Ontology Resources - Revision history

Cooperl: /* Publications */

2011-07-18T23:25:59Z

Publications

Cooperl: moved Ontology resources to Ontology Resources

2011-07-18T23:25:25Z

moved Ontology resources to Ontology Resources

Cooperl at 23:21, 18 July 2011

2011-07-18T23:21:15Z

Cooperl: /* Publications */

2011-07-18T23:19:24Z

Publications

Cooperl: /* List of projects working on ontologies */

2011-07-18T23:07:01Z

List of projects working on ontologies

Shuly at 02:29, 4 December 2008

2008-12-04T02:29:17Z

Shuly: New page: ==Internet resources and textbooks== [http://www.mobot.org/MOBOT/Research/APweb/top/glossaryA_H.html Angiosperm Phylogeny Web Glossary] Esau K. 1977: Anatomy of Seed Plants, 2nd Edition...

2008-11-25T02:02:23Z

New page: ==Internet resources and textbooks== *[http://www.mobot.org/MOBOT/Research/APweb/top/glossaryA_H.html Angiosperm Phylogeny Web Glossary] *Esau K. 1977: Anatomy of Seed Plants, 2nd Edition...

New page

==Internet resources and textbooks==

*[http://www.mobot.org/MOBOT/Research/APweb/top/glossaryA_H.html Angiosperm Phylogeny Web Glossary]
*Esau K. 1977: Anatomy of Seed Plants, 2nd Edition. Wiley &Sons, Inc. ISBN:0471245208.
*Gifford E. M. and. Foster A. S, 1989. Morphology and evolution of vascular plants, 3rd Edition. W.H. Freeman & Co., New York. ISBN:0716719460.
*Kiesselbach, T. A. 1999: The Structure and Reproduction of Corn. 1999, 50th Anniversary Edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York. ISBN:0879695560.

==List of projects working on ontologies==

*Controlled Vocabulary and Ontologies for cereal plants [http://www.gramene.org/plant_ontology/ (Gramene)]
*Ontologies & Controlled Vocabularies for Gene Annotation of Arabidopsis [http://godot.ncgr.org/info/ontologies/ (TAIR)]
*Ontologies and Controlled Vocabularies for Maize [http://www.maizemap.org/ontology.htm (Maize Mapping Project)]
*Ontologies to describe biochemical charateristics. Developed by Gene Ontology Consortium [http://www.geneontology.org (GO)]
*Open Biological Ontology Foundry: an open community for sharing ontologies [http://obo.sf.net (OBO)]
*FAO's agricultural thesaurus [http://www.fao.org/agrovoc/ (AGROVOC)]
*Agricultural Ontology Service Project [http://www.fao.org/agris/aos/ (AOS)]

==Publications==

*Bioinformatics and its applications in plant biology. [[http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.arplant.56.032604.144103 Abstract]] [[http://arjournals.annualreviews.org/doi/full/10.1146/annurev.arplant.56.032604.144103 Full Text]] [http://arjournals.annualreviews.org/loi/arplant Annual Review of Plant Biology], 2006, Vol 57: 335-360. 

*Ontologies for data and knowledge sharing in biology: plant ROS signaling as a case study. [[http://www3.interscience.wiley.com/cgi-bin/abstract/112279243/ABSTRACT?CRETRY=1&SRETRY=0 Abstract]] [[http://www3.interscience.wiley.com/cgi-bin/fulltext/112279243/PDFSTART Full Text]] [http://www3.interscience.wiley.com/cgi-bin/jhome/34201 Bioessays], 2006, Vol28(2): 199-210. 

*An ontology for cell types. [[http://genomebiology.com/2005/6/2/R21/abstract/ Abstract]] [[http://genomebiology.com/2005/6/2/R21 Full Text]] [http://genomebiology.com/ Genome Biology], 2005, Vol 6: R21. 

*The Gene Ontology (GO) database and informatics resource. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14681407 Abstract]] [[http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D258 Full Text]] [http://nar.oupjournals.org/ Nucleic Acids Research], 2004, Vol 32: D258-D261.

*Bio-ontologies-fast and furious. [[http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v22/n6/full/nbt0604-773.html Full Text]] [http://www.nature.com/nbt/ Nature Biotechnology], 2004, Vol 22(6): 773-774.

*Functional annotation of the Arabidopsis genome using controlled vocabularies. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15173566 Abstract]] [[http://www.plantphysiol.org/cgi/content/full/135/2/745 Full Text]] [http://www.plantphysiol.org/ Plant Physiology], 2004, Vol 135(2): 745-755.

*Ontologies in biology: design, applications and future challenges. [[http://www.nature.com/cgi-taf/DynaPage.taf?file=/nrg/journal/v5/n3/abs/nrg1295_fs.html&dynoptions=doi1090299222 Abstract]] [[http://www.nature.com/cgi-taf/DynaPage.taf?file=/nrg/journal/v5/n3/full/nrg1295_fs.html&filetype=pdf Full Text]] [http://www.nature.com/reviews/ Nature Reviews Genetics] 2004, Vol 5(3): 213-222.

*Zea mays ontology - a database of international terms [http://www.sciencedirect.com/science/journal/13601385 Trends in Plant Science], 2003, 8(11): 517-520 [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14607095&dopt=Abstract Abstract]] [[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD1-49R5G9N-2&_user=492137&_coverDate=11%2F30%2F2003&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000022719&_version=1&_urlVersion=0&_userid=492137&md5=fd11e32826061af2d4c652ea08a3c3e7 Full Text]] 

*Ontologies: Formalising biological knowledge for bioinformatics. [[http://www3.interscience.wiley.com/cgi-bin/abstract/104524933/ABSTRACT Abstract]] [[http://www3.interscience.wiley.com/cgi-bin/fulltext/104524933/PDFSTART Full Text]] [http://www3.interscience.wiley.com/cgi-bin/jhome/34201 Bioessays], 2003, Vol 25(5): 501-506.

*Extension and Integration of the Gene Ontology (GO): Combining GO Vocabularies With External Vocabularies. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12466303&dopt=Abstract Abstract]] [[http://www.genome.org/cgi/content/full/12/12/1982 Full Text]] [http://www.genome.org/ Genome research] 2002,12: 1982-1991.

*The Plant OntologyTM Consortium and Plant Ontologies [[http://www3.interscience.wiley.com/cgi-bin/abstract/91016119/START Abstract]] [[http://www3.interscience.wiley.com/cgi-bin/fulltext/91016119/HTMLSTART Full Text]] [http://www3.interscience.wiley.com/cgi-bin/jtoc?Type=DD&ID=91016119 Comparative and Functional Genomics], 2002, Vol 3(2), 137-142.

*Gramene: development and integration of trait and gene ontologies for rice [[http://www3.interscience.wiley.com/cgi-bin/abstract/91016047/START Abstract]] [[http://www3.interscience.wiley.com/cgi-bin/fulltext/91016047/HTMLSTART Full Text]] [http://www3.interscience.wiley.com/cgi-bin/jtoc?Type=DD&ID=91016119 Comparative and Functional Genomics], 2002, Vol 3(2), 132-136.

*Creating the gene ontology resource: design and implementation. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11483584&dopt=Abstract Abstract]] [[http://www.genome.org/cgi/content/full/11/8/1425 Full Text]] [http://www.genome.org/ Genome Research], 2001, Vol 11(8), 1425-1433.

*Gene Ontology: tool for the unification of biology. [[http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10802651&dopt=Abstract Abstract]] [[http://www.nature.com/cgi-taf/DynaPage.taf?file=/ng/journal/v25/n1/full/ng0500_25.html Full Text]] [http://www.nature.com/ng/ Nature Genetics], 2000, 25: 25-29.

*On the representation of gene function in genetic databases. by Michael Ashburner, ISMB 1998. [[http://www.geneontology.org/doc/gene_ontology_discussion.html HTML]]

@@ Line 16: / Line 16: @@
 *Agricultural Ontology Service Project [http://www.fao.org/agris/aos/ (AOS)]
-==Publications==
+==Ontology Publications==
 See the page: [[Related_Publications]]
 [[Category:Publications]]

@@ Line 17: / Line 17: @@
 ==Publications==
+See the page: [[Related_Publications]]
 [[Category:Publications]]

← Older revision		Revision as of 23:19, 18 July 2011
Line 18:		Line 18:
	==Publications==		==Publications==

−	*Bioinformatics and its applications in plant biology. [[http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.arplant.56.032604.144103 Abstract]] [[http://arjournals.annualreviews.org/doi/full/10.1146/annurev.arplant.56.032604.144103 Full Text]]<br />[http://arjournals.annualreviews.org/loi/arplant Annual Review of Plant Biology], 2006, Vol 57: 335-360.<br />
−
−	*Ontologies for data and knowledge sharing in biology: plant ROS signaling as a case study. [[http://www3.interscience.wiley.com/cgi-bin/abstract/112279243/ABSTRACT?CRETRY=1&SRETRY=0 Abstract]] [[http://www3.interscience.wiley.com/cgi-bin/fulltext/112279243/PDFSTART Full Text]]<br />[http://www3.interscience.wiley.com/cgi-bin/jhome/34201 Bioessays], 2006, Vol28(2): 199-210.<br />
−
−	*An ontology for cell types. [[http://genomebiology.com/2005/6/2/R21/abstract/ Abstract]] [[http://genomebiology.com/2005/6/2/R21 Full Text]]<br />[http://genomebiology.com/ Genome Biology], 2005, Vol 6: R21.<br />
−
−	*The Gene Ontology (GO) database and informatics resource. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14681407 Abstract]] [[http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D258 Full Text]] <br />[http://nar.oupjournals.org/ Nucleic Acids Research], 2004, Vol 32: D258-D261.
−
−	*Bio-ontologies-fast and furious. [[http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v22/n6/full/nbt0604-773.html Full Text]] <br />[http://www.nature.com/nbt/ Nature Biotechnology], 2004, Vol 22(6): 773-774.
−
−	*Functional annotation of the Arabidopsis genome using controlled vocabularies. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15173566 Abstract]] [[http://www.plantphysiol.org/cgi/content/full/135/2/745 Full Text]] <br />[http://www.plantphysiol.org/ Plant Physiology], 2004, Vol 135(2): 745-755.
−
−	*Ontologies in biology: design, applications and future challenges. [[http://www.nature.com/cgi-taf/DynaPage.taf?file=/nrg/journal/v5/n3/abs/nrg1295_fs.html&dynoptions=doi1090299222 Abstract]] [[http://www.nature.com/cgi-taf/DynaPage.taf?file=/nrg/journal/v5/n3/full/nrg1295_fs.html&filetype=pdf Full Text]] <br />[http://www.nature.com/reviews/ Nature Reviews Genetics] 2004, Vol 5(3): 213-222.
−
−	*Zea mays ontology - a database of international terms<br />[http://www.sciencedirect.com/science/journal/13601385 Trends in Plant Science], 2003, 8(11): 517-520 [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14607095&dopt=Abstract Abstract]] [[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD1-49R5G9N-2&_user=492137&_coverDate=11%2F30%2F2003&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000022719&_version=1&_urlVersion=0&_userid=492137&md5=fd11e32826061af2d4c652ea08a3c3e7 Full Text]]<br />
−
−	*Ontologies: Formalising biological knowledge for bioinformatics. [[http://www3.interscience.wiley.com/cgi-bin/abstract/104524933/ABSTRACT Abstract]] [[http://www3.interscience.wiley.com/cgi-bin/fulltext/104524933/PDFSTART Full Text]] <br />[http://www3.interscience.wiley.com/cgi-bin/jhome/34201 Bioessays], 2003, Vol 25(5): 501-506.
−
−	*Extension and Integration of the Gene Ontology (GO): Combining GO Vocabularies With External Vocabularies. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12466303&dopt=Abstract Abstract]] [[http://www.genome.org/cgi/content/full/12/12/1982 Full Text]] <br />[http://www.genome.org/ Genome research] 2002,12: 1982-1991.
−
−	*The Plant Ontology<sup>TM</sup> Consortium and Plant Ontologies [[http://www3.interscience.wiley.com/cgi-bin/abstract/91016119/START Abstract]] [[http://www3.interscience.wiley.com/cgi-bin/fulltext/91016119/HTMLSTART Full Text]] <br />[http://www3.interscience.wiley.com/cgi-bin/jtoc?Type=DD&ID=91016119 Comparative and Functional Genomics], 2002, Vol 3(2), 137-142.
−
−	*Gramene: development and integration of trait and gene ontologies for rice [[http://www3.interscience.wiley.com/cgi-bin/abstract/91016047/START Abstract]] [[http://www3.interscience.wiley.com/cgi-bin/fulltext/91016047/HTMLSTART Full Text]] <br />[http://www3.interscience.wiley.com/cgi-bin/jtoc?Type=DD&ID=91016119 Comparative and Functional Genomics], 2002, Vol 3(2), 132-136.
−
−	*Creating the gene ontology resource: design and implementation. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11483584&dopt=Abstract Abstract]] [[http://www.genome.org/cgi/content/full/11/8/1425 Full Text]] <br />[http://www.genome.org/ Genome Research], 2001, Vol 11(8), 1425-1433.
−
−	*Gene Ontology: tool for the unification of biology. [[http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10802651&dopt=Abstract Abstract]] [[http://www.nature.com/cgi-taf/DynaPage.taf?file=/ng/journal/v25/n1/full/ng0500_25.html Full Text]] <br />[http://www.nature.com/ng/ Nature Genetics], 2000, 25: 25-29.
−
−	*On the representation of gene function in genetic databases. by Michael Ashburner, ISMB 1998. [[http://www.geneontology.org/doc/gene_ontology_discussion.html HTML]]

	[[Category:Publications]]		[[Category:Publications]]

← Older revision		Revision as of 02:29, 4 December 2008
Line 47:		Line 47:

	*On the representation of gene function in genetic databases. by Michael Ashburner, ISMB 1998. [[http://www.geneontology.org/doc/gene_ontology_discussion.html HTML]]		*On the representation of gene function in genetic databases. by Michael Ashburner, ISMB 1998. [[http://www.geneontology.org/doc/gene_ontology_discussion.html HTML]]
		+
		+	[[Category:Publications]]

← Older revision	Revision as of 23:25, 18 July 2011
(No difference)

@@ Line 6: / Line 6: @@
 *Kiesselbach, T. A. 1999: The Structure and Reproduction of Corn. 1999, 50th Anniversary Edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York. ISBN:0879695560.
-==List of projects working on ontologies==
+==List of other projects working on ontologies==
 *Controlled Vocabulary and Ontologies for cereal plants [http://www.gramene.org/plant_ontology/ (Gramene)]

Ontology Resources - Revision history

Cooperl: /* Publications */

Cooperl: moved Ontology resources to Ontology Resources

Cooperl at 23:21, 18 July 2011

Cooperl: /* Publications */

Cooperl: /* List of projects working on ontologies */

Shuly at 02:29, 4 December 2008

Shuly: New page: ==Internet resources and textbooks== *[http://www.mobot.org/MOBOT/Research/APweb/top/glossaryA_H.html Angiosperm Phylogeny Web Glossary] *Esau K. 1977: Anatomy of Seed Plants, 2nd Edition...

Shuly: New page: ==Internet resources and textbooks== [http://www.mobot.org/MOBOT/Research/APweb/top/glossaryA_H.html Angiosperm Phylogeny Web Glossary] Esau K. 1977: Anatomy of Seed Plants, 2nd Edition...