A common layer of interoperability for biomedical ontologies based on OWL EL

Bioinformatics

Volumn 27, Issue 7, 2011, Pages 1001-1008

  Hoehndorf, Robert ^a   Dumontier, Michel ^b   Oellrich, Anika ^c   Wimalaratne, Sarala ^c   Rebholz Schuhmann, Dietrich ^c   Schofield, Paul ^a,d   Gkoutos, Georgios V ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b CARLETON UNIVERSITY   (Canada)

^c EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^d JACKSON LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUSES;

ARTICLE; COMPUTER PROGRAM; EVALUATION; FACTUAL DATABASE; LINGUISTICS; MEDICAL RESEARCH; SEMANTICS;

BIOMEDICAL RESEARCH; DATABASES, FACTUAL; SEMANTICS; SOFTWARE; VOCABULARY, CONTROLLED;

EID: 79953302403     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr058     Document Type: Article

References (45)

1. Ashburner, M. et al. (2000) Gene ontology: tool for the unification of biology. Nat. Genet., 25, 25-29.
2. Baader, F. et al. (2005) Pushing the EL envelope. In Proceedings of the Nineteenth International Joint Conference on Artificial Intelligence IJCAI-05. Morgan-Kaufmann Publishers, Edinburgh, UK.
3. Baader, F. et al. (2006a) 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. Springer, pp. 287-291.
4. +. In Proceedings of the 2006 International Workshop on Description Logics (DL2006), CEUR-WS.
5. Bard, J. et al. (2005) An ontology for cell types. Genome Biol., 6, R21.
6. Barwise, J. and Etchemendy, J. (2002) Language, Proof and Logic. Center for the Study of Language and Information (CSLI), Stanford, USA.
7. Battista, A.D.L. and Dumontier, M. (2009) A platform for reasoning with OWLEL knowledge bases in a peer-to-peer environment. In Proceedings of the 6th International Workshop on OWL: Experiences and Directions (OWLED 2009), Vol. 529, CEURS-WS.org, Innsbruck, Austria.
8. Burek, P. et al. (2006) A top-level ontology of functions and its application in the open biomedical ontologies. Bioinformatics, 22, e66-e73.
9. Ceusters, W. et al. (2006) Referent tracking: the problem of negative findings. Stud. Health Technol. Inform., 124, 741-746.
10. Courtot, M. et al. (2008) The OWL of biomedical investigations. In Dolbear,C. et al. (eds) Proceedings of the Fourth OWLED Workshop on OWL: Experiences and Directions, CEUR-WS.org, Innsbruck, Aachen.
11. Gkoutos, G.V. et al. (2004) Building mouse phenotype ontologies. Pac. Symp. Biocomput., 9, 178-189.
12. Golbreich, C. et al. (2006) The foundational model of anatomy in owl: Experience and perspectives. Web Semant., 4, 181-195.
13. Grau, B. et al. (2008) Owl 2: The next step for owl. Web Semant., 6, 309-322.
14. Gruber, T.R. (1993) Towards principles for the design of ontologies used for knowledge sharing. In Guarino,N. and Poli,R. (eds) Formal Ontology in Conceptual Analysis and Knowledge Representation, Kluwer Academic Publishers, Deventer, The Netherlands.
15. Guarino, N. (1998) Formal ontology and information systems. In Guarino,N. (ed.) Proceedings of the 1st International Conference on Formal Ontologies in Information Systems. IOS Press, pp. 3-15.
16. Hayamizu, T.F. et al. (2005) The adult mouse anatomical dictionary: a tool for annotating and integrating data. Genome Biol., 6, R29.
17. Hoehndorf, R. et al. (2007) Representing default knowledge in biomedical ontologies: application to the integration of anatomy and phenotype ontologies. BMC Bioinformatics, 8, 377.
18. Hoehndorf, R. et al. (2010a) Applying the functional abnormality ontology pattern to anatomical functions. J. Biomed. Semant., 1, 4.
19. Hoehndorf, R. et al. (2010b) Interoperability between phenotype and anatomy ontologies. Bioinformatics, 26, 3112-3118.
20. Hoehndorf, R. et al. (2010c) Relations as patterns: Bridging the gap between OBO and OWL. BMC Bioinformatics, 11, 441.
21. Horridge, M. et al. (2007) Igniting the OWL 1.1 touch paper: The OWL API. In Proceedings of the OWLED 2007 Workshop on OWL: Experiences and Directions, Vol. 258, CEUR-WS.org, Innsbruck, Austria.
22. Horrocks, I. et al. (2000) Practical reasoning for very expressive description logics. Logic J. IGPL, 8, 239-264.
23. Horrocks, I. et al. (2006) The even more irresistible SROIQ. In Proceedings of the 10th International Conference on Principles of Knowledge Representation and Reasoning (KR2006), AAAI Press, Menlo Park, California, USA, pp. 57-67.
24. Horrocks, I. (2007) Obo flat file format syntax and semantics and mapping to owl web ontology language. Technical report, University of Manchester.
25. Motik, B. et al. (2009a) Hypertableau reasoning for description logics. J. Art. Intell. Res., 36, 165-228.
26. Motik, B. et al. (2009b) OWL 2 Web Ontology Language: profiles. Recommendation, World Wide Web Consortium (W3C). Available at http://www.w3.org/TR/owl2-profiles/.
27. Mungall, C.J. et al. (2010a) Cross-product extensions of the gene ontology. J. Biomed. Inform., in press.
28. Mungall, C.J. et al. (2010b) Evolution of the sequence ontology terms and relationships. J. Biomed. Inform. in press.
29. Mungall, C. et al. (2010c) Integrating phenotype ontologies across multiple species. Genome Biol., 11, R2.
30. Mutharaju, R. et al. (2010)AMapReduce algorithm for EL+. In Proceedings of the 23rd InternationalWorkshop on Description Logics (DL2010), Vol. 573, CEUR-WS.org, Innsbruck, Austria, pp. 464-474.
31. Noy, N.F. et al. (2009) Bioportal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res., 37, W170-W173.
32. Rector, A.L. and Brandt,S. (2008) Why do it the hard way? The case for an expressive description logic for SNOMED. J. Am. Med. Inform. Assoc., 15, 744-751.
33. Robinson, P. N. et al. (2008) The human phenotype ontology: a tool for annotating and analyzing human hereditary disease. Am. J. Hum. Genet., 83, 610-615.
34. Rosse, C. and Mejino, J.L.V. (2003) A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J. Biomed. Inform., 36, 478-500.
35. Schulz, S. et al. (2009a) SNOMED reaching its adolescence: Ontologists' and logicians' health check. Int. J. Med. Inform., 78 (Suppl. 1), S86-S94.
36. Schulz, S. et al. (2009b) Strengths and limitations of formal ontologies in the biomedical domain. RECIIS-Electronic Journal of Communication, Information & Innovation in Health, 3, 31-45.
37. Sirin, E. and Parsia, B. (2004) Pellet: an OWL DL reasoner. In Haarslev,V. and Möller,R. (eds) Proceedings of the 2004 International Workshop on Description Logics, DL2004, Whistler, British Columbia, Canada, June 6-8, Vol. 104 of CEUR Workshop Proceedings. Aachen, Germany.
38. Smith, B. et al. (2005) Relations in biomedical ontologies. Genome Biol., 6, R46.
39. Smith, B. et al. (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotech., 25, 1251-1255.
40. Smith, C.L. et al. (2004) The mammalian phenotype ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol., 6, R7.
41. Suntisrivaraporn, B. (2008) Empirical evaluation of reasoning in lightweight DLs on life science ontologies. In Proceedings of the 2nd Mahasarakham International Workshop on AI (MIWAI'08),Mahasarakham University,Mahasarakham, Thailand.
42. Tobies, S. (2000) The complexity of reasoning with cardinality restrictions and nominals in expressive description logics. J. Artif. Int. Res., 12, 199-217.
43. Topalis, P. et al. (2010) A set of ontologies to drive tools for the control of vector-borne diseases. J. Biomed. Inform., in press.
44. Tsarkov, D. and Horrocks, I. (2006) FaCT++ description logic reasoner: System description. In Furbach,U. and Shankar,N. (eds) Automated Reasoning: Proceedings of the Third International Joint Conference, IJCAR 2006, Seattle, Washington, USA, August 17-20, Vol. 4130 of Lecture Notes in Computer Science. Springer, Berlin.
45. Wolstencroft, K. et al. (2006) Protein classification using ontology classification. Bioinformatics, 22, e530-e538.