OntologySummit2012 RecommendedReading

About this resource
This Recommended Reading list is a work in progress and will evolve over the course of OntologySummit2012 from community input.

Experimentally, references suggested by the community will be added to an online library, hosted at Zotero.org and belonging to the OntologySummit2012 Zotero Group. The group home page is at https://www.zotero.org/groups/ontologysummit2012. The Library view, best for viewing the items in Track-aligned collections and subcollections, is accessible directly at https://www.zotero.org/groups/ontologysummit2012/items/collectionKey/CMDDWSCG. This group library is viewable by anyone (public), editable by any member of the group. If you are a summit participant, are not yet a group member, and would like to be one, please send an email message, including the email address at which you'd prefer to receive an invitation to join the group, to amanda-dot-vizedom-at-gmail-dot-com.

All summit members are invited and encouraged to contribute to the group library directly. However, no one is required to do so in order to see or contribute recommended readings. For convenience, especially of those who prefer not to use a separate tool, text bibliographies will be exported regularly and updated here. Other formats, including metadata-rich formats for use with other tools, can also be exported from Zotero. If you have a particular format request, please let us know and we'll try to include it in the regular export routine.

''[Note: Beyond contributing, as all are encouraged to do, some additional-responsibility volunteers would be most welcome. The exporting task can probably be done more smoothly and effectively by someone with more tool and/or digital curation experience. Transferring references from summit email and chat, when the suggester doesn't wish to add them directly, could use an extra hand or two -AmandaVizedom]''

Bibliographies of Recommend Reading
Most recent export: 2012.02.01

Track-1&2: Ontology for Big Systems and Systems Engineering
[1] J. Rasmussen, A. M. Pejtersen, and L. P. Goodstein, Cognitive systems engineering. Wiley, 1994.

[2] C. Partridge, �ladseb_t_r_04-02.pdf.� Jun-2002.

[3] C. Masolo, L. Vieu, E. Bottazzi, C. Catenacci, R. Ferrario, A. Gangemi, and N. Guarino, �Social roles and their descriptions,� Procs. of KR�04, pp. 267�277, 2004.

[4] C. Masolo, G. Guizzardi, L. Vieu, E. Bottazzi, and R. Ferrario, �Relational roles and qua-individuals,� in Procs. of AAAI Fall Symposium Roles, 2005, vol. 5.

[5] H. S. Low, C. J. O. Baker, A. Garcia, and M. R. Wenk, �An OWL-DL Ontology for Classification of Lipids,� ICBO: International Conference on Biomedical Ontology, July 24-26, 2009, 2009.

[6] Guarino, N., �Artefactual Kinds, Functional Parts, and Functional Roles.�.

[7] W. Gielingh, �A theory for the modelling of complex and dynamic systems,� ITcon, vol. 13, pp. 421�475, 2008.

[8] M. J. Frisch, G. Trucks, H. Schlegel, G. Scuseria, M. Robb, J. Cheeseman, J. Montgomery, T. Vreven, K. Kudin, J. Burant, and others, �Ultra-Large-Scale Systems: The Software Challene of the Future 2006,� 2008.

[9] E. Bottazzi and R. Ferrario, �Introducing Perspectiles in Organizations.�

[10]�The pupose of a system is what it does.� [Online]. Available: http://en.wikipedia.org/wiki/POSIWID.

[11] H. Teijgeler, �Functional and Physical Objects - the big picture.� [Online]. Available: http://15926.info/functional-physical-object/index.htm.

[12] I.-I. O. for Standardization, �ISO - International Organization for Standardization.� [Online]. Available: http://www.iso.org/iso/iso_catalogue/catalogue_tc/catalogue_detail.htm?csnumber=43669. [Accessed: 01-Feb-2012].

[13] Semat, �SEMAT: Software Engineering Method and Theory.� [Online]. Available: www.semat.org.

[14] J. Rasmussen, A. M. Pejtersen, and L. P. Goodstein, Cognitive systems engineering. Wiley, 1994.

[15] E. W. Dijkstra, �Self stabilizing systems in spite of distributed control,� CACM, vol. 17, no. 11, pp. 643-644, 1974.

[16]VW Factory - Germany. 2009.

[17] S. Borgo, R. Mizoguchi, and B. Smith, �On the ontology of functions,� Applied Ontology, vol. 6, no. 2, pp. 99�104, 2011.

[18] I.-I. O. for Standardization, �ISO 10303-214:2010 Industrial automation systems and integration -- Product data representation and exchange -- Part 214: Application protocol: Core data for automotive mechanical design processes.� [Online]. Available: http://www.iso.org/iso/iso_catalogue/catalogue_tc/catalogue_detail.htm?csnumber=43669. [Accessed: 26-Jan-2012].

Cyc
[1] C. Sammut and G. I. Webb, Eds., Encyclopedia of Machine Learning, 1st ed. Springer, 2011.

[2] M. Witbrock, K. Panton, S. L. Reed, D. Schneider, B. Aldag, M. Reimers, and S. Bertolo, �Automated OWL annotation assisted by a large knowledge base,� in Workshop Notes of the 2004 Workshop on Knowledge Markup and Semantic Annotation at the 3rd International Semantic Web Conference ISWC2004, 2004, pp. 71�80.

[3] M. Witbrock, C. Matuszek, A. Brusseau, R. Kahlert, C. B. Fraser, and D. Lenat, �Knowledge begets knowledge: Steps towards assisted knowledge acquisition in Cyc,� in Proc. of the AAAI 2005 Spring Symposium on Knowledge Collection from Volunteer Contributors, 2005.

[4] M. Witbrock, E. Coppock, and R. Kahlert, �Uniting a priori and a posteriori knowledge: A research framework.�

[5] M. Witbrock, D. Baxter, J. Curtis, D. Schneider, R. Kahlert, P. Miraglia, P. Wagner, K. Panton, G. Matthews, and A. Vizedom, �An interactive dialogue system for knowledge acquisition in cyc,� in Proceedings of the Workshop on Mixed-Initiative Intelligent Systems, 2003, pp. 138�145.

[6] M. E. Taylor, C. Matuszek, P. R. Smith, and M. Witbrock, �Guiding Inference with Policy Search Reinforcement Learning,� in Proc. of FLAIRS, 2007.

[7] M. E. Taylor, C. Matuszek, B. Klimt, and M. Witbrock, �Autonomous classification of knowledge into an ontology,� in The 20th International FLAIRS Conference (FLAIRS), Key West, Florida, 2007.

[8] N. Siegel, B. Shepard, J. Cabral, and M. Witbrock, �Hypothesis Generation and Evidence Assembly for Intelligence Analysis: Cycorp�s No�scape Application,� in Proceedings of the 2005 International Conference on Intelligence Analysis (IA 2005), 2005.

[9] N. Siegel, G. Matthews, J. Masters, R. Kahlert, M. Witbrock, and K. Pittman, �Applying Cyc: Using the Knowledge-Based Data Monitor To Track Tests and Defects,� 2004.

[10] B. Shepard, C. Matuszek, C. B. Fraser, W. Wechtenhiser, D. Crabbe, Z. Gungordu, J. Jantos, T. Hughes, L. Lefkowitz, M. Witbrock, and others, �A Knowledge-based approach to network security: applying Cyc in the domain of network risk assessment,� in PROCEEDINGS OF THE NATIONAL CONFERENCE ON ARTIFICIAL IN&#8481;LIGENCE, 2005, vol. 20, p. 1563.

[11] P. Shah, D. Schneider, C. Matuszek, R. C. Kahlert, B. Aldag, D. Baxter, J. Cabral, M. Witbrock, and J. Curtis, �Automated population of Cyc: extracting information about named-entities from the web,� in Proceedings of the Nineteenth International FLAIRS Conference, 2006, pp. 153�158.

[12] D. Schneider, C. Matuszek, P. Shah, R. Kahlert, D. Baxter, J. Cabral, M. Witbrock, and D. Lenat, �Gathering and managing facts for intelligence analysis,� in Proceedings of the International Conference on Intelligence Analysis, 2005.

[13] B. Rode and others, �Towards a Model of Pattern Recovery in Relational Data,� in Proceedings of the 2005 International Conference on Intelligence Analysis, 2005.

[14] B. Rode and R. C. Kahlert, �Representational Reformulation in Hypothesis-Driven Recognition.�

[15] S. L. Reed and D. B. Lenat, �Mapping ontologies into Cyc,� in AAAI 2002 Conference Workshop on Ontologies For The Semantic Web, 2002, pp. 1�6.

[16] D. Ramachandran, P. Reagan, and K. Goolsbey, �First-orderized researchcyc: Expressivity and efficiency in a common-sense ontology,� in AAAI Workshop on Contexts and Ontologies: Theory, Practice and Applications, 2005.

[17] K. Panton, P. Miraglia, N. Salay, R. C. Kahlert, D. Baxter, and R. Reagan, �Knowledge formation and dialogue using the KRAKEN toolset,� in PROCEEDINGS OF THE NATIONAL CONFERENCE ON ARTIFICIAL IN&#8481;LIGENCE, 2002, pp. 900�905.

[18] K. Panton, C. Matuszek, D. Lenat, D. Schneider, M. Witbrock, N. Siegel, and B. Shepard, �Common sense reasoning�from Cyc to intelligent assistant,� Ambient Intelligence in Everyday Life, pp. 1�31, 2006.

[19] T. O�Hara, S. Bertolo, M. Witbrock, B. Aldag, J. Curtis, K. Panton, D. Schneider, and N. Salay, �Inferring parts of speech for lexical mappings via the Cyc KB,� in Proceedings of the 20th international conference on Computational Linguistics, 2004, p. 1305.

[20] T. O�Hara, N. Salay, M. Witbrock, D. Schneider, B. Aldag, S. Bertolo, K. Panton, F. Lehmann, M. Smith, D. Baxter, and others, �Inducing criteria for mass noun lexical mappings using the Cyc KB and its extension to WordNet,� in Proc. of the Fifth International Workshop on Computational Semantics (IWCS-5), 2003.

[21] C. Matuszek, M. Witbrock, R. C. Kahlert, J. Cabral, D. Schneider, P. Shah, and D. Lenat, �Searching for common sense: Populating Cyc� from the Web,� in Proceedings of the National Conference on Artificial Intelligence, 2005, vol. 20, p. 1430.

[22] C. Matuszek, J. Cabral, M. Witbrock, and J. DeOliveira, �An introduction to the syntax and content of Cyc,� in Proceedings of the 2006 AAAI Spring Symposium on Formalizing and Compiling Background Knowledge and Its Applications to Knowledge Representation and Question Answering, 2006, vol. 3864, pp. 44�49.

[23] J. Masters and Z. Gungordu, �Semantic knowledge source integration: a progress report,� in Integration of Knowledge Intensive Multi-Agent Systems, 2003. International Conference on, 2003, pp. 562�566.

[24] D. Mahler, �Holistic query expansion using graphical models,� New Directions in Question Answering, vol. 2004, pp. 203�227, 2004.

[25] J. Ludwig, A. Davis, M. Abrams, and J. Curtis, �Developing A Hidden Domain for Human and Electronic Students,� Proceedings of the 2-11 IJCAI Workshop on Agents Learning Interactively from Human Teachers, 2011.

[26] F. Lehman and D. Foxvog, �Putting Flesh on the Bones: Issues that Arise in Creating Anatomical Knowledge Bases with Rich Relational Structures,� in AAAI-98 Workshop on Sharing Information in Bioinformatics and Medical Knowledge Bases, 1998.

[27] K. D. Forbus, L. Birnbaum, E. Wagner, J. Baker, and M. Witbrock, �Analogy, Intelligent IR, and Knowledge Integration for Intelligence Analysis: Situation Tracking and the Whodunit problem,� in International Conference on Intelligence Analysis: The Office of the Assistant Director of Central Intelligence, 2005.

[28] D. Fensel, F. Van Harmelen, B. Andersson, P. Brennan, H. Cunningham, E. Della Valle, F. Fischer, Z. Huang, A. Kiryakov, T. K. Lee, and others, �Towards LarKC: a platform for web-scale reasoning,� in Semantic Computing, 2008 IEEE International Conference on, 2008, pp. 524�529.

[29] C. Deaton, B. Shepard, C. Klein, C. Mayans, B. Summers, A. Brusseau, M. Witbrock, and D. Lenat, �The comprehensive terrorism knowledge base in cyc,� in Proceedings of the 2005 International Conference on Intelligence Analysis, 2005.

[30] J. Davis, Semantic knowledge management&#8239;: integrating ontology management, knowledge discovery, and human language technologies. Berlin; Heidelberg: Springer, 2009.

[31] J. Curtis, G. Matthews, and D. Baxter, �On the effective use of Cyc in a question answering system,� in IJCAI Workshop on Knowledge and Reasoning for Answering Questions, 2005.

[32] J. Curtis, J. Cabral, and D. Baxter, �On the application of the Cyc ontology to word sense disambiguation,� in Proceedings of the 19th International Florida Artificial Intelligence Research Society Conference, 2006, pp. 652�657.

[33] J. Curtis, D. Baxter, P. Wagner, J. Cabral, D. Schneider, M. Witbrock, and others, �Methods of Rule Acquisition in the TextLearner System,� in Proceedings of the 2009 AAAI Spring Symposium on Learning by Reading and Learning to Read, 2009, pp. 22�28.

[34] J. Cabral, R. C. Kahlert, C. Matuszek, M. Witbrock, and B. Summers, �Converting Semantic Meta-knowledge into Inductive Bias,� in Inductive Logic Programming, vol. 3625, S. Kramer and B. Pfahringer, Eds. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005, pp. 38-50.

[35] A. Belasco, J. Curtis, R. Kahlert, C. Klein, C. Mayans, and P. Reagan, �Representing Knowledge Gaps Effectively,� Practical Aspects of Knowledge Management, pp. 159�164, 2004.

[36] D. Baxter, B. Shepard, N. Siegel, B. Gottesman, and D. Schneider, �Interactive natural language explanations of cyc inferences,� in Proceedings of AAAI, 2005.

[37] M. Assel, A. Cheptsov, G. Gallizo, I. Celino, D. Dell�Aglio, L. Brade�ko, M. Witbrock, and E. D. Valle, �Large knowledge collider: a service-oriented platform for large-scale semantic reasoning,� in Proceedings of the International Conference on Web Intelligence, Mining and Semantics, 2011, p. 41.

[38]�ekaw02-aitken-curtis.pdf.�.

[39]�fusion2002.pdf.�.

[40]�CEARCH-abstract-hpec-9-06.pdf.�.

[41]�fs-06-02.php.�.

[42] �DantosRecipeForClio.pdf.�.

[43]�Harnessing_Cyc_to_Answer_Clincal_Researchers_ad_hoc_Queries.pdf.�.

[44]�Translation_from_Logic_to_English.pdf.�.

[45] AAAI Fall Symposium, K. Murray, I. Harrison, and American Association for Artificial Intelligence., �Capturing and using patterns for evidence detection&#8239;: papers from the AAAI Fall Symposium,� Menlo Park, Calif., 2006.

Cross-Track-A1: Ontology Quality and Large-Scale Systems
[1] L. Yao, A. Divoli, I. Mayzus, J. A. Evans, and A. Rzhetsky, �Benchmarking ontologies: bigger or better?,� PLoS computational biology, vol. 7, no. 1, p. e1001055, 2011.

[2] D. Vrande&#269;i&#263; and Y. Sure, �How to design better ontology metrics,� The Semantic Web: Research and Applications, pp. 311�325, 2007.

[3] C. Vogel and J. Powers, �Quality metrics: How to ensure quality taxonomies,� in NATIONAL ONLINE MEETING, 2000, vol. 21, pp. 433�446.

[4] K. Verspoor, D. Dvorkin, K. B. Cohen, and L. Hunter, �Ontology quality assurance through analysis of term transformations,� Bioinformatics, vol. 25, no. 12, p. i77, 2009.

[5] P. Velardi, R. Navigli, A. Cuchiarelli, and R. Neri, �Evaluation of OntoLearn, a methodology for automatic learning of domain ontologies,� Ontology Learning from Text: Methods, evaluation and applications, pp. 92�106, 2005.

[6] M. Uschold and M. Gruninger, �Ontologies: Principles, methods and applications,� Knowledge engineering review, vol. 11, no. 2, pp. 93�136, 1996.

[7] J. Tane, P. Cimiano, and P. Hitzler, �Query-based multicontexts for knowledge base browsing: An evaluation,� Conceptual Structures: Inspiration and Application, pp. 413�426, 2006.

[8] N. Sugiura, Y. Shigeta, N. Fukuta, N. Izumi, and T. Yamaguchi, �Towards On-the-fly Ontology Construction�Focusing on Ontology Quality Improvement,� The Semantic Web: Research and Applications, pp. 1�15, 2004.

[9] A. Rector, N. Drummond, M. Horridge, J. Rogers, H. Knublauch, R. Stevens, H. Wang, and C. Wroe, �OWL pizzas: Practical experience of teaching OWL-DL: Common errors & common patterns,� Engineering Knowledge in the Age of the Semantic Web, pp. 63�81, 2004.

[10] C. Patel, K. Supekar, Y. Lee, and E. Park, � OntoKhoj : a semantic web portal for ontology searching, ranking and classification,� in Proceedings of the 5th ACM international workshop on Web information and data management, 2003, pp. 58�61.

[11] F. Neuhaus, E. Florescu, A. Galton, M. Gruninger, N. Guarino, L. Obrst, A. Sanchez, A. Vizedom, P. Yim, and B. Smith, �Creating the ontologists of the future,� Applied Ontology, vol. 6, no. 1, pp. 91�98, 2011.

[12] R. Navigli, P. Velardi, A. Cucchiarelli, and F. Neri, �Quantitative and qualitative evaluation of the OntoLearn ontology learning system,� in Proceedings of the 20th international conference on Computational Linguistics, 2004, p. 1043.

[13] R. Navigli, P. Velardi, A. Cucchiarelli, and F. Neri, �Automatic ontology learning: Supporting a per-concept evaluation by domain experts,� in Workshop on Ontology Learning and Population (ECAI 2004), Valencia, Spain, 2004.

[14] R. Navigli, �Consistent validation of manual and automatic sense annotations with the aid of semantic graphs,� Computational Linguistics, vol. 32, no. 2, pp. 273�281, 2006.

[15] D. L. McGuinness and P. F. Patel-Schneider, �Usability issues in knowledge representation systems,� in PROCEEDINGS OF THE NATIONAL CONFERENCE ON ARTIFICIAL IN&#8481;LIGENCE, 1998, pp. 608�614.

[16] G. MAIGA and D. WILLIAMS, �A Reference Model for Biomedical Ontology Evaluation: The Perspective of Granularity,� International Journal of Computing and ICT Research, p. 35.

[17] G. Maiga and D. Williams, �A Flexible Approach for User Evaluation of Biomedical Ontologies,� International Journal of Computing and ICT Research, p. 62, 2008.

[18] G. Maiga, �Towards a Reusable Evaluation Framework for Ontology based biomedical Systems Integration,� Strengthening the Role of ICT in Development, p. 215, 2007.

[19] J. Lubell, S. Rachuri, M. Mani, and E. Subrahmanian, �Sustaining engineering informatics: Toward methods and metrics for digital curation,� International Journal of Digital Curation, vol. 3, no. 2, 2008.

[20] N. Guarino and C. A. Welty, �An overview of OntoClean,� Handbook on ontologies, pp. 201�220, 2009.

[21] N. Guarino and C. Welty, �Evaluating ontological decisions with OntoClean,� Communications of the ACM, vol. 45, no. 2, pp. 61�65, 2002.

[22] A. G�mez-P�rez, �Some ideas and examples to evaluate ontologies,� in Artificial Intelligence for Applications, 1995. Proceedings., 11th Conference on, 1995, pp. 299�305.

[23] A. Gangemi, C. Catenacci, M. Ciaramita, and J. Lehmann, �A theoretical framework for ontology evaluation and validation,� in Semantic Web Applications and Perspectives (SWAP)�2nd Italian Semantic Web Workshop, 2005.

[24] N. S. Friedland, P. G. Allen, M. Witbrock, G. Matthews, N. Salay, P. Miraglia, J. Angele, S. Staab, D. Israel, V. Chaudhri, and others, �Towards a quantitative, platform-independent analysis of knowledge systems,� in Proc. Int�l Conf. Principles of Knowledge Representation, 2004, pp. 507�514.

[25] K. Dellschaft and S. Staab, �On how to perform a gold standard based evaluation of ontology learning,� The Semantic Web-ISWC 2006, pp. 228�241, 2006.

[26] P. R. Cohen, Empirical methods for artificial intelligence, vol. 55. MIT press Cambridge, Massachusetts, 1995.

[27] K. B. Cohen, C. Roeder, W. A. Baumgartner Jr, L. E. Hunter, and K. Verspoor, �Test suite design for ontology concept recognition systems,� 2010.

[28] C. Brewster, H. Alani, S. Dasmahapatra, and Y. Wilks, �Data driven ontology evaluation,� 2004.

[29] M. B. Almeida, �A proposal to evaluate ontology content,� Applied Ontology, vol. 4, no. 3, pp. 245�265, 2009.

[30] P. Alani, Harith and Brewster, Christopher, �Ontology Ranking based on the Analysis of Concept Structures,� in IUI 02: 2002 International Conference on Intelligent User Interfaces, San Francisco, California, USA, January 13-16, 2002, Banff, Alberta, Canada, 2002, p. 198.

[31] H. Alani and C. Brewster, �Metrics for ranking ontologies,� 2006.

[32] �AgainstIdiosyncrasyinOntologyDevelopment_Smith_2006.pdf.�.

General Issues in Ontology
[1] N. Guarino, D. Oberle, and S. Staab, �What Is an Ontology?,� in Handbook of Ontologies, 2nd ed., Springer Berlin Heidelberg, 2009.

Use Case Characterization
[1] F. Neuhaus, E. Florescu, A. Galton, M. Gruninger, N. Guarino, L. Obrst, A. Sanchez, A. Vizedom, P. Yim, and B. Smith, �Creating the ontologists of the future,� Applied Ontology, vol. 6, no. 1, pp. 91�98, 2011.