2008

Collecting Community-Based Mappings in an Ontology Repository by N.F. Noy, N. Griffith, M. A. Musen 7th International Semantic Web Conference (ISWC 2008), Karlsruhe, Germany, Springer. Available as BMIR technical report BMIR-2008-1343

Collaborative Ontology Development in Protege by T. Tudorache, N.F. Noy, S. Tu, M. A. Musen 7th International Semantic Web Conference (ISWC 2008), Karlsruhe, Germany, Springer. Available as BMIR technical report BMIR-2008-1331

Customizable Workflow Support for Collaborative Ontology Development by 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. Available as BMIR technical report BMIR-2008-1344

A Generic Ontology For Collaborative Ontology-Development Workflows by A. Sebastian, N. F. Noy, T. Tudorache, M. A. Musen 16th International Conference on Knowledge Engineering and Knowledge Management (EKAW 2008), Catania, Italy, Springer. Available as BMIR technical report BMIR-2008-1311

Developing Biomedical Ontologies Collaboratively by N. F. Noy, T. Tudorache, S. de Coronado, M. A. Musen AMIA 2008 Annual Symposium, Washington, DC. Available as BMIR technical report BMIR-2008-1309

Representing the NCI Thesaurus in OWL DL: Modeling tools help modeling languages by by N.F. Noy, S. de Coronado, H. Solbrig, G. Fragoso, F.W. Hartel, and M. A. Musen Applied Ontology Journal, 3(3), p. 173-190. 2008. Available as BMIR Technical Report SMI-2008-1308

Search NCI Thesaurus in BioPortal:

Collaborative Ontology Development on the (Semantic) Web by by N.F. Noy and T. Tudorache, AAAI Spring Symposium on "Semantic Web and Knowledge Engineering" (SWKE), Stanford, March 2008.

Translating the Foundational Model of Anatomy into OWL by N.F. Noy and D.L. Rubin. Journal of Web Semantics 6(2). Acces through ScienceDirect. Longer version available as SMI Technical Report SMI-2007-1234

The CKC Challenge: Exploring Tools for Collaborative Knowledge Construction by N.F. Noy, A. Chugh, H. Alani. IEEE Intelligent Systems, 23(1), 64-68. Longer version available as SMI Technical Report SMI-2007-1260

2007

Biomedical Ontologies: A Functional Perspective by D.L.Rubin, N. Shah, N.F. Noy. Briefings in Bioinformatics, 9 (1), 75-90. Available as SMI technical report SMI-2008-1288

Ontology Mapping - A User Survey by S. Falconer, N. Noy, M.-A. Storey The Second International Workshop on Ontology Matching (OM 2007) at ISWC 2007 + ASWC 2007 Busan, Korea. Available as SMI technical report SMI-2007-1283

Searching Ontologies Based on Content: Experiments in the Biomedical Domain by H. Alani, N.F. Noy, N. Shah, N. Shadbolt, M.A. Musen The Fourth International Conference on Knowledge Capture (K-CAP 2007), Whistler, BC, Canada, ACM, 55-62. Available as SMI technical report SMI-2007-1264

Protege: A Tool for Managing and Using Terminology in Radiology Applications by D. L. Rubin, N. F. Noy, M. A. Musen Journal of Digital Imaging 2007. Available as SMI technical report SMI-2007-1261

Collaborative Protege by T. Tudorache and N.Noy. Workshop on Social and Collaborative Construction of Structured Knowledge (CKC 2007) at WWW 2007, Banff, Canada. (PDF)

Using annotations from controlled vocabularies to find meaningful associations by W. Lee, L. Raschid, P. Srinivasan, N. H. Shah, D. L. Rubin, N. F. Noy Lecture Notes in Bioinformatics, LNBI , 4544, 247-263. Available as SMI technical report SMI-2007-1262

2006

Towards Understanding the Needs of Cognitive Support for Ontology Mapping by S. Falconer, N. Noy, M.-A. Storey International Workshop on Ontology Matching (OM 2006) at ISWC 2006 Athens, Georgia. Available as SMI technical report SMI-2006-1225

A Framework for Ontology Evolution in Collaborative Environments by N. Noy, A. Chugh, W. Liu, M. A. Musen Fifth International Conference on the Semantic Web (ISWC-2006), Athens, Georgia. Available as SMI technical report SMI-2006-1224

Defining N-ary Relations on the Semantic Web: Use With Individuals by N.Noy and A. Rector. W3C Working Group Note (HTML). Translation in Russian

Topic-Specific Trust and Open Rating Systems: An Approach for Ontology Evaluation by H. Lewen, K. Supekar, N.F. Noy, M. A. Musen. Workshop on Evaluation of Ontologies for the Web (EON2006) at the 15th International World Wide Web Conference (WWW 2006), Edinburgh, UK. Available as SMI technical report SMI-2006-1142

The National Center for Biomedical Ontology: Advancing Biomedicine through Structured Organization of Scientific Knowledge by D. L. Rubin, S. E. Lewis, C. J. Mungall, S. Misra, M. Westerfield, M. Ashburner, I. Sim, C. G. Chute, H. Solbrig, M. A. Storey, B. Smith, J. D. Richter, N. F. Noy, M. A. Musen. OMICS: A Journal of Integrative Biology (in press). Available as SMI technical report SMI-2006-1118

2005

Order from Chaos: How can ontologies and the Semantic Web help us structure the world's semi-structured information? by N. Noy, ACM Queue Magazine, Special Issue on Semi-Structured Data, 3(8), October 2005 (article)

The Protege OWL Experience by Knublauch, H., Horridge, M., Musen, M., Rector, A., Stevens, R., Drummond, N., Lord, P., Noy, N., Seidenberg, J., and Wang, H. Workshop on OWL: Experiences and Directions, Galway, Ireland (PDF)

Ontology Mapping Discovery with Uncertainty by P.Mitra, N.F. Noy, A.R. Jaiswal. Fourth International Conference on the Semantic Web (ISWC-2005), Galway, Ireland

User ratings of ontologies: Who will rate the raters? by N.F. Noy, R.V. Guha, and M.A. Musen. Proceedings of the AAAI 2005 Spring Symposium on Knowledge Collection from Volunteer Contributors, Stanford, CA. (PDF)

Representing Classes As Property Values on the Semantic Web by N.Noy (editor). W3C Working Group Note (HTML)

EZPAL: environment for Composing Constraint Axioms by Instantiating Templates by C.-S. J. Hou, M. A. Musen, N. F. Noy, International Journal of Human-Computer Studies, 62(5), 578-596 (PDF)

2004

Making Biomedical Ontologies and Ontology Repositories Work by N.F. Noy, D.L. Rubin, and M.A. Musen IEEE Intelligent Systems 19(6) pp. 78-81(PDF - subscription required, PDF - earlier draft)

Semantic Integration: A Survey Of Ontology-Based Approaches by N.F.Noy. SIGMOD Record, Special Issue on Semantic Integration, 33 (4), December, 2004. (PDF)

The Protege OWL Plugin: An Open Development Environment for Semantic Web Applications by H. Knublauch, R. Fergerson, N.F. Noy and M.A. Musen. Third International Conference on the Semantic Web (ISWC-2004), Hisroshima, Japan (PDF)

Specifying Ontology Views by Traversal by N.F. Noy and M.A. Musen. Third International Conference on the Semantic Web (ISWC-2004), Hisroshima, Japan (PDF)

Tracking Changes During Ontology Evolution by N. F. Noy, S. Kunnatur, M. Klein, M.A. Musen. Third International Conference on the Semantic Web (ISWC-2004), Hisroshima, Japan (PDF)

Accessing and Manipulating Ontologies Using Web Services by O. Dameron, N. F. Noy, H. Knublauch, M. A. Musen. Workshop on Semantic Web Services: Preparing to Meet the World of Business Applications at the Third International Conference on the Semantic Web (ISWC-2004), Hisroshima, Japan (PDF)

OMEN: A Probabilistic Ontology Mapping Tool by P. Mitra, N. F. Noy, A. R. Jaiswal. Workshop on Meaning coordination and negotiation at the Third International Conference on the Semantic Web (ISWC-2004), Hisroshima, Japan (PDF)

Using PROMPT Ontology-Comparison Tools in the EON Ontology Alignment Contest by N.F. Noy and M.A. Musen. Workshop on Evaluation of Ontology-based Tools (EON2004) at the Third International Conference on the Semantic Web (ISWC-2004), Hisroshima, Japan (PDF)

Why Evaluate Ontology Technologies? Because It Works! by Y. Sure, A. Gómez-Pérez, W. Daelemans, M. Reinberger, N. Guarino, N.F. Noy IEEE Intelligent Systems 19(4), Trends & Controversies, pp. 74-81 (PDF - subscription required)

Ontology Versioning in an Ontology-Management Framework by N.F. Noy and M.A. Musen IEEE Intelligent Systems, 19(4), pp. 6-13. Available as SMI technical report SMI-2003-0961 (PDF - subscription required)

Ontology Evolution: Not the Same as Schema Evolution by N. F. Noy & M. Klein. Knowledge and Information Systems, 6(4), pp. 428-440. Available as SMI technical report SMI-2002-0926

2003

Tools for Mapping and Merging Ontologies by N.F.Noy. Handbook on Ontologies, S.Staab and R. Studer, editors, pp. 365-384. Springer-Verlag.

The PROMPT Suite: Interactive Tools For Ontology Merging And Mapping by N.F. Noy and M.A. Musen International Journal of Human-Computer Studies, 59/6 pp. 983-1024. Available as SMI technical report SMI-2003-0973

Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO) by I. Yeh, P. Karp, N.F. Noy, R. Altman Bioinformatics, 19, pp. 241-248 (PDF)

The Evolution of Protege: An Environment for Knowledge-Based Systems Development by J. Gennari, M. A. Musen, R. W. Fergerson, W. E. Grosso, M. Crubezy, H. Eriksson, N. F. Noy, S. W. Tu International Journal of Human-Computer Studies, 58(1), pp. 89-123. Available as SMI technical report SMI-2002-0943

A Component-Based Framework for Ontology Evolution by M. Klein and N.F. Noy. Workshop on Ontologies and Distributed Systems at IJCAI-03, Acapulco, Mexico. (Available in the workshop proceedings and as SMI technical report SMI-2003-0960 )

Tracking Complex Changes During Ontology Evolution by N.F. Noy and M. Klein. Second International Semantic Web Conference (ISWC-2003) Poster Session, Sanibel Island, Florida (PDF)

2002

Evaluating Ontology-Mapping Tools: Requirements and Experience by N. F. Noy & M. A. Musen. In the Proceedings of the Workshop on Evaluation of Ontology Tools at EKAW'02 (EON2002), Siguenza, Spain, October 2002. Available as SMI technical report SMI-2002-0936 (2002)

A Template-Based Approach Toward Acquisition of Logical Sentences by C.J. Hou, N. F. Noy & M. A. Musen. In the Proceedings of the Conference on Intelligent Information Processing (IIP-2002), Montreal, Canada, August 2002. Available as SMI technical report SMI-2002-0933 (2002)

PromptDiff: A Fixed-Point Algorithm for Comparing Ontology Versions by N. F. Noy & M. A. Musen. In the Proceedings of the Eighteenth National Conference on Artificial Intelligence (AAAI-2002), Edmonton, Alberta, August 2002. Available as SMI technical report SMI-2002-0927 (2002)

Pushing the Envelope: Challenges in a Frame-Based Representation of Human Anatomy by N. F. Noy & M. A. Musen & J. L.V. Mejino, Jr. & C. Rosse. Data and Knowledge Engineering Journal, 48/3 pp. 335-359. Available as SMI technical report SMI-2002-0925 (2002)

2001

Anchor-PROMPT: Using Non-Local Context for Semantic Matching by N. F. Noy & M. A. Musen. In the Proceedings of the Workshop on Ontologies and Information Sharing at the Seventeenth International Joint Conference on Artificial Intelligence (IJCAI-2001), Seattle, WA, August 200. Available as SMI technical report SMI-2001-0889 (2001)

Ontology Development 101: A Guide to Creating Your First Ontology by Noy, N.F. and McGuinness, D.L. Download (preferred link). Translations in French, Russian, and Spanish. Available as SMI technical report SMI-2001-0880 (2001)

Creating Semantic Web Contents with Protege-2000 by Noy, N.F., Sintek, M., Decker, S., Crubézy, M., Fergerson, R., Musen, M.A In IEEE Intelligent Systems, Vol. 16, No. 2, March/April 2001, special issue on Semantic Web, pp. 60-71. Available as SMI technical report SMI-2001-0872 (2001)

Representation of Structural Relationships in the Foundational Model of Anatomy by JLV Mejino, N.F. Noy, M.A. Musen J.F. Brinkley, and C.Rosse. In the Proceedings of the AMIA Annual Symposium, p. 973. Washington DC (HTML)

2000

Component-Based Support for Building Knowledge-Acquisition Systems by M. A. Musen, R. W. Fergerson, W. E. Grosso, N. F. Noy, M. Crubezy, & J. H. Gennari. In the Proceedings of the Conference on Intelligent Information Processing (IIP 2000) of the International Federation for Information Processing World Computer Congress (WCC 2000), Beijing. Available as SMI technical report SMI-2000-0838 (2000)

PROMPT: Algorithm and Tool for Automated Ontology Merging and Alignment by N. F. Noy & M. A. Musen. In the Proceedings of the Seventeenth National Conference on Artificial Intelligence (AAAI-2000), Austin, TX. Available as SMI technical report SMI-2000-0831 (2000)

The knowledge model of Protege-2000: Combining interoperability and flexibility by N. F. Noy, R. W. Fergerson, & M. A. Musen. In the Proceedings of the 12th International Conference on Knowledge Engineering and Knowledge Management (EKAW'2000), Juan-les-Pins, France. Available as SMI technical report SMI-2000-0830 (2000)

Knowledge-Acquisition Interfaces for Domain Experts: An Empirical Evaluation of Protege-2000 by N. F. Noy, W. Grosso, & M. A. Musen. In the Proceedings of the Twelfth International Conference on Software Engineering and Knowledge Engineering (SEKE2000), Chicago,IL. Available as SMI technical report SMI-2000-0825 (2000)

Ontology Acquisition from On-line Knowledge Sources by Q. Li, P. Shilane, N. F. Noy, & M. A. Musen. In the Proceedings of the AMIA Annual Symposium, Los Angeles, CA. Available as SMI technical report SMI-2000-0850 (2000)

Ontological Foundations for Experimental Science Knowledge Bases by N.F. Noy and C.D. Hafner. Applied Artificial Intelligence 14 (6), Taylor and Francis, 2000

1999

SMART: Automated Support for Ontology Merging and Alignment by Noy, N.F. and Musen M.A. In the Proceedings of the Twelfth Workshop on Knowledge Acquisition, Modeling and Management. Banff, Canada. Available as SMI technical report SMI-1999-0813   (1999)

An Algorithm for Merging and Aligning Ontologies: Automation and Tool Support by Noy, N.F. and Musen M.A. In the Proceedings of the Workshop on Ontology Management at Sixteenth National Conference on Artificial Intelligence (AAAI-99), Orlando, FL. Available as SMI technical report SMI-1999-0799   (1999)

1998 and earlier

Representing Scientific Experiments: Implications for Ontology Design and Knowledge Sharing by  Noy, N.F.. and Hafner, C. In the Proceedings of the 15th National Conference on Artificial Intelligence (AAAI-98), Madison, WI. AAAI Press (1998)

The State of the Art in Ontology Design: A Survey and Comparative Review by  Noy, N.F. and Hafner, C. In AI Magazine, 18(3), 53-74 (1997)

Ontological Foundations for Biology Knowledge Models by Hafner, C. and Fridman, N. In the Proceedings of the 4th International Conference on Intelligent Systems for Molecular Biology (ISMB-96), 78-87. St. Louis, MO: AAAI Press  (1996)

Principles and Tools for Authoring Knowledge-Rich Documents by Futrelle, R.P. and Fridman, N.  In the Proceedings of the DEXA'95, 6th International Workshop and Conference on Database and Expert Systems Applications. London, UK (1995)

Creating a Knowledge Base of Biological Research Papers by Hafner, C., Baclawski, K., Futrelle, R., Fridman, N. and Sampath, S.  In the Proceedings of the 2d Intl. Conf. on Intelligent Systems for Molecular Biology (ISMB-94), 147-155. Stanford, CA: AAAI Press (1994)

Reuse of Adaptive Software through Opportunistic Parameterization by Fridman, N. and Lieberherr, K. Report NU- CCS-94-17, Northeastern University, Boston, MA (1994)

M&M-Query: Database support for the annotation and retrieval of biological research articles by Baclawski, K. and Fridman, N. Report NU-CCS-94-08. Northeastern University, Boston, MA (1994)

Database Techniques for Biological Materials and Methods by Baclawski, K., Fridman, N., Futrelle, R. and Pescitelli, M. In the Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology (ISMB-93), 21-29. Washington, DC: AAAI Press (1993)

Implementation of a Vectorized and Pipelined DLX Simulator by Fridman, N. and Bestavros, A. Report TR-18-92, Computer Science Department, Boston University, Boston, MA (1992)

Back to Natasha's home page