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GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts

(2005) NUCLEIC ACIDS RESEARCH. 33(suppl. 1). p.D641-D646
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Abstract
Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. It follows that, improved annotation will allow better data mining of genomes, and more secure planning and design of experiments. The purpose of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for Arabidopsis nuclear genes and gene products, and to enter them into an added-value database. This re-annotation project is being performed exhaustively on every member of each gene family. Performing a family-wide annotation makes the task easier and more efficient than a gene-by-gene approach since many features obtained for one gene can be extrapolated to some or all the other genes of a family. A complete annotation procedure based on the most efficient prediction tools available is being used by 16 partner laboratories, each contributing annotated families from its field of expertise. A database, named GeneFarm, and an associated user-friendly interface to query the annotations have been developed. More than 3000 genes distributed over 300 families have been annotated and are available at http://genoplante-info.infobiogen.fr/Genefarm/. Furthermore, collaboration with the Swiss Institute of Bioinformatics is underway to integrate the GeneFarm data into the protein knowledgebase Swiss-Prot.
Keywords
MODEL, INFORMATION, UNIPROT, GENOME ANNOTATION, SECONDARY STRUCTURE PREDICTION, DATABASE, SEQUENCES, THALIANA, KNOWLEDGEBASE, IDENTIFICATION

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MLA
Aubourg, Sébastien, Véronique Brunaud, Clémence Bruyère, et al. “GeneFarm, Structural and Functional Annotation of Arabidopsis Gene and Protein Families by a Network of Experts.” NUCLEIC ACIDS RESEARCH 33.suppl. 1 (2005): D641–D646. Print.
APA
Aubourg, S., Brunaud, V., Bruyère, C., Cock, M., Cooke, R., Cottet, A., Couloux, A., et al. (2005). GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts. NUCLEIC ACIDS RESEARCH, 33(suppl. 1), D641–D646.
Chicago author-date
Aubourg, Sébastien, Véronique Brunaud, Clémence Bruyère, Mark Cock, Richard Cooke, Annick Cottet, Arnaud Couloux, et al. 2005. “GeneFarm, Structural and Functional Annotation of Arabidopsis Gene and Protein Families by a Network of Experts.” Nucleic Acids Research 33 (suppl. 1): D641–D646.
Chicago author-date (all authors)
Aubourg, Sébastien, Véronique Brunaud, Clémence Bruyère, Mark Cock, Richard Cooke, Annick Cottet, Arnaud Couloux, Patrice Déhais, Gilbert Deléage, Aymeric Duclert, Manuel Echeverria, Aimée Eschbach, Denis Falconet, Ghislain Filippi, Christine Gaspin, Christophe Geourjon, Jean-Michel Grienenberger, Guy Houlné, Elisabeth Jamet, Frédéric Lechauve, Olivier Leleu, Philippe Leroy, Régis Mache, Christian Meyer, Hafed Nedjari, Ioan Negrutiu, Valérie Orsini, Eric Peyretaillade, Cyril Pommier, Jeroen Raes, Jean-Loup Risler, Stéphane Rivière, Stephane Rombauts, Pierre Rouzé, Michel Schneider, Philippe Schwob, Ian Small, Ghislain Soumayet-Kampetenga, Darko Stankovski, Claire Toffano, Michael Tognolli, Michel Caboche, and Alain Lecharny. 2005. “GeneFarm, Structural and Functional Annotation of Arabidopsis Gene and Protein Families by a Network of Experts.” Nucleic Acids Research 33 (suppl. 1): D641–D646.
Vancouver
1.
Aubourg S, Brunaud V, Bruyère C, Cock M, Cooke R, Cottet A, et al. GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts. NUCLEIC ACIDS RESEARCH. 2005;33(suppl. 1):D641–D646.
IEEE
[1]
S. Aubourg et al., “GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts,” NUCLEIC ACIDS RESEARCH, vol. 33, no. suppl. 1, pp. D641–D646, 2005.
@article{331343,
  abstract     = {Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. It follows that, improved annotation will allow better data mining of genomes, and more secure planning and design of experiments. The purpose of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for Arabidopsis nuclear genes and gene products, and to enter them into an added-value database. This re-annotation project is being performed exhaustively on every member of each gene family. Performing a family-wide annotation makes the task easier and more efficient than a gene-by-gene approach since many features obtained for one gene can be extrapolated to some or all the other genes of a family. A complete annotation procedure based on the most efficient prediction tools available is being used by 16 partner laboratories, each contributing annotated families from its field of expertise. A database, named GeneFarm, and an associated user-friendly interface to query the annotations have been developed. More than 3000 genes distributed over 300 families have been annotated and are available at http://genoplante-info.infobiogen.fr/Genefarm/. Furthermore, collaboration with the Swiss Institute of Bioinformatics is underway to integrate the GeneFarm data into the protein knowledgebase Swiss-Prot.},
  author       = {Aubourg, Sébastien and Brunaud, Véronique and Bruyère, Clémence and Cock, Mark and Cooke, Richard and Cottet, Annick and Couloux, Arnaud and Déhais, Patrice and Deléage, Gilbert and Duclert, Aymeric and Echeverria, Manuel and Eschbach, Aimée and Falconet, Denis and Filippi, Ghislain and Gaspin, Christine and Geourjon, Christophe and Grienenberger, Jean-Michel and Houlné, Guy and Jamet, Elisabeth and Lechauve, Frédéric and Leleu, Olivier and Leroy, Philippe and Mache, Régis and Meyer, Christian and Nedjari, Hafed and Negrutiu, Ioan and Orsini, Valérie and Peyretaillade, Eric and Pommier, Cyril and Raes, Jeroen and Risler, Jean-Loup and Rivière, Stéphane and Rombauts, Stephane and Rouzé, Pierre and Schneider, Michel and Schwob, Philippe and Small, Ian and Soumayet-Kampetenga, Ghislain and Stankovski, Darko and Toffano, Claire and Tognolli, Michael and Caboche, Michel and Lecharny, Alain},
  issn         = {0305-1048},
  journal      = {NUCLEIC ACIDS RESEARCH},
  keywords     = {MODEL,INFORMATION,UNIPROT,GENOME ANNOTATION,SECONDARY STRUCTURE PREDICTION,DATABASE,SEQUENCES,THALIANA,KNOWLEDGEBASE,IDENTIFICATION},
  language     = {eng},
  number       = {suppl. 1},
  pages        = {D641--D646},
  title        = {GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts},
  url          = {http://dx.doi.org/10.1093/nar/gki115},
  volume       = {33},
  year         = {2005},
}

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