Can Inferred Provenance and Its Visualisation Be Used to Detect Erroneous Annotation? A Case Study Using UniProtKB

PLoS ONE

Volumn 8, Issue 10, 2013, Pages

  Bell, Michael J ^a   Collison, Matthew ^a   Lord, Phillip ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ANALYTICAL ERROR; ARTICLE; CASE STUDY; COMPUTER LANGUAGE; COMPUTER SECURITY; COMPUTER SYSTEM; INFORMATION PROCESSING; INTERNET; KNOWLEDGE BASE; QUALITY CONTROL; STATISTICAL ANALYSIS;

COMPUTER GRAPHICS; CONFIDENCE INTERVALS; DATABASES, PROTEIN; INFORMATION STORAGE AND RETRIEVAL; MOLECULAR SEQUENCE ANNOTATION; RESEARCH DESIGN;

EID: 84885451642     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0075541     Document Type: Article

References (36)

1. Robbins RJ, (1994) Biological databases: A new scientific literature. Publishing Research Quarterly 10: 3-27.
2. Buza T, McCarthy F, Burgess S, (2007) Experimental-confirmation and functional-annotation of predicted proteins in the chicken genome. BMC Genomics 8: 425+.
3. Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, et al. (2008) Gene ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Research 36: D577-D581.
4. Dolan ME, Ni L, Camon E, Blake JA, (2005) A procedure for assessing GO annotation consistency. Bioinformatics 21: i136-143.
5. Buza TJ, McCarthy FM, Wang N, Bridges SM, Burgess SC, (2008) Gene ontology annotation quality analysis in model eukaryotes. Nucleic Acids Research 36: e12.
6. Magrane M, Consortium U, (2011) UniProt knowledgebase: a hub of integrated protein data. Database 2011: bar009.
7. Drysdale RA, Crosby MA, Consortium TF, (2005) FlyBase: genes and gene models. Nucleic Acids Research 33: D390-D395.
8. Bridge A, Poggioli D, O'Donovan C, (2010) UniRule- automatic annotation in UniProtKB. Nature Publishing Group pp. 713 doi:10.1038/npre.2010.5247.1 URL http://dx.doi.org/10.1038/npre.2010.5247.1.
9. Bell MJ, Gillespie CS, Swan D, Lord P, (2012) An approach to describing and analysing bulk biological annotation quality: a case study using UniProtKB. Bioinformatics 28: i562-i568.
10. Artamonova III, Frishman G, Gelfand MSS, Frishman D, (2005) Mining sequence annotation databanks for association patterns. Bioinformatics 21: iii49-iii57.
11. Eisenhaber F, Bork P, (1999) Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries. Bioinformatics 15: 528-535.
12. Gilks WR, Audit B, De Angelis D, Tsoka S, Ouzounis CA, (2002) Modeling the percolation of annotation errors in a database of protein sequences. Bioinformatics 18: 1641-1649.
13. Gilks WR, Audit B, de Angelis D, Tsoka S, Ouzounis CA, (2005) Percolation of annotation errors through hierarchically structured protein sequence databases. Mathematical Biosciences 193: 223-234.
14. Galperin MY, Koonin EV, (1998) Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption. In silico biology 1: 55-67.
15. Jones C, Brown A, Baumann U, (2007) Estimating the annotation error rate of curated GO database sequence annotations. BMC Bioinformatics 8: 170.
16. The UniProt Consortium (2012) Reorganizing the protein space at the universal protein resource (UniProt). Nucleic Acids Research 40: D71-D75.
17. The UniProt Consortium (2011) UniProt Knowledgebase User Manual. http://web.expasy.org/docs/userman.html [Online. last-accessed: 2013-02-25].
18. Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, et al. (2005) The universal protein resource (uniprot). Nucleic acids research 33: D154-D159.
19. Alias-i (2008) LingPipe 4.1.0. http://alias-i.com/lingpipe [Online. last-accessed: 2013-02-25].
20. Leinonen R, Nardone F, Zhu W, Apweiler R, (2006) UniSave: the UniProtKB Sequence/Annotation version database. Bioinformatics 22: 1284-1285.
21. Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, et al. (2004) UniProt: the universal protein knowledgebase. Nucleic Acids Research 32: D115-D119.
22. Smoot ME, Ono K, Ruscheinski J, Wang PLL, Ideker T, (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics (Oxford, England) 27: 431-432.
23. Viégas FB, Wattenberg M, Dave K (2004) Studying cooperation and conict between authors with history flow visualizations. In: Proceedings of the SIGCHI conference on Human factors in computing systems. New York, NY, USA: ACM, CHI '04, pp. 575-582. doi:10.1145/985692.985765. URL http://dx.doi.org/10.1145/985692.985765.
24. The UniProt Consortium (2011) Uniprot release 2011_03. http://www.uniprot.org/news/2011/03/08/release [Online. last-accessed: 2013-02-25].
25. Gross A, Hartung M, Kirsten T, Rahm E (2009) Estimating the quality of Ontology-Based annotations by considering evolutionary changes. In: DILS '09: Proceedings of the 6th International Workshop on Data Integration in the Life Sciences. Berlin, Heidelberg: Springer-Verlag, pp. 71-87. doi:10.1007/978-3-642-02879-3_7. URL http://dx.doi.org/10.1007/978-3-642-02879-3_7.
26. The UniProt Consortium (2013) Update on activities at the universal protein resource (UniProt) in 2013. Nucleic Acids Research 41: D43-D47.
27. O'Donovan C, Martin MJ, Gattiker A, Gasteiger E, Bairoch A, et al. (2002) High-quality protein knowledge resource: Swiss-prot and trembl. Briefings in Bioinformatics 3: 275-284.
28. Ussery DW, Hallin PF, (2004) Genome update: annotation quality in sequenced microbial genomes. Microbiology (Reading, England) 150: 2015-2017.
29. Schnoes AM, Ream DC, Thorman AW, Babbitt PC, Friedberg I (2013) Biases in the experimental annotations of protein function and their effect on our understanding of protein function space. URL http://arxiv.org/abs/1301.1740. 1301.1740.
30. Curwen V, Eyras E, Andrews TD, Clarke L, Mongin E, et al. (2004) The ensembl automatic gene annotation system. Genome Research 14: 942-950.
31. McQuilton P, (2012) Opportunities for text mining in the FlyBase genetic literature curation work-flow. Database 2012: bas039.
32. Jones KS, (1972) A statistical interpretation of term specificity and its application in retrieval. Journal of Documentation 28: 11-21.
33. Lord PW, Stevens RD, Brass A, Goble CA, (2003) Investigating semantic similarity measures across the gene ontology: the relationship between sequence and annotation. Bioinformatics 19: 1275-1283.
34. Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, et al. (2001) The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Research 29: 37-40.
35. Lane L, Argoud-Puy G, Britan A, Cusin I, Duek PD, et al. (2012) neXtProt: a knowledge platform for human proteins. Nucleic Acids Research 40: D76-D83.
36. Fernández-Suárez XM, Galperin MY, (2013) The 2013 nucleic acids research database issue and the online molecular biology database collection. Nucleic Acids Research 41: D1-D7.