PIML: the Pathogen Information Markup Language. - Yongqun He; Richard R. Vines; Alice R. Wattam; Georgiy V. Abramochkin; Allan Dickerman; J. Dana Eckart; Bruno W. S. Sobral (Bioinform., 2005)

BBP: Brucella genome annotation with literature mining and curation. - Zuoshuang Xiang; Wenjie Zheng; Yongqun He (BMC Bioinform., 2006)

miniTUBA: medical inference by network integration of temporal data using Bayesian analysis. - Zuoshuang Xiang; Rebecca M. Minter; Xiaoming Bi; Peter J. Woolf; Yongqun He (Bioinform., 2007)

CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clustering. - Zuoshuang Xiang; Zhaohui S. Qin; Yongqun He (Bioinform., 2007)

VIOLIN: vaccine investigation and online information network. - 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; et al. (Nucleic Acids Res., 2008)

Modeling biomedical experimental processes with OBI. - 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; et al. (J. Biomed. Semant., 2010)

AEO: A Realism-Based Biomedical Ontology for the Representation of Adverse Events. - Yongqun He; Zuoshuang Xiang; Sirarat Sarntivijai; Luca Toldo; Werner Ceusters (ICBO, 2011)

Towards a Semantic Web Application: Ontology-Driven Ortholog Clustering Analysis. - Yu Lin; Zuoshuang Xiang; Yongqun He (ICBO, 2011)

Cell Line Ontology: Redesigning the Cell Line Knowledgebase to Aid Integrative Translational Informatics. - 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 (ICBO, 2011)

OntoFox and its Application in Development of Brucellosis Ontology. - Zuoshuang Xiang; Yu Lin; Yongqun He (ICBO, 2011)

Ontobee: A Linked Data Server and Browser for Ontology Terms. - Zuoshuang Xiang; Chris Mungall; Alan Ruttenberg; Yongqun He (ICBO, 2011)

Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology. - Yu Lin; Zuoshuang Xiang; Yongqun He (J. Biomed. Semant., 2011)

Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology. - Arzucan Özgür; Zuoshuang Xiang; Dragomir R. Radev; Yongqun He (J. Biomed. Semant., 2011)

Protegen: a web-based protective antigen database and analysis system. - Brian Yang; Samantha Sayers; Zuoshuang Xiang; Yongqun He (Nucleic Acids Res., 2011)

Ontorat web server for automatic generation and annotations of new ontology terms. - Zuoshuang Xiang; Yu Lin; Yongqun He (ICBO, 2012)

Ontodog: A Web-based Ontology Community View Generator. - Jie Zheng 001; Zuoshuang Xiang; Christian J. Stoeckert Jr.; Yongqun He (ICBO, 2012)

A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012). - Yongqun He; Luca Toldo; Gully Burns; Cui Tao; Darrell R. Abernethy (J. Biomed. Semant., 2012)

Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining. - Junguk Hur; Arzucan Özgür; Zuoshuang Xiang; Yongqun He (J. Biomed. Semant., 2012)

Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses. - Yu Lin; Yongqun He (J. Biomed. Semant., 2012)

Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis. - Cui Tao; Yongqun He; Hannah Yang; Gregory A. Poland; Christopher G. Chute (J. Biomed. Semant., 2012)

Alignment of Cultured Cell Modeling Across OBO Foundry Ontologies: Key Outcomes, Insights. - Matthew H. Brush; Jie Zheng 001; Yongqun He; Sirarat Sarntivijai; Bjoern Peters; Alexander D. Diehl; Christian J. Stoeckert Jr.; Melissa A. Haendel (ICBO, 2013)

Ontology modeling of genetic susceptibility to adverse events following vaccination. - Yu Lin; Yongqun He (VDOS+DO@ICBO, 2013)

The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing vaccine adverse events. - Erica Marcos; Yongqun He (VDOS+DO@ICBO, 2013)

HINO: BFO-aligned ontology representation of human molecular interactions and pathways. - Zuoshuang Xiang; Yongqun He (ICBO, 2013)

Analysis of Vaccine-related Networks using Semantic MEDLINE and the Vaccine Ontology. - Yuji Zhang 001; Cui Tao; Yongqun He; Pradip Kanjamala; Hongfang Liu (VDOS+DO@ICBO, 2013)

The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines. - Erica Marcos; Bin Zhao; Yongqun He (J. Biomed. Semant., 2013)

Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology. - Yuji Zhang 001; Cui Tao; Yongqun He; Pradip Kanjamala; Hongfang Liu (J. Biomed. Semant., 2013)

Computational vaccinology and the ICoVax 2012 workshop. - Yongqun He; Zhiwei Cao; Anne S. De Groot; Vladimir Brusic; Christian Schönbach; Nikolai Petrovsky (BMC Bioinform., 2013)

Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. - Thomas E. Todd; Omar Tibi; Yu Lin; Samantha Sayers; Denise N. Bronner; Zuoshuang Xiang; Yongqun He (BMC Bioinform., 2013)

Genome-wide prediction of vaccine targets for human herpes simplex viruses using Vaxign reverse vaccinology. - Zuoshuang Xiang; Yongqun He (BMC Bioinform., 2013)

A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks. - Zuoshuang Xiang; Tingting Qin; Zhaohui S. Qin; Yongqun He (BMC Syst. Biol., 2013)

HINO: a BFO-aligned ontology representing human molecular interactions and pathways. - Yongqun He; Zuoshuang Xiang (CoRR, 2013)

Analysis of Content Coverage for Informed Consent Concepts. - Frank J. Manion; Elizabeth Eisenhauer; Alla Karnovsky; Yongqun He; Yu Lin; Marcelline R. Harris (AMIA, 2014)

OGG: a Biological Ontology for Representing Genes and Genomes in Specific Organisms. - Yongqun He; Yue Liu; Bin Zhao (ICBO, 2014)

Development of a BFO-Based Informed Consent Ontology (ICO). - Yu Lin; Marcelline R. Harris; Frank J. Manion; Elizabeth Eisenhauer; Bin Zhao; Wei Shi; Alla Karnovsky; Yongqun He (ICBO, 2014)

Ontobat: An Ontology-based Semantic Web Approach for Linked Data Processing and Analysis. - Zuoshuang Xiang; Yu Lin; Yongqun He (ICBO, 2014)

OBCS: The Ontology of Biological and Clinical Statistics. - Jie Zheng 001; Marcelline R. Harris; Anna Maria Masci; Yu Lin; Alfred O. Hero III; Barry Smith 001; Yongqun He (ICBO, 2014)

Ontodog: a web-based ontology community view generation tool. - Jie Zheng 001; Zuoshuang Xiang; Christian J. Stoeckert Jr.; Yongqun He (Bioinform., 2014)

OAE: The Ontology of Adverse Events. - Yongqun He; Sirarat Sarntivijai; Yu Lin; Zuoshuang Xiang; Abra Guo; Shelley Zhang 002; Desikan Jagannathan; Luca Toldo; Cui Tao; Barry Smith 001 (J. Biomed. Semant., 2014)

The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events. - Yu Lin; Yongqun He (J. Biomed. Semant., 2014)

CLO: The cell line ontology. - 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; et al. (J. Biomed. Semant., 2014)

A 2013 workshop: vaccine and drug ontology studies (VDOS 2013). - Cui Tao; Yongqun He; Sivaram Arabandi (J. Biomed. Semant., 2014)

ICoVax 2013: The 3rd ISV Pre-conference Computational Vaccinology Workshop. - Anne S. De Groot; Phoebe De Groot; Yongqun He (BMC Bioinform., 2014)

DNAVaxDB: the first web-based DNA vaccine database and its data analysis. - Rebecca Racz; Xinna Li; Mukti Patel; Zuoshuang Xiang; Yongqun He (BMC Bioinform., 2014)

Updates on the web-based VIOLIN vaccine database and analysis system. - 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; et al. (Nucleic Acids Res., 2014)

A domain ontology for the Non-Coding RNA field. - Jingshan Huang; Karen Eilbeck; Judith A. Blake; Dejing Dou; Darren A. Natale; Alan Ruttenberg; Barry Smith 001; Michael T. Zimmermann; Guoqian Jiang; Yu Lin; Bin Wu 008; Yongqun He; et al. (BIBM, 2015)

Bridging Vaccine Ontology and NCIt vaccine domain for cancer vaccine data integration and analysis. - Yongqun He; Guoqian Jiang (ICBO, 2015)

Ontoanimal tools for reusing ontologies, generating and editing ontology terms, and dereferencing ontology terms. - Yongqun He; Jie Zheng 001; Yu Lin (ICBO, 2015)

Ontorat: Automatic generation and editing of ontology terms. - Yongqun He; Jie Zheng 001; Yu Lin (ICBO, 2015)

GOfox: Semantics-based simplified hierarchical classification and interactive visualization to support GO enrichment analysis. - Edison Ong; Yongqun He (ICBO, 2015)

Extension of the Interaction Network Ontology for Literature Mining of Gene-gene Interaction Networks from Sentences with Multiple Interaction Keywords. - Arzucan Özgür; Junguk Hur; Yongqun He (BDM2I@ISWC, 2015)

Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions. - Junguk Hur; Arzucan Özgür; Zuoshuang Xiang; Yongqun He (J. Biomed. Semant., 2015)

Ontology-based representation and analysis of host-Brucella interactions. - Yu Lin; Zuoshuang Xiang; Yongqun He (J. Biomed. Semant., 2015)

Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns. - Zuoshuang Xiang; Jie Zheng 001; Yu Lin; Yongqun He (J. Biomed. Semant., 2015)

Ontology-Based Analysis of Adverse Drug Reactions Associated with Anti-infection Drugs in China. - Mei Li; Yuying Cao; Liwei Wang 010; Hongfang Liu; Yongqun He (AMIA, 2016)

Application of Ontobedia on Cell Line Ontology Development. - Edison Ong; Yongqun He (AMIA, 2016)

EGO: A Biomedical Ontology for Integrative Epigenome Representation and Analysis. - Yongqun He; Zhaohui S. Qin; Jie Zheng 001 (ICBO/BioCreative, 2016)

The Cell Line Ontology Integration and Analysis of the Knowledge of LINCS Cell Lines. - Edison Ong; Jiangan Xie; Zhaohui Ni; Qingping Liu; Yu Lin; Vasileios Stathias; Caty Chung; Stephan C. Schürer; Yongqun He (ICBO/BioCreative, 2016)

Ontobull and BFOConvert: Web-based Programs to Support Automatic Ontology Conversion. - Edison Ong; Zuoshuang Xiang; Jie Zheng 001; Barry Smith 001; Yongqun He (ICBO/BioCreative, 2016)

Ignet: A Centrality and INO-based Web System for Analyzing and Visualizing Literature-mined Networks. - Arzucan Özgür; Junguk Hur; Zuoshuang Xiang; Edison Ong; Dragomir R. Radev; Yongqun He (ICBO/BioCreative, 2016)

The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature. - Arzucan Özgür; Junguk Hur; Yongqun He (BioData Min., 2016)

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. - 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; et al. (J. Biomed. Semant., 2016)

Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events. - Abra Guo; Rebecca Racz; Junguk Hur; Yu Lin; Zuoshuang Xiang; Lili Zhao; Jordan Rinder; Guoqian Jiang; Qian Zhu 003; Yongqun He (J. Biomed. Semant., 2016)

The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology. - Jingshan Huang; Karen Eilbeck; Barry Smith 001; Judith A. Blake; Dejing Dou; Weili Huang; Darren A. Natale; Alan Ruttenberg; Jun Huan; Michael T. Zimmermann; Guoqian Jiang; Yu Lin; et al. (J. Biomed. Semant., 2016)

VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms. - Yu Lin; Jie Zheng 001; Yongqun He (J. Biomed. Semant., 2016)

Vaccine and Drug Ontology Studies (VDOS 2014). - Cui Tao; Yongqun He; Sivaram Arabandi (J. Biomed. Semant., 2016)

The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis. - Jie Zheng 001; Marcelline R. Harris; Anna Maria Masci; Yu Lin; Alfred O. Hero III; Barry Smith 001; Yongqun He (J. Biomed. Semant., 2016)

The development of non-coding RNA ontology. - Jingshan Huang; Karen Eilbeck; Barry Smith 001; Judith A. Blake; Dejing Dou; Weili Huang; Darren A. Natale; Alan Ruttenberg; Jun Huan; Michael T. Zimmermann; Guoqian Jiang; Yu Lin; et al. (Int. J. Data Min. Bioinform., 2016)

From Scoping Review to Metadata: An Evidence-Based Approach to Identifying Informed Consent Metadata for Biorepositories. - Marcelline R. Harris; Frank J. Manion; Hsing-yi Song; Yongqun He; Muhamamd F. Amith; Cui Tao (AMIA, 2017)

Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping and OAE-based representation and analysis of adverse events in patients treated with cancer drugs. - Meiu Wong; Rebecca Racz; Edison Ong; Yongqun He (AMIA, 2017)

OLOBO: A New Ontology for Linking and Integrating Open Biological and Biomedical Ontologies. - Edison Ong; Yongqun He (ICBO, 2017)

Extracting Adverse Drug Reactions using Deep Learning and Dictionary Based Approaches. - Mert Tiftikci; Arzucan Özgür; Yongqun He; Junguk Hur (TAC, 2017)

Large-scale adverse effects related to treatment evidence standardization (LAERTES): an open scalable system for linking pharmacovigilance evidence sources with clinical data. - 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; et al. (J. Biomed. Semant., 2017)

Ontology-based literature mining of E. coli vaccine-associated gene interaction networks. - Junguk Hur; Arzucan Özgür; Yongqun He (J. Biomed. Semant., 2017)

Comparison, alignment, and synchronization of cell line information between CLO and EFO. - Edison Ong; Sirarat Sarntivijai; Simon Jupp; Helen E. Parkinson; Yongqun He (BMC Bioinform., 2017)

Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses. - 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 (BMC Bioinform., 2017)

Cells in experimental life sciences - challenges and solution to the rapid evolution of knowledge. - Sirarat Sarntivijai; Alexander D. Diehl; Yongqun He (BMC Bioinform., 2017)

Ontology-based systematic representation and analysis of traditional Chinese drugs against rheumatism. - Qingping Liu; Jiahao Wang; Yan Zhu; Yongqun He (BMC Syst. Biol., 2017)

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration. - Edison Ong; Zuoshuang Xiang; Bin Zhao; Yue Liu; Yu Lin; Jie Zheng 001; Chris Mungall; Mélanie Courtot; Alan Ruttenberg; Yongqun He (Nucleic Acids Res., 2017)

The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines. - Jie Zheng 001; Huan Li; Qingzhi Liu; Yongqun He (Quant. Biol., 2017)

OntoKeeper: Semiotic-driven Ontology Evaluation Tool For Biomedical Ontologists. - Muhammad Amith; Frank J. Manion; Chen Liang 005; Marcelline R. Harris; Dennis Wang; Yongqun He; Cui Tao (BIBM, 2018)

KTAO: A Kidney Tissue Atlas Ontology to Support Community-Based Kidney Knowledge Base Development and Data Integration. - 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; et al. (ICBO, 2018)

eXtensible Ontology Development (XOD) using Web-based Ontoanimal Tools. - Edison Ong; Yongqun He; Jie Zheng 001 (ICBO, 2018)

Coordinated Evolution of Ontologies of Informed Consent. - 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 (ICBO, 2018)

VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria. - Jun Li; Cui Tai; Zixin Deng; Weihong Zhong; Yongqun He; Hong-Yu Ou (Briefings Bioinform., 2018)

The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability. - Yongqun He; Zuoshuang Xiang; Jie Zheng 001; Yu Lin; James A. Overton; Edison Ong (J. Biomed. Semant., 2018)

Ontology-based literature mining and class effect analysis of adverse drug reactions associated with neuropathy-inducing drugs. - Junguk Hur; Arzucan Özgür; Yongqun He (J. Biomed. Semant., 2018)

ICEO: a Biological Ontology for Representing and Analyzing the Bacterial Integrative and Conjugative Element. - Meng Liu 012; Hong-Yu Ou; Yongqun He (ICBO, 2019)

OGG-Bac: Ontological Representation of Orthologous Bacterial Genes. - Meng Liu 012; Hong-Yu Ou; Yongqun He (ICBO, 2019)

OPMI: the Ontology of Precision Medicine and Investigation and its Support for Clinical Data and Metadata Representation and Analysis. - Yongqun He; Edison Ong; Jennifer Schaub; Frederick Dowd; John F. O'Toole; Anastasios Siapos; Christian G. Reich; Sarah Seager; Ling Wang 001; Hong Yu 014; Jie Zheng 001; Christian J. Stoeckert Jr.; et al. (ICBO, 2019)

Alignment of the Ontology of Host-Microbiome Interactions (OHMI) High Level Terms with Existing OBO Ontologies. - Yongqun He; Jie Zheng 001; Anna Maria Masci; Jihad S. Obeid (ICBO, 2019)

Ontological Modeling of Two-Component Regulatory Systems. - Hsin-Hui Huang; Meng Liu 012; Yongqun He (ICBO, 2019)

Ontological Derivation of Mendeleev's Periodic Table of Chemical Elements. - Kaiyong Liu; Yongqun He (ICBO, 2019)

Ontolion: A Web-based Integrative Ontology Development Platform. - Edison Ong; Yongqun He (ICBO, 2019)

ICDO: Ontological Representation of the International Classification of Diseases (ICD) and its Application in English and Chinese Healthy Data Standardization. - Ling Wan; Edison Ong; Yongqun He (ICBO, 2019)

OHMI: the ontology of host-microbiome interactions. - Yongqun He; Haihe Wang; Jie Zheng 001; Daniel P. Beiting; Anna Maria Masci; Hong Yu 014; Kaiyong Liu; Jianmin Wu; Jeffrey L. Curtis; Barry Smith 001; Alexander V. Alekseyenko; Jihad S. Obeid (J. Biomed. Semant., 2019)

OSCI: standardized stem cell ontology representation and use cases for stem cell investigation. - 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 001; Sirarat Sarntivijai; et al. (BMC Bioinform., 2019)

A 2018 workshop: vaccine and drug ontology studies (VDOS 2018). - Junguk Hur; Cui Tao; Yongqun He (BMC Bioinform., 2019)

VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions. - Edison Ong; Peter Sun; Kimberly Berke; Jie Zheng 001; Guanming Wu; Yongqun He (BMC Bioinform., 2019)

The cell line ontology-based representation, integration and analysis of cell lines used in China. - Hongjie Pan; Xiaocui Bian; Sheng Yang; Yongqun He; Xiaolin Yang; Yuqin Liu (BMC Bioinform., 2019)

Cells in ExperimentaL Life Sciences (CELLS-2018): capturing the knowledge of normal and diseased cells with ontologies. - Sirarat Sarntivijai; Yongqun He; Alexander D. Diehl (BMC Bioinform., 2019)

Machine learning-based identification and rule-based normalization of adverse drug reactions in drug labels. - Mert Tiftikci; Arzucan Özgür; Yongqun He; Junguk Hur (BMC Bioinform., 2019)

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. - Hong Yu 014; Solomiya Nysak; Noemi Garg; Edison Ong; Xianwei Ye; Xiangyan Zhang; Yongqun He (BMC Bioinform., 2019)

Architecture and usability of OntoKeeper, an ontology evaluation tool. - Muhammad Amith; Frank J. Manion; Chen Liang 005; Marcelline R. Harris; Dennis Wang; Yongqun He; Cui Tao (BMC Medical Informatics Decis. Mak., 2019)

A statistical analysis of vaccine-adverse event data. - Jian-Jian Ren; Tingni Sun; Yongqun He; Yuji Zhang 001 (BMC Medical Informatics Decis. Mak., 2019)

Victors: a web-based knowledge base of virulence factors in human and animal pathogens. - Samantha Sayers; Li Li; Edison Ong; Shunzhou Deng; Guanghua Fu; Yu Lin; Brian Yang; Shelley Zhang 002; Zhenzong Fa; Bin Zhao; Zuoshuang Xiang; Yongqing Li; et al. (Nucleic Acids Res., 2019)

CIDO: The Community-Based Coronavirus Infectious Disease Ontology. - Yongqun He; Hong Yu 014; Edison Ong; Yang Wang; Yingtong Liu; Anthony Huffman; Hsin-Hui Huang; John Beverley; Asiyah Yu Lin; William D. Duncan; Sivaram Arabandi; Jiangan Xie; et al. (ICBO/ODLS, 2020)

OGG-CoV: Ontology Representation and Analysis of Genes and Genomes of Coronaviruses (short paper). - Anthony Huffman; Yongqun He (ICBO/ODLS, 2020)

Vaxign-ML: supervised machine learning reverse vaccinology model for improved prediction of bacterial protective antigens. - Edison Ong; Haihe Wang; Mei U. Wong; Meenakshi Seetharaman; Ninotchka Valdez; Yongqun He (Bioinform., 2020)

Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events. - Fang Li 011; Jingcheng Du; Yongqun He; Hsing-yi Song; Mohcine Madkour; Guozheng Rao; Yang Xiang 003; Yi Luo; Henry W. Chen; Sijia Liu 002; Liwei Wang 010; Hongfang Liu; et al. (J. Am. Medical Informatics Assoc., 2020)

OntoPlot: A Novel Visualisation for Non-hierarchical Associations in Large Ontologies. - Ying Yang; Michael Wybrow; Yuan-Fang Li; Tobias Czauderna; Yongqun He (IEEE Trans. Vis. Comput. Graph., 2020)

Perform Pathway Enrichment Analysis Using ReactomeFIViz. - Robin Haw; Fred Loney 001; Edison Ong; Yongqun He; Guanming Wu (Protein-Protein Interaction Networks, 2020)

Identification and Ontology Term Enrichment Analysis of Genes Associated with COVID-19 and Acute Kidney Disease. - Guirui Huang; Suyuan Peng; Luxia Zhang; Yongqun He (ICBO, 2021)

A Community Effort for COVID-19 Ontology Harmonization. - 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 (ICBO, 2021)

Ontology-based Modeling, Representation, and Analysis of Biomarkers in Healthy and Disease Kidney Tissue. - Yingtong Liu; Wenjun Ju; Becky Steck; Sanjay Jain; Matthias Kretzler; Yongqun He (ICBO, 2021)

Ontology Modeling and Analysis of COVID-19-associated Acute Kidney Injury and Its Underlying Molecular Mechanisms. - Easheta Shah; Roshan Desai; Suyuan Peng; Luxia Zhang; Yongqun He (ICBO, 2021)

Standardization of assay representation in the Ontology for Biomedical Investigations. - Randi Vita; Jie Zheng 001; 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; et al. (Database J. Biol. Databases Curation, 2021)

CIDO ontology updates and secondary analysis of host responses to COVID-19 infection based on ImmPort reports and literature. - Anthony Huffman; Anna Maria Masci; Jie Zheng 001; Nasim Sanati; Timothy Brunson; Guanming Wu; Yongqun He (J. Biomed. Semant., 2021)

Development of the International Classification of Diseases Ontology (ICDO) and its application for COVID-19 diagnostic data analysis. - Ling Wan; Justin Song; Virginia He; Jennifer Roman; Grace Whah; Suyuan Peng; Luxia Zhang; Yongqun He (BMC Bioinform., 2021)

An Open Natural Language Processing Development Framework for EHR-based Clinical Research: A case demonstration using the National COVID Cohort Collaborative (N3C). - Sijia Liu 002; Andrew Wen; Liwei Wang 010; Huan He; Sunyang Fu; Robert T. Miller; Andrew E. Williams; Daniel R. Harris; Ramakanth Kavuluru; Mei Liu; Noor Abu-El-Rub; Rui Zhang 028; et al. (CoRR, 2021)

Visual comprehension and orientation into the COVID-19 CIDO ontology. - Ling Zheng; Yehoshua Perl; Yongqun He; Christopher Ochs; James Geller; Hao Liu 025; Vipina Kuttichi Keloth (J. Biomed. Informatics, 2021)

The Human Phenotype Ontology in 2021. - Sebastian Köhler 001; 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; et al. (Nucleic Acids Res., 2021)

Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning. - Edison Ong; Michael F. Cooke; Anthony Huffman; Zuoshuang Xiang; Mei U. Wong; Haihe Wang; Meenakshi Seetharaman; Ninotchka Valdez; Yongqun He (Nucleic Acids Res., 2021)

Ontological Representation and Analysis of the Molecular Interactions Related to COVID-19-associated Acute Kidney Injury. - Ghida Arnous; Yongqun He (ICBO, 2022)

Coordinating Coronavirus Research: The Virus Infectious Disease Ontology. - John Beverley; Yongqun He; Barry Smith 001; Shane Babcock; Eric Merrell; Lindsay G. Cowell; Regina Hurley; Sebastian Deusing (ICBO, 2022)

Toward an Occupation Ontology, OccO. - Sam Smith; Damion M. Dooley; Eric Merrell; John Beverley; Yongqun He (ICBO, 2022)

OMOP-2-OPMI: Ontologization of OMOP CDM Using OPMI to Support Clinical Data interoperability and analysis. - Long Tran; Yongqun He (ICBO, 2022)

The Ontology of Adverse Events in 2022. - Qiuyue Yang; Jun Su; Xue Zhang; Yongqun He; Jiangan Xie (ICBO, 2022)

Foundational Development of an Occupation Ontology. - Yongqun He; Samuel Smith; Damion M. Dooley (JOWO, 2022)

COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning. - Anthony Huffman; Edison Ong; Junguk Hur; Adonis D'mello; Hervé Tettelin; Yongqun He (Briefings Bioinform., 2022)

A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology. - Yongqun He; Hong Yu 014; Anthony Huffman; Asiyah Yu Lin; Darren A. Natale; John Beverley; Ling Zheng; Yehoshua Perl; Zhigang Wang; Yingtong Liu; Edison Ong; Yang Wang; et al. (J. Biomed. Semant., 2022)

Identification of missing hierarchical relations in the vaccine ontology using acquired term pairs. - Warren Manuel; Rashmie Abeysinghe; Yongqun He; Cui Tao; Licong Cui (J. Biomed. Semant., 2022)

Mass spectrometry-based immunopeptidomics and computational vaccinology strategies for the identification of universal Shigella immunogenic candidates. - 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 (Comput. Biol. Medicine, 2022)

Ontology-based Representation and Analysis of Conditional Vaccine Immune Responses Using Omics Data. - Anthony Huffman; Edison Ong; Timothy Brunson; Nasim Sanati; Jie Zheng 001; Anna Maria Masci; Guanming Wu; Yongqun He (ICBO, 2023)

The Occupation Ontology (OccO): Building a Bridge between Global Occupational Standards. - John Beverley; Sam Smith; Matthew Diller; William D. Duncan; Jie Zheng 001; John W. Judkins; William R. Hogan; Robin McGill; Damion M. Dooley; Yongqun He (JOWO, 2023)

Evaluation of GPT and BERT-based models on identifying protein-protein interactions in biomedical text. - Hasin Rehana; Nur Bengisu Çam; Mert Basmaci; Yongqun He; Arzucan Özgür; Junguk Hur (CoRR, 2023)

An open natural language processing (NLP) framework for EHR-based clinical research: a case demonstration using the National COVID Cohort Collaborative (N3C). - Sijia Liu 002; Andrew Wen; Liwei Wang 010; Huan He; Sunyang Fu; Robert T. Miller; Andrew E. Williams; Daniel R. Harris; Ramakanth Kavuluru; Mei Liu; Noor Abu-El-Rub; Dalton Schutte; et al. (J. Am. Medical Informatics Assoc., 2023)

Big knowledge visualization of the COVID-19 CIDO ontology evolution. - Ling Zheng; Yehoshua Perl; Yongqun He (BMC Medical Informatics Decis. Mak., 2023)

Nested Named Entity Recognition using Multilayer BERT-based Model. - Hasin Rehana; Benu Bansal; Nur Bengisu Çam; Jie Zheng 001; Yongqun He; Arzucan Özgür; Junguk Hur (CLEF (Working Notes), 2024)

Enhancing Vaxign-DL for Vaccine Candidate Prediction with Added ESM-Generated Features. - Yichao Chen; Yuhan Zhang; Yongqun He (ER (Workshops), 2024)

Integrative Ontology of Bipolar Disorder (OBD): Advancing Bipolar Disorder Research Through an Interoperable Ontological Framework. - Yujia Tian; Yongqun He; Rachel L. Richesson; Melvin G. McInnis (ER (Workshops), 2024)

Credentials in the Occupation Ontology. - John Beverley; Robin McGill; Sam Smith; Jie Zheng 001; Giacomo De Colle; Finn Wilson; Matthew Diller; William D. Duncan; William R. Hogan; Yongqun He (ICBO, 2024)

CellCards: Development of a Dynamic Ontology-Derived ETL Pipeline for Automatic Cell Information Extraction and Analysis. - Mary Czelusniak; Emily Tran; Fatima Oudeif; Jie Zheng 001; William D. Duncan; Alexander D. Diehl; Yongqun He (ICBO, 2024)

Grounding Realizable Entities. - Michael Rabenberg; Carter Benson; Federico Donato; Yongqun He; Anthony Huffman; Shane Babcock; John Beverley (ICBO, 2024)

Ontological representation, modeling, and analysis of parasite vaccines. - Anthony Huffman; Xumeng Zhang; Meghana Lanka; Jie Zheng 001; Anna Maria Masci; Yongqun He (J. Biomed. Semant., 2024)

Mapping vaccine names in clinical trials to vaccine ontology using cascaded fine-tuned domain-specific language models. - Jianfu Li; Yiming Li; Yuanyi Pan; Jinjing Guo; Zenan Sun; Fang Li 011; Yongqun He; Cui Tao (J. Biomed. Semant., 2024)

Empowering standardization of cancer vaccines through ontology: enhanced modeling and data analysis. - Jie Zheng 001; 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; et al. (J. Biomed. Semant., 2024)

Cancer Vaccine Adjuvant Name Recognition from Biomedical Literature using Large Language Models. - Hasin Rehana; Jie Zheng 001; Leo Yeh; Benu Bansal; Nur Bengisu Çam; Christianah Jemiyo; Brett A. McGregor; Arzucan Özgür; Yongqun He; Junguk Hur (CoRR, 2025)

A fourfold pathogen reference ontology suite. - 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 (J. Biomed. Semant., 2025)