Jie Zheng

Publication Activity (10 Years)

Years Active: 2010-2024
Publications (10 Years): 31

Top Topics

Clinical Medicine

Semantically Enhanced

Top Venues

J. Biomed. Semant.

Nucleic Acids Res.

ICBO/BioCreative

Publications

Yuting Wu, Ling Wang, Jingfang Chen, Jie Zheng, Zixiao Pan
A reinforcement learning driven two-stage evolutionary optimisation for hybrid seru system scheduling with worker transfer. Int. J. Prod. Res. 62 (11) (2024)
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) (2024)
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)
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) (2024)
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 (2024)
Yile Liang, Haocheng Luo, Haining Duan, Donghui Li, Hongsen Liao, Jie Feng, Jiuxia Zhao, Hao Ren, Xuetao Ding, Ying Cha, Qingte Zhou, Chenqi Situ, Jinghua Hao, Ke Xing, Feifan Yin, Renqing He, Yang Sun, Yueqiang Zheng, Yipeng Feng, Zhizhao Sun, Jingfang Chen, Jie Zheng, Ling Wang
Meituan's Real-Time Intelligent Dispatching Algorithms Build the World's Largest Minute-Level Delivery Network. INFORMS J. Appl. Anal. 54 (1) (2024)
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)
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)
Beatrice Amos, Cristina Aurrecoechea, Matthieu Barba, Ana Barreto, Evelina Y. Basenko, Wojciech Bazant, Robert Belnap, Ann S. Blevins, Ulrike Böhme, John Brestelli, Brian P. Brunk, Mark J. Caddick, Danielle Callan, Lahcen I. Campbell, Mikkel B. Christensen, George K. Christophides, Kathryn Crouch, Kristina Davis, Jeremy D. DeBarry, Ryan Doherty, Yikun Duan, Michael Dunn, Dave Falke, Steve Fisher, Paul Flicek, Brett Fox, Bindu Gajria, Gloria I. Giraldo-Calderón, Omar S. Harb, Elizabeth Harper, Christiane Hertz-Fowler, Mark J. Hickman, Connor Howington, Sufen Hu, Jay Humphrey, John Iodice, Andrew Jones, John Judkins, Sarah A. Kelly, Jessica C. Kissinger, Dae Kun Kwon, Kristopher Lamoureux, Daniel Lawson, Wei Li, Kallie Lies, Disha Lodha, Jamie Long, Robert M. MacCallum, Gareth Maslen, Mary Ann McDowell, Jaroslaw Nabrzyski, David S. Roos, Samuel S. C. Rund, Stephanie wever Schulman, Achchuthan Shanmugasundram, Vasily Sitnik, Drew Spruill, David Starns, Christian J. Stoeckert Jr., Sheena Shah Tomko, Haiming Wang, Susanne Warrenfeltz, Robert Wieck, Paul A. Wilkinson, Lin Xu, Jie Zheng
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. Nucleic Acids Res. 50 (D1) (2022)
Rebecca C. Jackson, Nicolas Matentzoglu, James A. Overton, Randi Vita, James P. Balhoff, Pier Luigi Buttigieg, Seth Carbon, Mélanie Courtot, Alexander D. Diehl, Damion M. Dooley, William D. Duncan, Nomi L. Harris, Melissa A. Haendel, Suzanna E. Lewis, Darren A. Natale, David Osumi-Sutherland, Alan Ruttenberg, Lynn M. Schriml, Barry Smith, Christian J. Stoeckert Jr., Nicole A. Vasilevsky, Ramona L. Walls, Jie Zheng, Christopher J. Mungall, Bjoern Peters
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies. Database J. Biol. Databases Curation 2021 (2021)
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)
Behrouz Shamsaei, Szymon Chojnacki, Marcin Pilarczyk, Mehdi Fazel-Najafabadi, Wen Niu, Chuming Chen, Karen Ross, Andrea Matlock, Jeremy Muhlich, Somchai Chutipongtanate, Jie Zheng, John Turner, Dusica Vidovic, Jake Jaffe, Michael J. MacCoss, Cathy Wu, Ajay Pillai, Avi Ma'ayan, Stephan C. Schürer, Michal Kouril, Mario Medvedovic, Jarek Meller
piNET: a versatile web platform for downstream analysis and visualization of proteomics data. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
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. (21) (2019)
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) (2019)
Jie Zheng, John Judkins, Christian J. Stoeckert Jr.
OWLmaker: An Application for Generating OWL Files from Tabular Text. ICBO (2019)
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. (5) (2019)
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)
Sarah Bost, Niina Eklund, Kaisa Silander, Jie Zheng, Christian J. Stoeckert Jr., Mathias Brochhausen
Mapping Data Annotated with the Minimum Information About BIobank data Sharing (MIABIS) 2.0 to the Ontology for Biobanking (OBIB). ICBO (2019)
Anna Maria Masci, Shannon McCall, Alessandro Racioppi, Helena Judge Ellis, Jihad S. Obeid, Barry Smith, Christian J. Stoeckert Jr., Jie Zheng
Standardization of the Histopathology Cancer Report: An Ontological Approach. ICBO (2018)
Francislon S. Oliveira, John Brestelli, Shon Cade, Jie Zheng, John Iodice, Steve Fischer, Cristina Aurrecoechea, Jessica C. Kissinger, Brian P. Brunk, Christian J. Stoeckert Jr., Gabriel R. Fernandes, David S. Roos, Daniel P. Beiting
MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments. Nucleic Acids Res. 46 (Database-Issue) (2018)
Edison Ong, Yongqun He, Jie Zheng
eXtensible Ontology Development (XOD) using Web-based Ontoanimal Tools. ICBO (2018)
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) (2018)
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) (2017)
Cristina Aurrecoechea, Ana Barreto, Evelina Y. Basenko, John Brestelli, Brian P. Brunk, Shon Cade, Kathryn Crouch, Ryan Doherty, Dave Falke, Steve Fischer, Bindu Gajria, Omar S. Harb, Mark Heiges, Christiane Hertz-Fowler, Sufen Hu, John Iodice, Jessica C. Kissinger, Cris Lawrence, Wei Li, Deborah F. Pinney, Jane A. Pulman, David S. Roos, Achchuthan Shanmugasundram, Fatima Silva-Franco, Sascha Steinbiss, Christian J. Stoeckert Jr., Drew Spruill, Haiming Wang, Susanne Warrenfeltz, Jie Zheng
EuPathDB: the eukaryotic pathogen genomics database resource. Nucleic Acids Res. 45 (Database-Issue) (2017)
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) (2017)
Edison Ong, Zuoshuang Xiang, Jie Zheng, Barry Smith, Yongqun He
Ontobull and BFOConvert: Web-based Programs to Support Automatic Ontology Conversion. ICBO/BioCreative (2016)
Yu Lin, Jie Zheng, Yongqun He
VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms. J. Biomed. Semant. 7 (2016)
Yongqun He, Zhaohui S. Qin, Jie Zheng
EGO: A Biomedical Ontology for Integrative Epigenome Representation and Analysis. ICBO/BioCreative (2016)
Jie Zheng, Jashon Cade, Brian P. Brunk, David S. Roos, Christian J. Stoeckert Jr., San James, Emmanuel Arinaitwe, Bryan Greenhouse, Grant Dorsey, Steven Sullivan, Jane M. Carlton, Gabriel Carrasco-Escobar, Dionicia Gamboa, Paula Maguina-Mercedes, Joseph Vinetz
Malaria Study Data Integration and Information Retrieval Based on OBO Foundry Ontologies. ICBO/BioCreative (2016)
Mathias Brochhausen, Jie Zheng, David L. Birtwell, Heather Williams, Anna Maria Masci, Helena Judge Ellis, Christian J. Stoeckert Jr.
OBIB-a novel ontology for biobanking. J. Biomed. Semant. 7 (2016)
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 (2016)
Yongqun He, Jie Zheng, Yu Lin
Ontoanimal tools for reusing ontologies, generating and editing ontology terms, and dereferencing ontology terms. ICBO (2015)
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 (2015)
Yongqun He, Jie Zheng, Yu Lin
Ontorat: Automatic generation and editing of ontology terms. ICBO (2015)
Philippe Rocca-Serra, Ramona L. Walls, Jacob Parnell, Rachel Gallery, Jie Zheng, Susanna-Assunta Sansone, Alejandra N. González-Beltrán
Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach. Database J. Biol. Databases Curation 2015 (2015)
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 (2014)
Philippe Rocca-Serra, Ramona L. Walls, Jacob Parnell, Rachel Gallery, Jie Zheng, Susanna-Assunta Sansone, Alejandra N. González-Beltrán
Modeling a Microbial Community and Biodiversity Assay with OBI and PCO OBO Foundry Ontologies: the Interoperability Gains of a Modular Approach. ICBO (2014)
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)
Jie Zheng, Zuoshuang Xiang, Christian J. Stoeckert Jr., Yongqun He
Ontodog: a web-based ontology community view generation tool. Bioinform. 30 (9) (2014)
Jie Zheng, Elisabetta Manduchi, Christian J. Stoeckert Jr.
Development of an Application Ontology for Beta Cell Genomics Based On the Ontology for Biomedical Investigations. ICBO (2013)
Mélanie Courtot, Jie Zheng, Christian J. Stoeckert Jr., Ryan Remy Brinkman, Alan Ruttenberg
Diagnostic criteria and clinical guidelines standardization to automate case classification. ICBO (2013)
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)
Jie Zheng, Zuoshuang Xiang, Christian J. Stoeckert Jr., Yongqun He
Ontodog: A Web-based Ontology Community View Generator. ICBO (2012)
Alok Dhamanaskar, Michael E. Cotterell, Jie Zheng, Jessica C. Kissinger, Christian J. Stoeckert Jr., John A. Miller
Suggestions for Galaxy Workflow Design Using Semantically Annotated Services. FOIS (2012)
Priti Parikh, Jie Zheng, Flora J. Logan-Klumpler, Christian J. Stoeckert Jr., Christos Louis, Pantelis Topalis, Anna V. Protasio, Amit P. Sheth, Mark Carrington, Matthew Berriman, Satya Sanket Sahoo
The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms. J. Biomed. Semant. 3 (2012)
Jie Zheng, Julia Stoyanovich, Elisabetta Manduchi, Junmin Liu, Christian J. Stoeckert Jr.
AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments. Database J. Biol. Databases Curation 2011 (2011)
Chaitanya Guttula, Alok Dhamanaskar, Rui Wang, John A. Miller, Jessica C. Kissinger, Jie Zheng, Christian J. Stoeckert Jr.
Enriching the Ontology for Biomedical Investigations (OBI) to Improve its Suitability for Web Service Annotations. ICBO (2011)
Jie Zheng, Omar S. Harb, Christian J. Stoeckert Jr.
Ontology Driven Data Collection for EuPathDB. ICBO (2011)
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) (2010)
James Malone, Ele Holloway, Tomasz Adamusiak, Misha Kapushesky, Jie Zheng, Nikolay Kolesnikov, Anna Zhukova, Alvis Brazma, Helen E. Parkinson
Modeling sample variables with an Experimental Factor Ontology. Bioinform. 26 (8) (2010)