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Creating the gene ontology resource: design and implementation.

Gene Ontology Consortium..

Genome Res. 2001 Aug;11(8):1425-33.


The Gene Ontology (GO) database and informatics resource.

Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R; Gene Ontology Consortium..

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D258-61.


Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO).

Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM.

Nucleic Acids Res. 2002 Jan 1;30(1):69-72.


Gramene, a tool for grass genomics.

Ware DH, Jaiswal P, Ni J, Yap IV, Pan X, Clark KY, Teytelman L, Schmidt SC, Zhao W, Chang K, Cartinhour S, Stein LD, McCouch SR.

Plant Physiol. 2002 Dec;130(4):1606-13. Review.


Whole-plant growth stage ontology for angiosperms and its application in plant biology.

Pujar A, Jaiswal P, Kellogg EA, Ilic K, Vincent L, Avraham S, Stevens P, Zapata F, Reiser L, Rhee SY, Sachs MM, Schaeffer M, Stein L, Ware D, McCouch S.

Plant Physiol. 2006 Oct;142(2):414-28.


Applying the Gene Ontology in microbial annotation.

Giglio MG, Collmer CW, Lomax J, Ireland A.

Trends Microbiol. 2009 Jul;17(7):262-8. doi: 10.1016/j.tim.2009.04.003. Review.


The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation.

Yu C, Zavaljevski N, Desai V, Johnson S, Stevens FJ, Reifman J.

BMC Bioinformatics. 2008 Jan 25;9:52. doi: 10.1186/1471-2105-9-52.


The Gene Ontology (GO) project in 2006.

Gene Ontology Consortium..

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D322-6.


On ontologies for biologists: the Gene Ontology--untangling the web.

Ashburner M, Lewis S.

Novartis Found Symp. 2002;247:66-80; discussion 80-3, 84-90, 244-52. Review.


Ontology annotation: mapping genomic regions to biological function.

Thomas PD, Mi H, Lewis S.

Curr Opin Chem Biol. 2007 Feb;11(1):4-11. Review.


The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology.

Camon E, Magrane M, Barrell D, Lee V, Dimmer E, Maslen J, Binns D, Harte N, Lopez R, Apweiler R.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D262-6.


Combining multisource information through functional-annotation-based weighting: gene function prediction in yeast.

Ray SS, Bandyopadhyay S, Pal SK.

IEEE Trans Biomed Eng. 2009 Feb;56(2):229-36. doi: 10.1109/TBME.2008.2005955.


annot8r: GO, EC and KEGG annotation of EST datasets.

Schmid R, Blaxter ML.

BMC Bioinformatics. 2008 Apr 9;9:180. doi: 10.1186/1471-2105-9-180.


Automated Gene Ontology annotation for anonymous sequence data.

Hennig S, Groth D, Lehrach H.

Nucleic Acids Res. 2003 Jul 1;31(13):3712-5.


SEMEDA: ontology based semantic integration of biological databases.

Köhler J, Philippi S, Lange M.

Bioinformatics. 2003 Dec 12;19(18):2420-7.


Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO).

Yeh I, Karp PD, Noy NF, Altman RB.

Bioinformatics. 2003 Jan 22;19(2):241-8.


The Gene Ontology (GO) project: structured vocabularies for molecular biology and their application to genome and expression analysis.

Blake JA, Harris MA.

Curr Protoc Bioinformatics. 2008 Sep;Chapter 7:Unit 7.2. doi: 10.1002/0471250953.bi0702s23.


Get ready to GO! A biologist's guide to the Gene Ontology.

Lomax J.

Brief Bioinform. 2005 Sep;6(3):298-304. Review.


Annotated expressed sequence tags (ESTs) from pre-smolt Atlantic salmon (Salmo salar) in a searchable data resource.

Adzhubei AA, Vlasova AV, Hagen-Larsen H, Ruden TA, Laerdahl JK, Høyheim B.

BMC Genomics. 2007 Jul 2;8:209.

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