Logical properties of foundational relations in bio-ontologies

References 

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