Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt

The Gene Ontology Consortium: Gene ontology: tool for the unification of biology. Nat Genet. 2000, 25: 25-29. 10.1038/75556.

Skunca N, Altenhoff A, Dessimoz C: Quality of computationally inferred gene ontology annotations. PLoS Comput Biol. 2012, 8: e1002533-10.1371/journal.pcbi.1002533.

Blake JA, Dolan M, Drabkin H, Hill DP, Li N, Sitnikov D, Bridges S, Burgess S, Buza T, McCarthy F, Peddinti D, Pillai L, Carbon S, Dietze H, Ireland A, Lewis SE, Mungall CJ, Gaudet P, Chrisholm RL, Fey P, Kibbe WA, Basu S, Siegele DA, McIntosh BK, Renfro DP, Zweifel AE, Hu JC, Brown NH, Tweedie S, Alam-Faruque Y: Gene Ontology annotations and resources. Nucleic Acids Res. 2013, 41 (Database issue): D530-D535.

Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM: A guide to best practices for Gene Ontology (GO) manual annotation. Database. 2013, 2013: bat054-

Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O’Donovan C, Martin MJ, Bely B, Browne P, Mun Chan W, Eberhardt R, Gardner M, Laiho K, Legge D, Magrane M, Pichler K, Poggioli D, Sehra H, Auchincloss A, Axelsen K, Blatter M-C, Boutet E, Braconi-Quintaje S, Breuza L, Bridge A, Coudert E, Estreicher A, Famiglietti L, Ferro-Rojas S, Feuermann M, Gos A: The UniProt-GO annotation database in 2011. Nucleic Acids Res. 2011, 40 (Database issue): D565-D570.

Rhee SY, Wood V, Dolinski K, Draghici S: Use and misuse of the gene ontology annotations. Nat Rev Genet. 2008, 9: 509-515. 10.1038/nrg2363.

Du Plessis L, Skunca N, Dessimoz C: The what, where, how and why of gene ontology–a primer for bioinformaticians. Brief Bioinform. 2011, 12: 723-735. 10.1093/bib/bbr002.

Blake JA: Ten quick tips for using the gene ontology. PLoS Comput Biol. 2013, 9: e1003343-10.1371/journal.pcbi.1003343.

Burge S, Kelly E, Lonsdale D, Mutowo-Muellenet P, McAnulla C, Mitchell A, Sangrador-Vegas A, Yong S-Y, Mulder N, Hunter S: Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Database (Oxford). 2012, 2012: bar068-

: UniProt-GOA Latest Annotation File Release Notes. [ http://www.ebi.ac.uk/GOA ]

: UniProt-GOA Annotation File Downloads. [ http://www.ebi.ac.uk/GOA/downloads ]

Ontology Changes Mailing Lists. http://www.geneontology.org/GO.mailing.lists.shtml#no-post ]

Request Tracker for Ontology Updates. http://sourceforge.net/p/geneontology/ontology-requests/ ]

Request Tracker for Annotation Updates. http://sourceforge.net/p/geneontology/annotation-issues/ ]

Example of GO Discussions in QuickGO. http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0023052#info=2 ]

Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC: The representation of heart development in the gene ontology. Dev Biol. 2011, 354: 9-17. 10.1016/j.ydbio.2011.03.011.

Alam-Faruque Y, Dimmer EC, Huntley RP, O’Donovan C, Scambler P, Apweiler R: The renal gene ontology annotation initiative. Organogenesis. 2010, 6: 71-75. 10.4161/org.6.2.11294.

Subset of GO Terms Unsuitable for Direct Annotation. http://purl.obolibrary.org/obo/go/subsets/gocheck_do_not_annotate.owl ]

Subset of GO Terms Unsuitable for Direct Manual Annotation. http://purl.obolibrary.org/obo/go/subsets/gocheck_do_not_manually_annotate.owl ]

UniProt-GOA Gene Ontology browser QuickGO. http://www.ebi.ac.uk/QuickGO ]

Alam-Faruque Y, Huntley RP, Khodiyar VK, Camon EB, Dimmer EC, Sawford T, Martin MJ, O’Donovan C, Talmud PJ, Scambler P, Apweiler R, Lovering RC: The impact of focused gene ontology curation of specific mammalian systems. PLoS One. 2011, 6: e27541-10.1371/journal.pone.0027541.

Groß A, Hartung M, Prüfer K, Kelso J, Rahm E: Impact of ontology evolution on functional analyses. Bioinformatics. 2012, 28: 2671-2677. 10.1093/bioinformatics/bts498.

Mutowo-Meullenet P, Huntley RP, Dimmer EC, Alam-Faruque Y, Sawford T, Jesus Martin M, O’Donovan C, Apweiler R: Use of Gene Ontology Annotation to understand the peroxisome proteome in humans. Database (Oxford). 2013, 2013: bas062-

GO Reference Collection. http://www.geneontology.org/cgi-bin/references.cgi ]

Uhlen M, Oksvold P, Fagerberg L, Lundberg E, Jonasson K, Forsberg M, Zwahlen M, Kampf C, Wester K, Hober S, Wernerus H, Björling L, Ponten F: Towards a knowledge-based Human Protein Atlas. Nat Biotechnol. 2010, 28: 1248-1250. 10.1038/nbt1210-1248.

Mehrle A, Rosenfelder H, Schupp I, del Val C, Arlt D, Hahne F, Bechtel S, Simpson J, Hofmann O, Hide W, Glatting K-H, Huber W, Pepperkok R, Poustka A, Wiemann S: The LIFEdb database in 2006. Nucleic Acids Res. 2006, 34 (Database issue): D415-D418.

Schnoes AM, Ream DC, Thorman AW, Babbitt PC, Friedberg I: Biases in the experimental annotations of protein function and their effect on our understanding of protein function space. PLoS Comput Biol. 2013, 9: e1003063-10.1371/journal.pcbi.1003063.

Clark JI D n, Dimmer EC, Mungall CJ: Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development. BMC Bioinformatics. 2010, 11: 530-10.1186/1471-2105-11-530.

GO Taxon Constraints File Importer. http://purl.obolibrary.org/obo/go/extensions/x-taxon-importer.owl ]

UniProt-GOA Taxon Constraints Webservice. http://www.ebi.ac.uk/QuickGO/GValidate?service=taxon&action=getConstraints ]

Barrell D, Dimmer E, Huntley RP, Binns D, O’Donovan C, Apweiler R: The GOA database in 2009–an integrated Gene Ontology Annotation resource. Nucleic Acids Res. 2009, 37 (Database issue): D396-D403.

UniProt-GOA Annotation Blacklist Webservice. http://www.ebi.ac.uk/QuickGO/GValidate?service=taxon&action=getBlacklist&taxon=<tax id>