Gene Ontology - A Bibliography

Publications on GO by members of the GO Consortium  |  Annotations using GO  |  Prediction of GO terms  |  GO Tools  |  Other publications with substantive discussion of GO  |  Publications on other OBO ontologies  | 


Publications on GO by members of the GO Consortium

  • Ashburner M. 1998. On the representation of gene function in genetic databases. [HTML]

  • Ashburner M, Lewis SE. 2002. On ontologies for biologists: the Gene Ontology - uncoupling the web. In: In Silico Biology. Novartis Found Symp 247: 66-80; discussion 80-3, 84-90, 244-52. [ABSTRACT]

  • Blake, J.A. and Harris, M. 2003. The Gene Ontology Project: Structured vocabularies for molecular biology and their application to genome and expression analysis. In A.D. Baxevanis, D.B. Davison, R. Page, G. Stormo and L. Stein (eds.), Current Protocols in Bioinformatics. Wiley and Sons, Inc., New York.

  • Hill, D.P., Blake, J.A., Richardson, J.E. and Ringwald, M. 2002. Extension and Integration of the Gene Ontology (GO): Combining GO vocabularies with external vocabularies. Genome Res 12: 1982-1991. [ABSTRACT] [FULL TEXT]

  • The Gene Ontology Consortium. 2000. Gene Ontology: tool for the unification of biology. Nat Genet 25: 25-29. [PubMed][PDF]

  • The Gene Ontology Consortium. 2001. Creating the gene ontology resource: design and implementation. Genome Res 11: 1425-1433. [ABSTRACT]    [FULL TEXT]
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Annotations using GO

  • Drosophila genomic: Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, et al. 2000. The genome sequence of Drosophila melanogaster. Science 287: 2185-2195. [ABSTRACT]

  • Mouse hepatic and hippocampal genes: Berger A, Mutch DM, Bruce German J, Roberts MA. Dietary effects of arachidonate-rich fungal oil and fish oil on murine hepatic and hippocampal gene expression. Lipids Health Dis 1: 2. [ABSTRACT]

  • Parasites: Berriman M, Aslett M, Ivens A, Hall N. 2001. Parasites are GO. Trends Parasitol 17: 463-464. [ABSTRACT]

  • Mouse cDNAs: Bono H, Kasukawa T, Furuno M, Hayashizaki Y, Okazaki Y. 2002. FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones. Nucleic Acids Res 30: 116-118. [ABSTRACT]

  • Mouse transcripts: Bono H, Yagi K, Kasukawa T, Nikaido I, Tominaga N, Miki R, Mizuno Y, Tomaru Y, Goto H, Nitanda H, Shimizu D, Makino H, Morita T, Fujiyama J, Sakai T, Shimoji T, Hume DA, Hayashizaki Y, Okazaki Y. 2003. Systematic Expression Profiling of the Mouse Transcriptome Using RIKEN cDNA Microarrays. Genome Res 13: 1318-1323. [ABSTRACT]

  • Swiss-Prot/TrEMBL:Camon EB, Barrell D, Brooksbank C, Magrane M, Apweiler R. 2003. The Gene Ontology Annotation (GOA) Project - Application of GO in SWISS-PROT, TrEMBL and InterPro Compar Funct Genom 4: 71-74. Conference Review. [ABSTRACT]

  • Swiss-Prot/TrEMBL:Camon E, Magrane M, Barrell D, Binns D, Fleischmann W, Kersey P, Mulder N, Oinn T, Maslen J, Cox A, Apweiler R. 2003. The Gene Ontology Annotation (GOA) Project: Implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Res 13: 662-672. [ABSTRACT]

  • Human odontogenic tumors: Carinci F, Francioso F, Piattelli A, Rubini C, Fioroni M, Evangelisti R, Arcelli D, Tosi L, Pezzetti F, Carinci P, Volinia S. 2003. Genetic expression profiling of six odontogenic tumors. J Dent Res 82: 551-557. [ABSTRACT]

  • Plasmodium yoelii: Carlton et al. 2002. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature 419: 512-519. [ABSTRACT]

  • Mouse lung transcripts Clerch LB, Baras AS, Massaro GD, Hoffman EP, Massaro D. 2003. DNA Microarray Analysis of Neonatal Mouse Lung Connects Regulation of KDR with Dexamethasone-Induced Inhibition of Alveolar Formation. Am J Physiol Lung Cell Mol Physiol [Epub ahead of print] [ABSTRACT]

  • Human breast cancer cellsCunliffe HE, Ringner M, Bilke S, Walker RL, Cheung JM, Chen Y, Meltzer PS. 2003. Cancer Res 63: 7158-7166. [ABSTRACT]

  • Vertebrate nuclear proteins: Dellaire G, Farrall R, Bickmore WA. 2003. The Nuclear Protein Database (NPD): sub-nuclear localisation and functional annotation of the nuclear proteome. Nucleic Acids Res 31: 328-330. [ABSTRACT]

  • Saccharomyces: 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. 2002. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res 30: 69-72. [ABSTRACT]

  • Mouse dendritic cells: Edwards AD, Chaussabel D, Tomlinson S, Schulz O, Sher A, Reis E Sousa C. 2003. Relationships Among Murine CD11c(high) Dendritic Cell Subsets as Revealed by Baseline Gene Expression Patterns. J Immunol 171: 47-60. [ABSTRACT]

  • Paracoccidioides brasiliensis:Felipe MS et al. 2003. Transcriptome characterization of the dimorphic and pathogenic fungus Paracoccidioides brasiliensis by EST analysis. Yeast 20: 263-271. [ABSTRACT]

  • Human endothelial cells: Gallagher PG, Bao Y, Serrano SM, Kamiguti AS, Theakston RD, Fox JW. 2003. Use of microarrays for investigating the subtoxic effects of snake venoms: insights into venom-induced apoptosis in human umbilical vein endothelial cells. Toxicon 41: 429-440. [ABSTRACT]

  • RESID: Garavelli JS. 2003. The RESID Database of Protein Modifications: 2003 developments. Nucleic Acids Res 31: 499-501. [ABSTRACT]

  • Plasmodium falciparum: Gardner MJ et al. 2002. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419: 498-511. [ABSTRACT]

  • Plasmodium falciparum, chromosomes 2, 10, 11 and 14: Gardner MJ et al. 2002. Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14. Nature 419: 531-534. [ABSTRACT]

  • Dictyostelium chromosome 2 genomic: Glockner G, Eichinger L, Szafranski K, Pachebat JA, Bankier AT, Dear PH, Lehmann R, Baumgart C. et al. 2002. Sequence and analysis of chromosome 2 of Dictyostelium discoideum. Nature 418: 79-85. [ABSTRACT]

  • Rice genomic: Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100. [ABSTRACT]

  • Schizophyllum commune: Guettler S, Jackson EN, Lucchese SA, Honaas L, Green A, Hittinger CT, Tian Y, Lilly WW, Gathman AC. 2003. ESTs from the basidiomycete Schizophyllum commune grown on nitrogen-replete and nitrogen-limited media. Fungal Genet Biol 39: 191-198. [ABSTRACT]

  • TIGRFAMs protein families: Haft DH, Selengut JD, White O. 2003. The TIGRFAMs database of protein families. Nucleic Acids Res 31: 371-373. [ABSTRACT]

  • Plasmodium falciparum, chromosomes 1, 3-9 and 13: Hall N et al. 2002. Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13. Nature 419: 527-531. [ABSTRACT]

  • Livestock (cattle & swine) ESTs: Harhay GP, Keele JW. 2003. Positional candidate gene selection from livestock EST databases using Gene Ontology. Bioinformatics 19: 249-255. [ABSTRACT]

  • Human pseudogenes: Harrison PM, Hegyi H, Balasubramanian S, Luscombe NM, Bertone P, Echols N, Johnson T, Gerstein M. 2002. Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res 12: 272-280. [ABSTRACT]

  • Mouse: Hill DP, Davis AP, Richardson JE, Corradi JP, Ringwald M, Eppig JT, Blake JA. 2001. Program description: Strategies for biological annotation of mammalian systems: implementing gene ontologies in mouse genome informatics. Genomics 74: 121-128. [ABSTRACT]

  • Human GPCRs: Hodges PE, Carrico PM, Hogan JD, O'Neill KE, Owen JJ, Mangan M, Davis BP, Brooks JE, Garrels JI. 2002. Annotating the human proteome: the Human Proteome Survey Database (HumanPSD) and an in-depth target database for G protein-coupled receptors (GPCR-PD) from Incyte Genomics. Nucleic Acids Res 30: 137-141. [ABSTRACT]

  • Anopheles gambiae: Holt RA et al. 2002. The genome sequence of the malaria mosquito Anopheles gambiae. Science 298: 129-149. [ABSTRACT]

  • Plasmodium falciparum, chromosome 12: Hyman et al. 2002. Sequence of Plasmodium falciparum chromosome 12. Nature 419: 534-537. [ABSTRACT]

  • Plasmodium falciparum transcripts: Isokpehi RD, Hide WA. 2003. Integrative analysis of intraerythrocytic differentially expressed transcripts yields novel insights into the biology of Plasmodium falciparum. Malar J [epub ahead of print] [ABSTRACT]

  • Mouse proteome: Kanapin A, Batalov S, Davis MJ, Gough J, Grimmond S, Kawaji H, Magrane M, Matsuda H, Schonbach C, Teasdale RD, Yuan Z. 2003. Mouse proteome analysis. Genome Res 13: 1335-1344. [ABSTRACT]

  • Mouse cDNAs: Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y, et al. 2001. Functional annotation of a full-length mouse cDNA collection. Nature 409: 685-690. [ABSTRACT]

  • Mouse proteome (lung & liver): Kislinger T, Rahman K, Radulovic D, Cox B, Rossant J, Emili A. 2003. PRISM, a Generic Large Scale Proteomic Investigation Strategy for Mammals. Mol Cell Proteomics 2: 96-106. [ABSTRACT]

  • Affymetrix probes: Liu G, Loraine AE, Shigeta R, Cline M, Cheng J, Valmeekam V, Sun S, Kulp D, Siani-Rose MA. 2003. NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res 31: 82-86. [ABSTRACT]

  • Human fibrosarcoma cells: Liu YG, Gano J, Huang R, Lin Y, Wang SM, Huang RP. 2002. Analysis of gene expression in Egr-1 transfected human fibrosarcoma cells. J Surg Oncol 80: 190-196. [ABSTRACT]

  • Mouse tumors: Martinez-Chantar ML, Corrales FJ, Martinez-Cruz LA, Garcia-Trevijano ER, Huang ZZ, Chen L, Kanel G, Avila MA, MatoJ M, Lu SC. 2002. Spontaneous oxidative stress and liver tumors in mice lacking methionine adenosyltransferase 1A. FASEB J 16: 1292-1294. [ABSTRACT]

  • Human pancreatic carcinoma cells: Mazzolini G, Narvaiza I, Martinez-Cruz LA, Arina A, Barajas M, Galofre JC, Qian C, Mato JM, Prieto J, Melero I. 2003. Pancreatic cancer escape variants that evade immunogene therapy through loss of sensitivity to IFNgamma-induced apoptosis. Gene Ther 10: 1067-1078. [ABSTRACT]

  • Meloidogyne incognita: McCarter JP, Mitreva MD, Martin J, Dante M, Wylie T, Rao U, Pape D, Bowers Y, Thiesing B, Murphy CV, Kloek AP, Chiapelli BJ, Clifton SW, Bird DM, Waterston RH. 2003. Analysis and functional classification of transcripts from the nematode Meloidogyne incognita. Genome Biol 4: R26. [ABSTRACT] [FULL TEXT]

  • Plasmodium vivax ESTs: Merino EF, Fernandez-Becerra C, Madeira AM, Machado AL, Durham A, Gruber A, Hall N, Del Portillo HA. 2003. Pilot survey of expressed sequence tags (ESTs) from the asexual blood stages of Plasmodium vivax in human patients. Malar J 2: 21, [ABSTRACT]

  • Amblyomma variegatum ESTs: Nene V, Lee D, Quackenbush J, Skilton R, Mwaura S, Gardner MJ, Bishop R. 2002. AvGI, an index of genes transcribed in the salivary glands of the ixodid tick Amblyomma variegatum. Int J Parasitol 32: 1447. [ABSTRACT]

  • Canine ESTs: Palmer LE, O'Shaughnessy AL, Preston RR, Santos L, Balija VS, Nascimento LU, Zutavern TL, Henthorn PS, Hannon GJ, McCombie WR. 2003. A survey of canine expressed sequence tags and a display of their annotations through a flexible web-based interface. J Hered 94: 15-22. [ABSTRACT]

  • Drosophila genes during aging: Pletcher SD, Macdonald SJ, Marguerie R, Certa U, Stearns SC, Goldstein DB, Partridge L. 2002. Genome-Wide Transcript Profiles in Aging and Calorically Restricted Drosophila melanogaster. Curr Biol 12: 712-723. [ABSTRACT]

  • Arabidopsis thaliana: Rhee SY et al. 2003. The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res 31: 224-228. [ABSTRACT]

  • Drosophila embryos: Simin K, Scuderi A, Reamey J, Dunn D, Weiss R, Metherall JE, Letsou A. 2002. Profiling patterned transcripts in Drosophila embryos. Genome Res 12:1040-1047. [ABSTRACT]

  • Bovine ESTs: Sonstegard TS, Capuco AV, White J, Van Tassell CP, Connor EE, Cho J, Sultana R, Shade L, Wray JE, Wells KD, Quackenbush J. 2002. Analysis of bovine mammary gland EST and functional annotation of the Bos taurus gene index. Mamm Genome 13:373-379. [ABSTRACT]

  • Danio rerio: Sprague J, Clements D, Conlin T, Edwards P, Frazer K, Schaper K, Segerdell E, Song P, Sprunger B, Westerfield M. 2003. The Zebrafish Information Network (ZFIN): the zebrafish model organism database. Nucleic Acids Res 31: 241-243. [ABSTRACT]

  • PANTHER (human, Drosophila): Thomas PD, Kejariwal A, Campbell MJ, Mi H, Diemer K, Guo N, Ladunga I, Ulitsky-Lazareva B, Muruganujan A, Rabkin S, Vandergriff JA, Doremieux O. 2003. PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucleic Acids Res 31: 334-341. [ABSTRACT]

  • Human skeletal muscle transcripts: Toppo S, Cannata N, Fontana P, Romualdi C, Laveder P, Bertocco E, Lanfranchi G, Valle G. 2003. TRAIT (TRAnscript Integrated Table): a knowledgebase of human skeletal muscle transcripts. Bioinformatics 19: 661-662. [ABSTRACT]

  • Honey bee ESTs: Whitfield CW, Band MR, Bonaldo MF, Kumar CG, Liu L, Pardinas JR, Robertson HM, Soares MB, Robinson GE. 2002. Annotated expressed sequence tags and cDNA microarrays for studies of brain and behavior in the honey bee. Genome Res 12: 555-566. [ABSTRACT]

  • Schizosaccharomyces pombe: Wood V, Bahler J. 2002. How to get the best from fission yeast genome data. Compar Funct Genom 3: 282-288. [ABSTRACT] [FULL TEXT]

  • Human mRNAs during decay: Yang E, Van Nimwegen E, Zavolan M, Rajewsky N, Schroeder M, Magnasco M, Darnell JE Jr. 2003. Decay Rates of Human mRNAs: Correlation With Functional Characteristics and Sequence Attributes. Genome Res 13: 1863-1872. [ABSTRACT]

  • Rice genomic: Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79-92. [ABSTRACT]

  • Anopheles gambiae: Zdobnov et al. 2002. Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science 298: 149-159. [ABSTRACT]

  • Plant alternatively spliced genes: Zhou Y, Zhou C, Ye L, Dong J, Xu H, Cai L, Zhang L, Wei L. 2003. Database and analyses of known alternatively spliced genes in plants. Genomics 82: 584-595. [ABSTRACT]

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Prediction of GO terms

  • Blaschke C, Valencia A. 2003. Automatic classification of protein functions from the literature. Compar Funct Genom 4: 75-79. Conference Review. [ABSTRACT]

  • Chiang JH, Yu HC. 2003. MeKE: discovering the functions of gene products from biomedical literature via sentence alignment. Bioinformatics 19: 1417-1422. [ABSTRACT]

  • Chou KC, Cai YD. 2003. A new hybrid approach to predict subcellular localization of proteins by incorporating gene ontology. Biochem Biophys Res Commun 311: 743-747. [ABSTRACT]

  • Draghici S, Khatri P, Bhavsar P, Shah A, Krawetz SA, Tainsky MA. 2003. Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. Nucleic Acids Res 31: 3775-3781. [ABSTRACT]

  • Enright AJ, van Dongen S, Ouzounis C. 2002. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30: 1575-1585. [ABSTRACT]

  • Hennig S, Groth D, Lehrach H. 2003. Automated Gene Ontology annotation for anonymous sequence data. Nucleic Acids Res 31: 3712-3715. [ABSTRACT]

  • Hvidsten TR, Komorowski J, Sandvik AK, Laegreid A. 2002. Predicting gene function from gene expressions and ontologies. Pac Symp Biocomput: 299-310. [ABSTRACT]

  • Hvidsten TR, Laegreid A, Komorowski J. 2003. Learning rule-based models of biological process from gene expression time profiles using Gene Ontology. Bioinformatics 19: 1116-1123. [ABSTRACT]

  • Jensen LJ, Gupta R, Staerfeldt HH, Brunak S. 2003. Prediction of human protein function according to Gene Ontology categories. Bioinformatics 19: 635-642. [ABSTRACT]

  • Jenssen TK, Laegreid A, Komorowski J, Hovig E. 2001. A literature network of human genes for high-throughput analysis of gene expression. Nat Genet 28: 21-28. [ABSTRACT]

  • King OD, Foulger, RE, Dwight SS, White JV, and Roth FP. 2003. Predicting gene function from patterns of annotation. Genome Res 13: 896-904. [ABSTRACT]

  • Lagreid A, Hvidsten TR, Midelfart H, Komorowski J, Sandvik AK. 2003. Predicting Gene Ontology Biological Process From Temporal Gene Expression Patterns. Genome Res 13: 965-979. [ABSTRACT]

  • Letovsky S, Kasif S. 2003. Predicting protein function from protein/protein interaction data: a probabilistic approach. Bioinformatics 19: I197-I204. [ABSTRACT]

  • Pouliot Y, Gao J, Su QJ, Liu GG, Ling XB. 2001. DIAN: a novel algorithm for genome ontological classification. Genome Res 11: 1766-1779. [ABSTRACT]

  • Raychaudhuri S, Altman RB. 2003. A literature-based method for assessing the functional coherence of a gene group. Bioinformatics 19: 396-401. [ABSTRACT]

  • Raychaudhuri S, Chang JT, Sutphin PD, Altman RB. 2002. Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature. Genome Res 12: 203-214. [ABSTRACT]

  • Schug J, Diskin S, Mazzarelli J, Brunk BP, Stoeckert CJ Jr. 2002. Predicting Gene Ontology Functions from ProDom and CDD Protein Domains. Genome Res 12: 648-655. [ABSTRACT]

  • Troyanskaya OG, Dolinski K, Owen AB, Altman RB, Botstein D. 2003. A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci U S A 100: 8348-8353. [ABSTRACT]

  • Xie H, Wasserman A, Levine Z, Novik A, Grebinskiy V, Shoshan A, Mintz. 2002. Large scale protein annotation through Gene Ontology. Genome Res 12: 785-794. [ABSTRACT]

  • Zehetner G. 2003. OntoBlast function: from sequence similarities directly to potential functional annotations by ontology terms. Nucleic Acids Res 31: 3799-3803. [ABSTRACT]
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Publications on GO tools

  • Berriz GF, White JV, King OD, Roth FP. 2003. GoFish finds genes with combinations of Gene Ontology attributes. Bioinformatics 19: 788-789. [ABSTRACT]

  • Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. 2003. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4: P3. [ABSTRACT]

  • Doniger, SW, Salomonis N, Dahlquist, KD, Vranizan K, Lawlor, SC and Conklin, BR. 2003 MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol 4: R7. [ABSTRACT] [FULL TEXT]

  • Draghici S, Khatri P, Martins RP, Ostermeier GC, Krawetz SA. 2003. Global profiling of gene expression. Genomics 81: 98-104. [ABSTRACT]

  • Draghici S, Khatri P, Shah A, Tainsky MA. 2003. Assessing the functional bias of commercial microarrays using the onto-compare database. Biotechniques Mar;Suppl: 55-61. [ABSTRACT]

  • Herrero J, Al-Shahrour F, Diaz-Uriarte R, Mateos A, Vaquerizas JM, Santoyo J, Dopazo J. 2003. GEPAS: a web-based resource for microarray gene expression data analysis. Nucleic Acids Res 31: 3461-3467. [ABSTRACT]

  • Khatri P, Draghici S, Ostermeier GC, Krawetz SA. 2002. Profiling gene expression using onto-express. Genomics 79: 266-270. [ABSTRACT]

  • Martinez-Cruz LA, Rubio A, Martinez-Chantar ML, Labarga A, Barrio I, Podhorski A, Segura V, Sevilla Campo JL, Avila MA, Mato JM. 2003. GARBAN: genomic analysis and rapid biological annotation of cDNA microarray and proteomic data. Bioinformatics 19: 2158-2160. ] [ABSTRACT]

  • Tanoue J, Yoshikawa M, Uemura S. 2002. The GeneAround GO viewer. Bioinformatics 18: 1705-1706. [ABSTRACT]

  • Zhong S, Li C, Wong WH. 2003. ChipInfo: software for extracting gene annotation and gene ontology information for microarray analysis. Nucleic Acids Res 31: 3483-3486. [ABSTRACT]
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Other publications with substantive discussion of GO

  • Badea L. 2003. Functional discrimination of gene expression patterns in terms of the Gene Ontology. Pac Symp Biocomput 8: 565-576. [ABSTRACT]

  • Bard J. 2003. Ontologies: Formalising biological knowledge for bioinformatics. Bioessays 25: 501-506. [ABSTRACT]

  • Bernardi L, Rojas I, van der Vet P. 2003. The ESF programme on Integrated Approaches to Functional Genomics. Workshop on Ontology for Biology. Compar Funct Genom 4: 68-70. Conference Report. [CFG site (no abstract)]

  • Biswas M, O'Rourke JF, Camon E, Fraser G, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva E, Mittard V, Mulder N, Phan I, Servant F, Apweiler R. 2002. Applications of InterPro in protein annotation and genome analysis. Brief Bioinform 3: 285-295. [ABSTRACT]

  • Bodenreider O, Mitchell JA, McCray AT. 2002. Evaluation of the UMLS as a Terminology and Knowledge Resource for Biomedical Informatics. Proc AMIA Symp 2002: 61-65. [ABSTRACT]

  • Bono H, Nikaido I, Kasukawa T, Hayashizaki Y, Okazaki Y. 2003. Comprehensive analysis of the mouse metabolome based on the transcriptome. Genome Res 13: 1345-1349. [ABSTRACT]

  • Brenner S. 2002. Life sentences: Ontology recapitulates philology. Genome Biol 3: comment1006.1-comment1006.2. [PubMed] [HTML] [Only available to subscribers]

  • Cornell M, Paton NW, Hedeler C, Kirby P, Delneri D, Hayes A, Oliver SG. 2003. GIMS: an integrated data storage and analysis environment for genomic and functional data. Yeast 20: 1291-1306. [ABSTRACT]

  • Harris MA, Parkinson H. 2003. Standards and ontologies for functional genomics: towards unified ontologies for biology and biomedicine. Compar Funct Genom 4: 116-120. Conference Report. [CFG site (no abstract)]

  • Juty NS, Spence HD, Hotz HR, Tang H, Goryanin I, Hodgman TC. 2001. Simultaneous modelling of metabolic, genetic and product-interaction networks. Brief Bioinform 2: 223-232. [ABSTRACT]

  • King OD, Lee JC, Dudley AM, Janse DM, Church GM, Roth FP. 2003. Predicting phenotype from patterns of annotation. Bioinformatics 19: I183-I189. [ABSTRACT]

  • Kohler J, Schulze-Kremer S. 2002. The semantic metadatabase (SEMEDA): ontology based integration of federated molecular biological data sources. In Silico Biol 2: 219-231. [ABSTRACT]

  • Lambrix P, Edberg A. 2003. Evaluation of ontology merging tools in bioinformatics. Pac Symp Biocomput 8: 589-600. [ABSTRACT]

  • Lambrix P, Habbouche M, Perez M. 2003. Evaluation of ontology development tools for bioinformatics. Bioinformatics 19: 1564-1571. [ABSTRACT]

  • Lan N, Montelione GT, Gerstein M. 2003. Ontologies for proteomics: towards a systematic definition of structure and function that scales to the genome level. Curr Opin Chem Biol 7: 44-54. [ABSTRACT]

  • Lewis S, Ashburner M, Reese MG. 2000. Annotating eukaryote genomes. Curr Opin Struct Biol 10: 349-354. [ABSTRACT]

  • Lord PW, Stevens RD, Brass A, Goble CA. 2003. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 19: 1275-1283. [ABSTRACT]

  • Lord PW, Stevens RD, Brass A, Goble CA. 2003. Semantic similarity measures as tools for exploring the Gene Ontology. Pac Symp Biocomput 8: 601-612. [ABSTRACT]

  • McConnell P, Johnson K, Lin S. 2002. Applications of Tree-Maps to hierarchical biological data. Bioinformatics 18: 1278-1279. [ABSTRACT]

  • McCray AT. 2003. An upper-level ontology for the biomedical domain. Compar Funct Genom 4: 80-84. Conference Review. [ABSTRACT]

  • McCray AT, Browne AC, Bodenreider O. 2002. The lexical properties of the gene ontology. Proc AMIA Symp 2002: 504-508. [ABSTRACT]

  • Michalickova K, Bader GD, Dumontier M, Lieu HC, Betel D, Isserlin R, Hogue CW. 2002. SeqHound: biological sequence and structure database as a platform for bioinformatics research. BMC Bioinformatics 3: 32. [ABSTRACT]

  • Nembaware V, Crum K, Kelso J, Seoighe C. 2002. Impact of the presence of paralogs on sequence divergence in a set of mouse-human orthologs. Genome Res 12: 1370-1376. [ABSTRACT]

  • Perez-Iratxeta C, Bork P, Andrade, MA. 2002. Association of genes to genetically inherited diseases using data mining. Nat Genet 31: 316-319. [ABSTRACT]

  • Rector AL, Rogers J, Roberts A, Wroe C. 2002. Scale and CONTEXT: Issues in Ontologies to Link Health- and Bio-Informatics. Proc AMIA Symp 2002: 642-646. [ABSTRACT]

  • Rison SC, Hodgman TC, Thornton JM. 2000. Comparison of functional annotation schemes for genomes. Funct Integr Genomics 1: 56-69. [ABSTRACT]

  • Sarkar IN, Cantor MN, Gelman R, Hartel F, Lussier YA. 2003. Linking biomedical language information and knowledge resources in the 21st century: GO and UMLS. Pac Symp Biocomput 8: 427-450. [ABSTRACT]

  • Shakhnovich BE, Dokholyan NV, DeLisi C, Shakhnovich EI. 2003. Functional fingerprints of folds: evidence for correlated structure-function evolution. J Mol Biol 326: 1-9. [ABSTRACT]

  • Stevens R, Goble CA, Bechhofer S. 2000. Ontology-based knowledge representation for bioinformatics. Brief Bioinform 1: 398-414. Review. [ABSTRACT]

  • Stevens R, Wroe C, Bechhofer S, Lord P, Rector A, Goble C. 2003. Building ontologies in DAML + OIL. Compar Funct Genom 4: 133-141. Conference Review. [ABSTRACT]

  • Tulipano PK, Millar W, Cimino JJ. 2003. Linking molecular imaging terminology to the Gene Ontology (GO). Pac Symp Biocomput 8: 613-623. [ABSTRACT]

  • Williams J, Andersen W. 2003. Bringing ontology to the Gene Ontology. Compar Funct Genom 4: 90-93. Conference Review. [ABSTRACT]

  • Wroe CJ, Stevens R, Goble CA, Ashburner M. 2003. A methodology to migrate the Gene Ontology to a description logic environment using DAML+OIL. Pac Symp Biocomput 8: 624-635. [ABSTRACT]

  • Yeh I, Karp PD, Noy NF, Altman RB. 2003. Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO). Bioinformatics 19: 241-248. [ABSTRACT]

  • Zeeberg BR, Feng W, Wang G, Wang MD, Fojo AT, Sunshine M, Narasimhan S, Kane DW, Reinhold WC, Lababidi S, Bussey KJ, Riss J, Barrett JC, Weinstein JN. 2003. GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol 4: R28. [ABSTRACT] [FULL TEXT]

  • Zhang J, Carey V, Gentleman R. 2003. An extensible application for assembling annotation for genomic data. Bioinformatics 19: 155-156. [ABSTRACT]
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Publications on other OBO ontologies

  • Bard J, Winter R. 2001. Ontologies of developmental anatomy: their current and future roles. Briefings Bioinformatics 2: 289-299. [ABSTRACT]

  • Hunter A, Kaufman MH, McKay A, Baldock R, Simmen MW, Bard JB. 2003. An ontology of human developmental anatomy. J Anat 203: 347-355. [ABSTRACT]

  • Jaiswal P, Ware D, Ni J, Chang K, Zhao W, Schmidt S, Pan X, Clark K, Teytelman L, Cartinhour S, Stein L, McCouch S. 2002. Gramene: development and integration of trait and gene ontologies for rice. Compar Funct Genom 3: 132-136. Conference Review. [ABSTRACT]

  • Lee RYN, Sternberg PW. 2003. Building a cell and anatomy ontology of Caenorhabditis elegans. Compar Funct Genom 4: 121-126. Conference Review. [ABSTRACT]

  • The Plant OntologyTM Consortium. 2002. The Plant OntologyTM Consortium and Plant Ontologies. Compar Funct Genom 3: 137-142. Conference Review. [ABSTRACT]

  • Stoeckert CJ, Parkinson H. 2003. The MGED ontology: a framework for describing functional genomics experiments. Compar Funct Genom 4: 127-132. Conference Review. [ABSTRACT]

  • 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. 2002. Gramene, a tool for grass genomics. Plant Physiol 130: 1606-1613. [ABSTRACT]

Please send corrections and additions to Michael Ashburner ( or to the GO mailing list.

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