The confidence information ontology: A step towards a standard for asserting confidence in annotations

Database

Volumn 2015, Issue , 2015, Pages

  Bastian, Frederic B ^a,b   Chibucos, Marcus C ^c   Gaudet, Pascale ^b   Giglio, Michelle ^c   Holliday, Gemma L ^d   Huang, Hong ^e   Lewis, Suzanna E ^f   Niknejad, Anne ^a,b   Orchard, Sandra ^g   Poux, Sylvain ^b   Skunca, Nives ^b,h,i   Robinson Rechavi, Marc ^a,b  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^c UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e UNIVERSITY OF SOUTH FLORIDA   (United States)

^f LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^g EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^h ETH ZURICH   (Switzerland)

ⁱ UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL ONTOLOGY; INFORMATION PROCESSING; ORGANIZATION; STANDARDS;

BIOLOGICAL ONTOLOGIES; CONGRESSES AS TOPIC; DATA CURATION;

EID: 84943194552     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bav043     Document Type: Article

References (22)

1. Skunca, N., Altenhoff, A. and Dessimoz, C. (2012) Quality of computationally inferred gene ontology annotations. PLoS Comput. Biol., 8, e1002533.
2. Schnoes, A.M., Ream, D.C., Thorman, A.W. et al. (2013) Biases in the experimental annotations of protein function and their effect on our understanding of protein function space. PLoS Comput. Biol., 9, e1003063.
3. Du Plessis, L., Skunca, N. and Dessimoz, C. (2011) The what, where, how and why of gene ontology-a primer for bioinformaticians. Brief. Bioinform., 12, 723-735.
4. Chibucos, M.C., Mungall, C.J., Balakrishnan, R. et al. (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database, 2014, bau075 http://database.oxfordjournals.org/content/2014/bau075.long
5. Willighagen, E.L., Waagmeester, A., Spjuth, O. et al. (2013) The ChEMBL database as linked open data. J. Cheminform., 5, 23.
6. Niknejad, A., Comte, A., Parmentier, G. et al. (2012) vHOG, a multispecies vertebrate ontology of homologous organs groups. Bioinformatics, 28, 1017-1020.
7. Lane, L., Argoud-Puy, G., Britan, A. et al. (2012) neXtProt: a knowledge platform for human proteins. Nucleic Acids Res., 40, D76-83.
8. The UniProt Consortium (2014) Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res., 42, D191-D198.
9. Furnham, N., Holliday, G.L., de Beer, T.A.P. et al. (2014) The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. Nucleic Acids Res., 42, D485-9.
10. Holliday, G.L., Andreini, C., Fischer, J.D. et al. (2012) MACiE: exploring the diversity of biochemical reactions. Nucleic Acids Res., 40, D783-D789.
11. Pruitt, K.D., Brown, G.R., Hiatt, S.M. et al. (2014) RefSeq: an update on mammalian reference sequences. Nucleic Acids Res., 42, D756-D763.
12. Richardson, E.J. and Watson, M. (2013) The automatic annotation of bacterial genomes. Brief. Bioinform., 14, 1-12.
13. Altman, M. (2012) Mitigating threats to data quality throughout the curation lifecycle. In: Marciano G, Lee C, Bowden H (eds). Curating For Quality: Ensuring Data Quality to Enable New Science. National Science Foundation, Arlington County, VA, pp. 1-119.
14. Gaudet, P., Arighi, C., Bastian, F. et al. (2012) Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference. Database, 2012, bas036.
15. Kardong, K.V. (2006) Vertebrates: comparative anatomy, function, evolution. McGraw-Hill, NY.
16. Bentley, P.J. (1979) The vertebrate urinary bladder: osmoregulatory and other uses. Yale J. Biol. Med., 52, 563-568.
17. Orchard, S., Kerrien, S., Abbani, S. et al. (2012) Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat. Methods, 9, 345-350.
18. Nakayama, H., Izuta, M., Nakayama, N. et al. (2000) Depletion of the squalene synthase (ERG9) gene does not impair growth of Candida glabrata in mice. Antimicrob. Agents Chemother., 44, 2411-2418.
19. Amemiya, C.T., Alfö ldi, J., Lee, A.P. et al. (2013) The African coelacanth genome provides insights into tetrapod evolution. Nature, 496, 311-316.
20. Brinkman, R., Courtot, M., Derom, D. et al. (2010)Modeling biomedical experimental processes withOBI. J. Biomed. Semant., 1, S7.
21. Camon, E.B., Barrell, D.G., Dimmer, E.C. et al. (2005) An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. BMC Bioinformatics, 6(Suppl 1), S17.
22. Poux, S., Magrane, M., Arighi, C.N. et al. (2014) Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data. Database, 2014, bau016.