Logical properties of foundational relations in bio-ontologies

Artificial Intelligence in Medicine

Volumn 39, Issue 3, 2007, Pages 197-216

  Bittner, Thomas ^a   Donnelly, Maureen ^a  

^a UNIVERSITY AT BUFFALO   (United States)

Author keywords

Axiomatic theories; Biomedical ontologies; Description logic; Formal ontology; Mereology

Indexed keywords

FORMAL LANGUAGES; FORMAL LOGIC; ONTOLOGY; SEMANTICS;

AXIOMATIC THEORIES; BIOMEDICAL ONTOLOGIES; DESCRIPTION LOGIC; FORMAL ONTOLOGY; MEREOLOGY;

MEDICAL COMPUTING;

ARTICLE; BIOONTOLOGY; COMPUTER ANALYSIS; DESCRIPTION LOGIC; FIRST ORDER LOGIC; LANGUAGE PROCESSING; LOGIC; MATHEMATICAL ANALYSIS; NOMENCLATURE; PRIORITY JOURNAL; SEMANTICS;

BIOMEDICAL RESEARCH; COMPUTATIONAL BIOLOGY; DATABASES; DECISION TREES; EXPERT SYSTEMS; HUMANS; LOGIC; MODELS, THEORETICAL; NATURAL LANGUAGE PROCESSING; QUALITY CONTROL; SEMANTICS; SOFTWARE; SYSTEMS INTEGRATION; TERMINOLOGY; VOCABULARY, CONTROLLED;

EID: 34247137809     PISSN: 09333657     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.artmed.2006.12.005     Document Type: Article

References (50)

1. Mejino J.L.V., and Rosse C. Symbolic modeling of structural relationships in the Foundational Model of Anatomy. Proceedings of the KR 2004 workshop on formal biomedical knowledge representation. Whistler, BC, Canada, 1 June 2004 (2004) 48-62
2. Smith B., and Rosse C. The role of foundational relations in the alignment of biomedical ontologies. In: Fieschi M., Coiera E., and Li Y.J. (Eds). Proceedings of the 11th World Congress on Medical Informatics (2004) 444-448
3. Smith B., Williams J., and Schulze-Kremer S. The ontology of the gene ontology. Proc. Annual Symposium of the American Medical Informatics Association (2003) 609-613
4. In: Baader F., Calvanese D., McGuinness D., Nardi D., and Patel-Schneider P. (Eds). The description logic handbook (2002), Cambridge University Press
5. Burkhardt H., and Dufour C. Part/whole i: history. In: Burkhardt H., and Smith B. (Eds). Handbook of metaphysics and ontology (1991), Philosophia, Muenchen 663-673
6. Simons P. Part/whole ii: mereology since. In: Burkhardt H., and Smith B. (Eds). Handbook of metaphysics and ontology (1991), Philosophia, Muenchen 673-675
7. Winston M., Chaffin R., and Herrmann D. A taxonomy of part-whole relations. Cognitive Sci 11 (1987) 417-444
8. Guarino N., Pribbenow S., and Vieu L. Modeling parts and wholes. Data Knowledge Eng 20 3 (1996) 257-258
9. Gerstl P., and Pribbenow S. Midwinters, end games, and body parts: a classification of part-whole relations. Int J Hum Comput Stud 43 (1995) 865-889
10. Sattler U. Description logics for the representation of aggregated objects. In: Horn W. (Ed). Proceedings of the 14th European Conference on Artificial Intelligence (2000), IOS Press, Amsterdam 239-243
11. Lambrix P., and Padgham L. Conceptual modeling in a document management environment using part-of reasoning in description logics. Data Knowledge Eng 32 1 (2000) 51-86
12. Lambrix P. Part-whole reasoning in an object-centered framework, no. 1771 in lecture notes in artificial intelligence (2000), Springer Verlag
13. Hahn U., Schulz S., and Romacker M. Partonomic reasoning as taxonomic reasoning in medicine. Proceedings of the 16th National Conference on Artificial Intelligence and 11th Innovative Applications of Artificial Intelligence Conference (1998) 271-276
14. Schulz S., and Hahn U. Mereotopological reasoning about parts and (w)holes in bio-ontologies. In: Welty C., and Smith B. (Eds). Formal ontology in information systems. Collected papers from the 2nd International Conference (2001) 210-221
15. Rogers J., and Rector A. GALEN's model of parts and wholes: experience and comparisons. Proceedings of the AMIA Symp 2000 (2000) 714-718
16. Mejino J.L.V., Agoncillo A.V., Rickard K.L., and Rosse C. Representing complexity in part-whole relationships within the Foundational Model of Anatomy. Proceedings of the American Medical Informatics Association Fall Symposium (2003) 450-454
17. Rescher N. Axioms for the part relation. Philos Stud 6 (1955) 8-11
18. Rosse C., and Mejino J.L.V. A reference ontology for bioinformatics: the foundational model of anatomy. J Biomed Inf 36 (2003) 478-500
19. Donnelly M. Containment relations in anatomical ontologies. AIMA Annual Symposium Proceedings (2005) 206-210
20. Donnelly M., Bittner T., and Rosse C. A formal theory for spatial representation and reasoning in bio-medical ontologies. Artif Int Med 36 1 (2006) 1-27
21. Donnelly M., and Bittner T. Spatial relations between classes of individuals. In: Mark D., and Cohn T. (Eds). Spatial information theory. Cognitive and computational foundations of geographic information science. International Conference (COSIT 2005), no. 3693 in lecture notes in computer science (2005), Springer Verlag 182-199
22. Smith B., Ceusters W., Klagges B., Köhler J., Kumar A., Lomax J.,., et al. Relations in biomedical ontologies. Genome Biol 6 5 (2005) r46
23. Smith B. Fiat objects. Topoi 20 2 (2001) 131-148
24. Bittner T, Donnelly M, Goldberg LJ, Neuhaus F. Modeling principles and methodologies-spatial representation and reasoning. In: Burger A, Davidson D, Baldock R, editors. Anatomy ontologies for bioinformatics: principles and practice. Springer Verlag, in press.
25. Copi I. Symbolic logic (1979), Prentice Hall, Upper Saddle River, NJ 07458
26. Schulz S., Hahn U., and Romacker M. Modeling anatomical spatial relations with description logics. AMIA 2000-Proceedings of the Annual Symposium of the American Medical Informatics Association (2000) 779-783
27. Spackman K. Managing clinical terminology hierarchies using algorithmic calculation of subsumption: experience with snomed-rt. J Am Med Inf Assoc Fall Symp [Special Issue].
28. Spackman K. Normal forms for description logic expressions of clinical concepts in SNOMED RT. J Am Med Inf Assoc (2001) 627-631
29. Schulz S., and Hahn U. Parthood as spatial inclusion-evidence from biomedical conceptualizations. Proceedings of the Ninth International Conference on Principles of Knowledge Representation and Reasoning (KR2004) (2004) 55-63
30. Zhang S., Mork P., and Bodenreider O. Lessons learned from aligning two representations of anatomy. In: Hahn U. (Ed). Proceedings of KR-MED 2004: First International Workshop on Formal Biomedical Knowledge Representation (2004) 102-108
31. Simons P. Parts, a study in ontology (1987), Clarendon Press, Oxford
32. Stuckenschmidt H., van Harmelen F., Bouquet P., Giunchiglia F., and Serafini L. Using C-OWL for the alignment and merging of medical ontologies. In: Hahn U. (Ed). Proceedings of KR-MED 2004: First International Workshop on Formal Biomedical Knowledge Representation (2004) 88-101
33. Kaushik S., Wijesekera D., and Ammann P. An algebra for ontologies. International conference on formal ontology in information systems (FOIS 2006) (2006)
34. Antoine Zimmermann J.E., Krötzsch M., and Hitzler P. Formalizing ontology alignment and its operations with category theory. In: Bennett B., and Fellbaum C. (Eds). International conference on formal ontology in information systems (FOIS 2006) (2006)
35. Bechhofer S., Horrocks I., Goble C., and Stevens R. OilEd: a reason-able ontology editor for the semantic web. Proceedings of KI2001, Joint German/Austrian conference on artificial intelligence, no. 2174 in lecture notes in computer science (2001), Springer-Verlag, Vienna 396-408
36. Noy N.F., Sintek M., Decker S., Crubezy M., Fergerson R.W., and Musen M.A. Creating semantic web contents with protege-2000. IEEE Intel Syst 16 2 (2001) 60-71
37. Knublauch H., Dameron O., and Musen M.A. Weaving the biomedical semantic web with the prote'ge' owl plugin. Proceedings of KR-MED 2004: First International Workshop on Formal Biomedical Knowledge Representation (2004) 39-47
38. Noy N.F., Musen M.A., Mejino J.L.V., and Rosse C. Pushing the envelope: challenges in a frame-based representation of human anatomy. Data Knowledge Eng 48 (2004) 335-359
39. Schmidt-Schauß M. Subsumption in kl-one is undecidable. Proceedings of the 1st international conference on principles of knowledge representation and reasoning (KR89) (1989) 421-431
40. Baader F., and Sattler U. Description logics with aggregates and concrete domains. Inf Syst 28 8 (2003) 979-1004
41. Horrocks I., and Sattler U. Decidability of shiq with complex role inclusion axioms. Artif Intell 120 1-2 (2004) 79-104
42. Horrocks I., Patel-Schneider P.F., and van Harmelen F. From SHIQ and RDF to OWL: the making of a web ontology language. J Web Semant 1 1 (2003) 7-26
43. Wessel M. Obstacles on the way to qualitative spatial reasoning with description logics: some undecidability results. In: Goble C.A., McGuinness D.L., Möller R., and Patel-Schneider P.F. (Eds). Proceedings of the international workshop in description logics 2001, vol. 49 (2001)
44. Lutz C., and Sattler U. Mary likes all cats. In: Baader F., and Sattler U. (Eds). Proceedings of the international workshop in description logics (DL2000), no. 33 in CEUR-WS, RWTH Aachen (2000) 213-226
45. Baader F., Brandt S., and Lutz C. Pushing the E L envelope. Proceedings of the nineteenth international joint conference on artificial intelligence IJCAI-05 (2005), Morgan-Kaufmann Publishers, Edinburgh, UK 364-369
46. +. Proceedings of the 2006 international workshop on description logics (DL2006), CEUR-WS, in press.
47. Baader F., Lutz C., and Suntisrivaraporn B. CEL-a polynomial-time reasoner for life science ontologies. In: Furbach U., and Shankar N. (Eds). Proceedings of the 3rd international joint conference on automated reasoning (IJCAR'06), vol. 4130 of lecture notes in artificial intelligence (2006), Springer-Verlag 287-291
48. Baader F. Restricted role-value-maps in a description logic with existential restrictions and terminological cycles. In: Calvanese D., Giacomo G.D., and Franconi E. (Eds). Proceedings of the 2003 international workshop on description logics (DL2003), vol. 81 of CEUR-WS, CEUR-WS. org (2003)
49. Rector A., and Horrocks I. Experience building a large, re-usable medical ontology using a description logic with transitivity and concept inclusions. Proc. of AAAI'97 (1997), AAAI Press, Menlo Park, California. http://citeseer.ist.psu.edu/rector97experience.html [URL: http://citeseer.ist.psu.edu/rector97experience.html]
50. Sattler U. A concept language for an engineering application with part-whole relations. In: Borgida A., Lenzerini M., Nardi D., and Nebel B. (Eds). Proceedings of the international workshop on description logics. Rome (1995) 119-123