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2020 – today
- 2024
[j78]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): 4 (2024)- [j77]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): 12 (2024) - [j76]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): 14 (2024) - [c61]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: 197-206 - [c60]Yichao Chen, Yuhan Zhang, Yongqun He
:
Enhancing Vaxign-DL for Vaccine Candidate Prediction with Added ESM-Generated Features. ER (Workshops) 2024: 148-158 - [c59]Yujia Tian, Yongqun He, Rachel L. Richesson, Melvin G. McInnis:
Integrative Ontology of Bipolar Disorder (OBD): Advancing Bipolar Disorder Research Through an Interoperable Ontological Framework. ER (Workshops) 2024: 169-179 - [i7]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 abs/2405.00186 (2024) - [i6]Michael Rabenberg, Carter Benson, Federico Donato, Yongqun He, Anthony Huffman, Shane Babcock, John Beverley:
Grounding Realizable Entities. CoRR abs/2405.00197 (2024) - 2023
- [j75]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): 2036-2040 (2023) - [j74]Ling Zheng, Yehoshua Perl, Yongqun He:
Big knowledge visualization of the COVID-19 CIDO ontology evolution. BMC Medical Informatics Decis. Mak. 23(1): 88 (2023) - [c58]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: 1-12 - [c57]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 - [i5]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 abs/2303.17728 (2023) - 2022
- [j73]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) - [j72]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): 22 (2022) - [j71]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): 25 (2022) - [j70]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:
Mass spectrometry-based immunopeptidomics and computational vaccinology strategies for the identification of universal Shigella immunogenic candidates. Comput. Biol. Medicine 148: 105900 (2022) - [c56]Ghida Arnous, Yongqun He:
Ontological Representation and Analysis of the Molecular Interactions Related to COVID-19-associated Acute Kidney Injury. ICBO 2022: 1 - [c55]John Beverley, Yongqun He, Barry Smith, Shane Babcock, Eric Merrell, Lindsay G. Cowell, Regina Hurley, Sebastian Deusing:
Coordinating Coronavirus Research: The Virus Infectious Disease Ontology. ICBO 2022: 1-14 - [c54]Sam Smith, Damion M. Dooley, Eric Merrell, John Beverley, Yongqun He:
Toward an Occupation Ontology, OccO. ICBO 2022: 1 - [c53]Long Tran, Yongqun He:
OMOP-2-OPMI: Ontologization of OMOP CDM Using OPMI to Support Clinical Data interoperability and analysis. ICBO 2022: 1-11 - [c52]Qiuyue Yang, Jun Su, Xue Zhang, Yongqun He, Jiangan Xie:
The Ontology of Adverse Events in 2022. ICBO 2022: 1 - [c51]Yongqun He, Samuel Smith, Damion M. Dooley:
Foundational Development of an Occupation Ontology. JOWO 2022 - 2021
- [j69]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) - [j68]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): 18 (2021) - [j67]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. 22-S(6): 508 (2021) - [j66]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: 103861 (2021) - [j65]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): D1207-D1217 (2021) - [j64]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): 671-678 (2021) - [c50]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: 70-76 - [c49]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: 110-115 - [c48]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: 116-121 - [c47]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: 122-127 - [i4]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 abs/2110.10780 (2021) - 2020
- [j63]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): 3185-3191 (2020) - [j62]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): 1046-1056 (2020) - [j61]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): 1140-1150 (2020) - [c46]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: 1-10 - [c45]Anthony Huffman, Yongqun He:
OGG-CoV: Ontology Representation and Analysis of Genes and Genomes of Coronaviruses (short paper). ICBO/ODLS 2020: 1-5 - [p1]Robin Haw, Fred Loney, Edison Ong, Yongqun He, Guanming Wu:
Perform Pathway Enrichment Analysis Using ReactomeFIViz. Protein-Protein Interaction Networks 2020: 165-179
2010 – 2019
- 2019
- [j60]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): 25 (2019) - [j59]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. 20-S(5): 227-230 (2019) - [j58]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. 20-S(5): 237-247 (2019) - [j57]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. 20-S(5): 249-258 (2019) - [j56]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. 20-S(7): 117-128 (2019) - [j55]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. 20-S(21): 704 (2019) - [j54]Junguk Hur, Cui Tao, Yongqun He:
A 2018 workshop: vaccine and drug ontology studies (VDOS 2018). BMC Bioinform. 20-S(21): 705 (2019) - [j53]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. 20-S(21): 707 (2019) - [j52]Jian-Jian Ren, Tingni Sun, Yongqun He, Yuji Zhang:
A statistical analysis of vaccine-adverse event data. BMC Medical Informatics Decis. Mak. 19(1): 101:1-101:12 (2019) - [j51]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. 19-S(4): 152:1-152:18 (2019) - [j50]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): D693-D700 (2019) - [c44]Meng Liu, Hong-Yu Ou, Yongqun He:
ICEO: a Biological Ontology for Representing and Analyzing the Bacterial Integrative and Conjugative Element. ICBO 2019: 1-10 - [c43]Meng Liu, Hong-Yu Ou, Yongqun He:
OGG-Bac: Ontological Representation of Orthologous Bacterial Genes. ICBO 2019: 1 - [c42]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: 1-10 - [c41]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: 1 - [c40]Hsin-Hui Huang, Meng Liu, Yongqun He:
Ontological Modeling of Two-Component Regulatory Systems. ICBO 2019: 1 - [c39]Kaiyong Liu, Yongqun He:
Ontological Derivation of Mendeleev's Periodic Table of Chemical Elements. ICBO 2019: 1 - [c38]Edison Ong, Yongqun He:
Ontolion: A Web-based Integrative Ontology Development Platform. ICBO 2019: 1 - [c37]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: 1 - [i3]Ying Yang, Michael Wybrow, Yuan-Fang Li, Tobias Czauderna, Yongqun He:
OntoPlot: A Novel Visualisation for Non-hierarchical Associations in Large Ontologies. CoRR abs/1908.00688 (2019) - 2018
- [j49]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): 566-574 (2018) - [j48]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): 3:1-3:10 (2018) - [j47]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): 17:1-17:10 (2018) - [c36]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: 1614-1617 - [c35]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 - [c34]Edison Ong, Yongqun He, Jie Zheng:
eXtensible Ontology Development (XOD) using Web-based Ontoanimal Tools. ICBO 2018 - [c33]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 - 2017
- [j46]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): 11:1-11:15 (2017) - [j45]Junguk Hur, Arzucan Özgür, Yongqun He:
Ontology-based literature mining of E. coli vaccine-associated gene interaction networks. J. Biomed. Semant. 8(1): 12:1-12:10 (2017) - [j44]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): 25-33 (2017) - [j43]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): 43-53 (2017) - [j42]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): 560:1-560:5 (2017) - [j41]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): 113-125 (2017) - [j40]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): D347-D352 (2017) - [j39]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): 291-301 (2017) - [c32]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 - [c31]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 - [c30]Edison Ong, Yongqun He:
OLOBO: A New Ontology for Linking and Integrating Open Biological and Biomedical Ontologies. ICBO 2017 - [i2]Mert Tiftikci, Arzucan Özgür, Yongqun He, Junguk Hur:
Extracting Adverse Drug Reactions using Deep Learning and Dictionary Based Approaches. TAC 2017 - 2016
- [j38]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: 41:1-41:17 (2016) - [j37]Cui Tao, Yongqun He, Sivaram Arabandi:
Vaccine and Drug Ontology Studies (VDOS 2014). J. Biomed. Semant. 7: 6 (2016) - [j36]Yu Lin, Jie Zheng, Yongqun He:
VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms. J. Biomed. Semant. 7: 20 (2016) - [j35]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: 24 (2016) - [j34]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: 29 (2016) - [j33]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: 44 (2016) - [j32]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: 53 (2016) - [j31]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): 214-232 (2016) - [c29]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 - [c28]Edison Ong, Yongqun He:
Application of Ontobedia on Cell Line Ontology Development. AMIA 2016 - [c27]Yongqun He, Zhaohui S. Qin, Jie Zheng:
EGO: A Biomedical Ontology for Integrative Epigenome Representation and Analysis. ICBO/BioCreative 2016 - [c26]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 - [c25]Edison Ong, Zuoshuang Xiang, Jie Zheng, Barry Smith, Yongqun He:
Ontobull and BFOConvert: Web-based Programs to Support Automatic Ontology Conversion. ICBO/BioCreative 2016 - [c24]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 - 2015
- [j30]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: 2 (2015) - [j29]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: 4 (2015) - [j28]Yu Lin, Zuoshuang Xiang, Yongqun He:
Ontology-based representation and analysis of host-Brucella interactions. J. Biomed. Semant. 6: 37 (2015) - [c23]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: 621-624 - [c22]Yongqun He, Guoqian Jiang:
Bridging Vaccine Ontology and NCIt vaccine domain for cancer vaccine data integration and analysis. ICBO 2015 - [c21]Yongqun He, Jie Zheng, Yu Lin:
Ontoanimal tools for reusing ontologies, generating and editing ontology terms, and dereferencing ontology terms. ICBO 2015 - [c20]Yongqun He, Jie Zheng, Yu Lin:
Ontorat: Automatic generation and editing of ontology terms. ICBO 2015 - [c19]Edison Ong, Yongqun He:
GOfox: Semantics-based simplified hierarchical classification and interactive visualization to support GO enrichment analysis. ICBO 2015 - [c18]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 - 2014
- [j27]Jie Zheng, Zuoshuang Xiang, Christian J. Stoeckert Jr., Yongqun He:
Ontodog: a web-based ontology community view generation tool. Bioinform. 30(9): 1340-1342 (2014) - [j26]Cui Tao, Yongqun He, Sivaram Arabandi:
A 2013 workshop: vaccine and drug ontology studies (VDOS 2013). J. Biomed. Semant. 5: 16 (2014) - [j25]Yu Lin, Yongqun He:
The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events. J. Biomed. Semant. 5: 19 (2014) - [j24]Yongqun He, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao, Barry Smith:
OAE: The Ontology of Adverse Events. J. Biomed. Semant. 5: 29 (2014) - [j23]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: 37 (2014) - [j22]Anne S. De Groot, Phoebe De Groot, Yongqun He:
ICoVax 2013: The 3rd ISV Pre-conference Computational Vaccinology Workshop. BMC Bioinform. 15(S-4): I1 (2014) - [j21]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): S2 (2014) - [j20]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): 1124-1132 (2014) - [c17]Frank J. Manion, Elizabeth Eisenhauer, Alla Karnovsky, Yongqun He, Yu Lin, Marcelline R. Harris:
Analysis of Content Coverage for Informed Consent Concepts. AMIA 2014 - [c16]Yongqun He, Yue Liu, Bin Zhao:
OGG: a Biological Ontology for Representing Genes and Genomes in Specific Organisms. ICBO 2014: 13-20 - [c15]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: 65 - [c14]Yu Lin, Marcelline R. Harris, Frank J. Manion, Elizabeth Eisenhauer, Bin Zhao, Wei Shi, Alla Karnovsky, Yongqun He:
Development of a BFO-Based Informed Consent Ontology (ICO). ICBO 2014: 84-86 - [c13]Zuoshuang Xiang, Yu Lin, Yongqun He:
Ontobat: An Ontology-based Semantic Web Approach for Linked Data Processing and Analysis. ICBO 2014: 93-95 - 2013
- [j19]Yuji Zhang, Cui Tao, Yongqun He, Pradip Kanjamala, Hongfang Liu:
Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology. J. Biomed. Semant. 4: 33 (2013) - [j18]Erica Marcos, Bin Zhao, Yongqun He:
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. 4: 40 (2013) - [j17]Yongqun He, Zhiwei Cao, Anne S. De Groot, Vladimir Brusic, Christian Schönbach, Nikolai Petrovsky:
Computational vaccinology and the ICoVax 2012 workshop. BMC Bioinform. 14(S-4): I1 (2013) - [j16]Zuoshuang Xiang, Yongqun He:
Genome-wide prediction of vaccine targets for human herpes simplex viruses using Vaxign reverse vaccinology. BMC Bioinform. 14(S-4): S2 (2013) - [j15]Thomas E. Todd, Omar Tibi, Yu Lin, Samantha Sayers, Denise N. Bronner, Zuoshuang Xiang, Yongqun He:
Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. BMC Bioinform. 14(S-6): S3 (2013) - [j14]Zuoshuang Xiang, Tingting Qin, Zhaohui S. Qin, Yongqun He:
A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks. BMC Syst. Biol. 7(S-3): S9 (2013) - [c12]Matthew H. Brush, Jie Zheng, Yongqun He, Sirarat Sarntivijai, Bjoern Peters, Alexander D. Diehl, Christian J. Stoeckert Jr., Melissa A. Haendel:
Alignment of Cultured Cell Modeling Across OBO Foundry Ontologies: Key Outcomes, Insights. ICBO 2013: 120 - [c11]Yu Lin, Yongqun He:
Ontology modeling of genetic susceptibility to adverse events following vaccination. VDOS+DO@ICBO 2013 - [c10]Erica Marcos, Yongqun He:
The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing vaccine adverse events. VDOS+DO@ICBO 2013 - [c9]Zuoshuang Xiang, Yongqun He:
HINO: BFO-aligned ontology representation of human molecular interactions and pathways. ICBO 2013: 122 - [c8]Yuji Zhang, Cui Tao, Yongqun He, Pradip Kanjamala, Hongfang Liu:
Analysis of Vaccine-related Networks using Semantic MEDLINE and the Vaccine Ontology. VDOS+DO@ICBO 2013 - [e1]Cui Tao, Yongqun He, Luca Toldo, Sivaram Arabandi, Selja Seppälä, Alan Ruttenberg:
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. CEUR Workshop Proceedings 1061, CEUR-WS.org 2013 [contents] - [i1]Yongqun He, Zuoshuang Xiang:
HINO: a BFO-aligned ontology representing human molecular interactions and pathways. CoRR abs/1311.3355 (2013) - 2012
- [j13]Yongqun He, Luca Toldo, Gully Burns, Cui Tao, Darrell R. Abernethy:
A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012). J. Biomed. Semant. 3: 12 (2012) - [j12]Cui Tao, Yongqun He, Hannah Yang, Gregory A. Poland, Christopher G. Chute:
Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis. J. Biomed. Semant. 3: 13 (2012) - [j11]Yu Lin, Yongqun He:
Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses. J. Biomed. Semant. 3: 17 (2012) - [j10]Junguk Hur, Arzucan Özgür, Zuoshuang Xiang, Yongqun He:
Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining. J. Biomed. Semant. 3: 18 (2012) - [c7]Zuoshuang Xiang, Yu Lin, Yongqun He:
Ontorat web server for automatic generation and annotations of new ontology terms. ICBO 2012 - [c6]Jie Zheng, Zuoshuang Xiang, Christian J. Stoeckert Jr., Yongqun He:
Ontodog: A Web-based Ontology Community View Generator. ICBO 2012 - 2011
- [j9]Yu Lin, Zuoshuang Xiang, Yongqun He:
Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology. J. Biomed. Semant. 2: 9 (2011) - [j8]Arzucan Özgür, Zuoshuang Xiang, Dragomir R. Radev, Yongqun He:
Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology. J. Biomed. Semant. 2(S-2): S8 (2011) - [j7]Brian Yang, Samantha Sayers, Zuoshuang Xiang, Yongqun He:
Protegen: a web-based protective antigen database and analysis system. Nucleic Acids Res. 39(Database-Issue): 1073-1078 (2011) - [c5]Yongqun He, Zuoshuang Xiang, Sirarat Sarntivijai, Luca Toldo, Werner Ceusters:
AEO: A Realism-Based Biomedical Ontology for the Representation of Adverse Events. ICBO 2011 - [c4]Yu Lin, Zuoshuang Xiang, Yongqun He:
Towards a Semantic Web Application: Ontology-Driven Ortholog Clustering Analysis. ICBO 2011 - [c3]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:
Cell Line Ontology: Redesigning the Cell Line Knowledgebase to Aid Integrative Translational Informatics. ICBO 2011 - [c2]Zuoshuang Xiang, Yu Lin, Yongqun He:
OntoFox and its Application in Development of Brucellosis Ontology. ICBO 2011 - [c1]Zuoshuang Xiang, Chris Mungall, Alan Ruttenberg, Yongqun He:
Ontobee: A Linked Data Server and Browser for Ontology Terms. ICBO 2011 - 2010
- [j6]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.:
Modeling biomedical experimental processes with OBI. J. Biomed. Semant. 1(S-1): S7 (2010)
2000 – 2009
- 2008
- [j5]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:
VIOLIN: vaccine investigation and online information network. Nucleic Acids Res. 36(Database-Issue): 923-928 (2008) - 2007
- [j4]Zuoshuang Xiang, Zhaohui S. Qin, Yongqun He:
CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clustering. Bioinform. 23(14): 1843-1845 (2007) - [j3]Zuoshuang Xiang, Rebecca M. Minter, Xiaoming Bi, Peter J. Woolf, Yongqun He:
miniTUBA: medical inference by network integration of temporal data using Bayesian analysis. Bioinform. 23(18): 2423-2432 (2007) - 2006
- [j2]Zuoshuang Xiang, Wenjie Zheng, Yongqun He:
BBP: Brucella genome annotation with literature mining and curation. BMC Bioinform. 7: 347 (2006) - 2005
- [j1]Yongqun He, Richard R. Vines, Alice R. Wattam, Georgiy V. Abramochkin, Allan Dickerman, J. Dana Eckart, Bruno W. S. Sobral:
PIML: the Pathogen Information Markup Language. Bioinform. 21(1): 116-121 (2005)
Coauthor Index
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