From Top-Level to Domain Ontologies: Ecosystem Classifications as a Case Study

This paper shows how to use a top-level ontology to create robust and logically coherent domain ontology in a way that facilitates computational implementation and interoperability. It uses a domain ontology of ecosystem classification and delineation outlined informally Bailey's paper on 'Delineation of Ecoregions' as a running example. Baily's (from an ontological perspective) rather imprecise and ambiguous definitions are made more logically rigorous and precise by (a) restating the informal definitions formally using the top-level terms whose semantics was specified rigorously in a logic-based top-level ontology and (b) by enforcing the clear distinction of types of relations as specified at the top-level and specific relations of a given type as they occur in the ecosystem domain. In this way it becomes possible to formally distinguish a number of relations which logical interrelations are important but which have been confused and been taken to be a single relation before.

[1]  Sherri de Coronado,et al.  NCI Thesaurus: A semantic model integrating cancer-related clinical and molecular information , 2007, J. Biomed. Informatics.

[2]  A. Rector,et al.  Relations in biomedical ontologies , 2005, Genome Biology.

[3]  Anthony G. Cohn,et al.  Formalising bio-spatial knowledge , 2001, FOIS.

[4]  Kent A. Spackman,et al.  SNOMED RT: a reference terminology for health care , 1997, AMIA.

[5]  Barry Smith,et al.  SNAP and SPAN: Towards Dynamic Spatial Ontology , 2004, Spatial Cogn. Comput..

[6]  E. J. Lowe Opening plenary talk: Recent advances in metaphysics , 2001, FOIS.

[7]  Barry Smith,et al.  On the Application of Formal Principles to Life Science Data: a Case Study in the Gene Ontology , 2004, DILS.

[8]  Lynette Hirschman,et al.  MiTAP for Biosecurity: A Case Study , 2002, AI Mag..

[9]  Alan L. Rector,et al.  Ontological Issues in using a Description Logic to Represent Medical Concepts: Experience from GALEN , 2004 .

[10]  Chen-Chieh Feng,et al.  Modeling Surface Hydrology Concepts with Endurance and Perdurance , 2004, GIScience.

[11]  W. Köppen,et al.  Grundriss der Klimakunde , 1931 .

[12]  Stephan Winter,et al.  Spatial Information Theory, 8th International Conference, COSIT 2007, Melbourne, Australia, September 19-23, 2007, Proceedings , 2007, COSIT.

[13]  Olivier Bodenreider,et al.  The Unified Medical Language System (UMLS): integrating biomedical terminology , 2004, Nucleic Acids Res..

[14]  Maureen Donnelly,et al.  A formal theory of qualitative size and distance relations between regions , 2007 .

[15]  H. Gaifman,et al.  Symbolic Logic , 1881, Nature.

[16]  Alia I. Abdelmoty,et al.  A critical evaluation of ontology languages for geographic information retrieval on the Internet , 2005, J. Vis. Lang. Comput..

[17]  Barry Smith Fiat Objects , 2001 .

[18]  Peter F. Fisher,et al.  Developments in Spatial Data Handling, 11th International Symposium on Spatial Data Handling, Leicester, UK, August 23-25, 2004 , 2005, SDH.

[19]  David M. Mark,et al.  Ontology and Geographic Objects: An Empirical Study of Cognitive Categorization , 1999, COSIT.

[20]  Chris S. Renschler,et al.  Ontological Investigation of a Multiscale Ecosystem Classification Using the “National Hierarchical Framework of Ecological Units” as an Example , 2006, GeoInformatica.

[21]  Cornelius Rosse,et al.  A formal theory for spatial representation and reasoning in biomedical ontologies , 2006, Artif. Intell. Medicine.

[22]  Nicola Guarino,et al.  Sweetening WORDNET with DOLCE , 2003, AI Mag..

[23]  Nicola Guarino,et al.  Sweetening Ontologies with DOLCE , 2002, EKAW.

[24]  Alan L. Rector,et al.  Modularisation of domain ontologies implemented in description logics and related formalisms including OWL , 2003, K-CAP '03.

[25]  Thomas Bittner,et al.  Understanding Taxonomies of Ecosystems: a Case Study , 2004, SDH.

[26]  Barry Smith,et al.  Individuals, Universals, Collections: On the Foundational Relations of Ontology , 2004 .

[27]  Maureen Donnelly,et al.  Logical properties of foundational relations in bio-ontologies , 2007, Artif. Intell. Medicine.

[28]  Nicola Guarino,et al.  Formal Ontology and Information Systems , 1998 .

[29]  Achille C. Varzi Parts, Wholes, and Part-Whole Relations: The Prospects of Mereotopology , 1996, Data Knowl. Eng..

[30]  Barry Smith,et al.  The Role of Foundational Relations in the Alignment of Biomedical Ontologies , 2004, MedInfo.

[31]  Christian Freksa,et al.  Spatial Information Theory. Cognitive and Computational Foundations of Geographic Information Science , 1999, Lecture Notes in Computer Science.

[32]  J. Blake,et al.  Creating the Gene Ontology Resource : Design and Implementation The Gene Ontology Consortium 2 , 2001 .

[33]  Thomas Bittner,et al.  Ontological Investigation of Ecosystem Hierarchies and Formal Theory for Multiscale Ecosystem Classifications , 2004 .

[34]  Pragya Agarwal,et al.  Ontological considerations in GIScience , 2005, Int. J. Geogr. Inf. Sci..

[35]  Maureen Donnelly,et al.  Spatial Relations Between Classes of Individuals , 2005, COSIT.

[36]  R. Bailey Delineation of ecosystem regions , 1983 .