CAFA and the Open World of protein function predictions

Trends in Genetics

Volumn 29, Issue 11, 2013, Pages 609-610

  Dessimoz, Christophe ^a,b,c   Škunca, Nives ^c,d   Thomas, Paul D ^e  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^c SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^d ETH ZURICH   (Switzerland)

^e UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MANNOSE; PROTEIN;

ALGORITHM; BIOLOGICAL PHENOMENA AND FUNCTIONS CONCERNING THE ENTIRE ORGANISM; DNA SEQUENCE; GOLD STANDARD; LETTER; PREDICTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FUNCTION; REFERENCE DATABASE; SWISS-PROT;

COMMUNITY ASSESSMENT; COMPUTATIONAL METHODS; GENE ONTOLOGY; OPEN WORLD ASSUMPTION; PROTEIN DATABASES; PROTEIN FUNCTION PREDICTION;

COMPUTATIONAL BIOLOGY; HUMANS; PROTEINS; SEQUENCE ANALYSIS, DNA;

EID: 84886290642     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2013.09.005     Document Type: Letter

References (9)

1. Radivojac P., et al. A large-scale evaluation of computational protein function prediction. Nat. Methods 2013, 10:221-227.
2. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 2010, 38:331-335. Gene Ontology Consortium.
3. Thomas P.D., et al. On the use of gene ontology annotations to assess functional similarity among orthologs and paralogs: a short report. PLoS Comput. Biol. 2012, 8:e1002386.
4. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2012, 40:71-75. UniProt Consortium.
5. Hunter S., et al. InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. 2012, 40:306-312.
6. Yamasaki S., et al. C-type lectin Mincle is an activating receptor for pathogenic fungus, Malassezia. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:1897-1902.
7. Dimmer E.C., et al. The UniProt-GO annotation database in 2011. Nucleic Acids Res. 2011, 40:565-570.
8. Skunca N., et al. Quality of computationally inferred gene ontology annotations. PLoS Comput. Biol. 2012, 8:e1002533.
9. Huttenhower C., et al. The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction. Bioinformatics 2009, 25:2404-2410.