John H. Gennari, Ph.D. - Publications

Affiliations: 
University of Washington, Seattle, Seattle, WA 
Area:
biomedical and health informatics

78 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Welsh C, Nickerson DP, Rampadarath A, Neal ML, Sauro HM, Gennari JH. libOmexMeta: Enabling semantic annotation of models to support FAIR principles. Bioinformatics (Oxford, England). PMID 34132740 DOI: 10.1093/bioinformatics/btab445  0.64
2020 Neal ML, Gennari JH, Waltemath D, Nickerson DP, König M. Open modeling and exchange (OMEX) metadata specification version 1.0. Journal of Integrative Bioinformatics. PMID 32589606 DOI: 10.1515/Jib-2020-0020  0.64
2020 Colunga AL, Kim KG, Woodall NP, Dardas TF, Gennari JH, Olufsen MS, Carlson BE. Deep phenotyping of cardiac function in heart transplant patients using cardiovascular systems models. The Journal of Physiology. PMID 32372434 DOI: 10.1113/Jp279393  0.36
2019 Sarwar DM, Kalbasi R, Gennari JH, Carlson BE, Neal ML, Bono B, Atalag K, Hunter PJ, Nickerson DP. Model annotation and discovery with the Physiome Model Repository. Bmc Bioinformatics. 20: 457. PMID 31492098 DOI: 10.1186/S12859-019-2987-Y  0.64
2019 Madsen C, Goñi Moreno A, P U, Palchick Z, Roehner N, Atallah C, Bartley B, Choi K, Cox RS, Gorochowski T, Grünberg R, Macklin C, McLaughlin J, Meng X, Nguyen T, ... ... Gennari JH, et al. Synthetic Biology Open Language (SBOL) Version 2.3. Journal of Integrative Bioinformatics. PMID 31199770 DOI: 10.1515/Jib-2019-0025  0.36
2018 Neal ML, König M, Nickerson D, Misirli G, Kalbasi R, Dräger A, Atalag K, Chelliah V, Cooling MT, Cook DL, Crook S, de Alba M, Friedman SH, Garny A, Gennari JH, et al. Harmonizing semantic annotations for computational models in biology. Briefings in Bioinformatics. PMID 30462164 DOI: 10.1093/Bib/Bby087  0.64
2018 Neal ML, Thompson CT, Kim KG, James RC, Cook DL, Carlson BE, Gennari JH. SemGen: a tool for semantics-based annotation and composition of biosimulation models. Bioinformatics (Oxford, England). PMID 30256901 DOI: 10.1093/Bioinformatics/Bty829  0.64
2018 Cox RS, Madsen C, McLaughlin JA, Nguyen T, Roehner N, Bartley B, Beal J, Bissell M, Choi K, Clancy K, Grünberg R, Macklin C, Misirli G, Oberortner E, Pocock M, ... ... Gennari JH, et al. Synthetic Biology Open Language (SBOL) Version 2.2.0. Journal of Integrative Bioinformatics. PMID 29605823 DOI: 10.1515/Jib-2018-0001  0.36
2017 Kalet AM, Doctor JN, Gennari JH, Phillips MH. Developing Bayesian networks from a dependency-layered ontology: a proof-of-concept in radiation oncology. Medical Physics. PMID 28500765 DOI: 10.1002/Mp.12340  0.4
2016 Beal J, Cox RS, Grünberg R, McLaughlin J, Nguyen T, Bartley B, Bissell M, Choi K, Clancy K, Macklin C, Madsen C, Misirli G, Oberortner E, Pocock M, Roehner N, ... ... Gennari JH, et al. Synthetic Biology Open Language (SBOL) Version 2.1.0. Journal of Integrative Bioinformatics. 13: 30-132. PMID 29215992 DOI: 10.1515/jib-2016-291  0.36
2016 Neal ML, Gennari JH, Cook DL. Qualitative causal analyses of biosimulation models. Ceur Workshop Proceedings. 1747. PMID 28804276  0.64
2016 Beal J, Cox RS, Grünberg R, McLaughlin J, Nguyen T, Bartley B, Bissell M, Choi K, Clancy K, Macklin C, Madsen C, Misirli G, Oberortner E, Pocock M, Roehner N, ... ... Gennari J, et al. Synthetic Biology Open Language (SBOL) Version 2.1.0. Journal of Integrative Bioinformatics. 13: 291. PMID 28187407 DOI: 10.2390/biecoll-jib-2016-291  0.36
2016 Roehner N, Beal J, Clancy K, Bartley B, Misirli G, Gruenberg R, Oberortner E, Pocock M, Bissell M, Madsen C, Nguyen T, Zhang M, Zhang Z, Zundel Z, Densmore D, ... Gennari J, et al. Sharing Structure and Function in Biological Design with SBOL 2.0. Acs Synthetic Biology. PMID 27111421 DOI: 10.1021/Acssynbio.5B00215  0.36
2015 Bartley B, Beal J, Clancy K, Misirli G, Roehner N, Oberortner E, Pocock M, Bissell M, Madsen C, Nguyen T, Zhang Z, Gennari JH, Myers C, Wipat A, Sauro H. Synthetic Biology Open Language (SBOL) Version 2.0.0. Journal of Integrative Bioinformatics. 12: 902-991. PMID 29220967 DOI: 10.1515/jib-2015-272  0.36
2015 Neal ML, Carlson BE, Thompson CT, James RC, Kim KG, Tran K, Crampin EJ, Cook DL, Gennari JH. Semantics-Based Composition of Integrated Cardiomyocyte Models Motivated by Real-World Use Cases. Plos One. 10: e0145621. PMID 26716837 DOI: 10.1371/Journal.Pone.0145621  1
2015 Bartley B, Beal J, Clancy K, Misirli G, Roehner N, Oberortner E, Pocock M, Bissell M, Madsen C, Nguyen T, Zhang Z, Gennari JH, Myers C, Wipat A, Sauro H. Synthetic Biology Open Language (SBOL) Version 2.0.0. Journal of Integrative Bioinformatics. 12: 272. PMID 26528570 DOI: 10.1515/Jib-2016-291  0.36
2015 Kalet AM, Gennari JH, Ford EC, Phillips MH. Bayesian network models for error detection in radiotherapy plans. Physics in Medicine and Biology. 60: 2735-49. PMID 25768885 DOI: 10.1088/0031-9155/60/7/2735  1
2014 Neal ML, Cooling MT, Smith LP, Thompson CT, Sauro HM, Carlson BE, Cook DL, Gennari JH. A reappraisal of how to build modular, reusable models of biological systems. Plos Computational Biology. 10: e1003849. PMID 25275523 DOI: 10.1371/Journal.Pcbi.1003849  1
2014 Galdzicki M, Clancy KP, Oberortner E, Pocock M, Quinn JY, Rodriguez CA, Roehner N, Wilson ML, Adam L, Anderson JC, Bartley BA, Beal J, Chandran D, Chen J, Densmore D, ... ... Gennari JH, et al. The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nature Biotechnology. 32: 545-50. PMID 24911500 DOI: 10.1038/Nbt.2891  1
2013 Cook DL, Neal ML, Bookstein FL, Gennari JH. Ontology of physics for biology: representing physical dependencies as a basis for biological processes. Journal of Biomedical Semantics. 4: 41. PMID 24295137 DOI: 10.1186/2041-1480-4-41  1
2013 Petrochilos D, Shojaie A, Gennari J, Abernethy N. Using random walks to identify cancer-associated modules in expression data. Biodata Mining. 6: 17. PMID 24128261 DOI: 10.1186/1756-0381-6-17  1
2013 Cook DL, Neal ML, Hoehndorf R, Gkoutos GV, Gennari JH. Representing physiological processes and their participants with PhysioMaps. Journal of Biomedical Semantics. 4: S2. PMID 23735231 DOI: 10.1186/2041-1480-4-S1-S2  0.64
2013 Neal ML, Cook DL, Gennari JH. An OWL knowledge base for classifying and querying collections of physiological models: A prototype human physiome Ceur Workshop Proceedings. 1060: 16-21.  1
2011 Cook DL, Bookstein FL, Gennari JH. Physical properties of biological entities: an introduction to the ontology of physics for biology. Plos One. 6: e28708. PMID 22216106 DOI: 10.1371/Journal.Pone.0028708  1
2011 Lin CP, Gennari JH. Understanding the work of pediatric inpatient medicine teams: implications for information system requirements. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 2011: 455-64. PMID 22195099  1
2011 Hoehndorf R, Dumontier M, Gennari JH, Wimalaratne S, de Bono B, Cook DL, Gkoutos GV. Integrating systems biology models and biomedical ontologies. Bmc Systems Biology. 5: 124. PMID 21835028 DOI: 10.1186/1752-0509-5-124  1
2011 Galdzicki M, Rodriguez C, Chandran D, Sauro HM, Gennari JH. Standard biological parts knowledgebase. Plos One. 6: e17005. PMID 21390321 DOI: 10.1371/Journal.Pone.0017005  1
2011 Gennari JH, Neal ML, Galdzicki M, Cook DL. Multiple ontologies in action: composite annotations for biosimulation models. Journal of Biomedical Informatics. 44: 146-54. PMID 20601121 DOI: 10.1016/J.Jbi.2010.06.007  1
2011 Cook DL, Galdzicki M, Neal ML, Mejino JLV, Gennari JH. HeartCyc, a cardiac cycle process ontology based in the ontology of physics for biology Ceur Workshop Proceedings. 833: 41-46.  1
2010 Lin CP, Black RA, Laplante J, Keppel GA, Tuzzio L, Berg AO, Whitener RJ, Buchwald DS, Baldwin LM, Fishman PA, Greene SM, Gennari JH, Tarczy-Hornoch P, Stephens KA. Facilitating health data sharing across diverse practices and communities. Amia Joint Summits On Translational Science Proceedings Amia Summit On Translational Science. 2010: 16-20. PMID 21347138  0.36
2009 Cook DL, Mejino JL, Neal ML, Gennari JH. Composite annotations: requirements for mapping multiscale data and models to biomedical ontologies. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2009: 2791-4. PMID 19964601 DOI: 10.1109/IEMBS.2009.5333830  1
2009 Neal ML, Gennari JH, Arts T, Cook DL. Advances in semantic representation for multiscale biosimulation: a case study in merging models. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 304-15. PMID 19209710  1
2008 Overby CL, Galdzicki M, Gennari JH. Analysis of simulation environments utilized in biomedical research. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 1077. PMID 18999224  1
2008 Solti I, Gennari JH, Payne T, Payne T, Solti M, Tarczy-Hornoch P. Natural language processing of clinical trial announcements: exploratory-study of building an automated screening application. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 1142. PMID 18999081  1
2008 Solti I, Aaronson B, Fletcher G, Solti M, Gennari JH, Cooper M, Payne T. Building an automated problem list based on natural language processing: lessons learned in the early phase of development. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 687-91. PMID 18999050  1
2008 Cook DL, Mejino JL, Neal ML, Gennari JH. Bridging biological ontologies and biosimulation: the ontology of physics for biology. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 136-40. PMID 18999003  1
2008 Lin CP, Payne TH, Nichol WP, Hoey PJ, Anderson CL, Gennari JH. Evaluating clinical decision support systems: monitoring CPOE order check override rates in the Department of Veterans Affairs' Computerized Patient Record System. Journal of the American Medical Informatics Association : Jamia. 15: 620-6. PMID 18579840 DOI: 10.1197/Jamia.M2453  1
2008 Gennari JH, Neal ML, Carlson BE, Cook DL. Integration of multi-scale biosimulation models via light-weight semantics. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 414-25. PMID 18229704  1
2007 Lin CP, Gennari JH. Designing CPOE systems using an ecological approach. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 1033. PMID 18694131  1
2007 Li X, Gennari JH, Brinkley JF. XGI: a graphical interface for XQuery creation. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 453-7. PMID 18693877  1
2007 Cook DL, Wiley JC, Gennari JH. Chalkboard: ontology-based pathway modeling and qualitative inference of disease mechanisms. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 16-27. PMID 17992742  1
2007 Weng C, Gennari JH, Fridsma DB. User-centered semantic harmonization: a case study. Journal of Biomedical Informatics. 40: 353-64. PMID 17452021 DOI: 10.1016/J.Jbi.2007.03.004  1
2007 Weng C, McDonald DW, Sparks D, McCoy J, Gennari JH. Participatory design of a collaborative clinical trial protocol writing system. International Journal of Medical Informatics. 76: S245-51. PMID 16798070 DOI: 10.1016/J.Ijmedinf.2006.05.035  1
2006 Civan A, Gennari JH, Pratt W. Integrating protocol schedules with patients' personal calendars. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 892. PMID 17238511  1
2006 Li H, Gennari JH, Brinkley JF. Model driven laboratory information management systems. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 484-8. PMID 17238388  1
2006 Brinkley JF, Suciu D, Detwiler LT, Gennari JH, Rosse C. A framework for using reference ontologies as a foundation for the semantic web. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 96-100. PMID 17238310  1
2006 Au AP, Li X, Gennari JH. Differences among cell-structure ontologies: FMA, GO, & CCO. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 16-20. PMID 17238294  1
2005 Lin CP, Nichol WP, Hoey P, Roth TL, Anderson C, Gennari JH, Payne TH. Approach for analysis of order check overrides in a computerized practitioner order entry system. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 1033. PMID 16779320  1
2005 Travillian RS, Gennari JH, Shapiro LG. Of mice and men: design of a comparative anatomy information system. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 734-8. PMID 16779137  1
2005 Gennari JH, Weng C, Benedetti J, McDonald DW. Asynchronous communication among clinical researchers: a study for systems design. International Journal of Medical Informatics. 74: 797-807. PMID 16023408 DOI: 10.1016/J.Ijmedinf.2005.03.019  1
2005 Gennari JH, Silberfein A, Wiley JC. Integrating genomic knowledge sources through an anatomy ontology. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 115-26. PMID 15759619  1
2005 Gennari JH, Mork P, Li H. Knowledge transformations between frame systems and RDB systems Proceedings of the 3rd International Conference On Knowledge Capture, K-Cap'05. 197-198. DOI: 10.1145/1088622.1088666  1
2004 Weng C, Gennari JH, McDonald DW. A collaborative clinical trial protocol writing system. Studies in Health Technology and Informatics. 107: 1481-6. PMID 15361061  1
2004 Gennari JH, Weng C, McDonald DW, Benedetti J, Green S. An ethnographic study of collaborative clinical trial protocol writing. Studies in Health Technology and Informatics. 107: 1461-5. PMID 15361057  1
2004 Pratt W, Reddy MC, McDonald DW, Tarczy-Hornoch P, Gennari JH. Incorporating ideas from computer-supported cooperative work. Journal of Biomedical Informatics. 37: 128-37. PMID 15120659 DOI: 10.1016/J.Jbi.2004.04.001  1
2004 Weng C, Gennari JH. Asynchronous collaborative writing through annotations Proceedings of the Acm Conference On Computer Supported Cooperative Work, Cscw. 578-581.  1
2004 McDonald DW, Weng C, Gennari JH. The multiple views of inter-organizational authoring Proceedings of the Acm Conference On Computer Supported Cooperative Work, Cscw. 564-573.  1
2003 Weng C, Gennari JH, McDonald DW. Scenario-based participatory design of a collaborative clinical trial protocol authoring system. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 1051. PMID 14728554  1
2003 Gennari JH, Musen MA, Fergerson RW, Grosso WE, Crubezy M, Eriksson H, Noy NF, Tu SW. The evolution of Protégé: An environment for knowledge-based systems development International Journal of Human Computer Studies. 58: 89-123. DOI: 10.1016/S1071-5819(02)00127-1  1
2002 Weng C, Kahn M, Gennari J. Temporal knowledge representation for scheduling tasks in clinical trial protocols. Proceedings / Amia ... Annual Symposium. Amia Symposium. 879-83. PMID 12463951  1
2001 Gennari JH, Sklar D, Silva J. Cross-tool communication: from protocol authoring to eligibility determination. Proceedings / Amia ... Annual Symposium. Amia Symposium. 199-203. PMID 11825180  1
2000 Rubin DL, Gennari J, Musen MA. Knowledge representation and tool support for critiquing clinical trial protocols Proceedings / Amia ... Annual Symposium. Amia Symposium. 724-728. PMID 11079979  1
2000 Gennari JH, Reddy M. Participatory design and an eligibility screening tool. Proceedings / Amia ... Annual Symposium. Amia Symposium. 290-4. PMID 11079891  1
1999 Rubin DL, Gennari JH, Srinivas S, Yuen A, Kaizer H, Musen MA, Silva JS. Tool support for authoring eligibility criteria for cancer trials. Proceedings / Amia ... Annual Symposium. Amia Symposium. 369-73. PMID 10566383  1
1998 Ohno-Machado L, Gennari JH, Murphy SN, Jain NL, Tu SW, Oliver DE, Pattison-Gordon E, Greenes RA, Shortliffe EH, Barnett GO. The guideline interchange format: a model for representing guidelines. Journal of the American Medical Informatics Association : Jamia. 5: 357-72. PMID 9670133 DOI: 10.1136/Jamia.1998.0050357  1
1998 Gennari JH, Cheng H, Altman RB, Musen MA. Reuse, CORBA, and knowledge-based systems International Journal of Human Computer Studies. 49: 523-546. DOI: 10.1006/Ijhc.1998.0217  1
1996 Fridsma DB, Gennari JH, Musen MA. Making generic guidelines site-specific. Proceedings : a Conference of the American Medical Informatics Association / ... Amia Annual Fall Symposium. Amia Fall Symposium. 597-601. PMID 8947736  1
1996 Rothenfluh TE, Gennari JH, Eriksson H, Puerta AR, Tu SW, Musen MA. Reusable ontologies, knowledge-acquisition tools, and performance systems: PROTE´GE´-II solutions to Sisyphus-2 International Journal of Human-Computer Studies \/ International Journal of Man-Machine Studies. 44: 303-332. DOI: 10.1006/Ijhc.1996.0017  0.4
1996 Rothenfluh TE, Gennari JH, Eriksson H, Puerta AR, Tu SW, Musen MA. Reusable ontologies, knowledge-acquisition tools, and performance systems: PROTÉGÉ-II solutions to Sisyphus-2 International Journal of Human Computer Studies. 44: 303-332.  1
1995 Musen MA, Gennari JH, Eriksson H, Tu SW, Puerta AR. PROTEGE-II: computer support for development of intelligent systems from libraries of components. Medinfo. Medinfo. 8: 766-70. PMID 8591322  1
1995 Musen MA, Gennari JH, Wong WW. A rational reconstruction of INTERNIST-I using PROTEGE-II. Proceedings / the ... Annual Symposium On Computer Application [Sic] in Medical Care. Symposium On Computer Applications in Medical Care. 289-93. PMID 8563287  1
1995 Gennari JH, Oliver DE, Pratt W, Rice J, Musen MA. A web-based architecture for a medical vocabulary server. Proceedings / the ... Annual Symposium On Computer Application [Sic] in Medical Care. Symposium On Computer Applications in Medical Care. 275-9. PMID 8563284  1
1995 Tu SW, Eriksson H, Gennari JH, Shahar Y, Musen MA. 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. 7: 257-89. PMID 7581625 DOI: 10.1016/0933-3657(95)00006-R  1
1995 Gennari JH, Altman RB, Musen MA. Reuse with protege-II: from elevators to ribosomes Acm Sigsoft Symposium On Software Reusability - Ssr. 72-80.  1
1994 Musen MA, Eriksson H, Gennari JH, Tu SW, Puerta AR. PROTEGE-II: a suite of tools for development of intelligent systems from reusable components. Proceedings / the ... Annual Symposium On Computer Application [Sic] in Medical Care. Symposium On Computer Applications in Medical Care. 1065. PMID 7949900  1
1994 Gennari JH, Tu SW, Rothenfluh TE, Musen MA. Mapping domains to methods in support of reuse International Journal of Human - Computer Studies. 41: 399-424. DOI: 10.1006/Ijhc.1994.1066  1
1994 Puerta AR, Eriksson H, Gennari JH, Musen MA. Model-based automated generation of user interfaces Proceedings of the National Conference On Artificial Intelligence. 1: 471-477.  1
1989 Gennari JH, Langley P, Fisher D. Models of incremental concept formation Artificial Intelligence. 40: 11-61. DOI: 10.1016/0004-3702(89)90046-5  1
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