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Developing Ontologies within Decentralised Settings

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Semantic e-Science

Part of the book series: Annals of Information Systems ((AOIS,volume 11))

Abstract

This chapter addresses two research questions: “How should a well-engineered methodology facilitate the development of ontologies within communities of practice?” and “What methodology should be used?” If ontologies are to be developed by communities then the ontology development life cycle should be better understood within this context. This chapter presents the Melting Point (MP), a proposed new methodology for developing ontologies within decentralised settings. It describes how MP was developed by taking best practices from other methodologies, provides details on recommended steps and recommended processes, and compares MP with alternatives. The methodology presented here is the product of direct first-hand experience and observation of biological communities of practice in which some of the authors have been involved. The Melting Point is a methodology engineered for decentralised communities of practice for which the designers of technology and the users may be the same group. As such, MP provides a potential foundation for the establishment of standard practices for ontology engineering.

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Notes

  1. 1.

    http://purl.obofoundry.org/obo/obi/

  2. 2.

    http://obi-ontology.org/page/consortium

  3. 3.

    http://www.obofoundry.org/crit.shtml

  4. 4.

    http://www.neon-project.org

  5. 5.

    http://www.w3.org/TR/owl-ref/

  6. 6.

    http://www.w3.org/RDF/

  7. 7.

    http://www.ebi.ac.uk/ontology-lookup/

  8. 8.

    http://www.obofoundry.org/wiki/index.php/Naming

  9. 9.

    http://protege.stanford.edu/

  10. 10.

    http://carmen.org.uk/

  11. 11.

    http://www.obofoundry.org/crit.shtml

  12. 12.

    http://www.isi.edu/natural-language/projects/ONTOLOGIES.html

  13. 13.

    http://www.neon-project.org

References

  1. Editorial: Compete, collaborate, compel. Nat Genet 39(8) (Aug 2007) 931

    Google Scholar 

  2. Julian, S., J. Rector, A.: The state of multi-user ontology engineering. In: Proceedings of the 2nd International Workshop on Modular Ontologies, Canada (2007)

    Google Scholar 

  3. Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L., Eilbeck, K., Lewis, S.: The obo foundry: Coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology 25(11) (2007) 1251–1255

    Article  Google Scholar 

  4. Gruber, T.: Collective knowledge systems: Where social web meets the semantic web. In: Proceedings of the 5th International Semantic Web Conference, Athens, GA, USA (2006)

    Google Scholar 

  5. Tudorache, T., Noy, N.: Collaborative protege. In: Social and Collaborative Construction of Structured Knowledge, Proceedings of 16th International WWW Conference, Alberta, Canada (2007)

    Google Scholar 

  6. Feigenbaum, E., McCorduck, P.: The Fifth Generation. Addison-Wesley, Reading, MA (1983)

    Google Scholar 

  7. Kendal, S., Creen, M.: An Introduction to Knowledge Engineering. Springer, New York, NY (2007)

    Google Scholar 

  8. Sowa, J.: Knowledge Representation: Logical, Philosophical, and Computational Foundation. Brooks Cole Publishing, Pacific Grove, CA (2000)

    Google Scholar 

  9. Sure, Y.: Methodology, Tools and Case Studies for Ontology Based Knowledge Management. PhD Thesis, Universitat Fridericiana zu Karlsruhe (2003)

    Google Scholar 

  10. Uschold, M., King, M.: Towards methodology for building ontologies. In: Workshop on Basic Ontological Issues in Knowledge Sharing, Held in Conjunction with IJCAI-95. Cambridge, UK (1995)

    Google Scholar 

  11. Gruninger, M., Fox, M.S.: The role of competency questions in enterprise engineering. In: Proceedings of the IFIP WG5.7 Workshop on Benchmarking – Theory and Practice, Trondheim, Norway (1994)

    Google Scholar 

  12. Bernaras, A., Laresgoiti, I., Corera, J.: Building and reusing ontologies for electrical network applications, 12th European Conference on Artificial Intelligence ECAI. Wiley, Budapest, Hungary (1996) 298–302

    Google Scholar 

  13. Fernadez-Lopez, M., Perez, A.G., Pazos, S.J., Pazos, S.A.: Building a chemical ontology using methontology and the ontology design environment. IEEE Intelligent Systems and Their Applications 14 (1999) 37–46

    Article  Google Scholar 

  14. Swartout, B., Ramesh, P., Knight, K., Russ, T.: Toward distributed use of largescale ontologies. In: Symposium on Ontological Engineering of AAAI, Stanford, California (1997)

    Google Scholar 

  15. Pinto, H.S., Staab, S., Tempich, C.: Diligent: Towards a fine-grained methodology for distributed, loosely-controlled and evolving engineering of ontologies. In: European Conference on Artificial Intelligence, Valencia, Spain (2004) 393–397

    Google Scholar 

  16. Vrandecic, D., Pinto, H.S., Sure, Y., Tempich, C.: The diligent knowledge processes. Journal of Knowledge Management 9(5) (2005) 85–96

    Article  Google Scholar 

  17. Garcia, C.A., Rocca-Serra, P., Stevens, R., Taylor, C., Nashar, K., Ragan, M.A., Sansone, S.: The use of concept maps during knowledge elicitation in ontology development processes – the nutrigenomics use case. BMC Bioinformatics 7 (2006) 267

    Article  Google Scholar 

  18. Mirzaee, V.: An Ontological Approach to Representing Historical Knowledge. MSc Thesis. PhD Thesis, Department of Electrical and Computer Engineering, University of British Columbia (2004)

    Google Scholar 

  19. Moreira, D., Musen, M.A.: Obo to owl: A protege owl tab to read/save obo ontologies. Bioinformatics 23(14) (2007) 1868–1870

    Article  Google Scholar 

  20. Sathiamurthy, M., Peters, B., Bui, H.H., Sidney, J., Mokili, J., Wilson S.S., Fleri, W., McGuinness, D., Bourne, P., Sette, A.: An ontology for immune epitopes: Application to the design of a broad scope database of immune reactivities. BMC Immunology 1(2) (2005)

    Google Scholar 

  21. Bada, M., Stevens, R., Goble, C., Gil, Y., Ashbourner, M., Blake, J., Cherry, J., Harris, M., Lewis, S.: A short study on the success of the geneontology. Journal of Web Semantics 1 (2004) 235–240

    Article  Google Scholar 

  22. Berners-Lee, T., Hendler, J., Lassila, O., et al.: The semantic web. Scientific American 284(5) (2001) 28–37

    Article  Google Scholar 

  23. Shadbolt, N., Berners-Lee, T., Hall, W.: The semantic web revisited. IEEE Intelligent Systems (2006) 96–101

    Google Scholar 

  24. Degtyarenko, K., Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., Alcantara, R., Darsow, M., Guedj, M., Ashburner, M.: ChEBI: A database and ontology for chemical entities of biological interest. Nucleic Acids Research (2007)

    Google Scholar 

  25. Smith, B., Kumar, A., Bittner, T.: Basic formal ontology for bioinformatics. Retrieved Jul. 12, 2010 from http://www.uni-leipzig.de/~akumar/JAIS.pdf Journal of Information Systems (2005) 1–16

  26. Gangemi, A., Guarino, N., Masolo, C., Oltramari, A., Schneider, L.: Sweetening Ontologies with Dolce. Lecture Notes in Computer Science (2002) 166–181

    Google Scholar 

  27. Herre, H., Heller, B., Burek, P., Hoehndorf, R., Loebe, F., Michalek, H.: General Formal Ontology (GFO) – A Foundational Ontology Integrating Objects and Processes. Onto-Med Report 8

    Google Scholar 

  28. Eden, H.A., Hirshfeld, Y.: Principles in formal specification of object oriented design and architecture. In: Proceedings of the 2001 Conference of the Centre for Advanced Studies on Collaborative Research, Toronto, Canada, IBM Press (2001)

    Google Scholar 

  29. Pressman, S.R.: Software Engineering, A Practitioners Approach. 5th edn. McGraw-Hill Series in Computer Science. Thomas Casson, New York, NY (2001)

    Google Scholar 

  30. Martin, J.: Rapid Application Development. Prentice-Hall, Englewood Cliffs, NJ (1991)

    Google Scholar 

  31. Gilb, T.: Evolutionary project management: Multiple performance, quality and cost metrics for early and continuous stakeholder value delivery. In: International Conference on Enterprise Information Systems, Porto, Portugal (2004)

    Google Scholar 

  32. Perez, A.G.: Some Ideas and Examples to Evaluate Ontologies. Technical Report, Stanford University (1994a)

    Google Scholar 

  33. Gilb, T.: Principles of Software Engineering Management. Addison-Wesley Longman, Boston, MA (1988)

    Google Scholar 

  34. Garcia, A.: Developing Ontologies Within the Biomedical Domain. PhD, University of Queensland (2007)

    Google Scholar 

  35. Fernandez, M.: Overview of methodologies for building ontologies. In: Proceedings of the IJCAI-99 Workshop on Ontologies and Problem-Solving Methods(KRR5), Stockholm, Sweden (1999)

    Google Scholar 

  36. Corcho, O., Fernadez-Lopez, M., Gomez-Perez, A.: Methodologies, tools, and languages for building ontologies. Where is their meeting point? Data and Knowledge Engineering 46(1) (2003) 41–64

    Article  Google Scholar 

  37. Fernandez, M., Gomez-Perez, A., Juristo, N.: Methontology: From ontological art to ontological engineering. In: Workshop on Ontological Engineering. Spring Symposium Series. AAAI97, Stanford (1997)

    Google Scholar 

  38. Good, B., Tranfield, E.M., Tan, P.C., Shehata, M., Singhera, G., Gosselink, J., Okon, E.B., Wilkinson, M.: Fast, cheap, and out of control: A zero curation model for ontology development. In: Pacific Symposium on Biocomputing. Maui, Hawaii, USA. (2006)

    Google Scholar 

  39. Van Heijst, G., Van der Spek, R., Kruizinga, E.: Organizing corporate memories. In: Tenth Knowledge Acquisition for Knowledge-Based Systems Workshop (KAW’96). (1996)

    Google Scholar 

  40. Mizoguchi, R., Vanwelkenhuysen, J., Ikeda, M.: Task ontology for reuse of problem solving knowledge. In: Towards Very Large Knowledge Bases: Knowledge Building and Knowledge Sharing (KBKS’95). (1995) 46–57

    Google Scholar 

  41. Uschold, M., Gruninger, M.: Ontologies: Principles, methods and applications. Knowledge Engineering Review 11 (1996) 93–136

    Article  Google Scholar 

  42. Fernadez-Lopez, M., Gomez-Perez, A.: Overview and analysis of methodologies for building ontologies. The Knowledge Engineering Review 17(2) (2002) 129–156

    Google Scholar 

  43. Lakoff, G.: Women, Fire, and Dangerous Things: What Categories Reveal About the Mind. Chicago University Press, Chicago (1987)

    Google Scholar 

  44. Cooke, N.: Varieties of knowledge elicitation techniques. International Journal of Human-Computer Studies 41 (1994) 801–849

    Article  Google Scholar 

  45. Arpirez, J., Corcho, O., Fernadez-Lopez, M., Gomez-Perez, A.: Webode in a nutshell. AI Magazine 24(3) (2003) 37–47

    Google Scholar 

  46. Hinchcliffe, D.: Dion hinchcliffe’s web 2.0 blog web 2.0 (2008)

    Google Scholar 

  47. Stoeckert, C.J., Parkinson, H.: The mged ontology: A framework for describing functional genomics experiments. Comparative and Functional Genomics 4 (2003) 127–132

    Article  Google Scholar 

  48. Perez, A.G., Juristo, N., Pazos, J.: Evaluation and assessment of knowledge sharing technology. In Mars, N. (ed.) Towards Very Large Knowledge Bases: Knowledge Building and Knowledge Sharing(KBK95), IOS Press, Amsterdam, The Netherlands, (1995) 289–296

    Google Scholar 

  49. Pinto, H.S., Martins, P. J.: Ontologies: How can they be built? Knowledge and Information Systems 6 (2004) 441–463

    Article  Google Scholar 

  50. IEEE: IEEE standard for software quality assurance plans (1998)

    Google Scholar 

  51. Greenwood, E.: Metodologia de la investigacion social. Paidos, Buenos Aires (1973)

    Google Scholar 

  52. Gomez-Perez, A., Fernandez-Lopez, M., Corcho, O.: Ontological Engineering. Springer, London (2004)

    Google Scholar 

  53. IEEE: IEEE standard for developing software life cycle processes (1996)

    Google Scholar 

  54. Mooney, S.D., Baenziger, P.H.: Extensible open source content management systems and frameworks: A solution for many needs of a bioinformatics group. Brief Bioinform 9(1) (Jan 2008) 69–74

    Article  Google Scholar 

  55. Stevens, R., Goble, C., Bechhofer, S.: Ontology-based knowledge representation for bioinformatics. Briefings in Bioinformatics (2000) 398–414

    Google Scholar 

  56. Gaines, B.R., Shaw, M.L.Q.: Knowledge acquisition tools based on personal construct psychology. The Knowledge Engineering Review 8(1) (1993) 49–85

    Article  Google Scholar 

  57. Rubin, D., Lewis, S., Mungall, C., Misra, S., Westerfield, M., Ashburner, M., Sim, I., Chute, C., Solbrig, H., Storey, M., Smith, B., Day-Richter, J., Noy, N., Musen, M.: National center for biomedical ontology: Advancing biomedicine through structured organization of scientific knowledge. OMICS 10(2) (2006) 85–98

    Article  Google Scholar 

  58. Cote, R., Jones, P., Apweiler, R., Hermjakob, H.: The ontology lookup service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics 7(97) (2006)

    Google Scholar 

  59. Noy, N.F., McGuinness, D.L.: Ontology Development 101: A Guide to Creating Your First Ontology. Technical Report, Stanford University (2001)

    Google Scholar 

  60. Perez, A.G., Fernadez-Lopez, M., Corcho, O.: Ontological Engineering. Computer Sciences. Springer. London (2004)

    Google Scholar 

  61. Haarslev, V., Mller, R.: Racer: A core inference engine for the semantic web. In: Proceedings of the 2nd International Workshop on Evaluation of Ontology-based Tools (EON2003), Sanibel Island, Florida, USA (2003) 27–36

    Google Scholar 

  62. Sirin, E., Parsia, B., Cuenca-Grau, B., Kalyanpur, A., Katz, Y.: Pellet: A practical owl-dl resoner. Journal of Web Semantics 5(2) (2007)

    Google Scholar 

  63. Garcia, A., Zhang, Z., Rajapakse, M., Baker, C., Tang, S.: Capturing and modeling neuro-radiological knowledge on a community basis: The head injury scenario. In: Health and Life Sciences workshop at the WWW2008. (2008)

    Google Scholar 

  64. Orchard, S., Hermjakob, H., Apweiler, R.: The proteomics standards initiative. Proteomics 3(7) (2003) 1374–1376

    Article  Google Scholar 

  65. Taylor, C., Paton, N., Lilley, K., Binz, P., Julian, R.J., Jones, A., Zhu, W., Apweiler, R., Aebersold, R., Deutsch, E., Dunn, M., Heck, A., Leitner, A., Macht, M., Mann, M., Martens, L., Neubert, T., Patterson, S., Ping, P., Seymour, S., Souda, P., Tsugita, A., Vandekerckhove, J., Vondriska, T., Whitelegge, J., Wilkins, M., Xenarios, I., Yates, J.R., Hermjakob, H.: The minimum information about a proteomics experiment (miape). Nature Biotechnology 25(8) (2007) 887–93

    Article  Google Scholar 

  66. Jones, A., Gibson, F.: An update on data standards for gel electrophoresis. Proteomics 7(Suppl 1) (2007) 35–40

    Article  Google Scholar 

  67. Dagnino, A.: Coordination of hardware manufacturing and software development lifecycles for integrated systems development. In: IEEE International Conference on Systems, Man, and Cybernetics 3 (2001) 850–1855

    Google Scholar 

  68. Boehm, B.: A spiral model of software development and enhancement. ACM SIGSOFT Software Engineering Notes 11(4) (1986) 14–24

    Article  Google Scholar 

  69. McDermid, J., Rook, P.: Software development process models. In: Software Engineer’s Reference Book. CRC Press, Boca Raton, FL (1993) 15–28

    Google Scholar 

  70. Larman, C., Basili, R., V.: Iterative and incremental development: A brief history. Computer, IEEE Computer Society 36 (2003) 47–56

    Article  Google Scholar 

  71. May, L, E., Zimmer, A, B.: The evolutionary development model for software. HP Journal (1996) Retrieved Jul. 12, 2010 http://www.hpl.hp.com/hpjournal/96aug/aug96a4.pdf

  72. Fox, M.S.: The tove project: A common-sense model of the enterprise systems. In: Industrial and Engineering Applications of Artificial Intelligence and Expert Systems. (1992)

    Google Scholar 

  73. Arpirez, J., Corcho, O., Fernadez-Lopez, M., Gomez-Perez, A.: Webode in a nutshell. AI Magazine 24(3) (2003) 37–47

    Google Scholar 

  74. Fellbaum, C.: WordNet, An Electronic Lexical Database. The MIT Press, Cambridge, MA (2000)

    Google Scholar 

  75. Knight, K., Luk, S.: Building a large-scale knowledge base for machine translation. In: Proceedings of the National Conference on Artificial Intelligence. Wiley, New York (1994) 773–773

    Google Scholar 

  76. Knight, K., Chander, I.: Automated postediting of documents. In: Proceedings of the 12th National Conference on Artificial Intelligence (vol. 1) Table of Contents, American Association for Artificial Intelligence Menlo Park, CA, USA (1994) 779–784

    Google Scholar 

  77. Knight, K., Graehl, J.: Machine transliteration. Computational Linguistics 24(4) (1998) 599–612

    Google Scholar 

  78. Valente, A., Russ, T., MacGregor, R., Swartout, W.: Building and (Re) Using an Ontology of Air Campaign Planning. IEEE Intelligent Systems (1999) 27–36

    Google Scholar 

  79. Tempich, C., Pinto, H., Sure, Y., Vrandecic, D., Casellas, N., Casanovas, P.: Evaluating diligent ontology engineering in a legal case study. In: XXII World Congress of Philosophy of Law and Social Philosophy, IVR2005 Granada, May 24th, 29th (2005)

    Google Scholar 

  80. Garcia, A.: Developing Ontologies in the Biological Domain. PhD Thesis, University of Queensland (2007)

    Google Scholar 

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Author information

Authors and Affiliations

  1. University of Bremen, Bremen, Germany

    Alexander Garcia

  2. Terry Fox Laboratory, Vancouver, Canada

    Kieran O’Neill

  3. E-Business and Web Science Research Group, Bundeswehr University, Munich, Germany

    Leyla Jael Garcia

  4. School of Computing Science, Newcastle University, Newcastle upon Tyne, UK

    Phillip Lord

  5. Department of Computer Science, University of Manchester, Manchester, M13 9PL, UK

    Robert Stevens

  6. Ontology Engineering Group, Departamento de Inteligencia Artificial, Facultad de Informtica, Universidad Politecnica de Madrid, Campus de Montegancedo, Madrid, Spain

    Oscar Corcho

  7. Abcam plc, Cambridge, CB4 0WN, UK

    Frank Gibson

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  1. Alexander Garcia
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  2. Kieran O’Neill
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  3. Leyla Jael Garcia
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  4. Phillip Lord
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Correspondence to Alexander Garcia .

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Editors and Affiliations

  1. College of Computer Science, Zhejiang University, Zheda Road 38, Hangzhou, 310058, China, People's Republic

    Huajun Chen

  2. Drug Discovery Pte Ltd., Lilly Singapore Centre for, Biomedical Grove 8A, Singapore, 138648, Singapore

    Yimin Wang

  3. Center for Medical Informatics, Yale University School of Medicine, Cedar St. 333, New Haven, 06520-8009, Connecticut, USA

    Kei-Hoi Cheung

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Garcia, A. et al. (2010). Developing Ontologies within Decentralised Settings. In: Chen, H., Wang, Y., Cheung, KH. (eds) Semantic e-Science. Annals of Information Systems, vol 11. Springer, Boston, MA. https://doi.org/10.1007/978-1-4419-5908-9_4

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