Estimating the quality of ontology-based annotations by considering evolutionary changes

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 5647 LNBI, Issue , 2009, Pages 71-87

  Gross, Anika ^a   Hartung, Michael ^a   Kirsten, Toralf ^a   Rahm, Erhard ^a  

^a UNIVERSITY OF LEIPZIG   (Germany)

Author keywords

Annotation; Evolution; Quality

Indexed keywords

ANNOTATION; EVOLUTION; EVOLUTIONARY CHANGES; FUNCTIONAL PROTEINS; GENE ONTOLOGY; GENERATION METHOD; GENERIC EVALUATION; OBJECT PROPERTY; ONTOLOGY CONCEPTS; ONTOLOGY-BASED ANNOTATION; QUALITY; SWISS-PROT;

DATA HANDLING;

ONTOLOGY;

EID: 70350359462     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-02879-3_7     Document Type: Conference Paper

References (24)

1. Berriz, G.F., King, O.D., Bryant, B., et al.: Characterizing gene sets with FuncAssociate. Bioinformatics 19(18), 2502-2504 (2003)
2. Bose, R., Frew, J.: Lineage retrieval for scientific data processing: A survey. ACM Computing Surveys 37(1), 1-28 (2005)
3. Boutet, E., Lieberherr, D., Tognolli, M.: UniProtKB/Swiss-Prot. Methods in Molecular Biology 406, 89-112 (2007)
4. Boyle, E.I., Weng, S., Gollub, J., et al.: GO: TermFinder - open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 20(18), 3710-3715 (2004)
5. Buneman, P., Chapman, A., Cheney, J.: Provenance management in curated databases. In: Proc, of the 2006 ACM SIGMOD International Conference on Management of Data, pp. 539-550 (2006)
6. Buza, T.J., McCarty, F.M., Wang, N.: Gene Ontology annotation quality analysis in model eukaryotes. Nucleic Acids Research 36(2), e12 (2008)
7. Dahlquist, K.D., Salomonis, N., Vranizan, K., et al.: GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nature Genetics 31(1), 19-20 (2002)
8. Gene Ontology - Evidence Codes: http://www.geneontology.org/GO.evidence
9. The Gene Ontology Consortium: The Gene Ontology project in 2008. Nucleic Acids Research 36, D440-D441 (2008) (Database issue)
10. Hartung, M., Kirsten, T., Rahm, E.: Analyzing the Evolution of Life Science Ontologies and Mappings. In: Bairoch, A., Cohen-Boulakia, S., Froidevaux, C. (eds.) DILS 2008. LNCS (LNBI), vol. 5109, pp. 11-27. Springer, Heidelberg (2008)
11. Hubbard, T.J., Aken, B.L., Ayling, S., et al.: Ensembl 2009. Nucleic Acids Research 37, D690-D697 (2009) (Database issue)
12. Jones, C.E., Brown, A.L., Baumann, U.: Estimating the annotation error rate of curated GO database sequence annotations. BMC Bioinformatics 8(1), 170 (2007)
13. Kirsten, T., Thor, A., Rahm, E.: Instance-based matching of large life science ontologies. In: Cohen-Boulakia, S., Tannen, V. (eds.) DILS 2007. LNCS (LNBI), vol. 4544, pp. 172-187. Springer, Heidelberg (2007)
14. Klein, M.: Change Management for Distributed Ontologies. PhD thesis, Vrije Universiteit Amsterdam (2004)
15. Klein, M., Fensel, D.: Ontology versioning on the Semantic Web. In: Proceedings of the International Semantic Web Working Symposium (SWWS), pp. 75-91 (2001)
16. Naumann, F., Leser, U., Freytag, J.C.: Quality-driven Integration of Heterogeneous Information Systems. In: Proc, of the International Conference on Very Large Data Bases (VLDB), pp. 447-458 (1999)
17. Noy, N., Klein, M.: Ontology evolution: Not the same as schema evolution. Knowledge and Information Systems 6(4), 428-440 (2004)
18. Rahm, E., Do, H.H.: Data Cleaning: Problems and Current Approaches. IEEE Data Engineering Bulletin 23(4), 3-13 (2000)
19. Redman, T.C.: Data Quality for the Information Age. Artech House (1996)
20. Stojanovic, L., Maedche, A., Motik, B., Stojanovic, N.: User-driven ontology evolution management. In: Gómez-Pérez, A., Benjamins, V.R. (eds.) EKAW 2002. LNCS, vol. 2473, pp. 285-300. Springer, Heidelberg (2002)
21. Stojanovic, L., Motik, B.: Ontology evolution within ontology editors. In: Proceedings of the International Workshop on Evaluation of Ontology-based Tools, pp. 53-62 (2002)
22. Thomas, P.D., Mi, H., Lewis, S.: Ontology annotation: mapping genomic regions to biological function. Current Opinion in Chemical Biology 11(1), 4-11 (2007)
23. Thor, A., Hartung, M., Gross, A., Kirsten, T., Rahm, E.: An evolution-based approach for assessing ontology mappings - A case study in the life sciences. In: Proc. Conference of the Business, Technology and Web (BTW), pp. 277-286 (2009)
24. Yang, Z., Zhang, D., Ye, C.: Ontology Analysis on Complexity and Evolution Based on Conceptual Model. In: Leser, U., Naumann, F., Eckman, B. (eds.) DILS 2006. LNCS (LNBI), vol. 4075, pp. 216-223. Springer, Heidelberg (2006)