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Jie Zheng 0001
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Publications
- 2023
- [c22]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 - [c21]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 - 2022
- [j25]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) - 2021
- [j22]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) - [j21]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) - 2019
- [j19]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) - [j18]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) - [j17]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) - [c18]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 - [c17]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 - 2018
- [j16]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) - [c15]Edison Ong, Yongqun He, Jie Zheng:
eXtensible Ontology Development (XOD) using Web-based Ontoanimal Tools. ICBO 2018 - 2017
- [j14]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) - [j12]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) - 2016
- [j11]Yu Lin, Jie Zheng, Yongqun He:
VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms. J. Biomed. Semant. 7: 20 (2016) - [j9]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) - [c14]Yongqun He, Zhaohui S. Qin, Jie Zheng:
EGO: A Biomedical Ontology for Integrative Epigenome Representation and Analysis. ICBO/BioCreative 2016 - [c13]Edison Ong, Zuoshuang Xiang, Jie Zheng, Barry Smith, Yongqun He:
Ontobull and BFOConvert: Web-based Programs to Support Automatic Ontology Conversion. ICBO/BioCreative 2016 - 2015
- [j7]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) - [c11]Yongqun He, Jie Zheng, Yu Lin:
Ontoanimal tools for reusing ontologies, generating and editing ontology terms, and dereferencing ontology terms. ICBO 2015 - [c10]Yongqun He, Jie Zheng, Yu Lin:
Ontorat: Automatic generation and editing of ontology terms. ICBO 2015 - 2014
- [j6]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) - [j5]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) - [c8]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 - 2013
- [c5]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 - 2012
- [c3]Jie Zheng, Zuoshuang Xiang, Christian J. Stoeckert Jr., Yongqun He:
Ontodog: A Web-based Ontology Community View Generator. ICBO 2012 - 2010
- [j1]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)
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