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List of works by John H Gennari

Asynchronous communication among clinical researchers: a study for systems design

scientific article published on 01 October 2005

Bayesian network models for error detection in radiotherapy plans

scientific article published on 13 March 2015

Composite annotations: requirements for mapping multiscale data and models to biomedical ontologies.

scientific article

Developing Bayesian networks from a dependency-layered ontology: A proof-of-concept in radiation oncology.

scientific article published on 13 May 2017

Evaluating clinical decision support systems: monitoring CPOE order check override rates in the Department of Veterans Affairs' Computerized Patient Record System

scientific article published on 25 June 2008

Harmonizing semantic annotations for computational models in biology

Harmonizing semantic annotations for computational models in biology

scientific article published on 01 March 2019

Incorporating ideas from computer-supported cooperative work

scientific article published on April 2004

Integrating systems biology models and biomedical ontologies

scientific article (publication date: 11 August 2011)

Model annotation and discovery with the Physiome Model Repository

scientific article published on 06 September 2019

Multiple ontologies in action: composite annotations for biosimulation models

scientific article

OMEX metadata specification (version 1.2)

scientific article published in 2021

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

scientific article published on 02 December 2013

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

scientific article published on June 1995

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

scientific article published on 25 June 2020

Participatory design of a collaborative clinical trial protocol writing system.

scientific article published on 23 June 2006

Physical properties of biological entities: an introduction to the ontology of physics for biology

scientific article (publication date: 2011)

Practical resources for enhancing the reproducibility of mechanistic modeling in systems biology

scientific article published in September 2021

Predicting instances of pathway ontology classes for pathway integration.

scientific article

SBOL-OWL: An Ontological Approach for Formal and Semantic Representation of Synthetic Biology Information

scientific article published on 14 May 2019

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

scientific article published on 01 May 2019

Semantics-Based Composition of Integrated Cardiomyocyte Models Motivated by Real-World Use Cases

scientific article published on 30 December 2015

Sharing Structure and Function in Biological Design with SBOL 2.0.

scientific article published on 25 April 2016

Standard biological parts knowledgebase

scientific article

Synthetic Biology Open Language (SBOL) Version 2.0.0.

scientific article published on 04 September 2015

Synthetic Biology Open Language (SBOL) Version 2.1.0.

scientific article published on 18 December 2016

Synthetic Biology Open Language (SBOL) Version 2.2.0.

scientific article published on 2 April 2018

Synthetic Biology Open Language (SBOL) Version 2.3.

scientific article published on 13 June 2019

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.

scientific article

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

article

User-centered semantic harmonization: a case study.

scientific article published on 21 March 2007

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