Predicting the Extension of Biomedical Ontologies

PLoS Computational Biology

Volumn 8, Issue 9, 2012, Pages

  Pesquita, Catia ^a   Couto, Francisco M ^a  

^a UNIVERSITY OF LISBON   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGY; FORECASTING; GENE ONTOLOGY;

BIOLOGICAL PROCESS; BIOMEDICAL ONTOLOGIES; F MEASURE; GENE ONTOLOGY; HARD TASK; LIFE-SCIENCES; ONTOLOGY EVOLUTION; ONTOLOGY'S; STATE OF THE ART; TEST BED;

AUTOMATION;

ARTICLE; AUTOMATION; BIOMEDICAL ONTOLOGY; BIOMEDICINE; INFORMATION PROCESSING; METHODOLOGY; NOMENCLATURE; PREDICTION;

EID: 84866932669     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002630     Document Type: Article

References (38)

1. Rubin DL, Shah NH, Noy NF, (2008) Biomedical ontologies: a functional perspective. Brief Bioinform 9: 75-90.
2. Aranguren MEn, Antezana E, Kuiper M, Stevens R, (2008) Ontology Design Patterns for bioontologies: a case study on the. BMC Bioinformatics 13: 1-13.
3. Sure Y, Erdmann M, Angele J, Staab S, Studer R, et al. (2002) OntoEdit: Collaborative ontology development for the semantic web. In: ISWC 2002. Springer. pp. 221-235.
4. Pinto HS, Martins J, (2004) Ontologies: How can They be Built? Knowl Inf Syst 6: 441-464.
5. De Nicola A, Missikoff M, Navigli R, (2009) A software engineering approach to ontology building. Inf Syst 34: 258-275.
6. Gennari J, Musen M, Fergerson R, (2003) The Evolution of Protégé: An Environment for Knowledge-Based Systems Development. Int J Hum-Comput St 58: 189-123.
7. Day-Richter J, Harris Ma, Haendel M, Lewis S, (2007) OBO-Edit-an ontology editor for biologists. Bioinformatics (Oxford, England) 23: 2198-200.
8. Noy N, McGuinness D, Others (2001) Ontology development 101: A guide to creating your first ontology. Technical report, Stanford University.
9. Tempich C, Pinto H, Staab S, (2006) Ontology engineering revisited: An iterative case study. The Semantic Web: Research and Applications 411: 110-124.
10. 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 Biotechnol 25: 1251-5.
11. Noy NF, Klein M, (2004) Ontology Evolution: Not the Same as Schema Evolution. Knowl Inf Syst 6: 428-440.
12. Harris M, Clark J, Ireland A, Lomax J, Ashburner M, et al. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32: D258.
13. Frantzi K, Ananiadou S, (2000) Automatic recognition of multi-word terms:. the C-value/NC-value method. Int J Digit Lbr 3: 115-130.
14. Buitelaar P, Olejnik D, Sintek M (2004) A Protégé Plug-In for Ontology Extraction from Text Based on Linguistic Analysis. In: Proceedings of the 1st European Semantic Web Symposium; May 2004; Heraklion, Greece. ESWS. volume 5.
15. Cimiano P, Völker J (2005) text2Onto: A framework for ontology learning and data-driven change discovery. In: Natural language processing and information systems: 10th International Conference on Applications of Natural Language to Information Systems; 15-17 June 2005; Alicante, Spain. NLDB. Springer Verlag, volume 3513, p. 227.
16. Roitman H, Gal A, (2006) Ontobuilder: Fully automatic extraction and consolidation of ontologies from Web sources using sequence semantics. Current Trends in Database Technology pp. 573-576.
17. Lee JB, Kim Jj, Park JC, (2006) Automatic extension of Gene Ontology with exible identification of candidate terms. Bioinformatics (Oxford, England) 22: 665-70.
18. Buitelaar P, Cimiano P (2008) Ontology learning and population: bridging the gap between text and knowledge, volume 167. IOS Press.
19. Wächter T, Schroeder M, Dresden TU, (2010) Semi-automated ontology generation within OBOEdit. Bioinformatics 26: 88-96.
20. Brewster C, Jupp S, Luciano J, Shotton D, Stevens RD, et al. (2009) Issues in learning an ontology from text. BMC bioinformatics 10Suppl 5: S1.
21. Flouris G, Manakanatas D, Kondylakis H, Plexousakis D, Antoniou G, (2008) Ontology change: classification and survey. Knowl Eng Rev 23: 117-152.
22. Ceusters W, Smith B (2006) A realism-based approach to the evolution of biomedical ontologies. In: AMIA Annual Symposium Proceedings. American Medical Informatics Association 2006: 121. Available: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1839444/.
23. Pinto H, Gómez-Pérez A, Martins J (1999) Some issues on ontology integration. In: Proceedings of the IJCAI-99 workshop on Ontologies and Problem-Solving Methods; 2 August 1999; Stockholm, Sweden. KRR5. pp. 1-12.
24. Pesquita C, Couto FM (2011) Where GO is going and what it means for ontology extension. In: International Conference on Biomedical Ontologies; 26-30 July 2011, Buffalo, NY. ICBO.
25. Stojanovic L (2004) Methods and tools for ontology evolution [PhD dissertation]. Université of Karlsruhe.
26. Castano S, Ferrara A, Hess G (2006) Discovery-driven ontology evolution. In: The Semantic Web Applications and Perspectives, 3rd Italian Semantic Web Workshop; 18-20 December 2006; PISA, Italy. SWAP. Citeseer, pp. 18-20.
27. Leenheer PD, Mens T (2008) Ontology evolution: State of the Art and Future Directions. In: Hepp M, De Leenheer P, de Moor A, Sure Y, editors. Ontology Management for the Semantic Web, Semantic Web Services, and Business Applications, from Semantic Web and Beyond: Computing for Human Experience. Springer. volume 2. pp. 1-47.
28. Stojanovic L, Maedche A, Motik B, Stojanovic N (2002) User-driven ontology evolution management. In: Knowledge Engineering and Knowledge Management: Ontologies and the Semantic Web. Springer. volume 2473. pp. 133-140.
29. Haase P, Hotho A, Schmidt-Thieme L, Sure Y, (2005) Collaborative and usage-driven evolution of personal ontologies. The Semantic Web: Research and Applications pp. 125-226.
30. Ceusters W, (2009) Applying evolutionary terminology auditing to the Gene Ontology. J Biomed Inform 42: 518-29.
31. Hartung M, Gross A, Kirsten T (2010) Discovering evolving regions in life science ontologies. In: Data Integration in the Life Sciences. Springer. volume 6254. pp. 19-34. Available: http://www.springerlink.com/index/AK240444Q9Q81302.pdf.
32. Pesquita C, Grego T, Couto F (2009) Identifying Gene Ontology Areas for Automated Enrichment. In: Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living. Springer. volume 5518. pp. 934-941. Available: http://www.springerlink.com/index/ B6J21M301137M471.pdf.
33. Mungall C, Bada M, Berardini T, Deegan J, Ireland A, et al. (2011) Cross-product extensions of the Gene Ontology. J Biomed Inform 44: 80-86.
34. Alterovitz G, Xiang M, Hill DP, Lomax J, Liu J, et al. (2010) Ontology engineering. Nat Biotechnol 28: 128-130.
35. Leonelli S, Diehl AD, Christie KR, Harris Ma, Lomax J, (2011) How the Gene Ontology Evolves. BMC Bioinformatics 12: 325.
36. Hall M, Frank E, Holmes G, Pfahringer B, Reutemann P, et al. (2009) The WEKA data mining software: an update. ACM SIGKDD Explorations Newsletter 11: 10-18.
37. Chawla N, Bowyer K, Hall L, Kegelmeyer W, (2002) SMOTE: synthetic minority over-sampling technique. J Artif Intell Res 16: 321{pipe}-357.
38. Hartung M, Kirsten T, Gross A, Rahm E, (2009) OnEX: Exploring changes in life science ontologies. BMC bioinformatics 10: 250.