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P.G. Baker, A. Brass, S. Bechhofer, C. Goble, N. Paton, and R. Stevens.
TAMBIS: Transparent Access to Multiple Bioinformatics Information Sources. An Overview.
In Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB'98), pages 25-34, Menlow Park, California, June 28-July 1 1998. AAAI Press.

S. Schulze-Kremer.
Ontologies for Molecular Biology.
In Proceedings of the Third Pacific Symposium on Biocomputing, pages 693-704. AAAI Press, 1998.

S. Blackburn.
The Oxford Dictionary of Philosophy.
Oxford University Press, 1996.

D. B. Lenat.
Cyc: A Large-Scale Investment in Knowledge Infrastructure.
Communications of the ACM, 38(11):32-38, 1995.

M. Uschold, M. King, S. Moralee, and Y. Zorgios.
The Enterprise Ontology.
The Knowledge Engineering Review, 13(1):31-89, 1998.
SpecialIssue on Putting Ontologies to Use.

T.R. Gruber.
Towards Principles for the Design of Ontologies Used for Knowledge Sharing.
In Roberto Poli Nicola Guarino, editor, International Workshop on Formal Ontology, Padova, Italy, 1993.
Available as technical report KSL-93-04, Knowledge Systems Laboratory, Stanford University:

M. Winston, R. Chaffin, and D. Herrmann.
A Taxonomy of Part-Whole Relations.
Cognitive Science, 11:417-444, 1987.

J.J. Odell.
Six Different Kinds of Aggregation, pages 139-149.
Cambridge University Press, 1998.

R. J. Brachman, D. L. McGuinness, P. F. Patel-Schneider, L. A. Resnick, and A. Borgida.
Living with Classic: When and How to Use a KL-ONE-like Language.
In J. Sowa, editor, Principles of Semantic Networks: Explorations in the representation of knowledge, pages 401-456. Morgan Kaufmann, 1991.

R. Jasper and M. Uschold.
A Framework for Understanding and Classifying Ontology Applications.
In Twelfth Workshop on Knowledge Acquisition Modeling and Management KAW'99, 1999.
Published on-line

Nicola Guarino and C. Welty.
Identity, Unity, and Individuality: Towards a Formal Toolkit for Ontological Analysis.
In W Horn, editor, Proceedings of ECAI-2000: The European Conference on Artificial Intelligence, Amsterdam, August 2000. IOS Press.

International Union of Biochemistry .
Enzyme Nomenclature 1984 : Recommendations of the Nomenclature Committee of the International Union of Biochemistry on the Nomenclature and Classification of Enzyme-Catalyzed Reactions.
Academic Press (for The International Union of Biochemistry by), Orlando, FL, 1984.

R.O. Chen, R. Felciano, and R.B. Altman.
RiboWeb: Linking Structural Computations to a Knowledge Base of Published Experimental Data.
In Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, pages 84-87. AAAI Press, 1997.

R. Altman, M. Bada, X.J. Chai, M. Whirl Carillo, R.O. Chen, and N.F. Abernethy.
RiboWeb: An Ontology-Based System for Collaborative Molecular Biology.
IEEE Intelligent Systems, 14(5):68-76, 1999.

P. Karp and S. Paley.
Integrated Access to Metabolic and Genomic Data.
Journal of Computational Biology, 3(1):191-212, 1996.

P. Karp, M. Riley, S. Paley, A. Pellegrini-Toole, and M. Krummenacker.
EcoCyc: Electronic Encyclopedia of E. coli Genes and Metabolism.
Nucleic Acids Research, 27(1):55-58, 1999.

M. Riley.
Functions of the gene products of Escherichia coli.
Microbiological Reviews, 57:862-952, 1993.

The FlyBase Consortium.
The FlyBase database of Drosophila Genome Projects and Community Literature.
Nucleic Acids Research, 27(1):85-88, 1999. ).

P.G. Baker, C.A. Goble, S. Bechhofer, N.W. Paton, R. Stevens, and A Brass.
An Ontology for Bioinformatics Applications.
Bioinformatics, 15(6):510-520, 1999.

N.W. Paton, R.D. Stevens, P.G. Baker, C.A. Goble, S. Bechhofer, and A. Brass.
Query Processing in the TAMBIS Bioinformatics Source Integration System.
In et al. Z.M. Ozsoyoglo, editor, Proc. 11th Int. Conf. on Scientific and Statistical Database Management (SSDBM), pages 138-147, Los Alamitos, California, July 1999. IEEE Press.

M. Uschold and M. Gruninger.
Ontologies: Principles, Methods and Applications.
Knowledge Engineering Review, 11(2):93-113, June 1996.

M. Fernandez, A. Gomez-Perez, and N. Juristo.
METHODONTOLOGY: From Ontological Art to Ontological Engineering.
In Workshop on Knowledge Engineering: Spring Symposium Series (AAAI'97), pages 33-40, Menlow Park, Ca, 1997. AAAI Press.

M. Gruninger and M. S. Fox.
Methodology for the Design and Evaluation of Ontologies.
In IJCAI Workshop on Basic Ontological Issues in Knowledge Sharing, 1995.
Published on-line by Ceur Publication

D.M. Jones, T.J.M. Bench-Capon, and P.R.S. Visser.
Methodologies for Ontology Development.
In J. Cuena, editor, Proc. ITi and KNOWS Conference of the 15th IFIP World Computer Congress, pages 62-75, London, UK, 1998. Chapman and Hall Ltd.

A. Gomez-Perez.
Some Ideas and Examples to Evaluate Ontologies.
Technical Report Technical Report KSL-94-65, Knowledge Systems Laboratory , Stanford, 1994.

M.A. Ould.
Strategies for Software Engineering : The Management of Risk and Quality.
Chichester : Wiley, 1990.
(Wiley series in software engineering practice.

A.L. Rector, J.E. Rogers, and P Pole.
The Galen high level ontology.
Studies in Health Technology and Informatics, 34:174-178, 1996.

J. Sowa.
Top-level ontological categories.
International Journal of Human-Computer Studies, 43(5/6):669-686, 1995.

D.A. Duce G.A. Ringland.
Approaches to Knowledge Representation: An Introduction.
Knowledge-Based and Expert Systems Series. John Wiley, Chichester, 1988.

I. Horrocks, D. Fensel, J. Broekstra, M. Crubezy, S. Decker, M. Erdmann, W. Grosso, C. Goble, F. Van Harmelen, M. Klein, M. Musen, S. Staab, and R. Studer.
The ontology interchange language oil: The grease between ontologies.

A. Farquhar, R. Fikes, and J.P. Rice.
The ontolingua server: A tool for collaborative ontology construction.
Journal of Human-Computer Studies, 46:707-728, 1997.

V.K. Chaudhri, A. Farquhar, R. Fikes, P.D. Karp, and J.P. Rice.
OKBC: A programmatic foundation for knowledge base interoperability.
In Proc of 15th National Conf on At (AAAI-98) and the 10th Conf on Innovative Applications of AI (IAAI-98), pages 600-607, Menlow Park, Ca, 1998. AAAI Press.

A. Borgida.
Description Logics in Data Management.
IEEE Trans Knowledge and Data Engineering, 7(5):671-782, 1995.

W. A. Woods and J. G. Schmolze.
The KL-ONE Family.
Computers Math. Applic., 23(2-5):133-177, 1992.

S Bechhofer and C.A. Goble.
Delivering Terminological Services.
AI*IA Notizie, Periodico dell'Associazione Italiana per l'intelligenza Artificiale, 12(1), March 1999.

I. Horrocks.
Using an Expressive Description Logic: FaCT or Fiction?
In A.G.Cohn, L.K. Schubert, and S.C.Shapiro, editors, Principles of Knowledge Representation and Reasoning: Proceedings of the Sixth International Conference (KR'98). Morgan Kaufmann Publishers, San Fransisco, CA, 1998.

A. L. Rector, S. K. Bechhofer, C. A. Goble, I. Horrocks, W. A. Nowlan, and W. D. Solomon.
The GRAIL Concept Modelling Language for Medical Terminology.
Artificial Intelligence in Medicine, 9:139-171, 1996.

J.E. Rogers, W.D. Solomon, A.L. Rector, P.M. Pole, P. Zanstra, and van der Haring E.
Rubrics to Dissections to GRAIL to Classifications.
In Medical Informatics Europe '97, pages 241-245, Amsterdam, 1997. IOS Press Vol 43.

P.D. Karp, V.K. Chaudhri, and S.M Paley.
A Collaborative Environment for Authoring Large Knowledge Bases.
Journal of Intelligent Information Systems, 13(3):155-194, 1999.

J. Domingue.
Tadzebao and WebOnto: Discussing, Browsing, and Editing Ontologies on the Web.
In 11th Knowledge Acquisition for Knowledge-Based Systems Workshop, 1998.

A. J. Duineveld, R. Stoter, M.R. Weiden, B. Kenepa, and V. R. Benjamins.
Wondertools? A Comparative Study of Ontological Engineering Tools.
In Twelfth Workshop on Knowledge Acquisition, Modeling and Management, 1999.
Published on-line

W. E. Grosso, H. Eriksson, R. W. Fergerson, J. H. Gennari, S. W. Tu, and M. A. Musen.
Knowledge Modeling at the Millennium (The Design and Evolution of Protégé-2000).
Technical Report SMI-1999-0801, Stanford Medical Informatics (SMI), Stanford University School of Medicine, 1999.
[Online] at:

Robert Stevens 2001-07-19