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A Vocabulary of Topological and Containment Relations for a Practical Biological Ontology

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Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 8116))

Abstract

We describe the development of a formal language for expressing qualitative spatial knowledge. The language is intended as a practical tool for knowledge representation and has been designed with the particular aim of encoding the qualitative spatial information found in an introductory college level biology textbook. We have taken a corpus-driven approach in which we first identify the requirements by analysing the sentences in the book, design the vocabulary, and then check its adequacy by applying it to model the sentences containing spatial knowledge. Our technical solution extends the well-known Region Connection Calculus with predicates for referring to surfaces, cavities and different forms of containment. We illustrate the application of this vocabulary in encoding sample sentences from the book, and give empirical results regarding the correspondence between the defined relations of our formal theory and the actual usage of vocabulary pertaining to ‘surrounding’, ‘enclosure’ and ‘containment’ in the textbook.

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References

  • Agarwal, P.: Contested Nature of place: Knowledge Mapping for Resolving Ontological Distinctions Between Geographical Concepts. In: Egenhofer, M., Freksa, C., Miller, H.J. (eds.) GIScience 2004. LNCS, vol. 3234, pp. 1–21. Springer, Heidelberg (2004)

    Chapter  Google Scholar 

  • Bateman, J.A., Hois, J., Ross, R.J., Tenbrink, T.: A linguistic ontology of space for natural language processing. Artif. Intell. 174(14), 1027–1071 (2010)

    Article  Google Scholar 

  • Bennett, B.: A categorical axiomatisation of region-based geometry. Fundamenta Informaticae 46(1-2), 145–158 (2001)

    MathSciNet  MATH  Google Scholar 

  • Bennett, B.: What is a forest? on the vagueness of certain geographic concepts. Topoi 20(2), 189–201 (2001)

    Article  Google Scholar 

  • Bennett, B., Agarwal, P.: Semantic categories underlying the meaning of ‘place’. In: Winter, S., Duckham, M., Kulik, L., Kuipers, B. (eds.) COSIT 2007. LNCS, vol. 4736, pp. 78–95. Springer, Heidelberg (2007)

    Chapter  Google Scholar 

  • Bittner, T.: Logical properties of foundational mereogeometrical relations in bio-ontologies. Applied Ontology 4(2), 109–138 (2009)

    Google Scholar 

  • Casati, R., Varzi, A.: Holes and Other Superficialities. MIT Press, Cambridge (1994)

    Google Scholar 

  • Clementini, E., Di Felice, P., van Oosterom, P.: A small set of formal topological relationships suitable for end-user interaction. In: Abel, D.J., Ooi, B.-C. (eds.) SSD 1993. LNCS, vol. 692, pp. 277–295. Springer, Heidelberg (1993)

    Chapter  Google Scholar 

  • Cohn, A.: A hierarchcial representation of qualitative shape based on connection and convexity. In: Kuhn, W., Frank, A.U. (eds.) COSIT 1995. LNCS, vol. 988, pp. 311–326. Springer, Heidelberg (1995)

    Google Scholar 

  • Cohn, A.G., Mark, D.M. (eds.): COSIT 2005. LNCS, vol. 3693. Springer, Heidelberg (2005)

    MATH  Google Scholar 

  • Cohn, A.G., Varzi, A.C.: Mereotopological connection. Journal of Philosophical Logic 32(4), 357–390 (2003)

    Article  MathSciNet  MATH  Google Scholar 

  • Davis, E.: Representations of Commonsense Knowledge. Morgan Kaufmann, San Mateo (1990)

    Google Scholar 

  • Davis, E.: Qualitative spatial reasoning in interpreting text and narrative, Spatial Cognition and Computation (2012) (to appear)

    Google Scholar 

  • Donnelly, M., Bittner, T., Rosse, C.: A formal theory for spatial representation and reasoning in biomedical ontologies. Artificial Intelligence in Medicine 36(1), 1–27 (2006)

    Article  Google Scholar 

  • Edelsbrunner, H., Kirkpatrick, D.G., Seidel, R.: On the shape of a set of points in the plane. IEEE Transactions on Information Theory 29(4), 551–558 (1983)

    Article  MathSciNet  MATH  Google Scholar 

  • Egenhofer, M., Franzosa, R.: Point-set topological spatial relations. International Journal of Geographic Information Systems 5(2), 161–174 (1991)

    Article  Google Scholar 

  • Egenhofer, M., Giudice, N., Moratz, R., Worboys, M. (eds.): COSIT 2011. LNCS, vol. 6899. Springer, Heidelberg (2011)

    MATH  Google Scholar 

  • Fellbaum, C.: WordNet: an electronic lexical database. Bradford Books (1998)

    Google Scholar 

  • Gotts, N.M.: How far can we ‘C’? defining a ‘doughnut’ using connection alone. In: Doyle, J., Sandewall, E., Torasso, P. (eds.) Principles of Knowledge Representation and Reasoning: Proceedings of the 4th International Conference (KR 1994). Morgan Kaufmann (1994)

    Google Scholar 

  • Klippel, A., Li, R., Yang, J., Hardisty, F., Xu, S.: The egenhofer cohn hypothesis or, topological relativity? In: Raubal, M., Mark, D.M., Frank, A.U. (eds.) Cognitive and Linguistic Aspects of Geographic Space. Lecture Notes in Geoinformation and Cartography, pp. 195–215. Springer, Heidelberg (2013)

    Chapter  Google Scholar 

  • Knauff, M., Rauh, R., Renz, J.: A cognitive assessment of topological spatial relations: Results from an empirical investigation. In: Frank, A.U. (ed.) COSIT 1997. LNCS, vol. 1329, pp. 193–206. Springer, Heidelberg (1997)

    Chapter  Google Scholar 

  • Mark, D., Egenhofer, M.: Calibrating the meanings of spatial predicates form natural language: Line-region relations. In: Proceedings of the Sixth International Symposium on Spatial Data Handling (SDH), pp. 538–553. Edinborough (1994)

    Google Scholar 

  • Miller, G.: Wordnet: A lexical database for english. Communications of the ACM 38(11), 39–41 (1990)

    Article  Google Scholar 

  • Montello, D.R., Goodchild, M.F., Gottsegen, J., Fohl, P.: Where’s downtown?: Behavioral methods for determining referents of vague spatial queries. Spatial Cognition & Computation 3(2-3), 185–204 (2003)

    Article  Google Scholar 

  • Randell, D.A., Cui, Z., Cohn, A.G.: A spatial logic based on regions and connection. In: Proc. 3rd Int. Conf. on Knowledge Representation and Reasoning, pp. 165–176. Morgan Kaufmann, San Mateo (1992)

    Google Scholar 

  • Rector, A.L., Bechhofer, S., Goble, C.A., Horrocks, I., Nowlan, W.A., Solomon, W.D.: The grail concept modelling language for medical terminology. Artificial Intelligence in Medicine 9(2), 139–171 (1997)

    Article  Google Scholar 

  • Reece, J.B., Urry, L.A., Cain, M.L., Wasserman, S.A., Minorsky, P.V., Jackson, R.B.: Campbell Biology, 9th edn. Pearson (2011)

    Google Scholar 

  • Renz, J., Nebel, B.: On the complexity of qualitative spatial reasoning: A maximal tractable fragment of the Region Connection Calculus. Artificial Intelligence 108(1-2), 69–123 (1999)

    Article  MathSciNet  MATH  Google Scholar 

  • Riedemann, C.: Matching names and definitions of topological operators. In: Cohn, A.G., Mark, D.M. (eds.) COSIT 2005. LNCS, vol. 3693, pp. 165–181. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  • Rosse, C., Mejino Jr., J.L., et al.: A reference ontology for biomedical informatics: the foundational model of anatomy. Journal of Biomedical Informatics 36(6), 478–500 (2003)

    Article  Google Scholar 

  • Schulz, S., Jansen, L.: Molecular interactions: On the ambiguity of ordinary statements in biomedical literature. Applied Ontology 4(1), 21–34 (2009)

    Google Scholar 

  • Schulz, S., Kumar, A., Bittner, T.: Biomedical ontologies: What part-of is and isn’t. Journal of Biomedical Informatics 39(3), 350–361 (2006)

    Article  Google Scholar 

  • Shariff, A., Egenhofer, M., Mark, D.: Natural language spatial relations between linear and areal objects: the topology and metric of english-language terms. International Journal of Geographical Information Systems 12(3), 215–245 (1998)

    Google Scholar 

  • Shihong, D., Qiao, W., Qiming, Q.: Definitions of natural-language spatial relations: Combining topology and directions. Geospatial Information Science 9(1), 55–64 (2006)

    Article  Google Scholar 

  • Smith, B., Mejino Jr., J.L.V., Schulz, S., Kumar, A., Rosse, C.: Anatomical information science. In: Cohn, A.G., Mark, D.M. (eds.) COSIT 2005. LNCS, vol. 3693, pp. 149–164. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  • Stock, K., Cialone, C.: Universality, language-variability and individuality: Defining linguistic building blocks for spatial relations. In: Egenhofer, M., Giudice, N., Moratz, R., Worboys, M. (eds.) COSIT 2011. LNCS, vol. 6899, pp. 391–412. Springer, Heidelberg (2011)

    Chapter  Google Scholar 

  • Stock, K., Pasley, R.C., Gardner, Z., Brindley, P., Moreley, J., Cialone, C.: Creating a corpus of geospatial language. Draft available on web at, http://www.nottingham.ac.uk/~lgzwww/contacts/staffPages/kristinstock/documents/CorpusPaperv1.4forweb.pdf

  • Tenbrink, T., Kuhn, W.: A model of spatial reference frames in language. In: Egenhofer, M., Giudice, N., Moratz, R., Worboys, M. (eds.) COSIT 2011. LNCS, vol. 6899, pp. 371–390. Springer, Heidelberg (2011)

    Chapter  Google Scholar 

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Bennett, B., Chaudhri, V., Dinesh, N. (2013). A Vocabulary of Topological and Containment Relations for a Practical Biological Ontology. In: Tenbrink, T., Stell, J., Galton, A., Wood, Z. (eds) Spatial Information Theory. COSIT 2013. Lecture Notes in Computer Science, vol 8116. Springer, Cham. https://doi.org/10.1007/978-3-319-01790-7_23

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  • DOI: https://doi.org/10.1007/978-3-319-01790-7_23

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-01789-1

  • Online ISBN: 978-3-319-01790-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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