Improving ontologies by automatic reasoning and evaluation of logical definitions

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Köhler, Sebastian ^a   Bauer, Sebastian ^a   Mungall, Chris J ^b   Carletti, Gabriele ^c   Smith, Cynthia L ^d   Schofield, Paul ^d,e   Gkoutos, Georgios V ^e   Robinson, Peter N ^a,f  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF CAMERINO   (Italy)

^d JACKSON LABORATORY   (United States)

^e UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^f MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SOFTWARE; ERROR DETECTION; MAMMALS; QUALITY CONTROL; SEMANTICS; SYSTEMATIC ERRORS;

AUTOMATED REASONING; AUTOMATIC REASONING; BIOMEDICAL ONTOLOGIES; ONTOLOGY TERMS; OWL ONTOLOGIES; SEMANTIC RELATIONSHIPS;

ONTOLOGY;

MAMMALIA;

ANIMAL; ARTICLE; COMPUTER PROGRAM; HUMAN; KNOWLEDGE; LINGUISTICS; LOGIC; PHENOTYPE; SEMANTICS;

ANIMALS; HUMANS; KNOWLEDGE; LOGIC; PHENOTYPE; SEMANTICS; SOFTWARE; VOCABULARY, CONTROLLED;

EID: 80054915354     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-418     Document Type: Article

References (33)

1. Robinson PN, Bauer S. Introduction to Bio-Ontologies 2011, CRC Press Inc.
2. Ashburner M, Ball C, Blake JA, Botstein D. Gene Ontology: tool for the unification of biology. Nature Genetics 2000,
3. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Consortium OBI, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis SE. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 2007, 25(11):1251-1255. 10.1038/nbt1346, 2814061, 17989687.
4. Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. Cross-product extensions of the Gene Ontology. J Biomed Inform 2011, 44:80-6. 10.1016/j.jbi.2010.02.002, 20152934.
5. Smith CL, Goldsmith CAW, Eppig JT. The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol 2005, 6:R7. 10.1186/gb-2005-6-5-p7, 549068, 15642099.
6. Robinson PN, Köhler S, Bauer S, Seelow D, Horn D, Mundlos S. The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease. Am J Hum Genet 2008, 83(5):610-615. 10.1016/j.ajhg.2008.09.017, 2668030, 18950739.
7. Robinson PN, Mundlos S. The human phenotype ontology. Clin Genet 2010, 77(6):525-534. 10.1111/j.1399-0004.2010.01436.x, 20412080.
8. Human Phenotype Ontology. , http://www.human-phenotype-ontology.org
9. Schindelman G, Fernandes JS, Bastiani CA, Yook K, Sternberg PW. Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community. BMC Bioinformatics 2011, 12:32. 10.1186/1471-2105-12-32, 3039574, 21261995.
10. Gkoutos GV, Green ECJ, Mallon AM, Hancock JM, Davidson D. Building mouse phenotype ontologies. Pac Symp Biocomput 2004, 178-189.
11. Gkoutos GV, Green ECJ, Mallon AM, Hancock JM, Davidson D. Using ontologies to describe mouse phenotypes. Genome Biol 2005, 6:R8. 10.1186/gb-2005-6-5-p8, 549069, 15642100.
12. Sprague J, Bayraktaroglu L, Bradford Y, Conlin T, Dunn N, Fashena D, Frazer K, Haendel M, Howe DG, Knight J, Mani P, Moxon SAT, Pich C, Ramachandran S, Schaper K, Segerdell E, Shao X, Singer A, Song P, Sprunger B, Slyke CEV, Westerfield M. The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res 2008, (36 Database):D768-D772.
13. Hancock JM, Mallon AM, Beck T, Gkoutos GV, Mungall C, Schofield PN. Mouse, man, and meaning: bridging the semantics of mouse phenotype and human disease. Mamm Genome 2009, 20(8):457-461. 10.1007/s00335-009-9208-3, 2759022, 19649761.
14. Washington NL, Haendel MA, Mungall CJ, Ashburner M, Westerfield M, Lewis SE. Linking human diseases to animal models using ontology-based phenotype annotation. PLoS Biol 2009, 7(11):e1000247. 10.1371/journal.pbio.1000247, 2774506, 19956802.
15. Motik B, Patel-Schneider PF, Parsia B. OWL 2 Web Ontology Language: structural specification and functional-syle syntax 2008, , http://www.w3.org/TR/owl2-syntax/
16. Rosse C, Mejino JLV. A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J Biomed Inform 2003, 36(6):478-500. 10.1016/j.jbi.2003.11.007, 14759820.
17. Mungall CJ, Gkoutos GV, Smith CL, Haendel MA, Lewis SE, Ashburner M. Integrating phenotype ontologies across multiple species. Genome Biol 2010, 11:R2. 10.1186/gb-2010-11-1-r2, 2847714, 20064205.
18. Degtyarenko K, de Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alcántara R, Darsow M, Guedj M, Ashburner M. ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res 2008, (36 Database):D344-D350.
19. Sirin E, Parsia B, Cuenca Grau B, Kalyanpur A, Katz Y. Pellet: A practical OWL-DL reasoner. Web Semantics 2007, 5(2):51-53.
20. Motik B, Shearer R, Horrocks I. Optimized reasoning in description logics using hypertableaux. Proc of CADE-21, Volume 4603 of LNCS (LNAI), Heidelberg: Springer 2007, 67-83.
21. Noy NF, Crubezy M, Fergerson RW, Knublauch H, Tu SW, Vendetti J, Musen MA. Protégé-2000: an open-source ontology-development and knowledge-acquisition environment. AMIA Annu Symp Proc 2003, 2003:953.
22. Protégé. , http://protege.stanford.edu
23. TopQuadrant TopQuadrant -- products -- TopBraid Composer. 2011, TopQuadrant., http://www.topquadrant.com/products/TB_Composer.html
24. Bada M, Mungall C, Hunter L. A call for an abductive reasoning fature in OWL-reasoning tools toward ontology quality control. 5th OWL Experiences and Directions Workshop (OWLED 2008) 2008, , http://www.webont.org/owled/2008/papers/owled2008eu_submission_44.pdf
25. Bada M, Hunter L. Identification of OBO nonalignments and its implications for OBO enrichment. Bioinformatics 2008, 24(12):1448-1455. 10.1093/bioinformatics/btn194, 2427163, 18463117.
26. Verspoor K, Dvorkin D, Cohen KB, Hunter L. Ontology quality assurance through analysis of term transformations. Bioinformatics (Oxford, England) 2009, 25(12):i77-84.
27. Ceusters W, Smith B, Kumar A, Dhaen C. Mistakes in medical ontologies: where do they come from and how can they be detected?. Stud Health Technol Inform 2004, 102:145-63.
28. Gkoutos GV, Green ECJ, Mallon AM, Hancock JM, Davidson D. Using ontologies to describe mouse phenotypes. Genome Biol 2004, 6:R8. 10.1186/gb-2004-6-1-r8, 549069, 15642100.
29. Horridge M, Bechhofer S. The OWL API: A Java API for working with OWL 2 ontologies. 6th OWL Experienced and Directions Workshop, Chantilly, Virginia 2009,
30. oboformat library. , http://code.google.com/p/oboformat/
31. OWL Tools. , http://code.google.com/p/owltools/
32. Tsarkov D, Horrocks I. FaCT++ description logic reasoner: system description. Proc of the Int Joint Conf on Automated Reasoning (IJCAR 2006), Volume 4130 of Lecture Notes in Artificial Intelligence, Springer 2006, 292-297.
33. Haendel MA, Gkoutos GG, Lewis SE, Mungall C. Uberon: towards a comprehensive multi-species anatomy ontology. 2009, , http://precedings.nature.com/documents/3592/version/1