John H. Gennari

According to our database, John H. Gennari authored at least 76 papers between 1989 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

VSCode-Antimony: a source editor for building, analyzing, and translating antimony models.

Steve Ma, Longxuan Fan, Sai Anish Konanki, Eva Liu, John H. Gennari, Lucian P. Smith, Joseph L. Hellerstein, Herbert M. Sauro

Bioinform., December, 2023

An automated model annotation system (AMAS) for SBML models.

Woosub Shin, John H. Gennari, Joseph L. Hellerstein, Herbert M. Sauro

Bioinform., October, 2023

2022

BioSimulators: a central registry of simulation engines and services for recommending specific tools.

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

Nucleic Acids Res., 2022

BioSimulators: a central registry of simulation engines and services for recommending specific tools.

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

CoRR, 2022

2021

OMEX metadata specification (version 1.2).

John H. Gennari, Matthias König, Goksel Misirli, Maxwell Lewis Neal, David P. Nickerson, Dagmar Waltemath

J. Integr. Bioinform., 2021

libOmexMeta: enabling semantic annotation of models to support FAIR principles.

Ciaran M. Welsh, David P. Nickerson, Anand K. Rampadarath, Maxwell Lewis Neal, Herbert M. Sauro, John H. Gennari

Bioinform., 2021

2020

Open modeling and exchange (OMEX) metadata specification version 1.0.

Maxwell Lewis Neal, John H. Gennari, Dagmar Waltemath, David P. Nickerson, Matthias König

J. Integr. Bioinform., 2020

2019

Synthetic Biology Open Language (SBOL) Version 2.3.

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

J. Integr. Bioinform., 2019

Model annotation and discovery with the Physiome Model Repository.

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

BMC Bioinform., 2019

Predicting instances of pathway ontology classes for pathway integration.

Lucy Lu Wang, G. Thomas Hayman, Jennifer R. Smith, Monika Tutaj, Mary Shimoyama, John H. Gennari

J. Biomed. Semant., 2019

SemGen: a tool for semantics-based annotation and composition of biosimulation models.

Maxwell Lewis Neal, Christopher T. Thompson, Karam G. Kim, Ryan C. James, Daniel L. Cook, Brian E. Carlson, John H. Gennari

Bioinform., 2019

Harmonizing semantic annotations for computational models in biology.

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

Briefings Bioinform., 2019

The Ontology of Physics for Biology - A Companion to Basic Formal Ontology.

Daniel L. Cook, John H. Gennari, Maxwell Lewis Neal

Proceedings of the 10th International Conference on Biomedical Ontology (ICBO 2019), Buffalo, New York, USA, July 30, 2019

2018

Synthetic Biology Open Language (SBOL) Version 2.2.0.

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

J. Integr. Bioinform., 2018

Quantifying the effects of gene entity disambiguation for GSEA.

Lucy Lu Wang, John H. Gennari

Proceedings of the AMIA 2018, 2018

Counting Readmissions: Surprisingly difficult.

Ahmad K. Aljadaan, Peter Tarczy-Hornoch, Adam B. Wilcox, Todd F. Dardas, John H. Gennari

Proceedings of the AMIA 2018, 2018

2017

Similarity Metrics for Determining Overlap Among Biological Pathways.

Lucy Lu Wang, John H. Gennari

Proceedings of the 8th International Conference on Biomedical Ontology (ICBO 2017), Newcastle-upon-Tyne, United Kingdom, September 13th, 2017

Extending the Ontology of Physics for Biology with Thermodynamics.

Daniel L. Cook, John H. Gennari, Maxwell Lewis Neal

Proceedings of the 8th International Conference on Biomedical Ontology (ICBO 2017), Newcastle-upon-Tyne, United Kingdom, September 13th, 2017

2016

Synthetic Biology Open Language (SBOL) Version 2.1.0.

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

J. Integr. Bioinform., 2016

An Analysis of Differences in Biological Pathway Resources.

Lucy Lu Wang, John H. Gennari, Neil F. Abernethy

Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

Qualitative Causal Analyses of Biosimulation Models.

Maxwell Lewis Neal, John H. Gennari, Daniel L. Cook

Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

Discovering representational differences between pathway knowledge bases for pathway resource merging.

Lucy Lu Wang, John H. Gennari, Neil F. Abernethy

Proceedings of the AMIA 2016, 2016

Assessing patient and caregiver needs and challenges in information and symptom management: a study of primary brain tumors.

Rebecca J. Hazen, Amanda Lazar, John H. Gennari

Proceedings of the AMIA 2016, 2016

2015

Synthetic Biology Open Language (SBOL) Version 2.0.0.

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

J. Integr. Bioinform., 2015

Decision Analysis for Oropharyngeal Cancer in Radiotherapy.

Ahmad Aljadaan, John H. Gennari, Mark H. Phillips, Wade P. Smith

Proceedings of the AMIA 2015, 2015

2014

A Reappraisal of How to Build Modular, Reusable Models of Biological Systems.

Maxwell Lewis Neal, Michael T. Cooling, Lucian P. Smith, Christopher T. Thompson, Herbert M. Sauro, Brian E. Carlson, Daniel L. Cook, John H. Gennari

PLoS Comput. Biol., 2014

2013

Representing physiological processes and their participants with PhysioMaps.

Daniel L. Cook, Maxwell Lewis Neal, Robert Hoehndorf, Georgios V. Gkoutos, John H. Gennari

J. Biomed. Semant., 2013

Ontology of physics for biology: representing physical dependencies as a basis for biological processes.

Daniel L. Cook, Maxwell Lewis Neal, Fred L. Bookstein, John H. Gennari

J. Biomed. Semant., 2013

Using random walks to identify cancer-associated modules in expression data.

Deanna Petrochilos, Ali Shojaie, John H. Gennari, Neil F. Abernethy

BioData Min., 2013

An OWL knowledge base for classifying and querying collections of physiological models: A prototype human physiome.

Maxwell Lewis Neal, Daniel L. Cook, John H. Gennari

Proceedings of the 4th International Conference on Biomedical Ontology, 2013

Identifying High-Risk Components in Synthetic Biology.

Nikhil Gopal, Michal Galdzicki, Bryan Bartley, Evren Sirin, John H. Gennari

Proceedings of the AMIA 2013, 2013

2011

Multiple ontologies in action: Composite annotations for biosimulation models.

John H. Gennari, Maxwell Lewis Neal, Michal Galdzicki, Daniel L. Cook

J. Biomed. Informatics, 2011

Integrating systems biology models and biomedical ontologies.

Robert Hoehndorf, Michel Dumontier, John H. Gennari, Sarala M. Wimalaratne, Bernard de Bono, Daniel L. Cook, Georgios V. Gkoutos

BMC Syst. Biol., 2011

HeartCyc: A Cardiac Cycle Process Ontology Based in the Ontology of Physics for Biology.

Daniel L. Cook, Michal Galdzicki, Maxwell Lewis Neal, José L. V. Mejino Jr., John H. Gennari

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

2009

Advances in Semantic Representation for Multiscale Biosimulation: A Case Study in Merging Models.

Maxwell Lewis Neal, John H. Gennari, Theo Arts, Daniel L. Cook

Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009

2008

Research Paper: Evaluating Clinical Decision Support Systems: Monitoring CPOE Order Check Override Rates in the Department of Veterans Affairs' Computerized Patient Record System.

Ching-Ping Lin, Thomas H. Payne, W. Paul Nichol, Patricia J. Hoey, Curtis L. Anderson, John H. Gennari

J. Am. Medical Informatics Assoc., 2008

Integration of Multi-Scale Biosimulation Models via Light-Weight Semantics.

John H. Gennari, Maxwell Lewis Neal, Brian E. Carlson, Daniel L. Cook

Proceedings of the Biocomputing 2008, 2008

Building an Automated Problem List Based on Natural Language Processing: Lessons Learned in the Early Phase of Development.

Imre Solti, Barry Aaronson, Grant S. Fletcher, Magdolna Solti, John H. Gennari, Melissa Cooper, Thomas H. Payne

Proceedings of the AMIA 2008, 2008

Bridging Biological Ontologies and Biosimulation: The Ontology of Physics for Biology.

Daniel L. Cook, José L. V. Mejino Jr., Maxwell Lewis Neal, John H. Gennari

Proceedings of the AMIA 2008, 2008

2007

User-centered semantic harmonization: A case study.

Chunhua Weng, John H. Gennari, Douglas B. Fridsma

J. Biomed. Informatics, 2007

Participatory design of a collaborative clinical trial protocol writing system.

Chunhua Weng, David W. McDonald, Dana Sparks, Jason McCoy, John H. Gennari

Int. J. Medical Informatics, 2007

Chalkboard: Ontology-Based Pathway Modeling And Qualitative Inference Of Disease Mechanisms.

Daniel L. Cook, Jesse C. Wiley, John H. Gennari

Proceedings of the Biocomputing 2007, 2007

XGI: A Graphical Interface for XQuery Creation.

Xiang Li, John H. Gennari, James F. Brinkley

Proceedings of the AMIA 2007, 2007

2006

Model Driven Laboratory Information Management Systems.

Hao Li, John H. Gennari, James F. Brinkley

Proceedings of the AMIA 2006, 2006

Integrating Protocol Schedules with Patients' Personal Calendars.

Andrea Civan, John H. Gennari, Wanda Pratt

Proceedings of the AMIA 2006, 2006

A framework for using reference ontologies as a foundation for the semantic web.

James F. Brinkley, Dan Suciu, Landon Detwiler, John H. Gennari, Cornelius Rosse

Proceedings of the AMIA 2006, 2006

Differences Among Cell-structure Ontologies: FMA, GO, & CCO.

Alan Au, Xiang Li, John H. Gennari

Proceedings of the AMIA 2006, 2006

2005

Asynchronous communication among clinical researchers: A study for systems design.

John H. Gennari, Chunhua Weng, Jacqueline Benedetti, David W. McDonald

Int. J. Medical Informatics, 2005

Integrating Genomic Knowledge Sources Through an Anatomy Ontology.

John H. Gennari, Adam Silberfein, Jesse C. Wiley

Proceedings of the Biocomputing 2005, 2005

Knowledge transformations between frame systems and RDB systems.

John H. Gennari, Peter Mork, Hao Li

Proceedings of the 3rd International Conference on Knowledge Capture (K-CAP 2005), 2005

Of Mice and Men: Design of a Comparative Anatomy Information System.

Ravensara S. Travillian, John H. Gennari, Linda G. Shapiro

Proceedings of the AMIA 2005, 2005

Approach for Analysis of Order Check Overrides in a Computerized Practitioner Order Entry System.

Ching-Ping Lin, W. Paul Nichol, Patty Hoey, Terry L. Roth, Curtis L. Anderson, John H. Gennari, Thomas H. Payne

Proceedings of the AMIA 2005, 2005

2004

Incorporating ideas from computer-supported cooperative work.

Wanda Pratt, Madhu C. Reddy, David W. McDonald, Peter Tarczy-Hornoch, John H. Gennari

J. Biomed. Informatics, 2004

A Collaborative Clinical Trial Protocol Writing System.

Chunhua Weng, John H. Gennari, David W. McDonald

Proceedings of the MEDINFO 2004, 2004

An Ethnographic Study of Collaborative Clinical Trial Protocol Writing.

John H. Gennari, Chunhua Weng, David W. McDonald, Jacqueline Benedetti, Stephanie Green

Proceedings of the MEDINFO 2004, 2004

Asynchronous collaborative writing through annotations.

Chunhua Weng, John H. Gennari

Proceedings of the 2004 ACM Conference on Computer Supported Cooperative Work, 2004

The multiple views of inter-organizational authoring.

David W. McDonald, Chunhua Weng, John H. Gennari

Proceedings of the 2004 ACM Conference on Computer Supported Cooperative Work, 2004

2003

The evolution of Protégé: an environment for knowledge-based systems development.

John H. Gennari, Mark A. Musen, Ray W. Fergerson, William E. Grosso, Monica Crubézy, Henrik Eriksson, Natalya Fridman Noy, Samson W. Tu

Int. J. Hum. Comput. Stud., 2003

Interoperability of Protege 2.0 beta and OilEd 3.5 in the Domain Knowledge of Osteoporosis.

Franz Calvo, John H. Gennari

Proceedings of the EON2003, 2003

Scenario-based Participatory Design of A Collaborative Clinical Trial Protocol Authoring System.

Chunhua Weng, John H. Gennari, David W. McDonald

Proceedings of the AMIA 2003, 2003

2002

Temporal knowledge representation for scheduling tasks in clinical trial protocols.

Chunhua Weng, Michael G. Kahn, John H. Gennari

Proceedings of the AMIA 2002, 2002

2001

Cross-tool communication: from protocol authoring to eligibility determination.

John H. Gennari, David Sklar, John S. Silva

Proceedings of the AMIA 2001, 2001

2000

Knowledge representation and tool support for critiquing clinical trial protocols.

Daniel L. Rubin, John H. Gennari, Mark A. Musen

Proceedings of the AMIA 2000, 2000

Participatory design and an eligibility screening tool.

John H. Gennari, Madhu C. Reddy

Proceedings of the AMIA 2000, 2000

1999

Tool support for authoring eligibility criteria for cancer trials.

Daniel L. Rubin, John H. Gennari, Sandra Srinivas, Allen Yuen, Herbert Kaizer, Mark A. Musen, John S. Silva

Proceedings of the AMIA 1999, 1999

1998

Research Paper: The GuideLine Interchange Format: A Model for Representing Guidelines.

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

J. Am. Medical Informatics Assoc., 1998

Reuse, CORBA, and knowledge-based systems.

John H. Gennari, Heyning Cheng, Russ B. Altman, Mark A. Musen

Int. J. Hum. Comput. Stud., 1998

1996

Reusable ontologies, knowledge-acquisition tools, and performance systems: PROTÉGÉ-II solutions to Sisyphus-2.

Thomas E. Rothenfluh, John H. Gennari, Henrik Eriksson, Angel R. Puerta, Samson W. Tu, Mark A. Musen

Int. J. Hum. Comput. Stud., 1996

1995

Ontology-based configuration of problem-solving methods and generation of knowledge-acquisition tools: application of PROTEGE-II to protocol-based decision support.

Samson W. Tu, Henrik Eriksson, John H. Gennari, Yuval Shahar, Mark A. Musen

Artif. Intell. Medicine, 1995

Reuse with PROTÉgÉ-II: From Elevators to Ribosomes.

John H. Gennari, Russ B. Altman, Mark A. Musen

Proceedings of the ACM SIGSOFT Symposium on Software Reusability, 1995

1994

Mapping domains to methods in support of reuse.

John H. Gennari, Samson W. Tu, Thomas E. Rothenfluh, Mark A. Musen

Int. J. Hum. Comput. Stud., 1994

Beyond Data Models for Automated User Interface Generation.

Angel R. Puerta, Henrik Eriksson, John H. Gennari, Mark A. Musen

Proceedings of the People and Computers IX, 1994

Model-Based Automated Generation of User Interfaces.

Angel R. Puerta, Henrik Eriksson, John H. Gennari, Mark A. Musen

Proceedings of the 12th National Conference on Artificial Intelligence, Seattle, WA, USA, July 31, 1994

1991

Learning Spatial Relations from Images.

Kazuo Hiraki, John H. Gennari, Yoshinobu Yamamoto, Yuichiro Anzai

Proceedings of the Eighth International Workshop (ML91), 1991

1989

Models of Incremental Concept Formation.

John H. Gennari, Pat Langley, Douglas H. Fisher

Artif. Intell., 1989

Focused Concept Formation.

John H. Gennari

Proceedings of the Sixth International Workshop on Machine Learning (ML 1989), 1989