John H. Gennari

According to our database1, John H. Gennari authored at least 68 papers between 1989 and 2019.

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Bibliography

2019
Synthetic Biology Open Language (SBOL) Version 2.3.
J. Integrative Bioinformatics, 2019

Model annotation and discovery with the Physiome Model Repository.
BMC Bioinformatics, 2019

Predicting instances of pathway ontology classes for pathway integration.
J. Biomedical Semantics, 2019

SemGen: a tool for semantics-based annotation and composition of biosimulation models.
Bioinformatics, 2019

Harmonizing semantic annotations for computational models in biology.
Briefings in Bioinformatics, 2019

2018
Synthetic Biology Open Language (SBOL) Version 2.2.0.
J. Integrative Bioinformatics, 2018

Quantifying the effects of gene entity disambiguation for GSEA.
Proceedings of the AMIA 2018, 2018

Counting Readmissions: Surprisingly difficult.
Proceedings of the AMIA 2018, 2018

2017
Similarity Metrics for Determining Overlap Among Biological Pathways.
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.
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.
J. Integrative Bioinformatics, 2016

An Analysis of Differences in Biological Pathway Resources.
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

Qualitative Causal Analyses of Biosimulation Models.
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

Discovering representational differences between pathway knowledge bases for pathway resource merging.
Proceedings of the AMIA 2016, 2016

Assessing patient and caregiver needs and challenges in information and symptom management: a study of primary brain tumors.
Proceedings of the AMIA 2016, 2016

2015
Synthetic Biology Open Language (SBOL) Version 2.0.0.
J. Integrative Bioinformatics, 2015

Decision Analysis for Oropharyngeal Cancer in Radiotherapy.
Proceedings of the AMIA 2015, 2015

2014
A Reappraisal of How to Build Modular, Reusable Models of Biological Systems.
PLoS Computational Biology, 2014

2013
Representing physiological processes and their participants with PhysioMaps.
J. Biomedical Semantics, 2013

Ontology of physics for biology: representing physical dependencies as a basis for biological processes.
J. Biomedical Semantics, 2013

Using random walks to identify cancer-associated modules in expression data.
BioData Mining, 2013

An OWL knowledge base for classifying and querying collections of physiological models: A prototype human physiome.
Proceedings of the 4th International Conference on Biomedical Ontology, 2013

Identifying High-Risk Components in Synthetic Biology.
Proceedings of the AMIA 2013, 2013

2011
Multiple ontologies in action: Composite annotations for biosimulation models.
Journal of Biomedical Informatics, 2011

Integrating systems biology models and biomedical ontologies.
BMC Systems Biology, 2011

HeartCyc: A Cardiac Cycle Process Ontology Based in the Ontology of Physics for Biology.
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

2009
Advances in Semantic Representation for Multiscale Biosimulation: A Case Study in Merging Models.
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.
JAMIA, 2008

Integration of Multi-Scale Biosimulation Models via Light-Weight Semantics.
Proceedings of the Biocomputing 2008, 2008

Building an Automated Problem List Based on Natural Language Processing: Lessons Learned in the Early Phase of Development.
Proceedings of the AMIA 2008, 2008

Bridging Biological Ontologies and Biosimulation: The Ontology of Physics for Biology.
Proceedings of the AMIA 2008, 2008

2007
User-centered semantic harmonization: A case study.
Journal of Biomedical Informatics, 2007

Participatory design of a collaborative clinical trial protocol writing system.
I. J. Medical Informatics, 2007

Chalkboard: Ontology-Based Pathway Modeling And Qualitative Inference Of Disease Mechanisms.
Proceedings of the Biocomputing 2007, 2007

XGI: A Graphical Interface for XQuery Creation.
Proceedings of the AMIA 2007, 2007

2006
Model Driven Laboratory Information Management Systems.
Proceedings of the AMIA 2006, 2006

Integrating Protocol Schedules with Patients' Personal Calendars.
Proceedings of the AMIA 2006, 2006

A framework for using reference ontologies as a foundation for the semantic web.
Proceedings of the AMIA 2006, 2006

Differences Among Cell-structure Ontologies: FMA, GO, & CCO.
Proceedings of the AMIA 2006, 2006

2005
Asynchronous communication among clinical researchers: A study for systems design.
I. J. Medical Informatics, 2005

Integrating Genomic Knowledge Sources Through an Anatomy Ontology.
Proceedings of the Biocomputing 2005, 2005

Knowledge transformations between frame systems and RDB systems.
Proceedings of the 3rd International Conference on Knowledge Capture (K-CAP 2005), 2005

Of Mice and Men: Design of a Comparative Anatomy Information System.
Proceedings of the AMIA 2005, 2005

Approach for Analysis of Order Check Overrides in a Computerized Practitioner Order Entry System.
Proceedings of the AMIA 2005, 2005

2004
Incorporating ideas from computer-supported cooperative work.
Journal of Biomedical Informatics, 2004

A Collaborative Clinical Trial Protocol Writing System.
Proceedings of the MEDINFO 2004, 2004

An Ethnographic Study of Collaborative Clinical Trial Protocol Writing.
Proceedings of the MEDINFO 2004, 2004

Asynchronous collaborative writing through annotations.
Proceedings of the 2004 ACM Conference on Computer Supported Cooperative Work, 2004

The multiple views of inter-organizational authoring.
Proceedings of the 2004 ACM Conference on Computer Supported Cooperative Work, 2004

2003
The evolution of Protégé: an environment for knowledge-based systems development.
Int. J. Hum.-Comput. Stud., 2003

Interoperability of Protege 2.0 beta and OilEd 3.5 in the Domain Knowledge of Osteoporosis.
Proceedings of the EON2003, 2003

Scenario-based Participatory Design of A Collaborative Clinical Trial Protocol Authoring System.
Proceedings of the AMIA 2003, 2003

2002
Temporal knowledge representation for scheduling tasks in clinical trial protocols.
Proceedings of the AMIA 2002, 2002

2001
Cross-tool communication: from protocol authoring to eligibility determination.
Proceedings of the AMIA 2001, 2001

2000
Knowledge representation and tool support for critiquing clinical trial protocols.
Proceedings of the AMIA 2000, 2000

Participatory design and an eligibility screening tool.
Proceedings of the AMIA 2000, 2000

1999
Tool support for authoring eligibility criteria for cancer trials.
Proceedings of the AMIA 1999, 1999

1998
Research Paper: The GuideLine Interchange Format: A Model for Representing Guidelines.
JAMIA, 1998

Reuse, CORBA, and knowledge-based systems.
Int. J. Hum.-Comput. Stud., 1998

1996
Reusable ontologies, knowledge-acquisition tools, and performance systems: PROTÉGÉ-II solutions to Sisyphus-2.
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.
Artificial Intelligence in Medicine, 1995

Reuse with PROTÉgÉ-II: From Elevators to Ribosomes.
Proceedings of the ACM SIGSOFT Symposium on Software Reusability, 1995

1994
Mapping domains to methods in support of reuse.
Int. J. Hum.-Comput. Stud., 1994

Beyond Data Models for Automated User Interface Generation.
Proceedings of the People and Computers IX, 1994

Model-Based Automated Generation of User Interfaces.
Proceedings of the 12th National Conference on Artificial Intelligence, Seattle, WA, USA, July 31, 1994

1991
Learning Spatial Relations from Images.
Proceedings of the Eighth International Workshop (ML91), 1991

1989
Models of Incremental Concept Formation.
Artif. Intell., 1989

Focused Concept Formation.
Proceedings of the Sixth International Workshop on Machine Learning (ML 1989), 1989


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