John H. Gennari

79 papers A* 1A 2B 2Misc 25Journal 35Unranked 14
YearRankTypeTitle / Venue / Authors
2025 J jnl
LM-Merger: a workflow for merging logical models with an application to gene regulatory network models.
BMC Bioinform.
Luna Xingyu Li, Boris Aguilar, John H. Gennari, Guangrong Qin
2025 J jnl
Verification and reproducible curation of the BioModels repository.
PLoS Comput. Biol.
Lucian P. Smith, Rahuman S. Malik-Sheriff, Tung V. N. Nguyen, Henning Hermjakob, Jonathan R. Karr, Bilal Shaikh, Logan Drescher, Ion I. Moraru, James C. Schaff, Eran Agmon, Alexander A. Patrie, Michael L. Blinov, Joseph L. Hellerstein, Elebeoba E. May, David P. Nickerson, John H. Gennari, Herbert M. Sauro
2023 J jnl
An automated model annotation system (AMAS) for SBML models.
Bioinform.
Woosub Shin, John H. Gennari, Joseph L. Hellerstein, Herbert M. Sauro
2023 J jnl
VSCode-Antimony: a source editor for building, analyzing, and translating antimony models.
Bioinform.
Steve Ma, Longxuan Fan, Sai Anish Konanki, Eva Liu, John H. Gennari, Lucian P. Smith, Joseph L. Hellerstein, Herbert M. Sauro
2022 J jnl
BioSimulators: a central registry of simulation engines and services for recommending specific tools.
CoRR
Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Joseph L. Hellerstein, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr
2022 J jnl
BioSimulators: a central registry of simulation engines and services for recommending specific tools.
Nucleic Acids Res.
Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Rahuman S. Malik-Sheriff, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr
2021 J jnl
OMEX metadata specification (version 1.2).
J. Integr. Bioinform.
John H. Gennari, Matthias König, Goksel Misirli, Maxwell Lewis Neal, David P. Nickerson, Dagmar Waltemath
2021 J jnl
libOmexMeta: enabling semantic annotation of models to support FAIR principles.
Bioinform.
Ciaran M. Welsh, David P. Nickerson, Anand K. Rampadarath, Maxwell Lewis Neal, Herbert M. Sauro, John H. Gennari
2020 J jnl
Open modeling and exchange (OMEX) metadata specification version 1.0.
J. Integr. Bioinform.
Maxwell Lewis Neal, John H. Gennari, Dagmar Waltemath, David P. Nickerson, Matthias König
2019 J jnl
Harmonizing semantic annotations for computational models in biology.
Briefings Bioinform.
Maxwell Lewis Neal, Matthias König, David P. Nickerson, Goksel Misirli, Reza Kalbasi, Andreas Dräger, Koray Atalag, Vijayalakshmi Chelliah, Michael T. Cooling, Daniel L. Cook, Sharon M. Crook, Miguel de Alba, Samuel H. Friedman, Alan Garny, John H. Gennari, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nick S. Juty, Chris J. Myers, Brett G. Olivier, Herbert M. Sauro, Martin Scharm, Jacky L. Snoep, Vasundra Touré, Anil Wipat, Olaf Wolkenhauer, Dagmar Waltemath
2019 J jnl
Model annotation and discovery with the Physiome Model Repository.
BMC Bioinform.
Dewan M. Sarwar, Reza Kalbasi, John H. Gennari, Brian E. Carlson, Maxwell Lewis Neal, Bernard de Bono, Koray Atalag, Peter J. Hunter, David P. Nickerson
2019 J jnl
Predicting instances of pathway ontology classes for pathway integration.
J. Biomed. Semant.
Lucy Lu Wang, G. Thomas Hayman, Jennifer R. Smith, Monika Tutaj, Mary Shimoyama, John H. Gennari
2019 J jnl
SemGen: a tool for semantics-based annotation and composition of biosimulation models.
Bioinform.
Maxwell Lewis Neal, Christopher T. Thompson, Karam G. Kim, Ryan C. James, Daniel L. Cook, Brian E. Carlson, John H. Gennari
2019 J jnl
Synthetic Biology Open Language (SBOL) Version 2.3.
J. Integr. Bioinform.
Curtis Madsen, Ángel Goñi-Moreno, Umesh P, Zachary Palchick, Nicholas Roehner, Christian Atallah, Bryan Bartley, Kiri Choi, Robert Sidney Cox III, Thomas E. Gorochowski, Raik Grünberg, Chris Macklin, James Alastair McLaughlin, Xianwei Meng, Tramy Nguyen, Matthew R. Pocock, Meher Samineni, James Scott-Brown, Ysis Tarter, Michael Zhang, Zhen Zhang, Zach Zundel, Jacob Beal, Michael Bissell, Kevin Clancy, John H. Gennari, Goksel Misirli, Chris J. Myers, Ernst Oberortner, Herbert M. Sauro, Anil Wipat
2019 — conf
The Ontology of Physics for Biology - A Companion to Basic Formal Ontology.
ICBO
Daniel L. Cook, John H. Gennari, Maxwell Lewis Neal
2018 Misc conf
Counting Readmissions: Surprisingly difficult.
AMIA
Ahmad K. Aljadaan, Peter Tarczy-Hornoch, Adam B. Wilcox, Todd F. Dardas, John H. Gennari
2018 Misc conf
Quantifying the effects of gene entity disambiguation for GSEA.
AMIA
Lucy Lu Wang, John H. Gennari
2018 J jnl
Synthetic Biology Open Language (SBOL) Version 2.2.0.
J. Integr. Bioinform.
Robert Sidney Cox III, Curtis Madsen, James Alastair McLaughlin, Tramy Nguyen, Nicholas Roehner, Bryan Bartley, Jacob Beal, Michael Bissell, Kiri Choi, Kevin Clancy, Raik Grünberg, Chris Macklin, Goksel Misirli, Ernst Oberortner, Matthew R. Pocock, Meher Samineni, Michael Zhang, Zhen Zhang, Zach Zundel, John H. Gennari, Chris J. Myers, Herbert M. Sauro, Anil Wipat
2017 — conf
Extending the Ontology of Physics for Biology with Thermodynamics.
ICBO
Daniel L. Cook, John H. Gennari, Maxwell Lewis Neal
2017 — conf
Similarity Metrics for Determining Overlap Among Biological Pathways.
ICBO
Lucy Lu Wang, John H. Gennari
2016 — conf
An Analysis of Differences in Biological Pathway Resources.
ICBO/BioCreative
Lucy Lu Wang, John H. Gennari, Neil F. Abernethy
2016 Misc conf
Assessing patient and caregiver needs and challenges in information and symptom management: a study of primary brain tumors.
AMIA
Rebecca J. Hazen, Amanda Lazar, John H. Gennari
2016 Misc conf
Discovering representational differences between pathway knowledge bases for pathway resource merging.
AMIA
Lucy Lu Wang, John H. Gennari, Neil F. Abernethy
2016 — conf
Qualitative Causal Analyses of Biosimulation Models.
ICBO/BioCreative
Maxwell Lewis Neal, John H. Gennari, Daniel L. Cook
2016 J jnl
Synthetic Biology Open Language (SBOL) Version 2.1.0.
J. Integr. Bioinform.
Jacob Beal, Robert Sidney Cox III, Raik Grünberg, James Alastair McLaughlin, Tramy Nguyen, Bryan Bartley, Michael Bissell, Kiri Choi, Kevin Clancy, Chris Macklin, Curtis Madsen, Goksel Misirli, Ernst Oberortner, Matthew R. Pocock, Nicholas Roehner, Meher Samineni, Michael Zhang, Zhen Zhang, Zach Zundel, John H. Gennari, Chris J. Myers, Herbert M. Sauro, Anil Wipat
2015 Misc conf
Decision Analysis for Oropharyngeal Cancer in Radiotherapy.
AMIA
Ahmad Aljadaan, John H. Gennari, Mark H. Phillips, Wade P. Smith
2015 J jnl
Synthetic Biology Open Language (SBOL) Version 2.0.0.
J. Integr. Bioinform.
Bryan Bartley, Jacob Beal, Kevin Clancy, Goksel Misirli, Nicholas Roehner, Ernst Oberortner, Matthew R. Pocock, Michael Bissell, Curtis Madsen, Tramy Nguyen, Zhen Zhang, John H. Gennari, Chris J. Myers, Anil Wipat, Herbert M. Sauro
2014 J jnl
A Reappraisal of How to Build Modular, Reusable Models of Biological Systems.
PLoS Comput. Biol.
Maxwell Lewis Neal, Michael T. Cooling, Lucian P. Smith, Christopher T. Thompson, Herbert M. Sauro, Brian E. Carlson, Daniel L. Cook, John H. Gennari
2013 — conf
An OWL knowledge base for classifying and querying collections of physiological models: A prototype human physiome.
ICBO
Maxwell Lewis Neal, Daniel L. Cook, John H. Gennari
2013 Misc conf
Identifying High-Risk Components in Synthetic Biology.
AMIA
Nikhil Gopal, Michal Galdzicki, Bryan Bartley, Evren Sirin, John H. Gennari
2013 J jnl
Ontology of physics for biology: representing physical dependencies as a basis for biological processes.
J. Biomed. Semant.
Daniel L. Cook, Maxwell Lewis Neal, Fred L. Bookstein, John H. Gennari
2013 J jnl
Representing physiological processes and their participants with PhysioMaps.
J. Biomed. Semant.
Daniel L. Cook, Maxwell Lewis Neal, Robert Hoehndorf, Georgios V. Gkoutos, John H. Gennari
2013 J jnl
Using random walks to identify cancer-associated modules in expression data.
BioData Min.
Deanna Petrochilos, Ali Shojaie, John H. Gennari, Neil F. Abernethy
2011 — conf
HeartCyc: A Cardiac Cycle Process Ontology Based in the Ontology of Physics for Biology.
ICBO
Daniel L. Cook, Michal Galdzicki, Maxwell Lewis Neal, José L. V. Mejino Jr., John H. Gennari
2011 J jnl
Integrating systems biology models and biomedical ontologies.
BMC Syst. Biol.
Robert Hoehndorf, Michel Dumontier, John H. Gennari, Sarala M. Wimalaratne, Bernard de Bono, Daniel L. Cook, Georgios V. Gkoutos
2011 J jnl
Multiple ontologies in action: Composite annotations for biosimulation models.
J. Biomed. Informatics
John H. Gennari, Maxwell Lewis Neal, Michal Galdzicki, Daniel L. Cook
2009 Misc conf
Advances in Semantic Representation for Multiscale Biosimulation: A Case Study in Merging Models.
Pacific Symposium on Biocomputing
Maxwell Lewis Neal, John H. Gennari, Theo Arts, Daniel L. Cook
2008 Misc conf
Bridging Biological Ontologies and Biosimulation: The Ontology of Physics for Biology.
AMIA
Daniel L. Cook, José L. V. Mejino Jr., Maxwell Lewis Neal, John H. Gennari
2008 Misc conf
Building an Automated Problem List Based on Natural Language Processing: Lessons Learned in the Early Phase of Development.
AMIA
Imre Solti, Barry Aaronson, Grant S. Fletcher, Magdolna Solti, John H. Gennari, Melissa Cooper, Thomas H. Payne
2008 Misc conf
Integration of Multi-Scale Biosimulation Models via Light-Weight Semantics.
Pacific Symposium on Biocomputing
John H. Gennari, Maxwell Lewis Neal, Brian E. Carlson, Daniel L. Cook
2008 J jnl
Research Paper: Evaluating Clinical Decision Support Systems: Monitoring CPOE Order Check Override Rates in the Department of Veterans Affairs' Computerized Patient Record System.
J. Am. Medical Informatics Assoc.
Ching-Ping Lin, Thomas H. Payne, W. Paul Nichol, Patricia J. Hoey, Curtis L. Anderson, John H. Gennari
2007 Misc conf
Chalkboard: Ontology-Based Pathway Modeling And Qualitative Inference Of Disease Mechanisms.
Pacific Symposium on Biocomputing
Daniel L. Cook, Jesse C. Wiley, John H. Gennari
2007 J jnl
Participatory design of a collaborative clinical trial protocol writing system.
Int. J. Medical Informatics
Chunhua Weng, David W. McDonald, Dana Sparks, Jason McCoy, John H. Gennari
2007 J jnl
User-centered semantic harmonization: A case study.
J. Biomed. Informatics
Chunhua Weng, John H. Gennari, Douglas B. Fridsma
2007 Misc conf
XGI: A Graphical Interface for XQuery Creation.
AMIA
Xiang Li, John H. Gennari, James F. Brinkley
2006 Misc conf
A framework for using reference ontologies as a foundation for the semantic web.
AMIA
James F. Brinkley, Dan Suciu, Landon Detwiler, John H. Gennari, Cornelius Rosse
2006 Misc conf
Differences Among Cell-structure Ontologies: FMA, GO, & CCO.
AMIA
Alan Au, Xiang Li, John H. Gennari
2006 Misc conf
Integrating Protocol Schedules with Patients' Personal Calendars.
AMIA
Andrea Civan, John H. Gennari, Wanda Pratt
2006 Misc conf
Model Driven Laboratory Information Management Systems.
AMIA
Hao Li, John H. Gennari, James F. Brinkley
2005 Misc conf
Approach for Analysis of Order Check Overrides in a Computerized Practitioner Order Entry System.
AMIA
Ching-Ping Lin, W. Paul Nichol, Patty Hoey, Terry L. Roth, Curtis L. Anderson, John H. Gennari, Thomas H. Payne
2005 J jnl
Asynchronous communication among clinical researchers: A study for systems design.
Int. J. Medical Informatics
John H. Gennari, Chunhua Weng, Jacqueline Benedetti, David W. McDonald
2005 Misc conf
Integrating Genomic Knowledge Sources Through an Anatomy Ontology.
Pacific Symposium on Biocomputing
John H. Gennari, Adam Silberfein, Jesse C. Wiley
2005 B conf
Knowledge transformations between frame systems and RDB systems.
K-CAP
John H. Gennari, Peter Mork, Hao Li
2005 Misc conf
Of Mice and Men: Design of a Comparative Anatomy Information System.
AMIA
Ravensara S. Travillian, John H. Gennari, Linda G. Shapiro
2004 — conf
A Collaborative Clinical Trial Protocol Writing System.
MedInfo
Chunhua Weng, John H. Gennari, David W. McDonald
2004 — conf
An Ethnographic Study of Collaborative Clinical Trial Protocol Writing.
MedInfo
John H. Gennari, Chunhua Weng, David W. McDonald, Jacqueline Benedetti, Stephanie Green
2004 A conf
Asynchronous collaborative writing through annotations.
CSCW
Chunhua Weng, John H. Gennari
2004 J jnl
Incorporating ideas from computer-supported cooperative work.
J. Biomed. Informatics
Wanda Pratt, Madhu C. Reddy, David W. McDonald, Peter Tarczy-Hornoch, John H. Gennari
2004 A conf
The multiple views of inter-organizational authoring.
CSCW
David W. McDonald, Chunhua Weng, John H. Gennari
2003 — conf
Interoperability of Protege 2.0 beta and OilEd 3.5 in the Domain Knowledge of Osteoporosis.
EON
Franz Calvo, John H. Gennari
2003 B ed.
Proceedings of the 2nd International Conference on Knowledge Capture (K-CAP 2003), October 23-25, 2003, Sanibel Island, FL, USA
John H. Gennari, Bruce W. Porter, Yolanda Gil
2003 Misc conf
Scenario-based Participatory Design of A Collaborative Clinical Trial Protocol Authoring System.
AMIA
Chunhua Weng, John H. Gennari, David W. McDonald
2003 J jnl
The evolution of Protégé: an environment for knowledge-based systems development.
Int. J. Hum. Comput. Stud.
John H. Gennari, Mark A. Musen, Ray W. Fergerson, William E. Grosso, Monica Crubézy, Henrik Eriksson, Natalya Fridman Noy, Samson W. Tu
2002 Misc conf
Temporal knowledge representation for scheduling tasks in clinical trial protocols.
AMIA
Chunhua Weng, Michael G. Kahn, John H. Gennari
2001 Misc conf
Cross-tool communication: from protocol authoring to eligibility determination.
AMIA
John H. Gennari, David Sklar, John S. Silva
2000 Misc conf
Knowledge representation and tool support for critiquing clinical trial protocols.
AMIA
Daniel L. Rubin, John H. Gennari, Mark A. Musen
2000 Misc conf
Participatory design and an eligibility screening tool.
AMIA
John H. Gennari, Madhu C. Reddy
1999 Misc conf
Tool support for authoring eligibility criteria for cancer trials.
AMIA
Daniel L. Rubin, John H. Gennari, Sandra Srinivas, Allen Yuen, Herbert Kaizer, Mark A. Musen, John S. Silva
1998 J jnl
Research Paper: The GuideLine Interchange Format: A Model for Representing Guidelines.
J. Am. Medical Informatics Assoc.
Lucila Ohno-Machado, John H. Gennari, Shawn N. Murphy, Nilesh L. Jain, Samson W. Tu, Diane E. Oliver, Edward Pattison-Gordon, Robert A. Greenes, Edward H. Shortliffe, G. Octo Barnett
1998 J jnl
Reuse, CORBA, and knowledge-based systems.
Int. J. Hum. Comput. Stud.
John H. Gennari, Heyning Cheng, Russ B. Altman, Mark A. Musen
1996 J jnl
Reusable ontologies, knowledge-acquisition tools, and performance systems: PROTÉGÉ-II solutions to Sisyphus-2.
Int. J. Hum. Comput. Stud.
Thomas E. Rothenfluh, John H. Gennari, Henrik Eriksson, Angel R. Puerta, Samson W. Tu, Mark A. Musen
1995 J jnl
Ontology-based configuration of problem-solving methods and generation of knowledge-acquisition tools: application of PROTEGE-II to protocol-based decision support.
Artif. Intell. Medicine
Samson W. Tu, Henrik Eriksson, John H. Gennari, Yuval Shahar, Mark A. Musen
1995 — conf
Reuse with PROTÉgÉ-II: From Elevators to Ribosomes.
SSR
John H. Gennari, Russ B. Altman, Mark A. Musen
1994 — conf
Beyond Data Models for Automated User Interface Generation.
BCS HCI
Angel R. Puerta, Henrik Eriksson, John H. Gennari, Mark A. Musen
1994 J jnl
Mapping domains to methods in support of reuse.
Int. J. Hum. Comput. Stud.
John H. Gennari, Samson W. Tu, Thomas E. Rothenfluh, Mark A. Musen
1994 A* conf
Model-Based Automated Generation of User Interfaces.
AAAI
Angel R. Puerta, Henrik Eriksson, John H. Gennari, Mark A. Musen
1991 — conf
Learning Spatial Relations from Images.
ML
Kazuo Hiraki, John H. Gennari, Yoshinobu Yamamoto, Yuichiro Anzai
1989 — conf
Focused Concept Formation.
ML
John H. Gennari
1989 J jnl
Models of Incremental Concept Formation.
Artif. Intell.
John H. Gennari, Pat Langley, Douglas H. Fisher