GO Annotation in InterPro: Why Stability Does Not Indicate Accuracy in a Sea of Changing Annotations

Overview

Journal Database (Oxford)

Specialty Biology

Date 2016 Mar 21

PMID 26994912

Citations 10

Authors

Amaia Sangrador-Vegas

Alex L Mitchell

Hsin-Yu Chang

Siew-Yit Yong

Robert D Finn

Affiliations

Soon will be listed here.

Abstract

The removal of annotation from biological databases is often perceived as an indicator of erroneous annotation. As a corollary, annotation stability is considered to be a measure of reliability. However, diverse data-driven events can affect the stability of annotations in both primary protein sequence databases and the protein family databases that are built upon the sequence databases and used to help annotate them. Here, we describe some of these events and their consequences for the InterPro database, and demonstrate that annotation removal or reassignment is not always linked to incorrect annotation by the curator. Database URL: http://www.ebi.ac.uk/interpro.

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References

Sigrist C, de Castro E, Cerutti L, Cuche B, Hulo N, Bridge A . New and continuing developments at PROSITE. Nucleic Acids Res. 2012; 41(Database issue):D344-7. PMC: 3531220. DOI: 10.1093/nar/gks1067. View

Attwood T, Coletta A, Muirhead G, Pavlopoulou A, Philippou P, Popov I . The PRINTS database: a fine-grained protein sequence annotation and analysis resource--its status in 2012. Database (Oxford). 2012; 2012:bas019. PMC: 3326521. DOI: 10.1093/database/bas019. View

Weits D, Giuntoli B, Kosmacz M, Parlanti S, Hubberten H, Riegler H . Plant cysteine oxidases control the oxygen-dependent branch of the N-end-rule pathway. Nat Commun. 2014; 5:3425. PMC: 3959200. DOI: 10.1038/ncomms4425. View

Letunic I, Doerks T, Bork P . SMART: recent updates, new developments and status in 2015. Nucleic Acids Res. 2014; 43(Database issue):D257-60. PMC: 4384020. DOI: 10.1093/nar/gku949. View

Mitchell A, Chang H, Daugherty L, Fraser M, Hunter S, Lopez R . The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res. 2014; 43(Database issue):D213-21. PMC: 4383996. DOI: 10.1093/nar/gku1243. View

Wiertz E, Jones T, Sun L, Bogyo M, Geuze H, Ploegh H . The human cytomegalovirus US11 gene product dislocates MHC class I heavy chains from the endoplasmic reticulum to the cytosol. Cell. 1996; 84(5):769-79. DOI: 10.1016/s0092-8674(00)81054-5. View

Pedruzzi I, Rivoire C, Auchincloss A, Coudert E, Keller G, de Castro E . HAMAP in 2015: updates to the protein family classification and annotation system. Nucleic Acids Res. 2014; 43(Database issue):D1064-70. PMC: 4383873. DOI: 10.1093/nar/gku1002. View

Servant F, Bru C, Carrere S, Courcelle E, Gouzy J, Peyruc D . ProDom: automated clustering of homologous domains. Brief Bioinform. 2002; 3(3):246-51. DOI: 10.1093/bib/3.3.246. View

Mi H, Muruganujan A, Thomas P . PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res. 2012; 41(Database issue):D377-86. PMC: 3531194. DOI: 10.1093/nar/gks1118. View

10.

Huntley R, Sawford T, Martin M, ODonovan C . Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt. Gigascience. 2014; 3(1):4. PMC: 3995153. DOI: 10.1186/2047-217X-3-4. View

11.

Finn R, Bateman A, Clements J, Coggill P, Eberhardt R, Eddy S . Pfam: the protein families database. Nucleic Acids Res. 2013; 42(Database issue):D222-30. PMC: 3965110. DOI: 10.1093/nar/gkt1223. View

12.

Skunca N, Altenhoff A, Dessimoz C . Quality of computationally inferred gene ontology annotations. PLoS Comput Biol. 2012; 8(5):e1002533. PMC: 3364937. DOI: 10.1371/journal.pcbi.1002533. View

13.

Bilguvar K, Ozturk A, Louvi A, Kwan K, Choi M, Tatli B . Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations. Nature. 2010; 467(7312):207-10. PMC: 3129007. DOI: 10.1038/nature09327. View

14.

Haft D, Selengut J, Richter R, Harkins D, Basu M, Beck E . TIGRFAMs and Genome Properties in 2013. Nucleic Acids Res. 2012; 41(Database issue):D387-95. PMC: 3531188. DOI: 10.1093/nar/gks1234. View

15.

Mi H, Dong Q, Muruganujan A, Gaudet P, Lewis S, Thomas P . PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res. 2009; 38(Database issue):D204-10. PMC: 2808919. DOI: 10.1093/nar/gkp1019. View

16.

Rhee S, Wood V, Dolinski K, Draghici S . Use and misuse of the gene ontology annotations. Nat Rev Genet. 2008; 9(7):509-15. DOI: 10.1038/nrg2363. View

17.

Mi H, Poudel S, Muruganujan A, Casagrande J, Thomas P . PANTHER version 10: expanded protein families and functions, and analysis tools. Nucleic Acids Res. 2015; 44(D1):D336-42. PMC: 4702852. DOI: 10.1093/nar/gkv1194. View

18.

Bianchetti C, Takasuka T, Deutsch S, Udell H, Yik E, Bergeman L . Active site and laminarin binding in glycoside hydrolase family 55. J Biol Chem. 2015; 290(19):11819-32. PMC: 4424323. DOI: 10.1074/jbc.M114.623579. View

19.

Sillitoe I, Lewis T, Orengo C . Using CATH-Gene3D to Analyze the Sequence, Structure, and Function of Proteins. Curr Protoc Bioinformatics. 2015; 50:1.28.1-1.28.21. DOI: 10.1002/0471250953.bi0128s50. View

20.

Oates M, Stahlhacke J, Vavoulis D, Ben Smithers , Rackham O, Sardar A . The SUPERFAMILY 1.75 database in 2014: a doubling of data. Nucleic Acids Res. 2014; 43(Database issue):D227-33. PMC: 4383889. DOI: 10.1093/nar/gku1041. View