Yongqun He

According to our database1, Yongqun He authored at least 99 papers between 2005 and 2020.

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Bibliography

2020
Perform Pathway Enrichment Analysis Using ReactomeFIViz.
Proceedings of the Protein-Protein Interaction Networks, Methods and Protocols., 2020

OntoPlot: A Novel Visualisation for Non-hierarchical Associations in Large Ontologies.
IEEE Trans. Vis. Comput. Graph., 2020

2019
Victors: a web-based knowledge base of virulence factors in human and animal pathogens.
Nucleic Acids Res., 2019

A statistical analysis of vaccine-adverse event data.
BMC Med. Inf. & Decision Making, 2019

Architecture and usability of OntoKeeper, an ontology evaluation tool.
BMC Med. Inf. & Decision Making, 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.
BMC Bioinform., 2019

Machine learning-based identification and rule-based normalization of adverse drug reactions in drug labels.
BMC Bioinform., 2019

Cells in ExperimentaL Life Sciences (CELLS-2018): capturing the knowledge of normal and diseased cells with ontologies.
BMC Bioinform., 2019

The cell line ontology-based representation, integration and analysis of cell lines used in China.
BMC Bioinform., 2019

VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions.
BMC Bioinform., 2019

A 2018 workshop: vaccine and drug ontology studies (VDOS 2018).
BMC Bioinform., 2019

OSCI: standardized stem cell ontology representation and use cases for stem cell investigation.
BMC Bioinform., 2019

OHMI: the ontology of host-microbiome interactions.
J. Biomedical Semantics, 2019

2018
Ontology-based literature mining and class effect analysis of adverse drug reactions associated with neuropathy-inducing drugs.
J. Biomedical Semantics, 2018

The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability.
J. Biomedical Semantics, 2018

VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria.
Briefings in Bioinformatics, 2018

Coordinated Evolution of Ontologies of Informed Consent.
Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), 2018

eXtensible Ontology Development (XOD) using Web-based Ontoanimal Tools.
Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), 2018

KTAO: A Kidney Tissue Atlas Ontology to Support Community-Based Kidney Knowledge Base Development and Data Integration.
Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), 2018

OntoKeeper: Semiotic-driven Ontology Evaluation Tool For Biomedical Ontologists.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

2017
Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration.
Nucleic Acids Res., 2017

Ontology-based systematic representation and analysis of traditional Chinese drugs against rheumatism.
BMC Syst. Biol., 2017

Cells in experimental life sciences - challenges and solution to the rapid evolution of knowledge.
BMC Bioinform., 2017

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

Comparison, alignment, and synchronization of cell line information between CLO and EFO.
BMC Bioinform., 2017

Ontology-based literature mining of E. coli vaccine-associated gene interaction networks.
J. Biomedical Semantics, 2017

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

Extracting Adverse Drug Reactions using Deep Learning and Dictionary Based Approaches.
Proceedings of the 2017 Text Analysis Conference, 2017

OLOBO: A New Ontology for Linking and Integrating Open Biological and Biomedical Ontologies.
Proceedings of the 8th International Conference on Biomedical Ontology (ICBO 2017), Newcastle-upon-Tyne, United Kingdom, September 13th, 2017

Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping and OAE-based representation and analysis of adverse events in patients treated with cancer drugs.
Proceedings of the AMIA 2017, 2017

From Scoping Review to Metadata: An Evidence-Based Approach to Identifying Informed Consent Metadata for Biorepositories.
Proceedings of the AMIA 2017, 2017

2016
The development of non-coding RNA ontology.
Int. J. Data Min. Bioinform., 2016

The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis.
J. Biomedical Semantics, 2016

Vaccine and Drug Ontology Studies (VDOS 2014).
J. Biomedical Semantics, 2016

VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms.
J. Biomedical Semantics, 2016

The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology.
J. Biomedical Semantics, 2016

Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events.
J. Biomedical Semantics, 2016

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.
J. Biomedical Semantics, 2016

The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature.
BioData Min., 2016

Ignet: A Centrality and INO-based Web System for Analyzing and Visualizing Literature-mined Networks.
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

Ontobull and BFOConvert: Web-based Programs to Support Automatic Ontology Conversion.
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

The Cell Line Ontology Integration and Analysis of the Knowledge of LINCS Cell Lines.
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

EGO: A Biomedical Ontology for Integrative Epigenome Representation and Analysis.
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

Application of Ontobedia on Cell Line Ontology Development.
Proceedings of the AMIA 2016, 2016

Ontology-Based Analysis of Adverse Drug Reactions Associated with Anti-infection Drugs in China.
Proceedings of the AMIA 2016, 2016

2015
Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns.
J. Biomedical Semantics, 2015

Ontology-based representation and analysis of host-Brucella interactions.
J. Biomedical Semantics, 2015

Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions.
J. Biomedical Semantics, 2015

Extension of the Interaction Network Ontology for Literature Mining of Gene-gene Interaction Networks from Sentences with Multiple Interaction Keywords.
Proceedings of International Workshop on Biomedical Data Mining, 2015

GOfox: Semantics-based simplified hierarchical classification and interactive visualization to support GO enrichment analysis.
Proceedings of the International Conference on Biomedical Ontology, 2015

Ontorat: Automatic generation and editing of ontology terms.
Proceedings of the International Conference on Biomedical Ontology, 2015

Ontoanimal tools for reusing ontologies, generating and editing ontology terms, and dereferencing ontology terms.
Proceedings of the International Conference on Biomedical Ontology, 2015

Bridging Vaccine Ontology and NCIt vaccine domain for cancer vaccine data integration and analysis.
Proceedings of the International Conference on Biomedical Ontology, 2015

A domain ontology for the Non-Coding RNA field.
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

2014
Updates on the web-based VIOLIN vaccine database and analysis system.
Nucleic Acids Res., 2014

DNAVaxDB: the first web-based DNA vaccine database and its data analysis.
BMC Bioinform., 2014

ICoVax 2013: The 3rd ISV Pre-conference Computational Vaccinology Workshop.
BMC Bioinform., 2014

A 2013 workshop: vaccine and drug ontology studies (VDOS 2013).
J. Biomedical Semantics, 2014

CLO: The cell line ontology.
J. Biomedical Semantics, 2014

The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events.
J. Biomedical Semantics, 2014

OAE: The Ontology of Adverse Events.
J. Biomedical Semantics, 2014

Ontodog: a web-based ontology community view generation tool.
Bioinform., 2014

OBCS: The Ontology of Biological and Clinical Statistics.
Proceedings of the 5th International Conference on Biomedical Ontology, 2014

Ontobat: An Ontology-based Semantic Web Approach for Linked Data Processing and Analysis.
Proceedings of the 5th International Conference on Biomedical Ontology, 2014

Development of a BFO-Based Informed Consent Ontology (ICO).
Proceedings of the 5th International Conference on Biomedical Ontology, 2014

OGG: a Biological Ontology for Representing Genes and Genomes in Specific Organisms.
Proceedings of the 5th International Conference on Biomedical Ontology, 2014

Analysis of Content Coverage for Informed Consent Concepts.
Proceedings of the AMIA 2014, 2014

2013
HINO: a BFO-aligned ontology representing human molecular interactions and pathways.
CoRR, 2013

A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks.
BMC Syst. Biol., 2013

Genome-wide prediction of vaccine targets for human herpes simplex viruses using Vaxign reverse vaccinology.
BMC Bioinform., 2013

Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates.
BMC Bioinform., 2013

Computational vaccinology and the ICoVax 2012 workshop.
BMC Bioinform., 2013

Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology.
J. Biomedical Semantics, 2013

The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines.
J. Biomedical Semantics, 2013

Analysis of Vaccine-related Networks using Semantic MEDLINE and the Vaccine Ontology.
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, 2013

HINO: BFO-aligned ontology representation of human molecular interactions and pathways.
Proceedings of the 4th International Conference on Biomedical Ontology, 2013

The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing vaccine adverse events.
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, 2013

Ontology modeling of genetic susceptibility to adverse events following vaccination.
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, 2013

Alignment of Cultured Cell Modeling Across OBO Foundry Ontologies: Key Outcomes, Insights.
Proceedings of the 4th International Conference on Biomedical Ontology, 2013

2012
Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis.
J. Biomedical Semantics, 2012

Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses.
J. Biomedical Semantics, 2012

Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining.
J. Biomedical Semantics, 2012

A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012).
J. Biomedical Semantics, 2012

Ontodog: A Web-based Ontology Community View Generator.
Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), 2012

Ontorat web server for automatic generation and annotations of new ontology terms.
Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), 2012

2011
Protegen: a web-based protective antigen database and analysis system.
Nucleic Acids Res., 2011

Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology.
J. Biomedical Semantics, 2011

Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology.
J. Biomedical Semantics, 2011

Ontobee: A Linked Data Server and Browser for Ontology Terms.
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

OntoFox and its Application in Development of Brucellosis Ontology.
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

Cell Line Ontology: Redesigning the Cell Line Knowledgebase to Aid Integrative Translational Informatics.
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

Towards a Semantic Web Application: Ontology-Driven Ortholog Clustering Analysis.
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

AEO: A Realism-Based Biomedical Ontology for the Representation of Adverse Events.
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

2010
Modeling biomedical experimental processes with OBI.
J. Biomedical Semantics, 2010

2008
VIOLIN: vaccine investigation and online information network.
Nucleic Acids Res., 2008

2007
CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clustering.
Bioinform., 2007

miniTUBA: medical inference by network integration of temporal data using Bayesian analysis.
Bioinform., 2007

2006
BBP: Brucella genome annotation with literature mining and curation.
BMC Bioinform., 2006

2005
PIML: the Pathogen Information Markup Language.
Bioinform., 2005


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