Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning

PLoS ONE

Volumn 6, Issue 7, 2011, Pages

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

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b CARLETON UNIVERSITY   (Canada)

^c WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^d JACKSON LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; AUTOMATION; COMPUTER ANALYSIS; CONTROLLED STUDY; DATA ANALYSIS; DATA ANALYSIS SOFTWARE; DATA SYNTHESIS; INFORMATION PROCESSING; KNOWLEDGE DISCOVERY; MEDICAL RESEARCH; ODONTOLOGY; SEMANTICS; SYSTEM ANALYSIS; INFORMATION RETRIEVAL; KNOWLEDGE; NATURAL LANGUAGE PROCESSING;

AUTOMATION; BIOMEDICAL RESEARCH; INFORMATION STORAGE AND RETRIEVAL; KNOWLEDGE; NATURAL LANGUAGE PROCESSING;

EID: 79960592493     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0022006     Document Type: Article

References (48)

1. Smith B, Ashburner M, Rosse C, Bard J, Bug W, et al. (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotech 25: 1251-1255.
2. Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, et al. (2007) Advancing translational research with the semantic web. BMC Bioinformatics 8: S2+.
3. Schulz S, Hahn U, (2005) Part-whole representation and reasoning in formal biomedical ontologies. Artifical Intelligence in Medicine 34: 179-200.
4. Rector A, Rogers J, Bittner T, (2006) Granularity, scale and collectivity: When size does and does not matter. Journal of Biomedical Informatics 39: 333-349.
5. Schulz S, Beisswanger E, Wermter J, Hahn U, (2006) Towards an upper level ontology for molecular biology. AMIA Annu Symp Proc pp. 694-698.
6. Hoehndorf R, Loebe F, Poli R, Kelso J, Herre H, (2008) GFO-Bio: A biomedical core ontology. Applied Ontology 3: 219-227.
7. Wolstencroft K, Lord P, Tabernero L, Brass A, Stevens R, (2006) Protein classification using ontology classification. Bioinformatics 22: e530-e538.
8. Mungall C, Gkoutos G, Smith C, Haendel M, Lewis S, et al. (2010) Integrating phenotype ontologies across multiple species. Genome Biology 11: R2+.
9. Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, et al. (2010) Cross-product extensions of the gene ontology. Journal of biomedical informatics.
10. Washington NL, Haendel MA, Mungall CJ, Ashburner M, Westerfield M, et al. (2009) Linking human diseases to animal models using ontology-based phenotype annotation. PLoS Biol 7: e1000247.
11. Hoehndorf R, Dumontier M, Oellrich A, Wimalaratne S, Rebholz-Schuhmann D, et al. (2011) A common layer of interoperability for biomedical ontologies based on OWL EL. Bioinformatics 27: 1001-1008.
12. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. Nature Genetics 25.
13. Smith CL, Goldsmith CAW, Eppig JT, (2004) The mammalian phenotype ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biology 6: R7.
14. Robinson PN, Koehler S, Bauer S, Seelow D, Horn D, et al. (2008) The human phenotype ontology: a tool for annotating and analyzing human hereditary disease. American journal of human genetics 83: 610-615.
15. Jensen LJ, Bork P, (2010) Ontologies in quantitative biology: A basis for comparison, integration, and discovery. PLoS Biol 8: e1000374.
16. Gkoutos GV, Mungall C, Dolken S, Ashburner M, Lewis S, et al. (2009) Entity/quality-based logical definitions for the human skeletal phenome using PATO. Annual International Conference of the IEEE Engineering in Medicine and Biology Society 1: 7069-7072.
17. Horrocks I, (2007) OBO flat file format syntax and semantics and mapping to OWL Web Ontology Language. Technical report, University of Manchester. Available: http://www.cs.man.ac.uk/~horrocks/obo/. Accessed 2011 Jun 16.
18. Hoehndorf R, Oellrich A, Dumontier M, Kelso J, Rebholz-Schuhmann D, et al. (2010) Relations as patterns: Bridging the gap between OBO and OWL. BMC Bioinformatics 11: 441+.
19. Mungall CJ, (2011) OBO flat file format 1.4 syntax and semantics [draft]. Technical report, Lawrence Berkeley National Laboratory. Available: http://berkeleybop.org/~cjm/obo2owl/obo-syntax. html. Accessed 2011 Jun 16.
20. Grau B, Horrocks I, Motik B, Parsia B, Patelschneider P, et al. (2008) OWL 2: The next step for OWL. Web Semantics: Science, Services and Agents on the World Wide Web 6: 309-322.
21. Hoehndorf R, (2010) What is an upper-level ontology? Ontogenesis, Knowledge Blog Available: http://ontogenesis.knowledgeblog.org/740. Accessed 2011 Jun 16.
22. Gruber TR, (1995) Toward principles for the design of ontologies used for knowledge sharing. International Journal of Human-Computer Studies 43.
23. Guarino N, (1998) Formal ontology and information systems. In: Guarino N, editors. Proceedings of the 1st International Conference on Formal Ontologies in Information Systems IOS Press pp. 3-15.
24. Herre H, Heller B, Burek P, Hoehndorf R, Loebe F, et al. (2006) General Formal Ontology (GFO) - A foundational ontology integrating objects and processes [Version 1.0]. Onto-Med Report 8, IMISE, University of Leipzig, Leipzig, Germany.
25. Brachman RJ, (1983) What is-a is and isn't: An analysis of taxonomic links in semantic networks. Computer 16: 30-36.
26. Hilbert D, (1918) Axiomatisches Denken. Mathematische Annalen 78: 405-415.
27. Grenon P, (2003) BFO in a nutshell: A bi-categorial axiomatization of BFO and comparison with DOLCE. IFOMIS Report 06/2003, Institute for Formal Ontology and Medical Information Science (IFOMIS), University of Leipzig, Leipzig, Germany.
28. Masolo C, Borgo S, Gangemi A, Guarino N, Oltramari A, (2003) WonderWeb Deliverable D18: Ontology library (final). Technical report, Laboratory for Applied Ontology, ISTC-CNR, Trento, Italy.
29. Burek P, Hoehndorf R, Loebe F, Visagie J, Herre H, et al. (2006) A top-level ontology of functions and its application in the open biomedical ontologies. Bioinformatics 22: e66-e73.
30. Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D, (2004) Building mouse phenotype ontologies. Pac Symp Biocomput pp. 178-189.
31. Rosse C, Mejino JLV, (2003) A reference ontology for biomedical informatics: the Foundational Model of Anatomy. Journal of Biomedical Informatics 36: 478-500.
32. Hayamizu TF, Mangan M, Corradi JP, Kadin JA, Ringwald M, (2005) The adult mouse anatomical dictionary: a tool for annotating and integrating data. Genome Biology 6.
33. Bard J, Rhee SY, Ashburner M, (2005) An ontology for cell types. Genome Biology 6.
34. Natale D, Arighi C, Barker W, Blake J, Chang TC, et al. (2007) Framework for a protein ontology. BMC Bioinformatics 8: S1.
35. University of Cambridge (2010) European mutant mouse pathology database (Pathbase). Available: http://www.pathbase.net. Accessed 2010 Aug 2.
36. Degtyarenko K, Matos P, Ennis M, Hastings J, Zbinden M, et al. (2007) ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Research.
37. Smith B, Williams J, Schulze-Kremer S, (2003) The ontology of the gene ontology. AMIA Annual Symposium proceedings/AMIA Symposium AMIA Symposium pp. 609-613.
38. Smith B, Ceusters W, Klagges B, Köhler J, Kumar A, et al. (2005) Relations in biomedical ontologies. Genome Biol 6: R46.
39. W3C OWL Working Group (2009) OWL 2 Web Ontology Language: Document overview. Technical report, W3C. http://www.w3.org/TR/owl2-overview/. Accessed 2011 Jun 16.
40. Motik B, Shearer R, Horrocks I, (2009) Hypertableau Reasoning for Description Logics. Journal of Artificial Intelligence Research 36: 165-228.
41. Tsarkov D, Horrocks I, (2006) FaCT++ description logic reasoner: System description. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 4130 LNAI: 292-297.
42. Sirin E, Parsia B, Grau BC, Kalyanpur A, Katz Y, (2007) Pellet: A practical OWL-DL reasoner. Web Semant 5: 51-53.
43. Noy NF, Sintek M, Decker S, Crubezy M, Fergerson RW, et al. (2001) Creating semantic web contents with Protege-2000. IEEE Intelligent Systems 16: 60-71.
44. Horridge M, Bechhofer S, Noppens O, (2007) Igniting the OWL 1.1 touch paper: The OWL API. Proceedings of OWLED 2007: Third InternationalWorkshop on OWL Experiences and Directions.
45. Stevens R, Malone J, Williams S, Power R, (2010) Automating class definitions from OWL to English. Proceedings of Bio-Ontologies 2010: Semantic Applications in Life Sciences SIG at the 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2010).
46. Niles I, Pease A, (2001) Towards a standard upper ontology. Proceedings of the international conference on Formal Ontology in Information Systems- Volume 2001 New York, NY, USA ACM, FOIS '01 pp. 2-9.
47. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, et al. (2007) Database resources of the national center for biotechnology information. Nucleic Acids Research 35.
48. Mungall CJ, Batchelor C, Eilbeck K, (2010) Evolution of the sequence ontology terms and relationships. Journal of Biomedical Informatics.