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Developing Bayesian networks from a dependency-layered ontology: A proof-of-concept in radiation oncology.
Published in:
Medical Physics, 2017, v. 44, n. 8, p. 4350, doi. 10.1002/mp.12340
By:
- Kalet, Alan M.;
- Doctor, Jason N.;
- Gennari, John H.;
- Phillips, Mark H.
Publication type:
Article
VSCode-Antimony: a source editor for building, analyzing, and translating antimony models.
Published in:
Bioinformatics, 2023, v. 39, n. 12, p. 1, doi. 10.1093/bioinformatics/btad753
By:
- Ma, Steve;
- Fan, Longxuan;
- Konanki, Sai Anish;
- Liu, Eva;
- Gennari, John H;
- Smith, Lucian P;
- Hellerstein, Joseph L;
- Sauro, Herbert M
Publication type:
Article
An automated model annotation system (AMAS) for SBML models.
Published in:
Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad658
By:
- Shin, Woosub;
- Gennari, John H;
- Hellerstein, Joseph L;
- Sauro, Herbert M
Publication type:
Article
libOmexMeta: enabling semantic annotation of models to support FAIR principles.
Published in:
Bioinformatics, 2021, v. 37, n. 24, p. 4898, doi. 10.1093/bioinformatics/btab445
By:
- Welsh, Ciaran;
- Nickerson, David P;
- Rampadarath, Anand;
- Neal, Maxwell L;
- Sauro, Herbert M;
- Gennari, John H
Publication type:
Article
The guideline interchange format: a model for representing guidelines.
Published in:
1998
By:
- Ohno-Machado, Lucila;
- Gennari, John H;
- Murphy, Shawn N;
- Jain, Nilesh L;
- Tu, Samson W;
- Oliver, Diane E;
- Pattison-Gordon, Edward;
- Greenes, Robert A;
- Shortliffe, Edward H;
- Barnett, G Octo;
- Ohno-Machado, L;
- Gennari, J H;
- Murphy, S N;
- Jain, N L;
- Tu, S W;
- Oliver, D E;
- Pattison-Gordon, E;
- Greenes, R A;
- Shortliffe, E H;
- Barnett, G O
Publication type:
journal article
Predicting instances of pathway ontology classes for pathway integration.
Published in:
Journal of Biomedical Semantics, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1186/s13326-019-0202-8
By:
- Wang, Lucy Lu;
- Thomas Hayman, G.;
- Smith, Jennifer R.;
- Tutaj, Monika;
- Shimoyama, Mary E.;
- Gennari, John H.
Publication type:
Article
Ontology of physics for biology: representing physical dependencies as a basis for biological processes.
Published in:
Journal of Biomedical Semantics, 2013, v. 4, n. 1, p. 2, doi. 10.1186/2041-1480-4-41
By:
- Cook, Daniel L.;
- Neal, Maxwell L.;
- Bookstein, Fred L.;
- Gennari, John H.
Publication type:
Article
Representing physiological processes and their participants with PhysioMaps.
Published in:
Journal of Biomedical Semantics, 2013, v. 4, n. Suppl 1, p. 1, doi. 10.1186/2041-1480-4-S1-S2
By:
- Cook, Daniel L.;
- Neal, Maxwell L.;
- Hoehndorf, Robert;
- Gkoutos, Georgios V.;
- Gennari, John H.
Publication type:
Article
Physical Properties of Biological Entities: An Introduction to the Ontology of Physics for Biology.
Published in:
PLoS ONE, 2011, v. 6, n. 12, p. 1, doi. 10.1371/journal.pone.0028708
By:
- Cook, Daniel L.;
- Bookstein, Fred L.;
- Gennari, John H.
Publication type:
Article
Standard Biological Parts Knowledgebase.
Published in:
PLoS ONE, 2011, v. 6, n. 2, p. 1, doi. 10.1371/journal.pone.0017005
By:
- Galdzicki, Michal;
- Rodriguez, Cesar;
- Chandran, Deepak;
- Sauro, Herbert M.;
- Gennari, John H.
Publication type:
Article
OMEX metadata specification (version 1.2).
Published in:
Journal of Integrative Bioinformatics, 2021, v. 18, n. 3, p. 1, doi. 10.1515/jib-2021-0020
By:
- Gennari, John H.;
- König, Matthias;
- Misirli, Goksel;
- Neal, Maxwell L.;
- Nickerson, David P.;
- Waltemath, Dagmar
Publication type:
Article
Open modeling and exchange (OMEX) metadata specification version 1.0.
Published in:
Journal of Integrative Bioinformatics, 2020, v. 17, n. 2/3, p. 1, doi. 10.1515/jib-2020-0020
By:
- Neal, Maxwell L.;
- Gennari, John H.;
- Waltemath, Dagmar;
- Nickerson, David P.;
- König, Matthias
Publication type:
Article
Evaluating Clinical Decision Support Systems: Monitoring CPOE Order Check Override Rates in the Department of Veterans Affairs' Computerized Patient Record System.
Published in:
Journal of the American Medical Informatics Association, 2008, v. 15, n. 5, p. 620, doi. 10.1197/jamia.M2453
By:
- CHING-PING LIN;
- PAYNE, THOMAS H.;
- NICHOL, W. PAUL;
- HOEY, PATRICIA J.;
- ANDERSON, CURTIS L.;
- GENNARI, JOHN H.
Publication type:
Article
Model annotation and discovery with the Physiome Model Repository.
Published in:
BMC Bioinformatics, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s12859-019-2987-y
By:
- Sarwar, Dewan M.;
- Kalbasi, Reza;
- Gennari, John H.;
- Carlson, Brian E.;
- Neal, Maxwell L.;
- Bono, Bernard de;
- Atalag, Koray;
- Hunter, Peter J.;
- Nickerson, David P.
Publication type:
Article
A Reappraisal of How to Build Modular, Reusable Models of Biological Systems.
Published in:
2014
By:
- Neal, Maxwell L.;
- Cooling, Michael T.;
- Smith, Lucian P.;
- Thompson, Christopher T.;
- Sauro, Herbert M.;
- Carlson, Brian E.;
- Cook, Daniel L.;
- Gennari, John H.
Publication type:
Opinion
Harmonizing semantic annotations for computational models in biology.
Published in:
Briefings in Bioinformatics, 2019, v. 20, n. 2, p. 540, doi. 10.1093/bib/bby087
By:
- Neal, Maxwell Lewis;
- König, Matthias;
- Nickerson, David;
- Mısırlı, Göksel;
- Kalbasi, Reza;
- Dräger, Andreas;
- Atalag, Koray;
- Chelliah, Vijayalakshmi;
- Cooling, Michael T;
- Cook, Daniel L;
- Crook, Sharon;
- Alba, Miguel de;
- Friedman, Samuel H;
- Garny, Alan;
- Gennari, John H;
- Gleeson, Padraig;
- Golebiewski, Martin;
- Hucka, Michael;
- Juty, Nick;
- Myers, Chris
Publication type:
Article
Semantics-Based Composition of Integrated Cardiomyocyte Models Motivated by Real-World Use Cases.
Published in:
PLoS ONE, 2015, v. 10, n. 12, p. 1, doi. 10.1371/journal.pone.0145621
By:
- Neal, Maxwell L.;
- Carlson, Brian E.;
- Thompson, Christopher T.;
- James, Ryan C.;
- Kim, Karam G.;
- Tran, Kenneth;
- Crampin, Edmund J.;
- Cook, Daniel L.;
- Gennari, John H.
Publication type:
Article
Deep phenotyping of cardiac function in heart transplant patients using cardiovascular system models.
Published in:
Journal of Physiology, 2020, v. 598, n. 15, p. 3203, doi. 10.1113/JP279393
By:
- Colunga, Amanda L.;
- Kim, Karam G.;
- Woodall, N. Payton;
- Dardas, Todd F.;
- Gennari, John H.;
- Olufsen, Mette S.;
- Carlson, Brian E.
Publication type:
Article
NLIMED: Natural Language Interface for Model Entity Discovery in Biosimulation Model Repositories.
Published in:
Frontiers in Physiology, 2022, v. 13, p. 1, doi. 10.3389/fphys.2022.820683
By:
- Munarko, Yuda;
- Sarwar, Dewan M.;
- Rampadarath, Anand;
- Atalag, Koray;
- Gennari, John H.;
- Neal, Maxwell L.;
- Nickerson, David P.
Publication type:
Article
SemGen: a tool for semantics-based annotation and composition of biosimulation models.
Published in:
Bioinformatics, 2019, v. 35, n. 9, p. 1600, doi. 10.1093/bioinformatics/bty829
By:
- Neal, Maxwell L;
- Thompson, Christopher T;
- Carlson, Brian E;
- Kim, Karam G;
- James, Ryan C;
- Cook, Daniel L;
- Gennari, John H
Publication type:
Article

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