Primer on the gene ontology

Methods in Molecular Biology

Volumn 1446, Issue , 2017, Pages 25-37

  Gaudet, Pascale ^a,b   Škunca, Nives ^a,c,d   Hu, James C ^e   Dessimoz, Christophe ^a,d,f  

^a SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^b UNIVERSITY OF GENEVA   (Switzerland)

^c ETH ZURICH   (Switzerland)

^d UNIVERSITY COLLEGE LONDON   (United Kingdom)

^e TEXAS A AND M UNIVERSITY   (United States)

^f UNIVERSITY OF LAUSANNE   (Switzerland)

Author keywords

Annotation evidence; Annotations; Evidence codes; Function; Gene association file (GAF); Gene ontology structure; GO files; Vocabulary

Indexed keywords

AMINO ACID SEQUENCE; DATA ANALYSIS; GENE FUNCTION; GENE INTERACTION; GENE ONTOLOGY; GENE PRODUCT; GENETIC ASSOCIATION; HUMAN; PHYLOGENY; PREDICTION; PROTEIN PROTEIN INTERACTION; SUPERVISED MACHINE LEARNING; ANIMAL; BIOLOGY; GENETIC DATABASE; GENETICS; INTERNET; PROCEDURES;

DNA; PROTEIN; RNA;

ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA; GENE ONTOLOGY; HUMANS; INTERNET; PROTEINS; RNA;

EID: 84994493506     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-3743-1_3     Document Type: Chapter

References (43)

1. Ashburner M, Ball CA, Blake JA et al (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29
2. Friedmann HC (2004) From "butyribacterium" to "E. coli": an essay on unity in biochemistry. Perspect Biol Med 47: 47-66
3. Hastings J (2016) Primer on ontologies. In: Dessimoz C, Škunca N (eds) The gene ontology handbook. Methods in molecular biology, vol 1446. Humana Press. Chapter 1
4. Munoz-Torres M, Carbon S (2016) Get GO! retrieving GO data using AmiGO, QuickGO, API, files, and tools. In: Dessimoz C, Škunca N (eds) The gene ontology handbook. Methods in molecular biology, vol 1446. Humana Press. Chapter 11
5. Carbon S, Ireland A, Mungall CJ et al (2009) AmiGO: online access to ontology and annotation data. Bioinformatics 25: 288-289
6. Rhee SY, Wood V, Dolinski K et al (2008) Use and misuse of the gene ontology annotations. Nat Rev Genet 9: 509-515
7. Arnaud MB, Costanzo MC, Shah P et al (2009) Gene Ontology and the annotation of pathogen genomes: the case of Candida albicans. Trends Microbiol 17: 295-303
8. Pesquita C (2016) Semantic similarity in the gene ontology. In: Dessimoz C, Škunca N (eds) The gene ontology handbook. Methods in molecular biology, vol 1446. Humana Press. Chapter 12
9. Lovering RC, Camon EB, Blake JA et al (2008) Access to immunology through the Gene Ontology. Immunology 125: 154-160
10. Bauer S (2016) Gene-category analysis. In: Dessimoz C, Škunca N (eds) The gene ontology handbook. Methods in molecular biology, vol 1446. Humana Press. Chapter 13
11. Burge S, Kelly E, Lonsdale D, et al. (2012) Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Database: bar068
12. Pedruzzi I, Rivoire C, Auchincloss AH et al (2015) HAMAP in 2015: updates to the protein family classification and annotation system. Nucleic Acids Res 43: D1064-D1070
13. Cozzetto D, Jones DT (2016) Computational methods for annotation transfers from sequence. In: Dessimoz C, Škunca N (eds) The gene ontology handbook. Methods in molecular biology, vol 1446. Humana Press. Chapter 5
14. Gaudet P, Dessimoz C (2016) Gene ontology: pitfalls, biases, and remedies. In: Dessimoz C, Škunca N (eds) The gene ontology handbook. Methods in molecular biology, vol 1446. Humana Press. Chapter 14
15. Gene Ontology Consortium (2015) Gene Ontology Consortium: going forward. Nucleic Acids Res 43: D1049-D1056
16. The UniProt Consortium (2014) Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res 42: D191-D198
17. Drabkin HJ, Blake JA, Mouse Genome Informatics Database (2012) Manual gene ontology annotation workflow at the Mouse Genome Informatics Database. Database: bas045
18. Hong EL, Balakrishnan R, Dong Q et al (2008) Gene ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res 36: D577-D581
19. Davis P, WormBase Consortium (2009) WormBase - nematode biology and genomes. http://precedings.nature.com/documents/3127/version/1/files/npre20093127-1.pdf
20. dos Santos G, Schroeder AJ, Goodman JL et al (2015) FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations. Nucleic Acids Res 43: D690-D697
21. Gaudet P, Fey P, Basu S et al (2011) dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa. Nucleic Acids Res 39: D620-D624
22. Lamesch P, Berardini TZ, Li D et al (2012) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 40: D1202-D1210
23. Keseler IM, Bonavides-Martínez C, Collado-Vides J et al (2009) EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res 37: D464-D470
24. Buchan DWA, Ward SM, Lobley AE et al (2010) Protein annotation and modelling servers at University College London. Nucleic Acids Res 38: W563-W568
25. Burge S, Attwood TK, Bateman A, et al. (2012) Biocurators and biocuration: surveying the 21st century challenges. Database: bar059
26. Lovering RC (2016) How does the scientific community contribute to gene ontology? In: Dessimoz C, Škunca N (eds) The gene ontology handbook. Methods in molecular biology, vol 1446. Humana Press. Chapter 7
27. Poux S, Gaudet P (2016) Best practices in manual annotation with the gene ontology. In: Dessimoz C, Škunca N (eds) The gene ontology handbook. Methods in molecular biology, vol 1446. Humana Press. Chapter 4
28. Huntley RP, Lovering RC (2016) Annotation extensions. In: Dessimoz C, Škunca N (eds) The gene ontology handbook. Methods in molecular biology, vol 1446. Humana Press. Chapter 17
29. Hunter S, Jones P, Mitchell A et al (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res 40: D306-D312
30. Radivojac P, Clark WT, Oron TR et al (2013) A large-scale evaluation of computational protein function prediction. Nat Methods 10: 221-227
31. The Reference Genome Group of the Gene Ontology Consortium (2009) The Gene Ontology’s Reference Genome Project: a unified framework for functional annotation across species. PLoS Comput Biol 5: e1000431
32. Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 278: 631-637
33. Altenhoff AM, Studer RA, Robinson-Rechavi M et al (2012) Resolving the ortholog conjecture: orthologs tend to be weakly, but signifi- cantly, more similar in function than paralogs. PLoS Comput Biol 8: e1002514
34. Mi H, Muruganujan A, Casagrande JT et al (2013) Large-scale gene function analysis with the PANTHER classification system. Nat Protoc 8: 1551-1566
35. Altenhoff AM, Škunca N, Glover N et al (2015) The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. Nucleic Acids Res 43: D240-D249
36. Cai C (2003) SVM-Prot: web-based support vector machine software for functional classifi- cation of a protein from its primary sequence. Nucleic Acids Res 31: 3692-3697
37. Levy ED, Ouzounis CA, Gilks WR et al (2005) Probabilistic annotation of protein sequences based on functional classifications. BMC Bioinformatics 6: 302
38. Shen HB, Chou KC (2007) EzyPred: a topdown approach for predicting enzyme functional classes and subclasses. Biochem Biophys Res Commun 364: 53-59
39. Lobley AE, Nugent T, Orengo CA et al (2008) FFPred: an integrated feature-based function prediction server for vertebrate proteomes. Nucleic Acids Res 36: W297-W302
40. Gaudet P, Livstone MS, Lewis SE et al (2011) Phylogenetic-based propagation of functional annotations within the Gene Ontology Consortium. Brief Bioinform 12: 449-462
41. Škunca N, Altenhoff A, Dessimoz C (2012) Quality of computationally inferred gene ontology annotations. PLoS Comput Biol 8: e1002533
42. Chibucos MC, Mungall CJ, Balakrishnan R et al. (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database: bau075
43. Chibucos MC, Siegele DA, Hu JC, Giglio M (2016) The evidence and conclusion ontology (ECO): supporting GO annotations. In: Dessimoz C, Škunca N (eds) The gene ontology handbook. Methods in molecular biology, vol 1446. Humana Press. Chapter 18