Mark A. Musen - RankMe

395 papers A* 5A 3B 15C 1Misc 95Journal 151Unranked 119

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Author Once, Publish Everywhere: Portable Metadata Authoring with the CEDAR Embeddable Editor. Data Sci. J. Martin J. O'Connor, Marcos Martínez Romero, Attila L. Egyedi, Mete Ugur Akdogan, Michael Dorf, Mark A. Musen
2026	J	`jnl`	Knowledge Engineering for Open Science: Building and Deploying Knowledge Bases for Metadata Standards. AI Mag. Mark A. Musen, Martin J. O'Connor, Josef Hardi, Marcos Martínez Romero
2025	J	`jnl`	A General-Purpose Data Harmonization Framework: Supporting Reproducible and Scalable Data Integration in the RADx Data Hub. CoRR Jimmy K. Yu, Marcos Martínez Romero, Matthew Horridge, Mete Ugur Akdogan, Mark A. Musen
2025	J	`jnl`	A change language for ontologies and knowledge graphs. Database J. Biol. Databases Curation Harshad Hegde, Jennifer Vendetti, Damien Goutte-Gattat, J. Harry Caufield, John B. Graybeal, Nomi L. Harris, Naouel Karam, Christian Kindermann, Nicolas Matentzoglu, James A. Overton, Mark A. Musen, Christopher J. Mungall
2025	J	`jnl`	Author Once, Publish Everywhere: Portable Metadata Authoring with the CEDAR Embeddable Editor. CoRR Martin J. O'Connor, Marcos Martínez Romero, Attila L. Egyedi, Mete Ugur Akdogan, Michael Dorf, Mark A. Musen
2025	J	`jnl`	Knowledge engineering for open science: Building and deploying knowledge bases for metadata standards. CoRR Mark A. Musen, Martin J. O'Connor, Josef Hardi, Marcos Martínez Romero
2025	J	`jnl`	RADx Data Hub: A Cloud Platform for FAIR, Harmonized COVID-19 Data. CoRR Marcos Martínez Romero, Matthew Horridge, Nilesh Mistry, Aubrie Weyhmiller, Jimmy K. Yu, Alissa Fujimoto, Aria Henry, Martin J. O'Connor, Ashley Sier, Stephanie Suber, Mete Ugur Akdogan, Yan Cao, Somu Valliappan, Joanna O. Mieczkowska, RADx Data Hub team, Ashok Krishnamurthy, Michael A. Keller, Mark A. Musen
2025	J	`jnl`	Toward Total Recall: Enhancing FAIRness through AI-Driven Metadata Standardization. CoRR Sowmya S. Sundaram, Mark A. Musen
2024	J	`jnl`	A Change Language for Ontologies and Knowledge Graphs. CoRR Harshad Hegde, Jennifer Vendetti, Damien Goutte-Gattat, J. Harry Caufield, John B. Graybeal, Nomi L. Harris, Naouel Karam, Christian Kindermann, Nicolas Matentzoglu, James A. Overton, Mark A. Musen, Christopher J. Mungall
2024	J	`jnl`	Ensuring Adherence to Standards in Experiment-Related Metadata Entered Via Spreadsheets. CoRR Martin J. O'Connor, Josef Hardi, Marcos Martínez Romero, Sowmya Somasundaram, Brendan Honick, Stephen A. Fisher, Ajay Pillai, Mark A. Musen
2024	J	`jnl`	Use of a Structured Knowledge Base Enhances Metadata Curation by Large Language Models. CoRR Sowmya S. Sundaram, Benjamin Solomon, Avani Khatri, Anisha Laumas, Purvesh Khatri, Mark A. Musen
2023	J	`jnl`	A Comprehensive Approach to Ensuring Quality in Spreadsheet-Based Metadata. CoRR Martin J. O'Connor, Marcos Martínez Romero, Mete Ugur Akdogan, Josef Hardi, Mark A. Musen
2023	—	`conf`	Making Metadata More FAIR Using Large Language Models. DaMaLOS Sowmya S. Sundaram, Mark A. Musen
2023	J	`jnl`	Making Metadata More FAIR Using Large Language Models. CoRR Sowmya S. Sundaram, Mark A. Musen
2023	Misc	`conf`	Ontology Repositories and Semantic Artefact Catalogues with the OntoPortal Technology. ISWC Clément Jonquet, John B. Graybeal, Syphax Bouazzouni, Michael Dorf, Nicola Fiore, Xeni Kechagioglou, Timothy Redmond, Ilaria Rosati, Alex Skrenchuk, Jennifer Vendetti, Mark A. Musen
2023	J	`jnl`	The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information. Bioinform. John H. Morris, Karthik Soman, Rabia E. Akbas, Xiaoyuan Zhou, Brett Smith, Elaine C. Meng, Conrad C. Huang, Gabriel Cerono, Gundolf Schenk, Angela Rizk-Jackson, Adil Harroud, Lauren M. Sanders, Sylvain V. Costes, Krish Bharat, Arjun Chakraborty, Alexander R. Pico, Taline Mardirossian, Michael J. Keiser, Alice Tang, Josef Hardi, Yongmei Shi, Mark A. Musen, Sharat Israni, Sui Huang, Peter W. Rose, Charlotte A. Nelson, Sergio E. Baranzini
2022	J	`jnl`	A Biomedical Open Knowledge Network Harnesses the Power of AI to Understand Deep Human Biology. AI Mag. Sergio E. Baranzini, Katy Börner, John H. Morris, Charlotte A. Nelson, Karthik Soman, Erica Schleimer, Michael J. Keiser, Mark A. Musen, Roger Pearce, Tahsin Reza, Brett Smith, Bruce William Herr II, Boris Oskotsky, Angela Rizk-Jackson, Katherine P. Rankin, Stephan J. Sanders, Riley Bove, Peter W. Rose, Sharat Israni, Sui Huang
2022	—	`conf`	An Architecture for Attesting to the Provenance of Ontologies Using Blockchain Technologies. BMSD Simon Curty, Hans-Georg Fill, Rafael S. Gonçalves, Mark A. Musen
2022	—	`conf`	Data Harmonization through Use of Community Standards in the Common Fund Data Ecosystem. ICBO Michelle G. Giglio, Suvarna Nadendla, Arthur Brady, Amanda Charbonneau, Karl Czajkowski, Jeremy Yang, Tom Gillespie, Philippe Rocca-Serra, Jeffrey S. Grethe, Raja Mazumder, Bernard de Bono, Jonathan C. Silverstein, Daniel Clark, Mark A. Musen, Owen White
2022	J	`jnl`	Modeling community standards for metadata as templates makes data FAIR. CoRR Mark A. Musen, Martin J. O'Connor, Erik Schultes, Marcos Martínez Romero, Josef Hardi, John B. Graybeal
2022	Misc	`conf`	Ontologies in the Behavioral Sciences: Accelerating Research and the Accessibility and Use of Knowledge. AMIA Mark A. Musen, Jiang Bian, Bruce Chorpita, Vimla L. Patel, Cui Tao
2021	—	`conf`	A WebProtégé Plugin for Attesting to the Provenance of Ontologies on the Ethereum Blockchain. ISWC (Posters/Demos/Industry) Simon Curty, Hans-Georg Fill, Rafael S. Gonçalves, Mark A. Musen
2021	Misc	`conf`	Randomized user testing of recommender system clinical decision support. AMIA Andre Kumar, Rachael C. Aikens, Jason Horn, Lisa Shieh, Mark A. Musen, Michael T. M. Baiocchi, Russ B. Altman, Mary K. Goldstein, Steven M. Asch, Jonathan H. Chen
2021	J	`jnl`	Using Ethnographic Methods to Classify the Human Experience in Medicine: A Case Study of the Presence Ontology. CoRR Amrapali Maitra, Maulik R. Kamdar, Donna M. Zulman, Marie C. Haverfield, Cati Brown-Johnson, Rachel Schwartz, Sonoo Thadaney Israni, Abraham Verghese, Mark A. Musen
2021	J	`jnl`	Using ethnographic methods to classify the human experience in medicine: a case study of the presence ontology. J. Am. Medical Informatics Assoc. Amrapali Maitra, Maulik R. Kamdar, Donna M. Zulman, Marie C. Haverfield, Cati Brown-Johnson, Rachel Schwartz, Sonoo Thadaney Israni, Abraham Verghese, Mark A. Musen
2020	J	`jnl`	A more decentralized vision for Linked Data. Semantic Web Axel Polleres, Maulik R. Kamdar, Javier D. Fernández, Tania Tudorache, Mark A. Musen
2020	J	`jnl`	An Empirical Meta-analysis of the Life Sciences (Linked?) Open Data on the Web. CoRR Maulik R. Kamdar, Mark A. Musen
2020	J	`jnl`	Construction and Usage of a Human Body Common Coordinate Framework Comprising Clinical, Semantic, and Spatial Ontologies. CoRR Katy Börner, Ellen M. Quardokus, Bruce William Herr II, Leonard E. Cross, Elizabeth G. Record, Yingnan Ju, Andreas D. Bueckle, James P. Sluka, Jonathan C. Silverstein, Kristen M. Browne, Sanjay Jain, Clive H. Wasserfall, Marda L. Jorgensen, Jeffrey M. Spraggins, Nathan Heath Patterson, Mark A. Musen, Griffin M. Weber
2020	J	`jnl`	FAIR Convergence Matrix: Optimizing the Reuse of Existing FAIR-Related Resources. Data Intell. Hana Pergl Sustkova, Kristina Maria Hettne, Peter Wittenburg, Annika Jacobsen, Tobias Kuhn, Robert Pergl, Jan Slifka, Peter McQuilton, Barbara Magagna, Susanna-Assunta Sansone, Markus Stocker, Melanie Imming, Larry Lannom, Mark A. Musen, Erik Schultes
2020	J	`jnl`	OrderRex clinical user testing: a randomized trial of recommender system decision support on simulated cases. J. Am. Medical Informatics Assoc. Andre Kumar, Rachael C. Aikens, Jason Hom, Lisa Shieh, Jonathan Chiang, David Morales, Divya Saini, Mark A. Musen, Michael T. M. Baiocchi, Russ B. Altman, Mary K. Goldstein, Steven M. Asch, Jonathan H. Chen
2020	Misc	`conf`	Toward a Harmonized WHO Family of International Classifications Content Model. AMIA Samson W. Tu, Csongor Nyulas, Tania Tudorache, Mark A. Musen, Andrea Martinuzzi, Coen H. van Gool, Vincenzo Della Mea, Christopher G. Chute, Lucilla Frattura, Nicholas R. Hardiker, Huib ten Napel, Richard Madden, Ann-Helene Almborg, Jeewani Anupama Ginige, Catherine Sykes, Can Çelik, Robert Jakob
2020	—	`conf`	Toward a Harmonized WHO Family of International Classifications Content Model. MIE Samson W. Tu, Csongor I. Nyulas, Tania Tudorache, Mark A. Musen, Andrea Martinuzzi, Coen H. van Gool, Vincenzo Della Mea, Christopher G. Chute, Lucilla Frattura, Nick Hardiker, Huib ten Napel, Richard Madden, Ann-Helene Almborg, Jeewani Anupama Ginige, Catherine Sykes, Can Celik, Robert Jakob
2019	B	`conf`	Aligning Biomedical Metadata with Ontologies Using Clustering and Embeddings. ESWC Rafael S. Gonçalves, Maulik R. Kamdar, Mark A. Musen
2019	J	`jnl`	Aligning Biomedical Metadata with Ontologies Using Clustering and Embeddings. CoRR Rafael S. Gonçalves, Maulik R. Kamdar, Mark A. Musen
2019	J	`jnl`	Enabling Web-scale data integration in biomedicine through Linked Open Data. npj Digit. Medicine Maulik R. Kamdar, Javier D. Fernández, Axel Polleres, Tania Tudorache, Mark A. Musen
2019	A*	`conf`	HopRank: How Semantic Structure Influences Teleportation in PageRank (A Case Study on BioPortal). WWW Lisette Espín-Noboa, Florian Lemmerich, Simon Walk, Markus Strohmaier, Mark A. Musen
2019	J	`jnl`	HopRank: How Semantic Structure Influences Teleportation in PageRank (A Case Study on BioPortal). CoRR Lisette Espín-Noboa, Florian Lemmerich, Simon Walk, Markus Strohmaier, Mark A. Musen
2019	—	`conf`	Making Data FAIR Requires More than Just Principles: We Need Knowledge Technologies. eScience Mark A. Musen
2019	J	`jnl`	The CEDAR Workbench: An Ontology-Assisted Environment for Authoring Metadata that Describe Scientific Experiments. CoRR Rafael S. Gonçalves, Martin J. O'Connor, Marcos Martínez Romero, Attila L. Egyedi, Debra Willrett, John B. Graybeal, Mark A. Musen
2019	J	`jnl`	The FAIR Funder pilot programme to make it easy for funders to require and for grantees to produce FAIR Data. CoRR Peter Wittenburg, Hana Pergl Sustkova, Annalisa Montesanti, Margreet Bloemers, S. H. de Waard, Mark A. Musen, John B. Graybeal, Kristina M. Hettne, Annika Jacobsen, Robert Pergl, Rob W. W. Hooft, Christine Staiger, Celia W. G. van Gelder, Sebastiaan L. Knijnenburg, A. C. van Arkel, Bert Meerman, Mark D. Wilkinson, Susanna-Assunta Sansone, Philippe Rocca-Serra, Peter McQuilton, Alejandra N. González-Beltrán, G. J. C. Aben, Patrícia Henning, Maria Simone de Menezes Alencar, C. Ribeiro, C. R. L. Silva, Luís Fernando Sayão, Luana Sales, Viviane Veiga, Jefferson Lima, Simone Dib, Paula Xavier dos Santos, R. Murtinho, Jakob Tendel, B. F. Schaap, P. M. Brouwer, A. K. Gavai, Yamine Bouzembrak, Hans J. P. Marvin, Albert Mons, Tobias Kuhn, Alessa A. Gambardella, Ricardo de Miranda Azevedo, Vesa Muhonen, Mira van der Naald, N. W. Smit, M. J. Buys, Taco F. de Bruin, Fieke Schoots, H. J. E. Goodson, Henry S. Rzepa, Keith G. Jeffery, Hugh P. Shanahan, M. Axton, Veniamin Tkachenko, Anne Deslattes Mays, Natalie Meyers, Michael Conlon, Laurel L. Haak, Erik A. Schultes
2019	Misc	`conf`	Unleashing the value of Common Data Elements through the CEDAR Workbench. AMIA Martin J. O'Connor, Denise B. Warzel, Marcos Martínez Romero, Josef Hardi, Debra Willrett, Aras Efekhari, John B. Graybeal, Mark A. Musen
2019	—	`conf`	Use of OWL and Semantic Web Technologies at Pinterest. ISWC (2) Rafael S. Gonçalves, Matthew Horridge, Rui Li, Yu Liu, Mark A. Musen, Csongor I. Nyulas, Evelyn Obamos, Dhananjay Shrouty, David Temple
2019	J	`jnl`	Use of OWL and Semantic Web Technologies at Pinterest. CoRR Rafael S. Gonçalves, Matthew Horridge, Rui Li, Yu Liu, Mark A. Musen, Csongor I. Nyulas, Evelyn Obamos, Dhananjay Shrouty, David Temple
2019	J	`jnl`	Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases. Database J. Biol. Databases Curation Marcos Martínez Romero, Martin J. O'Connor, Attila L. Egyedi, Debra Willrett, Josef Hardi, John B. Graybeal, Mark A. Musen
2019	J	`jnl`	Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases. CoRR Marcos Martínez Romero, Martin J. O'Connor, Attila L. Egyedi, Debra Willrett, Josef Hardi, John B. Graybeal, Mark A. Musen
2019	—	`conf`	WebProtégé: A Cloud-Based Ontology Editor. WWW (Companion Volume) Matthew Horridge, Rafael S. Gonçalves, Csongor I. Nyulas, Tania Tudorache, Mark A. Musen
2019	J	`jnl`	WebProtégé: A Cloud-Based Ontology Editor. CoRR Matthew Horridge, Rafael S. Gonçalves, Csongor I. Nyulas, Tania Tudorache, Mark A. Musen
2018	—	`conf`	A More Decentralized Vision for Linked Data. DeSemWeb@ISWC Axel Polleres, Maulik R. Kamdar, Javier D. Fernández, Tania Tudorache, Mark A. Musen
2018	J	`jnl`	AgroPortal: A vocabulary and ontology repository for agronomy. Comput. Electron. Agric. Clément Jonquet, Anne Toulet, Elizabeth Arnaud, Sophie Aubin, Esther Dzalé Yeumo Kaboré, Vincent Emonet, John B. Graybeal, Marie-Angélique Laporte, Mark A. Musen, Valeria Pesce, Pierre Larmande
2018	J	`jnl`	Analyzing user interactions with biomedical ontologies: A visual perspective. J. Web Semant. Maulik R. Kamdar, Simon Walk, Tania Tudorache, Mark A. Musen
2018	J	`jnl`	CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata. BMC Bioinform. Syed Ahmad Chan Bukhari, Marcos Martínez Romero, Martin J. O'Connor, Attila L. Egyedi, Debra Willrett, John B. Graybeal, Mark A. Musen, Kei-Hoi Cheung, Steven H. Kleinstein
2018	—	`conf`	CEDAR: Semantic Web Technology to Support Open Science. WWW (Companion Volume) Mark A. Musen, Susanna-Assunta Sansone, Kei-Hoi Cheung, Steven H. Kleinstein, Morgan Crafts, Stephan C. Schürer, John B. Graybeal
2018	Misc	`conf`	How Sustainable are Biomedical Ontologies? AMIA James Geller, Vipina Kuttichi Keloth, Mark A. Musen
2018	—	`conf`	Protégé 5.5 - Improvements for Editing Biomedical Ontologies. ICBO Matthew Horridge, Rafael S. Gonçalves, Csongor I. Nyulas, Tania Tudorache, Mark A. Musen
2018	—	`conf`	Quality Assurance of Ontology Content Reuse. ICBO Michael Halper, Christopher Ochs, Yehoshua Perl, Sivaram Arabandi, Mark A. Musen
2018	—	`conf`	TOCSOC: A Temporal Ontology for Comparing the Survival Outcomes of Clinical Trials in Oncology. ICBO Deendayal Dinakarpandian, Michaela Liedtke, Mark A. Musen, Bhavish Dinakar
2018	J	`jnl`	The Variable Quality of Metadata About Biological Samples Used in Biomedical Experiments. CoRR Rafael S. Gonçalves, Mark A. Musen
2018	—	`conf`	Using Ontologies to Drive the Creation of High-Quality Metadata in CEDAR. ISWC (P&D/Industry/BlueSky) Rafael S. Gonçalves, Csongor I. Nyulas, Marcos Martínez Romero, Martin J. O'Connor, John B. Graybeal, Mark A. Musen
2018	—	`conf`	Using semantic technologies to enhance metadata submissions to public repositories in biomedicine. SWAT4LS Attila L. Egyedi, Martin J. O'Connor, Marcos Martínez Romero, Debra Willrett, Josef Hardi, John B. Graybeal, Mark A. Musen
2018	—	`conf`	WebProtégé 3.0 - Collaborative OWL Ontology Engineering in the Cloud. ISWC (P&D/Industry/BlueSky) Matthew Horridge, Rafael S. Gonçalves, Csongor I. Nyulas, Tania Tudorache, Mark A. Musen
2017	J	`jnl`	A systematic analysis of term reuse and term overlap across biomedical ontologies. Semantic Web Maulik R. Kamdar, Tania Tudorache, Mark A. Musen
2017	J	`jnl`	An empirical analysis of ontology reuse in BioPortal. J. Biomed. Informatics Christopher Ochs, Yehoshua Perl, James Geller, Sivaram Arabandi, Tania Tudorache, Mark A. Musen
2017	J	`jnl`	An ontology-driven tool for structured data acquisition using Web forms. J. Biomed. Semant. Rafael S. Gonçalves, Samson W. Tu, Csongor I. Nyulas, Michael J. Tierney, Mark A. Musen
2017	—	`conf`	BiOnIC: A Catalog of User Interactions with Biomedical Ontologies. ISWC (2) Maulik R. Kamdar, Simon Walk, Tania Tudorache, Mark A. Musen
2017	Misc	`conf`	Big Data to Knowledge (BD2K) and the Application of Metadata. AMIA Guoqian Jiang, Walter S. Campbell, Timothy Clark, Cui Tao, Mark A. Musen
2017	—	`conf`	Embracing Semantic Technology for Better Metadata Authoring in Biomedicine. SWAT4LS Attila L. Egyedi, Martin J. O'Connor, Marcos Martínez Romero, Debra Willrett, Josef Hardi, John B. Graybeal, Mark A. Musen
2017	Misc	`conf`	Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations. AMIA Marcos Martínez Romero, Martin J. O'Connor, Ravi D. Shankar, Maryam Panahiazar, Debra Willrett, Attila Levente Egyedi, Olivier Gevaert, John B. Graybeal, Mark A. Musen
2017	—	`conf`	High-Risk Drug-Drug Interactions Between Clinical Practice Guidelines for Management of Chronic Conditions. CRI Geoffrey J. Tso, Samson W. Tu, Mark A. Musen, Mary K. Goldstein
2017	A*	`conf`	How Users Explore Ontologies on the Web: A Study of NCBO's BioPortal Usage Logs. WWW Simon Walk, Lisette Espin Noboa, Denis Helic, Markus Strohmaier, Mark A. Musen
2017	—	`conf`	Making Online Datasets More Searchable and Accessible: The CEDAR project. SIMBig Mark A. Musen
2017	Misc	`conf`	Mechanism-based Pharmacovigilance over the Life Sciences Linked Open Data Cloud. AMIA Maulik R. Kamdar, Mark A. Musen
2017	—	`conf`	Metadata in the BioSample Online Repository are Impaired by Numerous Anomalies. SemSci@ISWC Rafael S. Gonçalves, Martin J. O'Connor, Marcos Martínez Romero, John B. Graybeal, Mark A. Musen
2017	J	`jnl`	Metadata in the BioSample Online Repository are Impaired by Numerous Anomalies. CoRR Rafael S. Gonçalves, Martin J. O'Connor, Marcos Martínez Romero, John B. Graybeal, Mark A. Musen
2017	J	`jnl`	NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation. J. Biomed. Semant. Marcos Martínez Romero, Clément Jonquet, Martin J. O'Connor, John B. Graybeal, Alejandro Pazos, Mark A. Musen
2017	A*	`conf`	PhLeGrA: Graph Analytics in Pharmacology over the Web of Life Sciences Linked Open Data. WWW Maulik R. Kamdar, Mark A. Musen
2017	—	`conf`	Real Time Summarization and Visualization of Ontology Change in Protégé. VOILA@ISWC Christopher Ochs, James Geller, Mark A. Musen, Yehoshua Perl
2017	—	`conf`	Supporting Ontology-Based Standardization of Biomedical Metadata in the CEDAR Workbench. ICBO Marcos Martínez Romero, Martin J. O'Connor, Michael Dorf, Jennifer Vendetti, Debra Willrett, Attila L. Egyedi, John B. Graybeal, Mark A. Musen
2017	—	`conf`	The CEDAR Workbench: An Ontology-Assisted Environment for Authoring Metadata that Describe Scientific Experiments. ISWC (2) Rafael S. Gonçalves, Martin J. O'Connor, Marcos Martínez Romero, Attila L. Egyedi, Debra Willrett, John B. Graybeal, Mark A. Musen
2017	—	`conf`	The New HIT: Human Health Information Technology. MedInfo Tiffany I. Leung, Mary K. Goldstein, Mark A. Musen, Ruth Cronkite, Jonathan H. Chen, Assaf Gottlieb, Eran Leitersdorf
2017	J	`jnl`	Use of ontology structure and Bayesian models to aid the crowdsourcing of ICD-11 sanctioning rules. J. Biomed. Informatics Yun Lou, Samson W. Tu, Csongor Nyulas, Tania Tudorache, Robert J. G. Chalmers, Mark A. Musen
2016	J	`jnl`	A unified software framework for deriving, visualizing, and exploring abstraction networks for ontologies. J. Biomed. Informatics Christopher Ochs, James Geller, Yehoshua Perl, Mark A. Musen
2016	B	`conf`	An Open Repository Model for Acquiring Knowledge About Scientific Experiments. EKAW Martin J. O'Connor, Marcos Martínez Romero, Attila L. Egyedi, Debra Willrett, John B. Graybeal, Mark A. Musen
2016	Misc	`conf`	CEDAR: Better Data Sharing Through the Authoring of Better Metadata. AMIA Mark A. Musen, Martin J. O'Connor, Marcos Martínez Romero, Attila Levente Egyedi, Debra Willrett, John B. Graybeal
2016	J	`jnl`	How Users Explore Ontologies on the Web: A Study of NCBO's BioPortal Usage Logs. CoRR Simon Walk, Lisette Espin Noboa, Denis Helic, Markus Strohmaier, Mark A. Musen
2016	J	`jnl`	Is the crowd better as an assistant or a replacement in ontology engineering? An exploration through the lens of the Gene Ontology. J. Biomed. Informatics Jonathan M. Mortensen, Natalie Telis, Jacob J. Hughey, Hua Fan-Minogue, Kimberly Van Auken, Michel Dumontier, Mark A. Musen
2016	J	`jnl`	NCBO Ontology Recommender 2.0: An Enhanced Approach for Biomedical Ontology Recommendation. CoRR Marcos Martínez Romero, Clément Jonquet, Martin J. O'Connor, John B. Graybeal, Alejandro Pazos, Mark A. Musen
2016	—	`conf`	Reusing the NCBO BioPortal Technology for Agronomy to Build AgroPortal. ICBO/BioCreative Clément Jonquet, Anne Toulet, Elizabeth Arnaud, Sophie Aubin, Esther Dzalé Yeumo Kaboré, Vincent Emonet, John B. Graybeal, Mark A. Musen, Cyril Pommier, Pierre Larmande
2016	J	`jnl`	Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies. J. Biomed. Informatics Christopher Ochs, Zhe He, Ling Zheng, James Geller, Yehoshua Perl, George Hripcsak, Mark A. Musen
2016	—	`conf`	Visualizing User Editing Behavior in Collaborative Ontology-engineering Projects. VOILA@ISWC Simon Walk, Tania Tudorache, Mark A. Musen
2015	Misc	`conf`	A Method to Compare ICF and SNOMED CT for Coverage of U.S. Social Security Administration's Disability Listing Criteria. AMIA Samson W. Tu, Csongor Nyulas, Tania Tudorache, Mark A. Musen
2015	J	`jnl`	Analysis and Prediction of User Editing Patterns in Ontology Development Projects. J. Data Semant. Hao Wang, Tania Tudorache, Dejing Dou, Natalya Fridman Noy, Mark A. Musen
2015	J	`jnl`	Applied ontology: The next decade begins. Appl. Ontology Nicola Guarino, Mark A. Musen
2015	A*	`conf`	Helping Users Bootstrap Ontologies: An Empirical Investigation. CHI Yuhao Zhang, Tania Tudorache, Matthew Horridge, Mark A. Musen
2015	J	`jnl`	How to apply Markov chains for modeling sequential edit patterns in collaborative ontology-engineering projects. Int. J. Hum. Comput. Stud. Simon Walk, Philipp Singer, Markus Strohmaier, Denis Helic, Natalya Fridman Noy, Mark A. Musen
2015	—	`conf`	Investigating term reuse and overlap in biomedical ontologies. ICBO Maulik R. Kamdar, Tania Tudorache, Mark A. Musen
2015	—	`conf`	Modeling and tools for supporting post-coordination in ICD-11. ICBO Csongor I. Nyulas, Samson W. Tu, Tania Tudorache, Mark A. Musen
2015	—	`conf`	NCBO BioPortal version 4. ICBO Ray W. Fergerson, Paul R. Alexander, Michael Dorf, Rafael S. Gonçalves, Manuel Salvadores, Alex Skrenchuk, Jennifer Vendetti, Mark A. Musen
2015	—	`conf`	OWL-based form generation and structured data acquisition. ICBO Rafael S. Gonçalves, Csongor I. Nyulas, Samson W. Tu, Mark A. Musen
2015	—	`conf`	Roadmap for a Multilingual BioPortal. MSW@ESWC Clément Jonquet, Vincent Emonet, Mark A. Musen
2015	—	`conf`	Snap-SPARQL: A Java Framework for Working with SPARQL and OWL. OWLED Matthew Horridge, Mark A. Musen
2015	—	`conf`	Structured data acquisition with ontology-based web forms. ICBO Rafael S. Gonçalves, Samson W. Tu, Csongor I. Nyulas, Michael J. Tierney, Mark A. Musen
2015	J	`jnl`	Ten years of Appl. Ontology Nicola Guarino, Mark A. Musen
2015	J	`jnl`	The center for expanded data annotation and retrieval. J. Am. Medical Informatics Assoc. Mark A. Musen, Carol A. Bean, Kei-Hoi Cheung, Michel Dumontier, Kim A. Durante, Olivier Gevaert, Alejandra N. González-Beltrán, Purvesh Khatri, Steven H. Kleinstein, Martin J. O'Connor, Yannick Pouliot, Philippe Rocca-Serra, Susanna-Assunta Sansone, Jeffrey A. Wiser
2015	J	`jnl`	The protégé project: a look back and a look forward. AI Matters Mark A. Musen
2015	J	`jnl`	Toward a science of learning systems: a research agenda for the high-functioning Learning Health System. J. Am. Medical Informatics Assoc. Charles P. Friedman, Joshua C. Rubin, Jeffrey S. Brown, Melinda Buntin, Milton Corn, Lynn Etheredge, Carl A. Gunter, Mark A. Musen, Richard Platt, William W. Stead, Kevin J. Sullivan, Douglas Van Houweling
2015	—	`conf`	Understanding How Users Edit Ontologies: Comparing Hypotheses About Four Real-World Projects. ISWC (1) Simon Walk, Philipp Singer, Lisette Espin Noboa, Tania Tudorache, Mark A. Musen, Markus Strohmaier
2015	—	`conf`	User Extensible System to Identify Problems in OWL Ontologies and SWRL Rules. RuleML João Paulo Orlando, Mark A. Musen, Dilvan A. Moreira
2015	—	`conf`	Using aggregate taxonomies to summarize SNOMED CT evolution. BIBM Christopher Ochs, Yehoshua Perl, James Geller, Mark A. Musen
2015	J	`jnl`	Using ontologies to model human navigation behavior in information networks: A study based on Wikipedia. Semantic Web Daniel Lamprecht, Markus Strohmaier, Denis Helic, Csongor Nyulas, Tania Tudorache, Natalya Fridman Noy, Mark A. Musen
2015	J	`jnl`	Using the wisdom of the crowds to find critical errors in biomedical ontologies: a study of SNOMED CT. J. Am. Medical Informatics Assoc. Jonathan M. Mortensen, Evan P. Minty, Michael Januszyk, Timothy E. Sweeney, Alan L. Rector, Natalya Fridman Noy, Mark A. Musen
2014	—	`conf`	A Study on the Atomic Decomposition of Ontologies. ISWC (2) Matthew Horridge, Jonathan Mortensen, Bijan Parsia, Ulrike Sattler, Mark A. Musen
2014	Misc	`conf`	An empirically derived taxonomy of errors in SNOMED CT. AMIA Jonathan M. Mortensen, Mark A. Musen, Natasha F. Noy
2014	Misc	`conf`	Automating Identification of Multiple Chronic Conditions in Clinical Practice Guidelines. AMIA Tiffany I. Leung, Hawre Jalal, Donna M. Zulman, Douglas K. Owens, Mark A. Musen, Michel Dumontier, Mary K. Goldstein
2014	J	`jnl`	Cross-domain targeted ontology subsets for annotation: The case of SNOMED CORE and RxNorm. J. Biomed. Informatics Pablo López-García, Paea LePendu, Mark A. Musen, Arantza Illarramendi
2014	Misc	`conf`	Crowdsourcing ICD-11 Sanctioning Rules. AMIA Vincent Lou, Samson W. Tu, Csongor Nyulas, Tania Tudorache, Robert J. G. Chalmers, Mark A. Musen
2014	J	`jnl`	Discovering Beaten Paths in Collaborative Ontology-Engineering Projects using Markov Chains. CoRR Simon Walk, Philipp Singer, Markus Strohmaier, Tania Tudorache, Mark A. Musen, Natalya Fridman Noy
2014	J	`jnl`	Discovering Beaten Paths in Collaborative Ontology-Engineering Projects using Markov Chains. J. Biomed. Informatics Simon Walk, Philipp Singer, Markus Strohmaier, Tania Tudorache, Mark A. Musen, Natalya Fridman Noy
2014	C	`conf`	Investigating Collaboration Dynamics in Different Ontology Development Environments. KSEM Marco Rospocher, Tania Tudorache, Mark A. Musen
2014	Misc	`conf`	Reasoning Based Quality Assurance of Medical Ontologies: A Case Study. AMIA Matthew Horridge, Bijan Parsia, Natasha F. Noy, Mark A. Musen
2014	J	`jnl`	Sequential Usage Patterns in Collaborative Ontology-Engineering Projects. CoRR Simon Walk, Philipp Singer, Markus Strohmaier, Denis Helic, Natasha F. Noy, Mark A. Musen
2014	—	`conf`	WebProtégé: a Web-based Development Environment for OWL Ontologies. OWLED Matthew Horridge, Tania Tudorache, Csongor Nyulas, Mark A. Musen
2014	J	`jnl`	WebProtégé: a collaborative Web-based platform for editing biomedical ontologies. Bioinform. Matthew Horridge, Tania Tudorache, Csongor Nyulas, Jennifer Vendetti, Natalya Fridman Noy, Mark A. Musen
2013	—	`conf`	Analysis of User Editing Patterns in Ontology Development Projects. OTM Conferences Hao Wang, Tania Tudorache, Dejing Dou, Natalya Fridman Noy, Mark A. Musen
2013	—	`conf`	Binary OWL. OWLED Matthew Horridge, Timothy Redmond, Tania Tudorache, Mark A. Musen
2013	J	`jnl`	BioPortal as a dataset of linked biomedical ontologies and terminologies in RDF. Semantic Web Manuel Salvadores, Paul R. Alexander, Mark A. Musen, Natalya Fridman Noy
2013	—	`conf`	Boosting RDF Adoption in Ruby with Goo. WaSABi@ISWC Manuel Salvadores, Paul R. Alexander, Ray W. Fergerson, Natalya Fridman Noy, Mark A. Musen
2013	—	`conf`	Crowdsourcing Ontology Verification. ICBO Jonathan Mortensen, Paul R. Alexander, Mark A. Musen, Natalya Fridman Noy
2013	Misc	`conf`	Crowdsourcing the Verification of Relationships in Biomedical Ontologies. AMIA Jonathan Mortensen, Mark A. Musen, Natasha F. Noy
2013	—	`conf`	Developing Crowdsourced Ontology Engineering Tasks: An iterative process. CrowdSem Jonathan Mortensen, Mark A. Musen, Natasha F. Noy
2013	—	`conf`	Getting Lucky in Ontology Search: A Data-Driven Evaluation Framework for Ontology Ranking. ISWC (1) Natalya Fridman Noy, Paul R. Alexander, Rave Harpaz, Patricia L. Whetzel, Ray W. Fergerson, Mark A. Musen
2013	J	`jnl`	Graph-Grammar Assistance for Automated Generation of Influence Diagrams CoRR John W. Egar, Mark A. Musen
2013	J	`jnl`	How ontologies are made: Studying the hidden social dynamics behind collaborative ontology engineering projects. J. Web Semant. Markus Strohmaier, Simon Walk, Jan Pöschko, Daniel Lamprecht, Tania Tudorache, Csongor Nyulas, Mark A. Musen, Natalya Fridman Noy
2013	—	`conf`	Introducing WebProtégé 2 as a Collaborative Platform for Editing Biomedical Ontologies. ICBO Matthew Horridge, Jonathan Mortensen, Tania Tudorache, Jennifer Vendetti, Csongor Nyulas, Mark A. Musen, Natalya Fridman Noy
2013	—	`conf`	Mechanical turk as an ontology engineer?: using microtasks as a component of an ontology-engineering workflow. WebSci Natalya Fridman Noy, Jonathan Mortensen, Mark A. Musen, Paul R. Alexander
2013	—	`conf`	Ontology Quality Assurance with the Crowd. HCOMP (Works in Progress / Demos) Jonathan Mortensen, Mark A. Musen, Natalya Fridman Noy
2013	J	`jnl`	PragmatiX: An Interactive Tool for Visualizing the Creation Process Behind Collaboratively Engineered Ontologies. Int. J. Semantic Web Inf. Syst. Simon Walk, Jan Pöschko, Markus Strohmaier, Keith Andrews, Tania Tudorache, Natalya Fridman Noy, Csongor Nyulas, Mark A. Musen
2013	—	`conf`	Simplified OWL Ontology Editing for the Web: Is WebProtégé Enough? ISWC (1) Matthew Horridge, Tania Tudorache, Jennifer Vendetti, Csongor Nyulas, Mark A. Musen, Natalya Fridman Noy
2013	J	`jnl`	The knowledge acquisition workshops: A remarkable convergence of ideas. Int. J. Hum. Comput. Stud. Mark A. Musen
2013	—	`conf`	Using Semantic Web in ICD-11: Three Years Down the Road. ISWC (2) Tania Tudorache, Csongor Nyulas, Natalya Fridman Noy, Mark A. Musen
2013	J	`jnl`	WebProtégé: A collaborative ontology editor and knowledge acquisition tool for the Web. Semantic Web Tania Tudorache, Csongor Nyulas, Natalya Fridman Noy, Mark A. Musen
2012	J	`jnl`	AMIA Board white paper: definition of biomedical informatics and specification of core competencies for graduate education in the discipline. J. Am. Medical Informatics Assoc. Casimir A. Kulikowski, Edward H. Shortliffe, Leanne M. Currie, Peter L. Elkin, Lawrence E. Hunter, Todd R. Johnson, Ira J. Kalet, Leslie A. Lenert, Mark A. Musen, Judy G. Ozbolt, Jack W. Smith, Peter Tarczy-Hornoch, Jeffrey J. Williamson
2012	Misc	`conf`	Application of Preference-Oriented Decision Making to Multimorbidity for Computerized Decision Support: Decision Analysis and Analytic Hierarchy. AMIA Joshua Goldner, Samson W. Tu, Mary K. Goldstein, Susana B. Martins, Pamela Kum, Csongor Nyulas, Mark A. Musen
2012	Misc	`conf`	Applications of Ontology Design Patterns in Biomedical Ontologies. AMIA Jonathan Mortensen, Matthew Horridge, Mark A. Musen, Natalya Fridman Noy
2012	J	`jnl`	Chapter 9: Analyses Using Disease Ontologies. PLoS Comput. Biol. Nigam H. Shah, Tyler Cole, Mark A. Musen
2012	Misc	`conf`	Deriving an Abstraction Network to Support Quality Assurance in OCRe. AMIA Christopher Ochs, Ankur Agrawal, Yehoshua Perl, Michael Halper, Samson W. Tu, Simona Carini, Ida Sim, Natalya Fridman Noy, Mark A. Musen, James Geller
2012	—	`conf`	Experiences with Multilingual Modeling in the Development of the International Classification of Traditional Medicine Ontology. MSW Csongor Nyulas, Tania Tudorache, Samson W. Tu, Mark A. Musen
2012	—	`conf`	Modest Use of Ontology Design Patterns in a Repository of Biomedical Ontologies. WOP Jonathan Mortensen, Matthew Horridge, Mark A. Musen, Natalya Fridman Noy
2012	—	`conf`	Ontology Design Pattern Language Expressivity Requirements. WOP Matthew Horridge, Mikel Egaña Aranguren, Jonathan Mortensen, Mark A. Musen, Natalya Fridman Noy
2012	Misc	`conf`	Opportunities to Support Complex Medical Decisions Through Informatics. AMIA Mary K. Goldstein, Donna M. Zulman, Mark A. Musen, Roberto A. Rocha
2012	—	`conf`	Pragmatic Analysis of Crowd-Based Knowledge Production Systems with iCAT Analytics: Visualizing Changes to the ICD-11 Ontology. AAAI Spring Symposium: Wisdom of the Crowd Jan Pöschko, Markus Strohmaier, Tania Tudorache, Natalya Fridman Noy, Mark A. Musen
2012	—	`conf`	Recommending Concepts to Experts: An Exploration of Recommender Techniques for Collaborative Ontology Engineering Platforms in the Biomedical Domain. ICBO Simon Walk, Markus Strohmaier, Tania Tudorache, Natalya Fridman Noy, Csongor Nyulas, Mark A. Musen
2012	J	`jnl`	The National Center for Biomedical Ontology. J. Am. Medical Informatics Assoc. Mark A. Musen, Natalya Fridman Noy, Nigam H. Shah, Patricia L. Whetzel, Christopher G. Chute, Margaret-Anne D. Storey, Barry Smith
2012	J	`jnl`	Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis. J. Am. Medical Informatics Assoc. Stephen T. Wu, Hongfang Liu, Dingcheng Li, Cui Tao, Mark A. Musen, Christopher G. Chute, Nigam H. Shah
2012	—	`conf`	Using SPARQL to Query BioPortal Ontologies and Metadata. ISWC (2) Manuel Salvadores, Matthew Horridge, Paul R. Alexander, Ray W. Fergerson, Mark A. Musen, Natalya Fridman Noy
2011	A	`conf`	A knowledge base driven user interface for collaborative ontology development. IUI Tania Tudorache, Natalya Fridman Noy, Sean M. Falconer, Mark A. Musen
2011	J	`jnl`	BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. Patricia L. Whetzel, Natalya Fridman Noy, Nigam H. Shah, Paul R. Alexander, Csongor Nyulas, Tania Tudorache, Mark A. Musen
2011	—	`conf`	Bioportal: Ontologies and Integrated Data Resources at the Click of a Mouse. ICBO Patricia L. Whetzel, Natasha F. Noy, Nigam Shah, Paul R. Alexander, Michael Dorf, Ray W. Fergerson, Margaret-Anne D. Storey, Barry Smith, Christopher G. Chute, Mark A. Musen
2011	J	`jnl`	Enabling enrichment analysis with the Human Disease Ontology. J. Biomed. Informatics Paea LePendu, Mark A. Musen, Nigam H. Shah
2011	B	`conf`	From mappings to modules: using mappings to identify domain-specific modules in large ontologies. K-CAP Amir Ghazvinian, Natalya Fridman Noy, Mark A. Musen
2011	J	`jnl`	How orthogonal are the OBO Foundry ontologies? J. Biomed. Semant. Amir Ghazvinian, Natalya Fridman Noy, Mark A. Musen
2011	J	`jnl`	Integration and publication of heterogeneous text-mined relationships on the Semantic Web. J. Biomed. Semant. Adrien Coulet, Yael Garten, Michel Dumontier, Russ B. Altman, Mark A. Musen, Nigam H. Shah
2011	J	`jnl`	NCBO Resource Index: Ontology-based search and mining of biomedical resources. J. Web Semant. Clément Jonquet, Paea LePendu, Sean M. Falconer, Adrien Coulet, Natalya Fridman Noy, Mark A. Musen, Nigam H. Shah
2011	B	`ed.`	Proceedings of the 6th International Conference on Knowledge Capture (K-CAP 2011), June 26-29, 2011, Banff, Alberta, Canada K-CAP Mark A. Musen, Óscar Corcho
2011	—	`conf`	Proposed SKOS Extensions for BioPortal Terminology Services. JIST Cui Tao, Natalya Fridman Noy, Harold R. Solbrig, Nigam H. Shah, Mark A. Musen, Christopher G. Chute
2011	—	`conf`	SWRL-F: a fuzzy logic extension of the semantic web rule language. WIMS Tomasz Wiktor Wlodarczyk, Chunming Rong, Martin J. O'Connor, Mark A. Musen
2011	—	`conf`	Semantic infrastructure to enable collaboration in ontology development. CTS Paul R. Alexander, Csongor Nyulas, Tania Tudorache, Patricia L. Whetzel, Natalya Fridman Noy, Mark A. Musen
2011	—	`conf`	The Age of Data-Driven Medicine: Mining the Electronic Health Record. ICBO Paea LePendu, Mark A. Musen, Nigam H. Shah
2011	—	`conf`	The BioPortal Import Plugin for Protégé. ICBO Jithun Nair, Tania Tudorache, Trish Whetzel, Natalya Fridman Noy, Mark A. Musen
2011	J	`jnl`	The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research. J. Biomed. Informatics Jessica D. Tenenbaum, Patricia L. Whetzel, Kent Anderson, Charles D. Borromeo, Ivo D. Dinov, Davera Gabriel, Beth A. Kirschner, Barbara Mirel, Timothy D. Morris, Natasha Fridman Noy, Csongor Nyulas, David Rubenson, Paul R. Saxman, Harpreet Singh, Nancy Whelan, Zach Wright, Brian D. Athey, Michael J. Becich, Geoffrey S. Ginsburg, Mark A. Musen, Kevin A. Smith, Alice F. Tarantal, Daniel L. Rubin, Peter Lyster
2011	—	`conf`	The NCBO Annotator: Ontology-Based Annotation as a Web Service. ICBO Patricia L. Whetzel, Clément Jonquet, Cherie Youn, Michael Dorf, Ray W. Fergerson, Mark A. Musen, Nigam Shah
2010	—	`conf`	A Typology for Modeling Processes in Clinical Guidelines and Protocols. SUComS Samson W. Tu, Mark A. Musen
2010	—	`conf`	An efficient approach to intelligent real-time monitoring using ontologies and Hadoop. HPCS Tomasz Wiktor Wlodarczyk, Chunming Rong, Csongor Nyulas, Mark A. Musen
2010	J	`jnl`	Building a biomedical ontology recommender web service. J. Biomed. Semant. Clément Jonquet, Mark A. Musen, Nigam H. Shah
2010	B	`conf`	DataStorm. SERVICES Tomasz Wiktor Wlodarczyk, Chunming Rong, Baodong Jia, Laurentiu Cocanu, Csongor Nyulas, Mark A. Musen
2010	—	`conf`	From mappings to modules: using mappings to identify domain-specific modules in large ontologies. OM Amir Ghazvinian, Natasha Fridman Noy, Mark A. Musen
2010	—	`conf`	Indexation et intégration de ressources textuelles à l'aide d'ontologies : application au domaine biomédical. IC Clément Jonquet, Adrien Coulet, Nigam H. Shah, Mark A. Musen
2010	—	`conf`	Lost in translation? Empirical analysis of mapping compositions for large ontologies. OM Anna Tordai, Amir Ghazvinian, Jacco van Ossenbruggen, Mark A. Musen, Natasha Fridman Noy
2010	—	`conf`	M OWLED Martin J. O'Connor, Christian Halaschek-Wiener, Mark A. Musen
2010	—	`conf`	Mapping Master: A Flexible Approach for Mapping Spreadsheets to OWL. ISWC (2) Martin J. O'Connor, Christian Halaschek-Wiener, Mark A. Musen
2010	B	`conf`	Ontology Development for the Masses: Creating ICD-11 in WebProtégé. EKAW Tania Tudorache, Sean M. Falconer, Natalya Fridman Noy, Csongor Nyulas, Tevfik Bedirhan Üstün, Margaret-Anne D. Storey, Mark A. Musen
2010	—	`conf`	Optimize First, Buy Later: Analyzing Metrics to Ramp-Up Very Large Knowledge Bases. ISWC (1) Paea LePendu, Natalya Fridman Noy, Clément Jonquet, Paul R. Alexander, Nigam H. Shah, Mark A. Musen
2010	—	`conf`	SWRL-F - A Fuzzy Logic Extension of the Semantic Web Rule Language. URSW Tomasz Wiktor Wlodarczyk, Martin J. O'Connor, Chunming Rong, Mark A. Musen
2010	J	`jnl`	Using text to build semantic networks for pharmacogenomics. J. Biomed. Informatics Adrien Coulet, Nigam H. Shah, Yael Garten, Mark A. Musen, Russ B. Altman
2010	—	`conf`	WebProtégé: Supporting the Creation of ICD-11. ISWC (Posters & Demos) Sean M. Falconer, Tania Tudorache, Csongor Nyulas, Natalya Fridman Noy, Mark A. Musen
2010	—	`conf`	Will Semantic Web Technologies Work for the Development of ICD-11? ISWC (2) Tania Tudorache, Sean M. Falconer, Csongor Nyulas, Natalya Fridman Noy, Mark A. Musen
2009	Misc	`conf`	A Bayesian Network Model for Analysis of Detection Performance in Surveillance Systems. AMIA Masoumeh T. Izadi, David L. Buckeridge, Anna Okhmatovskaia, Samson W. Tu, Martin J. O'Connor, Csongor Nyulas, Mark A. Musen
2009	J	`jnl`	BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res. Natalya Fridman Noy, Nigam H. Shah, Patricia L. Whetzel, Benjamin Dai, Michael Dorf, Nicholas Griffith, Clément Jonquet, Daniel L. Rubin, Margaret-Anne D. Storey, Christopher G. Chute, Mark A. Musen
2009	J	`jnl`	Comparison of concept recognizers for building the Open Biomedical Annotator. BMC Bioinform. Nigam H. Shah, Nipun Bhatia, Clément Jonquet, Daniel L. Rubin, Annie P. Chiang, Mark A. Musen
2009	J	`jnl`	Computational neuroanatomy: ontology-based representation of neural components and connectivity. BMC Bioinform. Daniel L. Rubin, Ion-Florin Talos, Michael Halle, Mark A. Musen, Ron Kikinis
2009	Misc	`conf`	Creating Mappings For Ontologies in Biomedicine: Simple Methods Work. AMIA Amir Ghazvinian, Natalya Fridman Noy, Mark A. Musen
2009	—	`ch.`	Ontologies for Formal Representation of Biological Systems. Handbook on Ontologies Nigam H. Shah, Mark A. Musen
2009	J	`jnl`	Ontology-driven indexing of public datasets for translational bioinformatics. BMC Bioinform. Nigam H. Shah, Clément Jonquet, Annie P. Chiang, Atul J. Butte, Rong Chen, Mark A. Musen
2009	B	`conf`	Semantic Wiki Search. ESWC Peter Haase, Daniel M. Herzig, Mark A. Musen, Thanh Tran
2009	J	`jnl`	Software-engineering challenges of building and deploying reusable problem solvers. Artif. Intell. Eng. Des. Anal. Manuf. Martin J. O'Connor, Csongor Nyulas, Samson W. Tu, David L. Buckeridge, Anna Okhmatovskaia, Mark A. Musen
2009	—	`ch.`	Traversing Ontologies to Extract Views. Modular Ontologies Natalya Fridman Noy, Mark A. Musen
2009	Misc	`conf`	What Four Million Mappings Can Tell You about Two Hundred Ontologies. ISWC Amir Ghazvinian, Natalya Fridman Noy, Clément Jonquet, Nigam H. Shah, Mark A. Musen
2008	B	`conf`	A Generic Ontology for Collaborative Ontology-Development Workflows. EKAW Abraham Sebastian, Natalya Fridman Noy, Tania Tudorache, Mark A. Musen
2008	—	`conf`	A System for Ontology-Based Annotation of Biomedical Data. DILS Clément Jonquet, Mark A. Musen, Nigam Shah
2008	J	`jnl`	A prototype symbolic model of canonical functional neuroanatomy of the motor system. J. Biomed. Informatics Ion-Florin Talos, Daniel L. Rubin, Michael Halle, Mark A. Musen, Ron Kikinis
2008	J	`jnl`	AAAI 2008 Spring Symposia Reports. AI Mag. Marcello Balduccini, Chitta Baral, Boyan Brodaric, Simon Colton, Peter Fox, David Gutelius, Knut Hinkelmann, Ian Horswill, Bernardo A. Huberman, Eva Hudlicka, Kristina Lerman, Christine L. Lisetti, Deborah L. McGuinness, Mary Lou Maher, Mark A. Musen, Mehran Sahami, Derek H. Sleeman, Barbara Thönssen, Juan D. Velásquez, Dan Ventura
2008	—	`conf`	An Ontology-Driven Framework for Deploying JADE Agent Systems. IAT Csongor Nyulas, Martin J. O'Connor, Samson W. Tu, David L. Buckeridge, Anna Okhmatovskaia, Mark A. Musen
2008	—	`conf`	BioPortal: A Web Portal to Biomedical Ontologies. AAAI Spring Symposium: Symbiotic Relationships between Semantic Web and Knowledge Engineering Daniel L. Rubin, Dilvan A. Moreira, Pradip Kanjamala, Mark A. Musen
2008	—	`conf`	BioPortal: A Web Repository for Biomedical Ontologies and Data Resources. ISWC (Posters & Demos) Natalya Fridman Noy, Nigam Shah, Benjamin Dai, Michael Dorf, Nicholas Griffith, Clément Jonquet, Michael Montegut, Daniel L. Rubin, Cherie Youn, Mark A. Musen
2008	—	`conf`	Collaborative Protege: Enabling Community-based Authoring of Ontologies. ISWC (Posters & Demos) Tania Tudorache, Natalya Fridman Noy, Mark A. Musen
2008	Misc	`conf`	Collecting Community-Based Mappings in an Ontology Repository. ISWC Natalya Fridman Noy, Nicholas Griffith, Mark A. Musen
2008	Misc	`conf`	Comparison of Ontology-based Semantic-Similarity Measures. AMIA Wei-Nchih Lee, Nigam Shah, Karanjot Sundlass, Mark A. Musen
2008	Misc	`conf`	Developing Biomedical Ontologies Collaboratively. AMIA Natalya Fridman Noy, Tania Tudorache, Sherri de Coronado, Mark A. Musen
2008	J	`jnl`	Model Formulation: Understanding Detection Performance in Public Health Surveillance: Modeling Aberrancy-detection Algorithms. J. Am. Medical Informatics Assoc. David L. Buckeridge, Anna Okhmatovskaia, Samson W. Tu, Martin J. O'Connor, Csongor Nyulas, Mark A. Musen
2008	J	`jnl`	Network Analysis of Intrinsic Functional Brain Connectivity in Alzheimer's Disease. PLoS Comput. Biol. Kaustubh Supekar, Vinod Menon, Daniel L. Rubin, Mark A. Musen, Michael D. Greicius
2008	—	`conf`	Organizing Committee. AAAI Spring Symposium: Symbiotic Relationships between Semantic Web and Knowledge Engineering Derek H. Sleeman, Mark A. Musen
2008	Misc	`conf`	Predicting Outbreak Detection in Public Health Surveillance: Quantitative Analysis to Enable Evidence-Based Method Selection. AMIA David L. Buckeridge, Anna Okhmatovskaia, Samson W. Tu, Martin J. O'Connor, Csongor Nyulas, Mark A. Musen
2008	—	`conf`	Preface. AAAI Spring Symposium: Symbiotic Relationships between Semantic Web and Knowledge Engineering Derek H. Sleeman, Mark A. Musen
2008	J	`jnl`	Representing the NCI Thesaurus in OWL DL: Modeling tools help modeling languages. Appl. Ontology Natalya Fridman Noy, Sherri de Coronado, Harold R. Solbrig, Gilberto Fragoso, Frank W. Hartel, Mark A. Musen
2008	Misc	`conf`	Supporting Collaborative Ontology Development in Protégé. ISWC Tania Tudorache, Natalya Fridman Noy, Samson W. Tu, Mark A. Musen
2008	—	`conf`	The SWRLAPI: A Development Environment for Working with SWRL Rules. OWLED Martin J. O'Connor, Ravi D. Shankar, Mark A. Musen, Amar K. Das, Csongor Nyulas
2008	Misc	`conf`	UMLS-Query: A Perl Module for Querying the UMLS. AMIA Nigam H. Shah, Mark A. Musen
2007	—	`conf`	07132 Report - Towards Interoperability of Biomedical Ontologies. Towards Interoperability of Biomedical Ontologies Mark A. Musen, Michael Schroeder, Barry Smith
2007	J	`jnl`	Annotation and query of tissue microarray data using the NCI Thesaurus. BMC Bioinform. Nigam H. Shah, Daniel L. Rubin, Inigo Espinosa, Kelli Montgomery, Mark A. Musen
2007	B	`conf`	Document-Oriented Views of Guideline Knowledge Bases. AIME Samson W. Tu, Shantha Condamoor, Tim Mather, Richard W. Hall, Neill Jones, Mark A. Musen
2007	—	`conf`	Efficiently Querying Relational Databases Using OWL and SWRL. RR Martin J. O'Connor, Ravi D. Shankar, Samson W. Tu, Csongor Nyulas, Amar K. Das, Mark A. Musen
2007	Misc	`conf`	Interpretation Errors related to the GO Annotation File Format. AMIA Dilvan A. Moreira, Nigam H. Shah, Mark A. Musen
2007	—	`conf`	Knowledge Zone: A Public Repository of Peer-Reviewed Biomedical Ontologies. MedInfo Kaustubh Supekar, Daniel L. Rubin, Natasha F. Noy, Mark A. Musen
2007	J	`jnl`	OBO to OWL: a protégé OWL tab to read/save OBO ontologies. Bioinform. Dilvan A. Moreira, Mark A. Musen
2007	—	`conf`	Querying the Semantic Web with SWRL. RuleML Martin J. O'Connor, Samson W. Tu, Csongor Nyulas, Amar K. Das, Mark A. Musen
2007	B	`conf`	Searching ontologies based on content: experiments in the biomedical domain. K-CAP Harith Alani, Natasha Fridman Noy, Nigam Shah, Nigel Shadbolt, Mark A. Musen
2007	J	`jnl`	Synthesis of Research Paper: The SAGE Guideline Model: Achievements and Overview. J. Am. Medical Informatics Assoc. Samson W. Tu, James R. Campbell, Julie Glasgow, Mark A. Nyman, Robert C. McClure, James C. McClay, Craig G. Parker, Karen M. Hrabak, David Berg, Tony Weida, James G. Mansfield, Mark A. Musen, Robert M. Abarbanel
2007	—	`ed.`	Towards Interoperability of Biomedical Ontologies, 27.03. - 30.03.2007 Towards Interoperability of Biomedical Ontologies Mark A. Musen, Michael Schroeder, Barry Smith
2007	B	`conf`	Using Semantic Web Technologies for Knowledge-Driven Querying of Biomedical Data. AIME Martin J. O'Connor, Ravi D. Shankar, Samson W. Tu, Csongor Nyulas, Dave Parrish, Mark A. Musen, Amar K. Das
2007	J	`jnl`	Using semantic dependencies for consistency management of an ontology of brain-cortex anatomy. Artif. Intell. Medicine Olivier Dameron, Mark A. Musen, Bernard Gibaud
2006	Misc	`conf`	A Framework for Ontology Evolution in Collaborative Environments. ISWC Natalya Fridman Noy, Abhita Chugh, William Liu, Mark A. Musen
2006	Misc	`conf`	Identifying Barriers to Hypertension Guideline Adherence Using Clinician Feedback at the Point of Care. AMIA N. D. Lin, Susana B. Martins, Albert Chan, Robert W. Coleman, Hayden B. Bosworth, Eugene Oddone, Ravi D. Shankar, Mark A. Musen, Brian B. Hoffman, Mary K. Goldstein
2006	—	`conf`	Medical Arguments in an Automated Health Care System. AAAI Spring Symposium: Argumentation for Consumers of Healthcare Ravi D. Shankar, Samson W. Tu, Mark A. Musen
2006	Misc	`conf`	Ontology-Based Representation of Simulation Models of Physiology. AMIA Daniel L. Rubin, David Grossman, Maxwell Lewis Neal, Daniel L. Cook, James B. Bassingthwaighte, Mark A. Musen
2006	Misc	`conf`	Ontology-based Annotation and Query of Tissue Microarray Data. AMIA Nigam H. Shah, Daniel L. Rubin, Kaustubh S. Supekar, Mark A. Musen
2006	—	`conf`	Topic-Specific Trust and Open Rating Systems: An Approach for Ontology Evaluation. EON@WWW Holger Lewen, Kaustubh Supekar, Natalya Fridman Noy, Mark A. Musen
2006	Misc	`conf`	Use of Declarative Statements in Creating and Maintaining Computer-Interpretable Knowledge Bases for Guideline-Based Care. AMIA Samson W. Tu, Karen M. Hrabak, James R. Campbell, Julie Glasgow, Mark A. Nyman, Robert C. McClure, James C. McClay, Robert M. Abarbanel, James G. Mansfield, Susana B. Martins, Mary K. Goldstein, Mark A. Musen
2006	J	`jnl`	Using ontologies linked with geometric models to reason about penetrating injuries. Artif. Intell. Medicine Daniel L. Rubin, Olivier Dameron, Yasser Bashir, David Grossman, Parvati Dev, Mark A. Musen
2005	J	`jnl`	Applied Ontology: Focusing on content. Appl. Ontology Nicola Guarino, Mark A. Musen
2005	Misc	`conf`	Challenges in Converting Frame-Based Ontology into OWL: the Foundational Model of Anatomy Case-Study. AMIA Olivier Dameron, Daniel L. Rubin, Mark A. Musen
2005	J	`jnl`	EZPAL: Environment for composing constraint axioms by instantiating templates. Int. J. Hum. Comput. Stud. Chih-Sheng Johnson Hou, Mark A. Musen, Natalya Fridman Noy
2005	—	`conf`	Knowledge-Based Syndromic Surveillance for Bioterrorism. AAAI Spring Symposium: AI Technologies for Homeland Security Mark A. Musen, Monica Crubézy, Martin J. O'Connor, David L. Buckeridge
2005	Misc	`conf`	Ontology Metadata to Support the Building of a Library of Biomedical Ontologies. AMIA Kaustubh Supekar, Mark A. Musen
2005	J	`jnl`	Ontology-Centered Syndromic Surveillance for Bioterrorism. IEEE Intell. Syst. Monica Crubézy, Martin J. O'Connor, David L. Buckeridge, Zachary Pincus, Mark A. Musen
2005	Misc	`conf`	Protégé-OWL: Creating Ontology-Driven Reasoning Applications with the Web Ontology Language. AMIA Daniel L. Rubin, Holger Knublauch, Ray W. Fergerson, Olivier Dameron, Mark A. Musen
2005	J	`jnl`	Protégé: Community is Everything. Int. J. Hum. Comput. Stud. Mark A. Musen
2005	Misc	`conf`	Semantic Clinical Guideline Documents. AMIA Henrik Eriksson, Samson W. Tu, Mark A. Musen
2005	Misc	`conf`	Supporting Rule System Interoperability on the Semantic Web with SWRL. ISWC Martin J. O'Connor, Holger Knublauch, Samson W. Tu, Benjamin N. Grosof, Mike Dean, William E. Grosso, Mark A. Musen
2005	—	`conf`	The Protege OWL Experience. OWLED Holger Knublauch, Matthew Horridge, Mark A. Musen, Alan L. Rector, Robert Stevens, Nick Drummond, Phillip W. Lord, Natalya Fridman Noy, Julian Seidenberg, Hai Wang
2005	Misc	`ed.`	The Semantic Web - ISWC 2005, 4th International Semantic Web Conference, ISWC 2005, Galway, Ireland, November 6-10, 2005, Proceedings ISWC Yolanda Gil, Enrico Motta, V. Richard Benjamins, Mark A. Musen
2005	Misc	`conf`	Use of Description Logic Classification to Reason about Consequences of Penetrating Injuries. AMIA Daniel L. Rubin, Olivier Dameron, Mark A. Musen
2005	—	`conf`	User Ratings of Ontologies: Who Will Rate the Raters? AAAI Spring Symposium: Knowledge Collection from Volunteer Contributors Natalya Fridman Noy, Ramanathan V. Guha, Mark A. Musen
2004	Misc	`conf`	A Knowledge-Based Framework for Deploying Surveillance Problem Solvers. IKE David L. Buckeridge, Martin J. O'Connor, Haobo Xu, Mark A. Musen
2004	—	`conf`	Accessing and Manipulating Ontologies Using Web Services. SWS@ISWC Olivier Dameron, Natalya Fridman Noy, Holger Knublauch, Mark A. Musen
2004	—	`conf`	An Intelligent Case-Adjustment Algorithm for the Automated Design of Population-based Quality Auditing Protocols. MedInfo Aneel A. Advani, Neill Jones, Yuval Shahar, Mary K. Goldstein, Mark A. Musen
2004	J	`jnl`	Application of Information Technology: Translating Research into Practice: Organizational Issues in Implementing Automated Decision Support for Hypertension in Three Medical Centers. J. Am. Medical Informatics Assoc. Mary K. Goldstein, Robert W. Coleman, Samson W. Tu, Ravi D. Shankar, Martin J. O'Connor, Mark A. Musen, Susana B. Martins, Philip W. Lavori, Michael G. Shlipak, Eugene Oddone, Aneel A. Advani, Parisa Gholami, Brian B. Hoffman
2004	—	`conf`	Editing Description Logic Ontologies with the Protégé OWL Plugin. Description Logics Holger Knublauch, Mark A. Musen, Alan L. Rector
2004	—	`conf`	Evaluating Provider Adherence in a Trial of a Guideline-Based Decision Support System for Hypertension. MedInfo Albert Chan, Robert W. Coleman, Susana B. Martins, Aneel A. Advani, Mark A. Musen, Hayden B. Bosworth, Eugene Oddone, Michael G. Shlipak, Brian B. Hoffman, Mary K. Goldstein
2004	J	`jnl`	Knowledge Representation with Ontologies: The Present and Future. IEEE Intell. Syst. Christopher Brewster, Kieron O'Hara, Steve Fuller, Yorick Wilks, Enrico Franconi, Mark A. Musen, Jeremy Ellman, Simon Buckingham Shum
2004	J	`jnl`	Making Biomedical Ontologies and Ontology Repositories Work. IEEE Intell. Syst. Natalya Fridman Noy, Daniel L. Rubin, Mark A. Musen
2004	—	`conf`	Modeling Guidelines for Integration into Clinical Workflow. MedInfo Samson W. Tu, Mark A. Musen, Ravi D. Shankar, James R. Campbell, Karen M. Hrabak, James C. McClay, Stanley M. Huff, Robert C. McClure, Craig G. Parker, Roberto A. Rocha, Robert M. Abarbanel, Nick Beard, Julie Glasgow, Guy Mansfield, Prabhu Ram, Qin Ye, Eric Mays, Tony Weida, Christopher G. Chute, Kevin McDonald, David N. Mohr, Mark A. Nyman, Sidna M. Scheitel, Harold Solbrig, David A. Zill, Mary K. Goldstein
2004	—	`ch.`	Ontologies in Support of Problem Solving. Handbook on Ontologies Monica Crubézy, Mark A. Musen
2004	J	`jnl`	Ontology Versioning in an Ontology Management Framework. IEEE Intell. Syst. Natalya Fridman Noy, Mark A. Musen
2004	J	`jnl`	Pushing the envelope: challenges in a frame-based representation of human anatomy. Data Knowl. Eng. Natalya Fridman Noy, Mark A. Musen, José L. V. Mejino Jr., Cornelius Rosse
2004	Misc	`conf`	Specifying Ontology Views by Traversal. ISWC Natalya Fridman Noy, Mark A. Musen
2004	Misc	`conf`	The Protégé OWL Plugin: An Open Development Environment for Semantic Web Applications. ISWC Holger Knublauch, Ray W. Fergerson, Natalya Fridman Noy, Mark A. Musen
2004	—	`conf`	The SAGE Guideline Modeling: Motivation and Methodology. CGP Samson W. Tu, James R. Campbell, Mark A. Musen
2004	Misc	`conf`	Tracking Changes During Ontology Evolution. ISWC Natalya Fridman Noy, Sandhya Kunnatur, Michel C. A. Klein, Mark A. Musen
2004	—	`conf`	Using Prompt Ontology-Comparison Tools in the EON Ontology Alignment Contest. EON Natalya Fridman Noy, Mark A. Musen
2004	—	`conf`	Using semantic dependencies for consistency management of an ontology of brain-cortex anatomy. KR-MED Olivier Dameron, Bernard Gibaud, Mark A. Musen
2004	—	`conf`	Weaving the biomedical Semantic Web with the Prote'ge' OWL Plugin. KR-MED Holger Knublauch, Olivier Dameron, Mark A. Musen
2003	Misc	`conf`	A Knowledge-Acquisition Wizard to Encode Guidelines. AMIA Ravi D. Shankar, Samson W. Tu, Mark A. Musen
2003	Misc	`conf`	An Analytic Framework for Space-Time Aberrancy Detection in Public Health Surveillance Data. AMIA David L. Buckeridge, Mark A. Musen, Paul Switzer, Monica Crubézy
2003	Misc	`conf`	BioSTORM: A System for Automated Surveillance of Diverse Data Sources. AMIA Martin J. O'Connor, David L. Buckeridge, Michael Choy, Monica Crubézy, Zachary Pincus, Mark A. Musen
2003	J	`jnl`	Configuring Online Problem-Solving Resources with the Internet Reasoning Service. IEEE Intell. Syst. Monica Crubézy, Mark A. Musen, Enrico Motta, Wenjin Lu
2003	Misc	`conf`	Contextualizing Heterogeneous Data for Integration and Inference. AMIA Zachary Pincus, Mark A. Musen
2003	Misc	`conf`	Developing Quality Indicators and Auditing Protocols from Formal Guideline Models: Knowledge Representation and Transformations. AMIA Aneel A. Advani, Mary K. Goldstein, Yuval Shahar, Mark A. Musen
2003	J	`jnl`	IFIP Conference on Intelligent Information Processing. IEEE Intell. Syst. Mark A. Musen, Bernd Neumann, Rudi Studer
2003	Misc	`conf`	Protégé-2000: An Open-Source Ontology-Development and Knowledge-Acquisition Environment: AMIA 2003 Open Source Expo. AMIA Natalya Fridman Noy, Monica Crubézy, Ray W. Fergerson, Holger Knublauch, Samson W. Tu, Jennifer Vendetti, Mark A. Musen
2003	J	`jnl`	The PROMPT suite: interactive tools for ontology merging and mapping. Int. J. Hum. Comput. Stud. Natalya Fridman Noy, Mark A. Musen
2003	Misc	`conf`	The Structure of Guideline Recommendations: A Synthesis. AMIA Samson W. Tu, James R. Campbell, Mark A. Musen
2003	J	`jnl`	The Unified Problem-Solving Method Development Language UPML. Knowl. Inf. Syst. Dieter Fensel, Enrico Motta, Frank van Harmelen, V. Richard Benjamins, Monica Crubézy, Stefan Decker, Mauro Gaspari, Rix Groenboom, William E. Grosso, Mark A. Musen, Enric Plaza, Guus Schreiber, Rudi Studer, Bob J. Wielinga
2003	J	`jnl`	The evolution of Protégé: an environment for knowledge-based systems development. Int. J. Hum. Comput. Stud. John H. Gennari, Mark A. Musen, Ray W. Fergerson, William E. Grosso, Monica Crubézy, Henrik Eriksson, Natalya Fridman Noy, Samson W. Tu
2003	—	`conf`	UPML: The Language and Tool Support for Making the Semantic Web Alive. Spinning the Semantic Web Borys Omelayenko, Monica Crubézy, Dieter Fensel, V. Richard Benjamins, Bob J. Wielinga, Enrico Motta, Mark A. Musen, Ying Ding
2002	—	`conf`	A Template-Based Approach Toward Acquisition of Logical Sentences. IIP Chih-Sheng Johnson Hou, Natalya Fridman Noy, Mark A. Musen
2002	Misc	`conf`	A Typology for Modeling Processes in Clinical Guidelines and Protocols. AMIA Samson W. Tu, Peter D. Johnson, Mark A. Musen
2002	Misc	`conf`	A framework for evidence-adaptive quality assessment that unifies guideline-based and performance-indicator approaches. AMIA Aneel A. Advani, Mary K. Goldstein, Mark A. Musen
2002	Misc	`conf`	Conceptual Heterogeneity Complicates Automated Syndromic Surveillance for Bioterrorism. AMIA Justin Graham, David L. Buckeridge, Michael Choy, Mark A. Musen
2002	—	`conf`	Configuring Online Problem-Solving Resources with the Internet Reasoning Service. IIP Monica Crubézy, Wenjin Lu, Enrico Motta, Mark A. Musen
2002	—	`conf`	Evaluating Ontology-Mapping Tools: Requirements and Experience. EON Natalya Fridman Noy, Mark A. Musen
2002	—	`ed.`	Intelligent Information Processing, IFIP 17 IIP Mark A. Musen, Bernd Neumann, Rudi Studer
2002	A	`conf`	Jambalaya: an interactive environment for exploring ontologies. IUI Margaret-Anne D. Storey, Natasha F. Noy, Mark A. Musen, Casey Best, Ray W. Fergerson, Neil A. Ernst
2002	Misc	`conf`	Knowledge-based bioterrorism surveillance. AMIA David L. Buckeridge, Justin Graham, Martin J. O'Connor, Michael Choy, Samson W. Tu, Mark A. Musen
2002	J	`jnl`	Medical Quality Assessment by Scoring Adherence to Guideline Intentions. J. Am. Medical Informatics Assoc. Aneel A. Advani, Yuval Shahar, Mark A. Musen
2002	—	`conf`	PROMPTDIFF: A Fixed-Point Algorithm for Comparing Ontology Versions. AAAI/IAAI Natalya Fridman Noy, Mark A. Musen
2002	J	`jnl`	Patient Safety in Guideline-Based Decision Support for Hypertension Management: ATHENA DSS. J. Am. Medical Informatics Assoc. Mary K. Goldstein, Brian B. Hoffman, Robert W. Coleman, Samson W. Tu, Ravi D. Shankar, Martin J. O'Connor, Susana B. Martins, Aneel A. Advani, Mark A. Musen
2002	Misc	`conf`	Protocol Design Patterns: Domain-oriented Abstractions to Support the Authoring of Computer-executable Clinical Trials. AMIA John H. Nguyen, Michael G. Kahn, Carol A. Broverman, Mark A. Musen
2002	J	`jnl`	Report on the First International Conference on Knowledge Capture (K-CAP). AI Mag. Yolanda Gil, Mark A. Musen, Jude W. Shavlik
2002	—	`conf`	SHriMP views: an interactive environment for information visualization and navigation. CHI Extended Abstracts Margaret-Anne D. Storey, Casey Best, Jeff Michaud, Derek Rayside, Marin Litoiu, Mark A. Musen
2002	Misc	`conf`	SYNCHRONUS: a reusable software module for temporal integration. AMIA Amar K. Das, Mark A. Musen
2002	Misc	`conf`	Standards-based Sharable Active Guideline Environment (SAGE): A Project to Develop a Universal Framework for Encoding and Disseminating Electronic Clinical Practice Guidelines. AMIA Nick Beard, James R. Campbell, Stanley M. Huff, Mauricio Leon, James G. Mansfield, Eric Mays, James C. McClay, David N. Mohr, Mark A. Musen, David O'Brien, Roberto A. Rocha, Anne Saulovich, Sidna M. Scheitel, Samson W. Tu
2002	Misc	`conf`	The Chronus II temporal database mediator. AMIA Martin J. O'Connor, Samson W. Tu, Mark A. Musen
2002	Misc	`conf`	Use of Protégé-2000 to Encode Clinical Guidelines. AMIA Ravi D. Shankar, Samson W. Tu, Mark A. Musen
2001	Misc	`conf`	A Client-Server Framework for Deploying a Decision-support System in a Resource-constrained Environment. AMIA Martin J. O'Connor, Ravi D. Shankar, Samson W. Tu, Aneel A. Advani, Mary K. Goldstein, Robert W. Coleman, Mark A. Musen
2001	Misc	`conf`	A formal method to resolve temporal mismatches in clinical databases. AMIA Amar K. Das, Mark A. Musen
2001	Misc	`conf`	A virtual medical record for guideline-based decision support. AMIA Peter D. Johnson, Samson W. Tu, Mark A. Musen, Ian N. Purves
2001	—	`conf`	Anchor-PROMPT: Using Non-Local Context for Semantic Matching. OIS@IJCAI Natalya Fridman Noy, Mark A. Musen
2001	—	`conf`	Building an Explanation Function for a Hypertension Decision-Support System. MedInfo Ravi D. Shankar, Susana B. Martins, Samson W. Tu, Mary K. Goldstein, Mark A. Musen
2001	—	`ed.`	Computer-Based Support for Clinical Guidelines and Protocols - Proceedings of EWGLP 2000, Leipzig, Germany EWGLP Barbara Heller, Markus Löffler, Mark A. Musen, Mario Stefanelli
2001	J	`jnl`	Creating Semantic Web Contents with Protégé-2000. IEEE Intell. Syst. Natalya Fridman Noy, Michael Sintek, Stefan Decker, Monica Crubézy, Ray W. Fergerson, Mark A. Musen
2001	—	`conf`	Creating and Using Ontologies: What Informatics is All About. MedInfo Mark A. Musen
2001	J	`jnl`	Guest Editors' Introduction: A Brain for Humankind. IEEE Intell. Syst. Dieter Fensel, Mark A. Musen
2001	Misc	`conf`	Integration of textual guideline documents with formal guideline knowledge bases. AMIA Ravi D. Shankar, Samson W. Tu, Susana B. Martins, Lawrence M. Fagan, Mary K. Goldstein, Mark A. Musen
2001	Misc	`conf`	Medical quality assessment by scoring adherence to guideline intentions. AMIA Aneel A. Advani, Yuval Shahar, Mark A. Musen
2001	—	`conf`	Modeling Data and Knowledge in the EON Guideline Architecture. MedInfo Samson W. Tu, Mark A. Musen
2001	Misc	`conf`	Patient safety in guideline-based decision support for hypertension management: ATHENA DSS. AMIA Mary K. Goldstein, Brian B. Hoffman, Robert W. Coleman, Samson W. Tu, Ravi D. Shankar, Martin J. O'Connor, Susana B. Martins, Aneel A. Advani, Mark A. Musen
2001	Misc	`conf`	Protege-2000: A Plug-in Architecture to Support Knowledge Acquisition, Knowledge Visualization, and the Semantic Web. AMIA Mark A. Musen, Ray W. Fergerson, Natalya Fridman Noy, Monica Crubézy
2001	—	`conf`	RASTA: A Distributed Temporal Abstraction System to Facilitate Knowledge-Driven Monitoring of Clinical Databases. MedInfo Martin J. O'Connor, William E. Grosso, Samson W. Tu, Mark A. Musen
2001	Misc	`conf`	Representation of Structural Relationships in the Foundational Model of Anatomy. AMIA José L. V. Mejino Jr., Natalya Fridman Noy, Mark A. Musen, James F. Brinkley, Cornelius Rosse
2001	—	`conf`	Workshop on the Future of Academic Research on Electronic Patient Records IMIA Working Group 17 on Electronic Patient Records. MedInfo Johan van der Lei, Mark A. Musen
2000	B	`conf`	A Case Study in Using Protégé-2000 as a Tool for CommonKADS. EKAW Guus Schreiber, Monica Crubézy, Mark A. Musen
2000	J	`jnl`	Discussion Forum: Integration and Beyond: Panel Discussion. J. Am. Medical Informatics Assoc. William W. Stead, Randolph A. Miller, Mark A. Musen, William R. Hersh
2000	Misc	`conf`	Explanations for a Hypertension Decision Support System. AMIA Ravi D. Shankar, Samson W. Tu, Mary K. Goldstein, Mark A. Musen
2000	Misc	`conf`	From guideline modeling to guideline execution: defining guideline-based decision-support services. AMIA Samson W. Tu, Mark A. Musen
2000	Misc	`conf`	Implementing clinical practice guidelines while taking account of changing evidence: ATHENA DSS, an easily modifiable decision-support system for managing hypertension in primary care. AMIA Mary K. Goldstein, Brian B. Hoffman, Robert W. Coleman, Mark A. Musen, Samson W. Tu, Aneel A. Advani, Ravi D. Shankar, Martin J. O'Connor
2000	Misc	`conf`	Knowledge representation and tool support for critiquing clinical trial protocols. AMIA Daniel L. Rubin, John H. Gennari, Mark A. Musen
2000	Misc	`conf`	Ontology acquisition from on-line knowledge sources. AMIA Qi Li, Philip Shilane, Natalya Fridman Noy, Mark A. Musen
2000	—	`conf`	PROMPT: Algorithm and Tool for Automated Ontology Merging and Alignment. AAAI/IAAI Natalya Fridman Noy, Mark A. Musen
2000	Misc	`conf`	Quality Assessment of Guideline-oriented Medical Care Using Recognition of Clinician Intentions. AMIA Aneel A. Advani, Yuval Shahar, Mark A. Musen
2000	—	`conf`	Representation Formalisms and Computational Methods for Modeling Guideline-Based Patient Care. EWGLP Samson W. Tu, Mark A. Musen
2000	Misc	`conf`	Representation of Nursing Guidelines Using the EON Guideline Model. AMIA Zhen Lin, Samson W. Tu, Mark A. Musen
2000	Misc	`conf`	Representation of temporal indeterminacy in clinical databases. AMIA Martin J. O'Connor, Samson W. Tu, Mark A. Musen
2000	J	`jnl`	Review Paper: Integration and Beyond: Linking Information from Disparate Sources and into Workflow. J. Am. Medical Informatics Assoc. William W. Stead, Randolph A. Miller, Mark A. Musen, William R. Hersh
2000	B	`conf`	The Knowledge Model of Protégé-2000: Combining Interoperability and Flexibility. EKAW Natalya Fridman Noy, Ray W. Fergerson, Mark A. Musen
2000	Misc	`conf`	The impact of displayed awards on the credibility and retention of Web site information. AMIA John Shon, Jonathan Marshall, Mark A. Musen
1999	Misc	`conf`	A flexible approach to guideline modeling. AMIA Samson W. Tu, Mark A. Musen
1999	Misc	`conf`	Applying temporal joins to clinical databases. AMIA Martin J. O'Connor, Samson W. Tu, Mark A. Musen
1999	Misc	`conf`	EON 2.0: Enhanced Middleware for Automation of Protocol-Directed Therapy. AMIA Mark A. Musen, Samson W. Tu, Ravi D. Shankar, Martin J. O'Connor, Aneel A. Advani
1999	Misc	`conf`	Effects of Evidence-Based Explanations of Clinical Guideline Recommendations on Clinical Decision-Making. AMIA John Shon, Mark A. Musen
1999	Misc	`conf`	Integrating a modern knowledge-based system architecture with a legacy VA database: the ATHENA and EON projects at Stanford. AMIA Aneel A. Advani, Samson W. Tu, Martin J. O'Connor, Robert W. Coleman, Mary K. Goldstein, Mark A. Musen
1999	J	`jnl`	Integration of Temporal Reasoning and Temporal-Data Maintenance into a Reusable Database Mediator to Answer Abstract, Time-Oriented Queries: The Tzolkin System. J. Intell. Inf. Syst. John H. Nguyen, Yuval Shahar, Samson W. Tu, Amar K. Das, Mark A. Musen
1999	Misc	`conf`	Justification of automated decision-making: medical explanations as medical arguments. AMIA Ravi D. Shankar, Mark A. Musen
1999	J	`jnl`	Original Investigation: Semi-automated Entry of Clinical Temporal-abstraction Knowledge. J. Am. Medical Informatics Assoc. Yuval Shahar, Hai Chen, Daniel P. Stites, Lawrence V. Basso, Herbert Kaizer, Darrell M. Wilson, Mark A. Musen
1999	J	`jnl`	Representation of change in controlled medical terminologies. Artif. Intell. Medicine Diane E. Oliver, Yuval Shahar, Edward H. Shortliffe, Mark A. Musen
1999	Misc	`conf`	Representing the Digital Anatomist Foundational Model as a Protege Ontology. AMIA Jin S. Hahn, Elizabeth S. Burnside, James F. Brinkley, Cornelius Rosse, Mark A. Musen
1999	Misc	`conf`	The low availability of metadata elements for evaluating the quality of medical information on the World Wide Web. AMIA John Shon, Mark A. Musen
1999	Misc	`conf`	Tool support for authoring eligibility criteria for cancer trials. AMIA Daniel L. Rubin, John H. Gennari, Sandra Srinivas, Allen Yuen, Herbert Kaizer, Mark A. Musen, John S. Silva
1999	J	`jnl`	Use of a domain model to drive an interactive knowledge-editing tool. Int. J. Hum. Comput. Stud. Mark A. Musen, Lawrence M. Fagan, David M. Combs, Edward H. Shortliffe
1998	Misc	`conf`	A declarative explanation framework that uses a collection of visualization agents. AMIA Ravi D. Shankar, Samson W. Tu, Mark A. Musen
1998	J	`jnl`	Episodic refinement of episodic skeletal-plan refinement. Int. J. Hum. Comput. Stud. Samson W. Tu, Mark A. Musen
1998	J	`jnl`	Forum Paper: How Should We Organize to J. Am. Medical Informatics Assoc. Charles P. Friedman, Mark E. Frisse, Mark A. Musen, Warner V. Slack, William W. Stead
1998	Misc	`conf`	Modern architectures for intelligent systems: reusable ontologies and problem-solving methods. AMIA Mark A. Musen
1998	J	`jnl`	Reuse, CORBA, and knowledge-based systems. Int. J. Hum. Comput. Stud. John H. Gennari, Heyning Cheng, Russ B. Altman, Mark A. Musen
1998	Misc	`conf`	Therapy planning as constraint satisfaction: a computer-based antiretroviral therapy advisor for the management of HIV. AMIA D. Scott Smith, John Y. Park, Mark A. Musen
1998	—	`conf`	VM-in-Protégé: A Study of Software Reuse. MedInfo John Y. Park, Mark A. Musen
1997	Misc	`conf`	A foundational model of time for heterogeneous clinical databases. AMIA Amar K. Das, Mark A. Musen
1997	Misc	`conf`	A temporal database mediator for protocol-based decision support. AMIA John H. Nguyen, Yuval Shahar, Samson W. Tu, Amar K. Das, Mark A. Musen
1997	Misc	`conf`	Domain Modeling with Integrated Ontologies: Principles for Reconciliation and Reuse. AMIA Aneel A. Advani, Samson W. Tu, Mark A. Musen
1997	J	`jnl`	Modular Neural Networks for Medical Prognosis: Quantifying the Benefits of Combining Neural Networks for Survival Prediction. Connect. Sci. Lucila Ohno-Machado, Mark A. Musen
1997	J	`jnl`	Sequential versus standard neural networks for pattern recognition: An example using the domain of coronary heart disease. Comput. Biol. Medicine Lucila Ohno-Machado, Mark A. Musen
1997	Misc	`conf`	Theater-Style Demonstration: EON: CORBA-Based Middleware for Automation of Protocol-Directed Therapy. AMIA Mark A. Musen, Samson W. Tu, Aneel A. Advani, Amar K. Das, Zaki Hasan, John H. Nguyen, Yuval Shahar
1996	J	`jnl`	Knowledge-based temporal abstraction in clinical domains. Artif. Intell. Medicine Yuval Shahar, Mark A. Musen
1996	J	`jnl`	Reusable ontologies, knowledge-acquisition tools, and performance systems: PROTÉGÉ-II solutions to Sisyphus-2. Int. J. Hum. Comput. Stud. Thomas E. Rothenfluh, John H. Gennari, Henrik Eriksson, Angel R. Puerta, Samson W. Tu, Mark A. Musen
1996	J	`jnl`	Synthesis of Research: EON: A Component-Based Approach to Automation of Protocol-Directed Therapy. J. Am. Medical Informatics Assoc. Mark A. Musen, Samson W. Tu, Amar K. Das, Yuval Shahar
1995	B	`conf`	A Component-Based Architecture for Automation of Protocol-Directed Therapy. AIME Mark A. Musen, Samson W. Tu, Amar K. Das, Yuval Shahar
1995	J	`jnl`	Architectures for intelligent systems based on reusable components. Artif. Intell. Medicine Mark A. Musen, Guus Schreiber
1995	—	`conf`	Learning Rare Categories in Backpropagation. SBIA Lucila Ohno-Machado, Mark A. Musen
1995	J	`jnl`	Ontology-based configuration of problem-solving methods and generation of knowledge-acquisition tools: application of PROTEGE-II to protocol-based decision support. Artif. Intell. Medicine Samson W. Tu, Henrik Eriksson, John H. Gennari, Yuval Shahar, Mark A. Musen
1995	—	`conf`	Reuse with PROTÉgÉ-II: From Elevators to Ribosomes. SSR John H. Gennari, Russ B. Altman, Mark A. Musen
1995	J	`jnl`	Task Modeling with Reusable Problem-Solving Methods. Artif. Intell. Henrik Eriksson, Yuval Shahar, Samson W. Tu, Angel R. Puerta, Mark A. Musen
1994	—	`conf`	Beyond Data Models for Automated User Interface Generation. BCS HCI Angel R. Puerta, Henrik Eriksson, John H. Gennari, Mark A. Musen
1994	J	`jnl`	Generation of knowledge-acquisition tools from domain ontologies. Int. J. Hum. Comput. Stud. Henrik Eriksson, Angel R. Puerta, Mark A. Musen
1994	J	`jnl`	Graph-Grammar Assistance for Automated Generation of Influence Diagrams. IEEE Trans. Syst. Man Cybern. Syst. John W. Egar, Mark A. Musen
1994	J	`jnl`	Mapping domains to methods in support of reuse. Int. J. Hum. Comput. Stud. John H. Gennari, Samson W. Tu, Thomas E. Rothenfluh, Mark A. Musen
1994	A*	`conf`	Model-Based Automated Generation of User Interfaces. AAAI Angel R. Puerta, Henrik Eriksson, John H. Gennari, Mark A. Musen
1994	J	`jnl`	Research Paper: A Logical Foundation for Representation of Clinical Data. J. Am. Medical Informatics Assoc. Keith E. Campbell, Amar K. Das, Mark A. Musen
1993	J	`jnl`	Conceptual models for automatic generation of knowledge-acquisition tools. Knowl. Eng. Rev. Henrik Eriksson, Mark A. Musen
1993	A	`conf`	Graph-Grammar Assistance for Automated Generation of Influence Diagrams. UAI John W. Egar, Mark A. Musen
1993	J	`jnl`	Metatools for Knowledge Acquisition. IEEE Softw. Henrik Eriksson, Mark A. Musen
1993	J	`jnl`	Modeling tasks with mechanisms. Int. J. Intell. Syst. Angel R. Puerta, Samson W. Tu, Mark A. Musen
1993	J	`jnl`	There's no theory better than that of a practical tool. Knowl. Eng. Rev. Mark A. Musen
1992	J	`jnl`	A multiple-method knowledge-acquisition shell for the automatic generation of knowledge-acquisition tools. Knowl. Acquis. Angel R. Puerta, John W. Egar, Samson W. Tu, Mark A. Musen
1992	J	`jnl`	A problem-solving model for episodic skeletal-plan refinement. Knowl. Acquis. Samson W. Tu, Yuval Shahar, John Dawes, James Winkles, Angel R. Puerta, Mark A. Musen
1992	B	`conf`	Conceptual Models for Automatic Generation of Knowledge-Acquisition Tools. EKAW Henrik Eriksson, Mark A. Musen
1992	J	`jnl`	Knowledge acquisition for temporal-abstraction mechanisms. Knowl. Acquis. Yuval Shahar, Samson W. Tu, Mark A. Musen
1992	J	`jnl`	Overcoming the limitations of role-limiting methods. Knowl. Acquis. Mark A. Musen
1992	—	`conf`	Problem-Solving Models for Generation of Task-Specific Knowledge-Acquisition Tools. AIFIPP Mark A. Musen, Samson W. Tu
1992	J	`jnl`	Use of KADS to create a conceptual model of the ONCOCIN task. Knowl. Acquis. Marc Linster, Mark A. Musen
1990	J	`jnl`	Die Suche nach der Wissensebene. Künstliche Intell. Mark A. Musen
1990	J	`jnl`	The 1990 AAAI Spring Symposium on Artificial Intelligence in Medicine. Artif. Intell. Medicine Gregory F. Cooper, Mark A. Musen
1989	J	`jnl`	An Editor for the Conceptual Models of Interactive Knowledge-Acquisition Tools. Int. J. Man Mach. Stud. Mark A. Musen
1989	J	`jnl`	Automated Support for Building and Extending Expert Models. Mach. Learn. Mark A. Musen
1989	J	`jnl`	Conceptual models of interactive knowledge acquisition tools. Knowl. Acquis. Mark A. Musen
1989	J	`jnl`	Episodic Skeletal-Plan Refinement Based on Temporal Data. Commun. ACM Samson W. Tu, Michael G. Kahn, Mark A. Musen, Jay C. Ferguson, Edward H. Shortliffe, Lawrence M. Fagan
1989	J	`jnl`	Knowledge acquisition at the metalevel: creation of custom-tailored knowledge-acquisition tools. SIGART Newsl. Mark A. Musen
1987	J	`jnl`	Use of a Domain Model to Drive an Interactive Knowledge-Editing Tool. Int. J. Man Mach. Stud. Mark A. Musen, Lawrence M. Fagan, David M. Combs, Edward H. Shortliffe