Generic Model Organism Database (English Wikipedia)

Noronha, Antonio; Cui, Changhai; Harris, Robert Adron; Crabbe, John C. (2014). Neurobiology of Alcohol Dependence. Elsevier. ISBN 978-0-12-407155-1.

cshlp.org

genome.cshlp.org

Tassy, Olivier; Dauga, Delphine; Daian, Fabrice; Sobral, Daniel; Robin, François; Khoueiry, Pierre; Salgado, David; Fox, Vanessa; Caillol, Danièle; Schiappa, Renaud; Laporte, Baptiste; Rios, Anne; Luxardi, Guillaume; Kusakabe, Takehiro; Joly, Jean-Stéphane; Darras, Sébastien; Christiaen, Lionel; Contensin, Magali; Auger, Hélène; Lamy, Clément; Hudson, Clare; Rothbächer, Ute; Gilchrist, Michael J.; Makabe, Kazuhiro W.; Hotta, Kohji; Fujiwara, Shigeki; Satoh, Nori; Satou, Yutaka; Lemaire, Patrick (1 October 2010). "The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program". Genome Research. 20 (10): 1459–1468. doi:10.1101/gr.108175.110. ISSN 1088-9051. PMC 2945195. PMID 20647237.

doi.org

Christopher J. Mungall; David B. Emmert; The FlyBase Consortium (2007). "A Chado case study: an ontology-based modular schema for representing genome-associated biological information". Bioinformatics. 23 (13): i337–i346. doi:10.1093/bioinformatics/btm189. PMID 17646315.
Stein LD; Mungall C; Shu S; Caudy M; Mangone M; Day A; Nickerson E; Stajich JE; Harris TW; Arva A; Lewis S. (2002). "The generic genome browser: a building block for a model organism system database". Genome Res. 12 (10): 1599–610. doi:10.1101/gr.403602. PMC 187535. PMID 12368253.
Afgan, E.; Baker, D.; van den Beek, M.; Blankenberg, D.; Bouvier, D.; Čech, M.; Chilton, J.; Clements, D.; Coraor, N.; Eberhard, C.; Grüning, B.; Guerler, A.; Hillman-Jackson, J.; Von Kuster, G.; Rasche, E.; Soranzo, N.; Turaga, N.; Taylor, J.; Nekrutenko, A.; Goecks, J. (8 July 2016). "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update". Nucleic Acids Research. 44 (W1): W3–W10. doi:10.1093/nar/gkw343. PMC 4987906. PMID 27137889.
Cantarel, Brandi L.; Korf, Ian; Robb, Sofia M. C.; Parra, Genis; Ross, Eric; Moore, Barry; Holt, Carson; Sánchez Alvarado, Alejandro; Yandell, Mark (January 2008). "MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes". Genome Research. 18: 188–196. doi:10.1101/gr.6743907. PMC 2134774.
Tassy, Olivier; Dauga, Delphine; Daian, Fabrice; Sobral, Daniel; Robin, François; Khoueiry, Pierre; Salgado, David; Fox, Vanessa; Caillol, Danièle; Schiappa, Renaud; Laporte, Baptiste; Rios, Anne; Luxardi, Guillaume; Kusakabe, Takehiro; Joly, Jean-Stéphane; Darras, Sébastien; Christiaen, Lionel; Contensin, Magali; Auger, Hélène; Lamy, Clément; Hudson, Clare; Rothbächer, Ute; Gilchrist, Michael J.; Makabe, Kazuhiro W.; Hotta, Kohji; Fujiwara, Shigeki; Satoh, Nori; Satou, Yutaka; Lemaire, Patrick (1 October 2010). "The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program". Genome Research. 20 (10): 1459–1468. doi:10.1101/gr.108175.110. ISSN 1088-9051. PMC 2945195. PMID 20647237.
Weems, Danforth; Miller, Neil; Garcia-Hernandez, Margarita; Huala, Eva; Rhee, Seung Y. (2004). "Design, Implementation and Maintenance of a Model Organism Database for Arabidopsis thaliana". Comparative and Functional Genomics. 5 (4): 362–369. doi:10.1002/cfg.408. ISSN 1531-6912. PMC 2447457. PMID 18629167.
Wang L; Wang S; Li Y; Paradesi MS; Brown SJ. (2007). "BeetleBase: the model organism database for Tribolium castaneum". Nucleic Acids Res. 35 (Database issue): D476–9. doi:10.1093/nar/gkl776. PMC 1669707. PMID 17090595.
Chisholm RL; Gaudet P; Just EM; Pilcher KE; Fey P; Merchant SN; Kibbe WA. (2006). "dictyBase, the model organism database for Dictyostelium discoideum". Nucleic Acids Res. 34 (Database issue): D423–7. doi:10.1093/nar/gkj090. PMC 1347453. PMID 16381903.
Arnaiz O; Cain S; Cohen J; Sperling L. (2007). "ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data". Nucleic Acids Res. 35 (Database issue): D439–44. doi:10.1093/nar/gkl777. PMC 1669747. PMID 17142227.
Colbourne JK; Singan VR; Gilbert DG. (2005). "wFleaBase: the Daphnia genome database". BMC Bioinformatics. 6: 45. doi:10.1186/1471-2105-6-45. PMC 555599. PMID 15752432.

genomearchitect.readthedocs.io

"Apollo — Apollo 2.7.0 documentation". genomearchitect.readthedocs.io.

gmod.org

"GMOD Components - GMOD". gmod.org.
"Chado - Getting Started - GMOD". gmod.org.
"XORT - GMOD". gmod.org.
"GMODTools - GMOD". gmod.org.
"Tripal". gmod.org.
"Apollo - GMOD". gmod.org.
"GBrowse - GMOD". gmod.org.
"JBrowse - GMOD". gmod.org.
"GBrowse syn - GMOD". gmod.org.
"CMap - GMOD". gmod.org.
"Textpresso". gmod.org.
Cantarel, Brandi L.; Korf, Ian; Robb, Sofia M. C.; Parra, Genis; Ross, Eric; Moore, Barry; Holt, Carson; Sánchez Alvarado, Alejandro; Yandell, Mark (January 2008). "MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes". Genome Research. 18: 188–196. doi:10.1101/gr.6743907. PMC 2134774.

ksu.edu

bioinformatics.ksu.edu

"BeetleBase". www.bioinformatics.ksu.edu/Be. Archived from the original on 13 July 2006.

nih.gov

pubmed.ncbi.nlm.nih.gov

Christopher J. Mungall; David B. Emmert; The FlyBase Consortium (2007). "A Chado case study: an ontology-based modular schema for representing genome-associated biological information". Bioinformatics. 23 (13): i337–i346. doi:10.1093/bioinformatics/btm189. PMID 17646315.
Stein LD; Mungall C; Shu S; Caudy M; Mangone M; Day A; Nickerson E; Stajich JE; Harris TW; Arva A; Lewis S. (2002). "The generic genome browser: a building block for a model organism system database". Genome Res. 12 (10): 1599–610. doi:10.1101/gr.403602. PMC 187535. PMID 12368253.
Afgan, E.; Baker, D.; van den Beek, M.; Blankenberg, D.; Bouvier, D.; Čech, M.; Chilton, J.; Clements, D.; Coraor, N.; Eberhard, C.; Grüning, B.; Guerler, A.; Hillman-Jackson, J.; Von Kuster, G.; Rasche, E.; Soranzo, N.; Turaga, N.; Taylor, J.; Nekrutenko, A.; Goecks, J. (8 July 2016). "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update". Nucleic Acids Research. 44 (W1): W3–W10. doi:10.1093/nar/gkw343. PMC 4987906. PMID 27137889.
Tassy, Olivier; Dauga, Delphine; Daian, Fabrice; Sobral, Daniel; Robin, François; Khoueiry, Pierre; Salgado, David; Fox, Vanessa; Caillol, Danièle; Schiappa, Renaud; Laporte, Baptiste; Rios, Anne; Luxardi, Guillaume; Kusakabe, Takehiro; Joly, Jean-Stéphane; Darras, Sébastien; Christiaen, Lionel; Contensin, Magali; Auger, Hélène; Lamy, Clément; Hudson, Clare; Rothbächer, Ute; Gilchrist, Michael J.; Makabe, Kazuhiro W.; Hotta, Kohji; Fujiwara, Shigeki; Satoh, Nori; Satou, Yutaka; Lemaire, Patrick (1 October 2010). "The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program". Genome Research. 20 (10): 1459–1468. doi:10.1101/gr.108175.110. ISSN 1088-9051. PMC 2945195. PMID 20647237.
Weems, Danforth; Miller, Neil; Garcia-Hernandez, Margarita; Huala, Eva; Rhee, Seung Y. (2004). "Design, Implementation and Maintenance of a Model Organism Database for Arabidopsis thaliana". Comparative and Functional Genomics. 5 (4): 362–369. doi:10.1002/cfg.408. ISSN 1531-6912. PMC 2447457. PMID 18629167.
Wang L; Wang S; Li Y; Paradesi MS; Brown SJ. (2007). "BeetleBase: the model organism database for Tribolium castaneum". Nucleic Acids Res. 35 (Database issue): D476–9. doi:10.1093/nar/gkl776. PMC 1669707. PMID 17090595.
Chisholm RL; Gaudet P; Just EM; Pilcher KE; Fey P; Merchant SN; Kibbe WA. (2006). "dictyBase, the model organism database for Dictyostelium discoideum". Nucleic Acids Res. 34 (Database issue): D423–7. doi:10.1093/nar/gkj090. PMC 1347453. PMID 16381903.
Arnaiz O; Cain S; Cohen J; Sperling L. (2007). "ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data". Nucleic Acids Res. 35 (Database issue): D439–44. doi:10.1093/nar/gkl777. PMC 1669747. PMID 17142227.
Colbourne JK; Singan VR; Gilbert DG. (2005). "wFleaBase: the Daphnia genome database". BMC Bioinformatics. 6: 45. doi:10.1186/1471-2105-6-45. PMC 555599. PMID 15752432.

ncbi.nlm.nih.gov

Stein LD; Mungall C; Shu S; Caudy M; Mangone M; Day A; Nickerson E; Stajich JE; Harris TW; Arva A; Lewis S. (2002). "The generic genome browser: a building block for a model organism system database". Genome Res. 12 (10): 1599–610. doi:10.1101/gr.403602. PMC 187535. PMID 12368253.
Afgan, E.; Baker, D.; van den Beek, M.; Blankenberg, D.; Bouvier, D.; Čech, M.; Chilton, J.; Clements, D.; Coraor, N.; Eberhard, C.; Grüning, B.; Guerler, A.; Hillman-Jackson, J.; Von Kuster, G.; Rasche, E.; Soranzo, N.; Turaga, N.; Taylor, J.; Nekrutenko, A.; Goecks, J. (8 July 2016). "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update". Nucleic Acids Research. 44 (W1): W3–W10. doi:10.1093/nar/gkw343. PMC 4987906. PMID 27137889.
Cantarel, Brandi L.; Korf, Ian; Robb, Sofia M. C.; Parra, Genis; Ross, Eric; Moore, Barry; Holt, Carson; Sánchez Alvarado, Alejandro; Yandell, Mark (January 2008). "MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes". Genome Research. 18: 188–196. doi:10.1101/gr.6743907. PMC 2134774.
Tassy, Olivier; Dauga, Delphine; Daian, Fabrice; Sobral, Daniel; Robin, François; Khoueiry, Pierre; Salgado, David; Fox, Vanessa; Caillol, Danièle; Schiappa, Renaud; Laporte, Baptiste; Rios, Anne; Luxardi, Guillaume; Kusakabe, Takehiro; Joly, Jean-Stéphane; Darras, Sébastien; Christiaen, Lionel; Contensin, Magali; Auger, Hélène; Lamy, Clément; Hudson, Clare; Rothbächer, Ute; Gilchrist, Michael J.; Makabe, Kazuhiro W.; Hotta, Kohji; Fujiwara, Shigeki; Satoh, Nori; Satou, Yutaka; Lemaire, Patrick (1 October 2010). "The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program". Genome Research. 20 (10): 1459–1468. doi:10.1101/gr.108175.110. ISSN 1088-9051. PMC 2945195. PMID 20647237.
Weems, Danforth; Miller, Neil; Garcia-Hernandez, Margarita; Huala, Eva; Rhee, Seung Y. (2004). "Design, Implementation and Maintenance of a Model Organism Database for Arabidopsis thaliana". Comparative and Functional Genomics. 5 (4): 362–369. doi:10.1002/cfg.408. ISSN 1531-6912. PMC 2447457. PMID 18629167.
Wang L; Wang S; Li Y; Paradesi MS; Brown SJ. (2007). "BeetleBase: the model organism database for Tribolium castaneum". Nucleic Acids Res. 35 (Database issue): D476–9. doi:10.1093/nar/gkl776. PMC 1669707. PMID 17090595.
Chisholm RL; Gaudet P; Just EM; Pilcher KE; Fey P; Merchant SN; Kibbe WA. (2006). "dictyBase, the model organism database for Dictyostelium discoideum". Nucleic Acids Res. 34 (Database issue): D423–7. doi:10.1093/nar/gkj090. PMC 1347453. PMID 16381903.
Arnaiz O; Cain S; Cohen J; Sperling L. (2007). "ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data". Nucleic Acids Res. 35 (Database issue): D439–44. doi:10.1093/nar/gkl777. PMC 1669747. PMID 17142227.
Colbourne JK; Singan VR; Gilbert DG. (2005). "wFleaBase: the Daphnia genome database". BMC Bioinformatics. 6: 45. doi:10.1186/1471-2105-6-45. PMC 555599. PMID 15752432.

web.archive.org

"BeetleBase". www.bioinformatics.ksu.edu/Be. Archived from the original on 13 July 2006.

worldcat.org

Tassy, Olivier; Dauga, Delphine; Daian, Fabrice; Sobral, Daniel; Robin, François; Khoueiry, Pierre; Salgado, David; Fox, Vanessa; Caillol, Danièle; Schiappa, Renaud; Laporte, Baptiste; Rios, Anne; Luxardi, Guillaume; Kusakabe, Takehiro; Joly, Jean-Stéphane; Darras, Sébastien; Christiaen, Lionel; Contensin, Magali; Auger, Hélène; Lamy, Clément; Hudson, Clare; Rothbächer, Ute; Gilchrist, Michael J.; Makabe, Kazuhiro W.; Hotta, Kohji; Fujiwara, Shigeki; Satoh, Nori; Satou, Yutaka; Lemaire, Patrick (1 October 2010). "The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program". Genome Research. 20 (10): 1459–1468. doi:10.1101/gr.108175.110. ISSN 1088-9051. PMC 2945195. PMID 20647237.
Weems, Danforth; Miller, Neil; Garcia-Hernandez, Margarita; Huala, Eva; Rhee, Seung Y. (2004). "Design, Implementation and Maintenance of a Model Organism Database for Arabidopsis thaliana". Comparative and Functional Genomics. 5 (4): 362–369. doi:10.1002/cfg.408. ISSN 1531-6912. PMC 2447457. PMID 18629167.