jie Zheng, John W. Judkins, William R. Hogan, Robin McGill, Damion M. Dooley, Yongqun He
2022 J jnl
A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology.
J. Biomed. Semant.
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
2022 J jnl
COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning.
Briefings Bioinform.
Anthony Huffman, Edison Ong, Junguk Hur, Adonis D'mello, Hervé Tettelin, Yongqun He
2022 — conf
Coordinating Coronavirus Research: The Virus Infectious Disease Ontology.
ICBO
John Beverley, Yongqun He, Barry Smith, Shane Babcock, Eric Merrell, Lindsay G. Cowell, Regina Hurley, Sebastian Deusing
2022 — conf
Foundational Development of an Occupation Ontology.
JOWO
Yongqun He, Samuel Smith, Damion M. Dooley
2022 J jnl
Identification of missing hierarchical relations in the vaccine ontology using acquired term pairs.
J. Biomed. Semant.
Warren Manuel, Rashmie Abeysinghe, Yongqun He, Cui Tao, Licong Cui
2022 J jnl
Mass spectrometry-based immunopeptidomics and computational vaccinology strategies for the identification of universal
Comput. Biol. Medicine
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
2022 — conf
OMOP-2-OPMI: Ontologization of OMOP CDM Using OPMI to Support Clinical Data interoperability and analysis.
ICBO
Long Tran, Yongqun He
2022 — conf
Ontological Representation and Analysis of the Molecular Interactions Related to COVID-19-associated Acute Kidney Injury.
ICBO
Ghida Arnous, Yongqun He
2022 — conf
The Ontology of Adverse Events in 2022.
ICBO
Qiuyue Yang, Jun Su, Xue Zhang, Yongqun He, Jiangan Xie
2022 — conf
Toward an Occupation Ontology, OccO.
ICBO
Sam Smith, Damion M. Dooley, Eric Merrell, John Beverley, Yongqun He
2021 — conf
A Community Effort for COVID-19 Ontology Harmonization.
ICBO
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
2021 J jnl
An Open Natural Language Processing Development Framework for EHR-based Clinical Research: A case demonstration using the National COVID Cohort Collaborative (N3C).
CoRR
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
2021 J jnl
CIDO ontology updates and secondary analysis of host responses to COVID-19 infection based on ImmPort reports and literature.
J. Biomed. Semant.
Anthony Huffman, Anna Maria Masci, Jie Zheng, Nasim Sanati, Timothy Brunson, Guanming Wu, Yongqun He
2021 J jnl
Development of the International Classification of Diseases Ontology (ICDO) and its application for COVID-19 diagnostic data analysis.
BMC Bioinform.
Ling Wan, Justin Song, Virginia He, Jennifer Roman, Grace Whah, Suyuan Peng, Luxia Zhang, Yongqun He
2021 — conf
Identification and Ontology Term Enrichment Analysis of Genes Associated with COVID-19 and Acute Kidney Disease.
ICBO
Guirui Huang, Suyuan Peng, Luxia Zhang, Yongqun He
2021 — conf
Ontology Modeling and Analysis of COVID-19-associated Acute Kidney Injury and Its Underlying Molecular Mechanisms.
ICBO
Easheta Shah, Roshan Desai, Suyuan Peng, Luxia Zhang, Yongqun He
2021 — conf
Ontology-based Modeling, Representation, and Analysis of Biomarkers in Healthy and Disease Kidney Tissue.
ICBO
Yingtong Liu, Wenjun Ju, Becky Steck, Sanjay Jain, Matthias Kretzler, Yongqun He
2021 J jnl
Standardization of assay representation in the Ontology for Biomedical Investigations.
Database J. Biol. Databases Curation
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.
2021 J jnl
The Human Phenotype Ontology in 2021.
Nucleic Acids Res.
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
2021 J jnl
Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning.
Nucleic Acids Res.
Edison Ong, Michael F. Cooke, Anthony Huffman, Zuoshuang Xiang, Mei U. Wong, Haihe Wang, Meenakshi Seetharaman, Ninotchka Valdez, Yongqun He
2021 J jnl
Visual comprehension and orientation into the COVID-19 CIDO ontology.
J. Biomed. Informatics
Ling Zheng, Yehoshua Perl, Yongqun He, Christopher Ochs, James Geller, Hao Liu, Vipina Kuttichi Keloth
2020 — conf
CIDO: The Community-Based Coronavirus Infectious Disease Ontology.
ICBO/ODLS
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
2020 — conf
OGG-CoV: Ontology Representation and Analysis of Genes and Genomes of Coronaviruses (short paper).
ICBO/ODLS
Anthony Huffman, Yongqun He
2020 J jnl
OntoPlot: A Novel Visualisation for Non-hierarchical Associations in Large Ontologies.
IEEE Trans. Vis. Comput. Graph.
Ying Yang, Michael Wybrow, Yuan-Fang Li, Tobias Czauderna, Yongqun He
2020 — ch.
Perform Pathway Enrichment Analysis Using ReactomeFIViz.
Protein-Protein Interaction Networks
Robin Haw, Fred Loney, Edison Ong, Yongqun He, Guanming Wu
2020 J jnl
Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events.
J. Am. Medical Informatics Assoc.
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
2020 J jnl
Vaxign-ML: supervised machine learning reverse vaccinology model for improved prediction of bacterial protective antigens.
Bioinform.
Edison Ong, Haihe Wang, Mei U. Wong, Meenakshi Seetharaman, Ninotchka Valdez, Yongqun He
2019 J jnl
A 2018 workshop: vaccine and drug ontology studies (VDOS 2018).
BMC Bioinform.
Junguk Hur, Cui Tao, Yongqun He
2019 J jnl
A statistical analysis of vaccine-adverse event data.
BMC Medical Informatics Decis. Mak.
Jian-Jian Ren, Tingni Sun, Yongqun He, Yuji Zhang
2019 — conf
Alignment of the Ontology of Host-Microbiome Interactions (OHMI) High Level Terms with Existing OBO Ontologies.
ICBO
Yongqun He, Jie Zheng, Anna Maria Masci, Jihad S. Obeid
2019 J jnl
Architecture and usability of OntoKeeper, an ontology evaluation tool.
BMC Medical Informatics Decis. Mak.
Muhammad Amith, Frank J. Manion, Chen Liang, Marcelline R. Harris, Dennis Wang, Yongqun He, Cui Tao
2019 J jnl
Cells in ExperimentaL Life Sciences (CELLS-2018): capturing the knowledge of normal and diseased cells with ontologies.
BMC Bioinform.
Sirarat Sarntivijai, Yongqun He, Alexander D. Diehl
2019 — conf
ICDO: Ontological Representation of the International Classification of Diseases (ICD) and its Application in English and Chinese Healthy Data Standardization.
ICBO
Ling Wan, Edison Ong, Yongqun He
2019 — conf
ICEO: a Biological Ontology for Representing and Analyzing the Bacterial Integrative and Conjugative Element.
ICBO
Meng Liu, Hong-Yu Ou, Yongqun He
2019 J jnl
Machine learning-based identification and rule-based normalization of adverse drug reactions in drug labels.
BMC Bioinform.
Mert Tiftikci, Arzucan Özgür, Yongqun He, Junguk Hur
2019 J jnl
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.
Hong Yu, Solomiya Nysak, Noemi Garg, Edison Ong, Xianwei Ye, Xiangyan Zhang, Yongqun He
2019 — conf
OGG-Bac: Ontological Representation of Orthologous Bacterial Genes.
ICBO
Meng Liu, Hong-Yu Ou, Yongqun He
2019 J jnl
OHMI: the ontology of host-microbiome interactions.
J. Biomed. Semant.
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
2019 — conf
OPMI: the Ontology of Precision Medicine and Investigation and its Support for Clinical Data and Metadata Representation and Analysis.
ICBO
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
2019 J jnl
OSCI: standardized stem cell ontology representation and use cases for stem cell investigation.
BMC Bioinform.
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
2019 J jnl
OntoPlot: A Novel Visualisation for Non-hierarchical Associations in Large Ontologies.
CoRR
Ying Yang, Michael Wybrow, Yuan-Fang Li, Tobias Czauderna, Yongqun He
2019 — conf
Ontolion: A Web-based Integrative Ontology Development Platform.
ICBO
Edison Ong, Yongqun He
2019 — conf
Ontological Derivation of Mendeleev's Periodic Table of Chemical Elements.
ICBO
Kaiyong Liu, Yongqun He
2019 — conf
Ontological Modeling of Two-Component Regulatory Systems.
ICBO
Hsin-Hui Huang, Meng Liu, Yongqun He
2019 J jnl
The cell line ontology-based representation, integration and analysis of cell lines used in China.
BMC Bioinform.
Hongjie Pan, Xiaocui Bian, Sheng Yang, Yongqun He, Xiaolin Yang, Yuqin Liu
2019 J jnl
VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions.
BMC Bioinform.
Edison Ong, Peter Sun, Kimberly Berke, Jie Zheng, Guanming Wu, Yongqun He
2019 J jnl
Victors: a web-based knowledge base of virulence factors in human and animal pathogens.
Nucleic Acids Res.
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
2018 — conf
Coordinated Evolution of Ontologies of Informed Consent.
ICBO
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
2018 — conf
KTAO: A Kidney Tissue Atlas Ontology to Support Community-Based Kidney Knowledge Base Development and Data Integration.
ICBO
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
2018 — conf
OntoKeeper: Semiotic-driven Ontology Evaluation Tool For Biomedical Ontologists.
BIBM
Muhammad Amith, Frank J. Manion, Chen Liang, Marcelline R. Harris, Dennis Wang, Yongqun He, Cui Tao
2018 J jnl
Ontology-based literature mining and class effect analysis of adverse drug reactions associated with neuropathy-inducing drugs.
J. Biomed. Semant.
Junguk Hur, Arzucan Özgür, Yongqun He
2018 J jnl
The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability.
J. Biomed. Semant.
Yongqun He, Zuoshuang Xiang, Jie Zheng, Yu Lin, James A. Overton, Edison Ong
2018 J jnl
VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria.
Briefings Bioinform.
Jun Li, Cui Tai, Zixin Deng, Weihong Zhong, Yongqun He, Hong-Yu Ou
2018 — conf
eXtensible Ontology Development (XOD) using Web-based Ontoanimal Tools.
ICBO
Edison Ong, Yongqun He, Jie Zheng
2017 J jnl
Cells in experimental life sciences - challenges and solution to the rapid evolution of knowledge.
BMC Bioinform.
Sirarat Sarntivijai, Alexander D. Diehl, Yongqun He
2017 J jnl
Comparison, alignment, and synchronization of cell line information between CLO and EFO.
BMC Bioinform.
Edison Ong, Sirarat Sarntivijai, Simon Jupp, Helen E. Parkinson, Yongqun He
2017 — conf
Extracting Adverse Drug Reactions using Deep Learning and Dictionary Based Approaches.
TAC
Mert Tiftikci, Arzucan Özgür, Yongqun He, Junguk Hur
2017 Misc conf
From Scoping Review to Metadata: An Evidence-Based Approach to Identifying Informed Consent Metadata for Biorepositories.
AMIA
Marcelline R. Harris, Frank J. Manion, Hsing-yi Song, Yongqun He, Muhamamd F. Amith, Cui Tao
2017 J jnl
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.
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
2017 — conf
OLOBO: A New Ontology for Linking and Integrating Open Biological and Biomedical Ontologies.
ICBO
Edison Ong, Yongqun He
2017 J jnl
Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration.
Nucleic Acids Res.
Edison Ong, Zuoshuang Xiang, Bin Zhao, Yue Liu, Yu Lin, Jie Zheng, Chris Mungall, Mélanie Courtot, Alan Ruttenberg, Yongqun He
2017 J jnl
Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses.
BMC Bioinform.
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
2017 J jnl
Ontology-based literature mining of E. coli vaccine-associated gene interaction networks.
J. Biomed. Semant.
Junguk Hur, Arzucan Özgür, Yongqun He
2017 J jnl
Ontology-based systematic representation and analysis of traditional Chinese drugs against rheumatism.
BMC Syst. Biol.
Qingping Liu, Jiahao Wang, Yan Zhu, Yongqun He
2017 J jnl
The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines.
Quant. Biol.
Jie Zheng, Huan Li, Qingzhi Liu, Yongqun He
2017 Misc conf
Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping and OAE-based representation and analysis of adverse events in patients treated with cancer drugs.
AMIA
Meiu Wong, Rebecca Racz, Edison Ong, Yongqun He
2016 Misc conf
Application of Ontobedia on Cell Line Ontology Development.
AMIA
Edison Ong, Yongqun He
2016 — conf
EGO: A Biomedical Ontology for Integrative Epigenome Representation and Analysis.
ICBO/BioCreative
Yongqun He, Zhaohui S. Qin, Jie Zheng
2016 — conf
Ignet: A Centrality and INO-based Web System for Analyzing and Visualizing Literature-mined Networks.
ICBO/BioCreative
Arzucan Özgür, Junguk Hur, Zuoshuang Xiang, Edison Ong, Dragomir R. Radev, Yongqun He
2016 — conf
Ontobull and BFOConvert: Web-based Programs to Support Automatic Ontology Conversion.
ICBO/BioCreative
Edison Ong, Zuoshuang Xiang, Jie Zheng, Barry Smith, Yongqun He
2016 Misc conf
Ontology-Based Analysis of Adverse Drug Reactions Associated with Anti-infection Drugs in China.
AMIA
Mei Li, Yuying Cao, Liwei Wang, Hongfang Liu, Yongqun He
2016 J jnl
Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events.
J. Biomed. Semant.
Abra Guo, Rebecca Racz, Junguk Hur, Yu Lin, Zuoshuang Xiang, Lili Zhao, Jordan Rinder, Guoqian Jiang, Qian Zhu, Yongqun He
2016 — conf
The Cell Line Ontology Integration and Analysis of the Knowledge of LINCS Cell Lines.
ICBO/BioCreative
Edison Ong, Jiangan Xie, Zhaohui Ni, Qingping Liu, Yu Lin, Vasileios Stathias, Caty Chung, Stephan C. Schürer, Yongqun He
2016 J jnl
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.
J. Biomed. Semant.
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
2016 J jnl
The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature.
BioData Min.
Arzucan Özgür, Junguk Hur, Yongqun He
2016 J jnl
The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology.
J. Biomed. Semant.
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
2016 J jnl
The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis.
J. Biomed. Semant.
Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Yu Lin, Alfred O. Hero III, Barry Smith, Yongqun He
2016 J jnl
The development of non-coding RNA ontology.
Int. J. Data Min. Bioinform.
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
2016 J jnl
VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms.
J. Biomed. Semant.
Yu Lin, Jie Zheng, Yongqun He
2016 J jnl
Vaccine and Drug Ontology Studies (VDOS 2014).
J. Biomed. Semant.
Cui Tao, Yongqun He, Sivaram Arabandi
2015 — conf
A domain ontology for the Non-Coding RNA field.
BIBM
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
2015 — conf
Bridging Vaccine Ontology and NCIt vaccine domain for cancer vaccine data integration and analysis.
ICBO
Yongqun He, Guoqian Jiang
2015 J jnl
Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions.
J. Biomed. Semant.
Junguk Hur, Arzucan Özgür, Zuoshuang Xiang, Yongqun He
2015 — conf
Extension of the Interaction Network Ontology for Literature Mining of Gene-gene Interaction Networks from Sentences with Multiple Interaction Keywords.
BDM2I@ISWC
Arzucan Özgür, Junguk Hur, Yongqun He
2015 — conf
GOfox: Semantics-based simplified hierarchical classification and interactive visualization to support GO enrichment analysis.
ICBO
Edison Ong, Yongqun He
2015 — conf
Ontoanimal tools for reusing ontologies, generating and editing ontology terms, and dereferencing ontology terms.
ICBO
Yongqun He, Jie Zheng, Yu Lin
2015 J jnl
Ontology-based representation and analysis of host-Brucella interactions.
J. Biomed. Semant.
Yu Lin, Zuoshuang Xiang, Yongqun He
2015 — conf
Ontorat: Automatic generation and editing of ontology terms.
ICBO
Yongqun He, Jie Zheng, Yu Lin
2015 J jnl
Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns.
J. Biomed. Semant.
Zuoshuang Xiang, Jie Zheng, Yu Lin, Yongqun He
2014 J jnl
A 2013 workshop: vaccine and drug ontology studies (VDOS 2013).
J. Biomed. Semant.
Cui Tao, Yongqun He, Sivaram Arabandi
2014 Misc conf
Analysis of Content Coverage for Informed Consent Concepts.
AMIA
Frank J. Manion, Elizabeth Eisenhauer, Alla Karnovsky, Yongqun He, Yu Lin, Marcelline R. Harris
2014 J jnl
CLO: The cell line ontology.
J. Biomed. Semant.
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
2014 J jnl
DNAVaxDB: the first web-based DNA vaccine database and its data analysis.
BMC Bioinform.
Rebecca Racz, Xinna Li, Mukti Patel, Zuoshuang Xiang, Yongqun He
2014 — conf
Development of a BFO-Based Informed Consent Ontology (ICO).
ICBO
Yu Lin, Marcelline R. Harris, Frank J. Manion, Elizabeth Eisenhauer, Bin Zhao, Wei Shi, Alla Karnovsky, Yongqun He
2014 J jnl
ICoVax 2013: The 3
BMC Bioinform.
Anne S. De Groot, Phoebe De Groot, Yongqun He
2014 J jnl
OAE: The Ontology of Adverse Events.
J. Biomed. Semant.
Yongqun He, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao, Barry Smith
2014 — conf
OBCS: The Ontology of Biological and Clinical Statistics.
ICBO
Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Yu Lin, Alfred O. Hero III, Barry Smith, Yongqun He
2014 — conf
OGG: a Biological Ontology for Representing Genes and Genomes in Specific Organisms.
ICBO
Yongqun He, Yue Liu, Bin Zhao
2014 — conf
Ontobat: An Ontology-based Semantic Web Approach for Linked Data Processing and Analysis.
ICBO
Zuoshuang Xiang, Yu Lin, Yongqun He
2014 J jnl
Ontodog: a web-based ontology community view generation tool.
Bioinform.
Jie Zheng, Zuoshuang Xiang, Christian J. Stoeckert Jr., Yongqun He
2014 J jnl
The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events.
J. Biomed. Semant.
Yu Lin, Yongqun He
2014 J jnl
Updates on the web-based VIOLIN vaccine database and analysis system.
Nucleic Acids Res.
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
2013 J jnl
A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks.
BMC Syst. Biol.
Zuoshuang Xiang, Tingting Qin, Zhaohui S. Qin, Yongqun He
2013 — conf
Alignment of Cultured Cell Modeling Across OBO Foundry Ontologies: Key Outcomes, Insights.
ICBO
Matthew H. Brush, Jie Zheng, Yongqun He, Sirarat Sarntivijai, Bjoern Peters, Alexander D. Diehl, Christian J. Stoeckert Jr., Melissa A. Haendel
2013 — conf
Analysis of Vaccine-related Networks using Semantic MEDLINE and the Vaccine Ontology.
VDOS+DO@ICBO
Yuji Zhang, Cui Tao, Yongqun He, Pradip Kanjamala, Hongfang Liu
2013 J jnl
Computational vaccinology and the ICoVax 2012 workshop.
BMC Bioinform.
Yongqun He, Zhiwei Cao, Anne S. De Groot, Vladimir Brusic, Christian Schönbach, Nikolai Petrovsky
2013 J jnl
Genome-wide prediction of vaccine targets for human herpes simplex viruses using Vaxign reverse vaccinology.
BMC Bioinform.
Zuoshuang Xiang, Yongqun He
2013 — conf
HINO: BFO-aligned ontology representation of human molecular interactions and pathways.
ICBO
Zuoshuang Xiang, Yongqun He
2013 J jnl
HINO: a BFO-aligned ontology representing human molecular interactions and pathways.
CoRR
Yongqun He, Zuoshuang Xiang
2013 J jnl
Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates.
BMC Bioinform.
Thomas E. Todd, Omar Tibi, Yu Lin, Samantha Sayers, Denise N. Bronner, Zuoshuang Xiang, Yongqun He
2013 J jnl
Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology.
J. Biomed. Semant.
Yuji Zhang, Cui Tao, Yongqun He, Pradip Kanjamala, Hongfang Liu
2013 — conf
Ontology modeling of genetic susceptibility to adverse events following vaccination.
VDOS+DO@ICBO
Yu Lin, Yongqun He
2013 — ed.
Proceedings of the ICBO2013 Workshops: International Workshop on Vaccine and Drug Ontology Studies (VDOS 2013), International Workshop on Definitions in Ontologies (DO 2013), part of the Semantic Trilogy 2013 , Montreal, Quebec, Canada, July 6th - 12th 2013.
VDOS+DO@ICBO
Cui Tao, Yongqun He, Luca Toldo, Sivaram Arabandi, Selja Seppälä, Alan Ruttenberg
2013 J jnl
The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines.
J. Biomed. Semant.
Erica Marcos, Bin Zhao, Yongqun He
2013 — conf
The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing vaccine adverse events.
VDOS+DO@ICBO
Erica Marcos, Yongqun He
2012 J jnl
A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012).
J. Biomed. Semant.
Yongqun He, Luca Toldo, Gully Burns, Cui Tao, Darrell R. Abernethy
2012 J jnl
Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining.
J. Biomed. Semant.
Junguk Hur, Arzucan Özgür, Zuoshuang Xiang, Yongqun He
2012 — conf
Ontodog: A Web-based Ontology Community View Generator.
ICBO
Jie Zheng, Zuoshuang Xiang, Christian J. Stoeckert Jr., Yongqun He
2012 J jnl
Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses.
J. Biomed. Semant.
Yu Lin, Yongqun He
2012 J jnl
Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis.
J. Biomed. Semant.
Cui Tao, Yongqun He, Hannah Yang, Gregory A. Poland, Christopher G. Chute
2012 — conf
Ontorat web server for automatic generation and annotations of new ontology terms.
ICBO
Zuoshuang Xiang, Yu Lin, Yongqun He
2011 — conf
AEO: A Realism-Based Biomedical Ontology for the Representation of Adverse Events.
ICBO
Yongqun He, Zuoshuang Xiang, Sirarat Sarntivijai, Luca Toldo, Werner Ceusters
2011 J jnl
Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology.
J. Biomed. Semant.
Yu Lin, Zuoshuang Xiang, Yongqun He
2011 — conf
Cell Line Ontology: Redesigning the Cell Line Knowledgebase to Aid Integrative Translational Informatics.
ICBO
Sirarat Sarntivijai, Zuoshuang Xiang, Terrence F. Meehan, Alexander D. Diehl, Uma Vempati, Stephan C. Schürer, Chao Pang, James Malone, Helen E. Parkinson, Brian D. Athey, Yongqun He
2011 J jnl
Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology.
J. Biomed. Semant.
Arzucan Özgür, Zuoshuang Xiang, Dragomir R. Radev, Yongqun He
2011 — conf
OntoFox and its Application in Development of Brucellosis Ontology.
ICBO
Zuoshuang Xiang, Yu Lin, Yongqun He
2011 — conf
Ontobee: A Linked Data Server and Browser for Ontology Terms.
ICBO
Zuoshuang Xiang, Chris Mungall, Alan Ruttenberg, Yongqun He
2011 J jnl
Protegen: a web-based protective antigen database and analysis system.
Nucleic Acids Res.
Brian Yang, Samantha Sayers, Zuoshuang Xiang, Yongqun He
2011 — conf
Towards a Semantic Web Application: Ontology-Driven Ortholog Clustering Analysis.
ICBO
Yu Lin, Zuoshuang Xiang, Yongqun He
2010 J jnl
Modeling biomedical experimental processes with OBI.
J. Biomed. Semant.
Ryan Remy Brinkman, Mélanie Courtot, Dirk Derom, Jennifer Fostel, Yongqun He, Phillip W. Lord, James Malone, Helen E. Parkinson, Björn Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Larisa N. Soldatova, Christian J. Stoeckert Jr., Jessica A. Turner, Jie Zheng, et al.
2008 J jnl
VIOLIN: vaccine investigation and online information network.
Nucleic Acids Res.
Zuoshuang Xiang, Thomas E. Todd, Kim P. Ku, Bethany L. Kovacic, Charles B. Larson, Fang Chen, Andrew P. Hodges, Yuying Tian, Elizabeth A. Olenzek, Boyang Zhao, Lesley A. Colby, Howard G. Rush, Janet R. Gilsdorf, George W. Jourdian, Yongqun He
2007 J jnl
CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clustering.
Bioinform.
Zuoshuang Xiang, Zhaohui S. Qin, Yongqun He
2007 J jnl
miniTUBA: medical inference by network integration of temporal data using Bayesian analysis.
Bioinform.
Zuoshuang Xiang, Rebecca M. Minter, Xiaoming Bi, Peter J. Woolf, Yongqun He
2006 J jnl
BBP:
BMC Bioinform.
Zuoshuang Xiang, Wenjie Zheng, Yongqun He
2005 J jnl
PIML: the Pathogen Information Markup Language.
Bioinform.
Yongqun He, Richard R. Vines, Alice R. Wattam, Georgiy V. Abramochkin, Allan Dickerman, J. Dana Eckart, Bruno W. S. Sobral