Daniel L. Cook

According to our database, Daniel L. Cook authored at least 21 papers between 2004 and 2019.

Collaborative distances:

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

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

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

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

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

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

Innovative Use of Ontologies: Association of Physiological Pathways to Corresponding Computational Models and Disparate Data Types.

Nazanin Tabesh-Saleki, Brian E. Carlson, Christopher T. Thompson, Maxwell Lewis Neal, Daniel L. Cook, Mary Shimoyama

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

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

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

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

A Model Browser for Biosimulation.

Gary Yngve, James F. Brinkley, Daniel L. Cook, Linda G. Shapiro

Proceedings of the AMIA 2007, 2007

2006

Ontology-Based Representation of Simulation Models of Physiology.

Daniel L. Rubin, David Grossman, Maxwell Lewis Neal, Daniel L. Cook, James B. Bassingthwaighte, Mark A. Musen

Proceedings of the AMIA 2006, 2006

2005

A Strategy for Improving and Integrating Biomedical Ontologies.

Cornelius Rosse, Anand Kumar, José L. V. Mejino Jr., Daniel L. Cook, Landon T. Detwiler, Barry Smith

Proceedings of the AMIA 2005, 2005

2004

Evolution of a Foundational Model of Physiology: Symbolic Representation for Functional Bioinformatics.

Daniel L. Cook, José L. V. Mejino Jr., Cornelius Rosse

Proceedings of the MEDINFO 2004, 2004