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Publications
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Publications by Project
There are 49 publications for the project "Protégé".
- BMIR-2009-1395
- SQWRL: a Query Language for OWL
- M. J. O'Connor, A. K. Das
- OWL: Experiences and Directions (OWLED), Fifth International Workshop, Chantilly, VA. Published in 2009
 - BMIR-2009-1379
- Using the Semantic Web Rule Language in the Development of Ontology-Driven Applications
- M. J. O'Connor, M. A. Musen, A. K. Das
- Handbook of Research on Emerging Rule-Based Languages and Technologies: Open Solutions and Approaches, Adrian Giurca, Dragan Gasevic, and Kuldar Taveter, IGI Global, Hershey, Pennsylvania, U.S.A, 525-539. Published in 2009
- BMIR-2008-1366
- Managing Change: An Ontology Version Control System
- T. Redmond, M. Smith, N. Drummond, T. Tudorache
- OWLED 2008, Karslruhe, Germany. Published in 2008
- BMIR-2008-1344
- Customizable Workflow Support for Collaborative Ontology Development
- A. Sebastian, T. Tudorache, N. F. Noy, M. A. Musen
- 4th International Workshop on Semantic Web Enabled Software Engineering (SWESE) at ISWC 2008, Karlsruhe, Germany. Published in 2008
 - BMIR-2008-1336
- The SWRLAPI: A Development Environment for Working with SWRL Rules
- M. J. O'Connor, C. I. Nyulas, R. D. Shankar, A. K. Das, M. A. Musen
- OWL: Experiences and Directions (OWLED), Fifth International Workshop, held with 7th International Semantic Web Conference, Karlsruhe, Germany. Published in 2008
- BMIR-2008-1331
- Supporting collaborative ontology development in Protege
- T. Tudorache, N. F. Noy, S. W. Tu, M. A. Musen
- Seventh International Semantic Web Conference, Karlsruhe, Germany, Springer. Published in 2008
- BMIR-2008-1311
- A Generic Ontology For Collaborative Ontology-Development Workflows
- A. Sebastian, N. F. Noy, T. Tudorache, M. A. Musen
- 16th International Conference on Knowledge Engineering and Knowledge Management (EKAW 2008), Catania, Italy, Springer. Published in 2008
- BMIR-2008-1309
- Developing Biomedical Ontologies Collaboratively
- N. F. Noy, T. Tudorache, S. de Coronado, M. A. Musen
- AMIA 2008 Annual Symposium, Washington, DC. Published in 2008
- BMIR-2008-1308
- Representing the NCI Thesaurus in OWL DL: Modeling tools help modeling languages
- N. F. Noy, S. de Coronado, H. Solbrig, G. Fragoso, F. W. Hartel, M. A. Musen
- Applied Ontology Journal, 3, 3, 173-190. Published in 2008
 - BMIR-2008-1287
- Developing a Web-Based Application using OWL and SWRL
- M. J. O'Connor, R. D. Shankar, S. W. Tu, C. I. Nyulas, A. K. Das
- AAAI Spring Symposium, Stanford, CA, USA. Published in 2008
 - BMIR-2007-1328
- Reusable Semantic Web-based Methods to Query Temporal Patterns: Application to Clinical Trials Management
- M. J. O'Connor, R. D. Shankar, A. K. Das
- Intelligent Data Analysis in Biomedicine and Pharmacology Workshop (IDAMAP), held with 11th Conference on Artificial Intelligence in Medicine. Published in 2007
- BMIR-2007-1261
- Protege: A Tool for Managing and Using Terminology in Radiology Applications
- D. L. Rubin, N. F. Noy, M. A. Musen
- Journal of Digital Imaging, J Digit Imaging. Published in 2007
- BMIR-2007-1260
- The CKC Challenge: Exploring Tools for Collaborative Knowledge
- N. F. Noy, A. Chugh, H. Alani
- . Published in 2007
- BMIR-2006-1225
- Towards understanding the needs of cognitive support for ontology mapping
- S. M. Falconer, N. F. Noy, M. Storey
- International Workshop on Ontology Matching (OM 2006) at ISWC 2006, Athens, GA. Published in 2006
- BMIR-2005-1117
- Use case: Ontology with rules for identifying brain anatomical structures.
- C. Golbreich, O. Bierlaire, O. Dameron, B. Gibaud
- W3C Workshop on Rule Languages for Interoperability. Published in 2005
- BMIR-2005-1116
- What reasoning support for ontology and rules? the brain anatomy case study: workshop on Protégé and rules
- C. Golbreich, O. Bierlaire, O. Dameron, B. Gibaud
- 8th International Protégé Conference. Published in 2005
- BMIR-2005-1115
- Using OWL and Description Logics based classification for reasoning in biomedical applications.
- D. L. Rubin, O. Dameron, M. A. Musen
- 8th International Protégé Conference, Madrid, Spain. Published in 2005
- BMIR-2005-1113
- Representing Classes As Property Values on the Semantic Web: W3C Technical Report
- N. F. Noy
- . Published in 2005
- BMIR-2005-1112
- User ratings of ontologies: Who will rate the raters?
- N. F. Noy, R. V. Guha, M. A. Musen
- Proceedings of the AAAI 2005 Spring Symposium on Knowledge Collection from Volunteer Contributors, Stanford, CA, American Association for Artificial Intelligence (www.aaai.org). Published in 2005
- BMIR-2005-1111
- Ontology Mapping Discovery with Uncertainty
- P. Mitra, N. F. Noy, A. R. Jaiswal
- Fourth International Conference on the Semantic Web (ISWC-2005), Galway, Ireland. Published in 2005
- BMIR-2005-1110
- The Protege OWL Experience: workshop on OWL: Experiences and Directions
- H. Knublauch, M. Horridge, A. L. Rector, R. Stevens, N. Drummond, P. Lord, N. F. Noy, J. Seidenberg, H. Wang, M. A. Musen
- Fourth International Semantic Web Conference (ISWC2005), Galway, Ireland. Published in 2005
- BMIR-2005-1109
- Order from Chaos: How can ontologies and the Semantic Web help us structure the world's semi-structured information?
- N. F. Noy
- ACM Queue Magazine, 3, 8, 1-4. Published in 2005
- BMIR-2005-1086
- A Knowledge-Based Mediator for Temporal Pattern Discovery in Biomedical Databases
- M. J. O'Connor, A. K. Das
- . Published in 2005
- BMIR-2005-1084
- Using an ontology of human anatomy to inform reasoning with geometric models
- D. L. Rubin, O. Dameron, Y. Bashir, D. Grossman, M. A. Musen
- Stud Health Technol Inform, 111, 429-35. Published in 2005
 - BMIR-2005-1080
- Supporting Rule System Interoperability on the Semantic Web with SWRL
- M. J. O'Connor, H. Knublauch, S. W. Tu, B. Grossof, M. Dean, W. E. Grosso, M. A. Musen
- Fourth International Semantic Web Conference (ISWC2005), Galway, Ireland. Published in 2005
- BMIR-2005-1068
- Keeping modular and platform-independent software up-to-date: benefits from the Semantic Web
- O. Dameron
- 8th International Protege conference, Madrid, Spain. Published in 2005
- BMIR-2005-1067
- Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study
- O. Dameron, D. L. Rubin, M. A. Musen
- AMIA Annual Symposium, Washington DC, 181-185. Published in 2005
- BMIR-2004-1071
- JOT: a scripting environment for creating and managing ontologies
- O. Dameron
- 7th International Protégé Conference, Bethesda, MD (USA). Published in 2004
- BMIR-2004-1070
- Accessing and manipulating ontologies using web services.
- O. Dameron, N. F. Noy, H. Knublauch, M. A. Musen
- Third International Semantic Web Conference (ISWC2004), Hiroshima, Japan. Published in 2004
- BMIR-2004-1069
- Using semantic dependencies for consistency management of an ontology of brain-cortex anatomy
- O. Dameron, B. Gibaud, M. A. Musen
- First International Workshop on Formal Biomedical Knowledge Representation KRMED04, Whistler, Canada, 30-38. Published in 2004
- BMIR-2004-1013
- OWL Pizzas: Practical Experience of Teaching OWL-DL: Common Errors & Common Patterns
- A. L. Rector, N. Drummond, M. Horridge, J. Rogers, H. Knublauch, R. Stevens, H. Wang, C. Wroe
- 14th International Conference on Knowledge Engineering and Knowledge Management (EKAW), Whittlebury Hall, UK. Published in 2004
- BMIR-2004-1012
- Ontology-Driven Software Development in the Context of the Semantic Web: An Example Scenario with Protégé/OWL
- H. Knublauch
- International Workshop on the Model-Driven Semantic Web, Monterey, CA. Published in 2004
- BMIR-2004-1011
- The Protégé OWL Plugin: An Open Development Environment for Semantic Web Applications
- H. Knublauch, R. Fergerson, N. F. Noy, M. A. Musen
- Third International Semantic Web Conference, Hiroshima, Japan. Published in 2004
- BMIR-2004-1007
- Editing Description Logic Ontologies with the Protégé OWL Plugin
- H. Knublauch, A. L. Rector, M. A. Musen
- International Workshop on Description Logics (DL2004), Whistler, Canada. Published in 2004
- BMIR-2004-1006
- Weaving the Biomedical Semantic Web with the Protégé OWL Plugin
- H. Knublauch, O. Dameron, M. A. Musen
- First International Workshop on Formal Biomedical Knowledge Representation, Whistler, Canada. Published in 2004
- BMIR-2003-0989
- Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO)
- I. Yeh, P. Karp, N. F. Noy, R. B. Altman
- Bioinformatics, 2, January 22, 241-8. Published in 2003
- BMIR-2003-0973
- The PROMPT Suite: Interactive Tools For Ontology Merging And Mapping
- N. F. Noy, M. A. Musen
- International Journal of Human-Computer Studies. Published in 2003
- BMIR-2003-0961
- Ontology Versioning as an Element of an Ontology-Evolution Framework
- N. F. Noy, M. A. Musen
- IEEE Intelligent Systems. Published in 2003
- BMIR-2002-0944
- Use of Protégé-2000 to Encode Clinical Guidelines
- R. D. Shankar, S. W. Tu, M. A. Musen
- . Published in 2002
- BMIR-2002-0943
- The Evolution of Protégé: An Environment for Knowledge-Based Systems Development
- J. Gennari, R. Fergerson, W. E. Grosso, M. Crubezy, H. Eriksson, N. F. Noy, S. W. Tu, M. A. Musen
- . Published in 2002
- BMIR-2002-0936
- Evaluating Ontology-Mapping Tools: Requirements and Experience
- N. F. Noy, M. A. Musen
- . Published in 2002
- BMIR-2002-0925
- Pushing the Envelope: Challenges in a Frame-Based Representation of Human Anatomy
- N. F. Noy, J. L. Mejino, C. Rosse, M. A. Musen
- . Published in 2002
- BMIR-2001-1269
- Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base.
- T. E. Klein, J. T. Chang, M. K. Cho, K. L. Easton, R. Fergerson, M. Hewett, Z. Lin, S. Liu, D. E. Oliver, D. L. Rubin, F. Shafa, J. M. Stuart, R. B. Altman
- The Pharmacogenomics Journal, Pharmacogenomics J, 1, 3, 167-170. Published in 2001
- BMIR-2001-0894
- A Case Study in Using Protege-2000 as a Tool for CommonKADS
- A. T. Schreiber, M. Crubezy, M. A. Musen
- 12th International Conference on Knowledge Engineering and Knowledge Management (EKAW'2000), Juan-les-Pins, France. Published in 2001
- BMIR-2001-0889
- Anchor-PROMPT: Using Non-Local Context for Semantic Matching
- N. F. Noy, M. A. Musen
- Workshop on Ontologies and Information Sharing at the Seventeenth International Joint Conference on Artificial Intelligence (IJCAI-2001), Seattle, WA. Published in 2001
- BMIR-2001-0880
- Ontology Development 101: A Guide to Creating Your First Ontology
- N. F. Noy, D. L. McGuinness
- . Published in 2001
- BMIR-2001-0872
- Creating Semantic Web Contents with Protege-2000
- N. F. Noy, M. Sintek, S. Decker, M. Crubezy, R. Fergerson, M. A. Musen
- IEEE Intelligent Systems, 16, 2, 60-71. Published in 2001
- BMIR-2000-1106
- Designing a Knowledge Base for Pharmacogenomics: an Ontology for Genetic Information
- D. L. Rubin, R. B. Altman
- Biomedical Computation at Stanford, Stanford, CA. Published in 2000
- BMIR-2000-0830
- The knowledge model of Protege-2000: Combining interoperability and flexibility
- N. F. Noy, R. Fergerson, M. A. Musen
- 2th International Conference on Knowledge Engineering and Knowledge Management (EKAW'2000), Juan-les-Pins, France. Published in 2000
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