Difference between revisions of "Related Publications"

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*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 />
 
*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 />
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==2008==
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*The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration”, Nature Biotechnology,25 (11), November 2007, 1251 -1255. [[http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf Smith et al, 2007]]
 +
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*Relations in Biomedical Ontologies”, Genome Biology (2005), 6 (5), R46. [[http://genomebiology.com/2005/6/5/R46 Smith etal, 2005]]
 +
 +
*Plant Structure Ontology (PSO) - A morphological and anatomical ontology of flowering plants. In ''Anatomy Ontologies for Bioinformatics'', Springer, 2008, p 27-42. [[http://www.springer.com/computer/computational+biology+and+bioinformatics/book/978-1-84628-884-5 Book]]<br />
 +
 +
*The Plant Ontology Database: a community resource for plant structure and development stages controlled vocabulary and annotations. [[http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D449 Abstract]] [[http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D449 Full Text]]<br />[http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D449 Nucleic Acid Research], 2008, 36(Database issue):D449-D454<br />
 +
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*The Plant Structure Ontology, a unified vocabulary of anatomy and morphology of a flowering plant. [[http://www.plantphysiol.org/cgi/content/abstract/143/2/587 Abstract]] [[http://www.plantphysiol.org/cgi/content/full/143/2/587 Full Text]]<br />[http://www.plantphysiol.org/ Plant Physiology], 2007, 143: 587-599 <br />
 +
 +
*Whole-plant growth stage ontology for angiosperms and its application in plant biology. [[http://www.plantphysiol.org/cgi/content/abstract/142/2/414 Abstract]] [[http://www.plantphysiol.org/cgi/content/full/142/2/414 Full Text]]<br />[http://www.plantphysiol.org/ Plant Physiology], 2006, 142: 414-428
 +
 +
*Plant Ontology (PO): a controlled vocabulary of plant structures and growth stages. [[http://www.hindawi.com/GetArticle.aspx?doi=10.1002/cfg.496&e=CTA Abstract]] [[http://www.hindawi.com/GetPDF.aspx?doi=10.1002/cfg.496 Full Text]]<br />[http://www3.interscience.wiley.com/cgi-bin/jhome/77002016 Comparative and Functional Genomics], 2005, Volume 6(7-8), 388 - 397
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 +
*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.
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*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.
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*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 />
 
*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 />
  
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==2004==
 
*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.
 
*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.
  
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*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.
 
*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.
  
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==2003==
 
*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 />
 
*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.
 
*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.
  
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==2002==
 
*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.
 
*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.
  
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*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.
 
*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.
  
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*Surrounding Space: On the Ontology of Organism-Environment Relations.  Theory in Biosciences 120:2 (2002), 139–162 [[http://ontology.buffalo.edu/smith/articles/Surrounding_space.pdf Smith and Varzi, 2002]]
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==2001==
 
*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.
 
*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.
  
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==2000 and Older==
 
*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.
 
*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]]
 
*On the representation of gene function in genetic databases. by Michael Ashburner, ISMB 1998. [[http://www.geneontology.org/doc/gene_ontology_discussion.html HTML]]
  
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*Surrounding Space: On the Ontology of Organism-Environment Relations.  Theory in Biosciences 120:2 (2002), 139–162 [[http://ontology.buffalo.edu/smith/articles/Surrounding_space.pdf Smith and Varzi, 2002]]
 
−
 
−
*The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration”, Nature Biotechnology,25 (11), November 2007, 1251 -1255. [[http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf Smith et al, 2007]]
 
−
 
−
*Relations in Biomedical Ontologies”, Genome Biology (2005), 6 (5), R46. [[http://genomebiology.com/2005/6/5/R46 Smith etal, 2005]]
 
−
 
−
*Plant Structure Ontology (PSO) - A morphological and anatomical ontology of flowering plants. In ''Anatomy Ontologies for Bioinformatics'', Springer, 2008, p 27-42. [[http://www.springer.com/computer/computational+biology+and+bioinformatics/book/978-1-84628-884-5 Book]]<br />
 
−
 
−
*The Plant Ontology Database: a community resource for plant structure and development stages controlled vocabulary and annotations. [[http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D449 Abstract]] [[http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D449 Full Text]]<br />[http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D449 Nucleic Acid Research], 2008, 36(Database issue):D449-D454<br />
 
−
 
−
*The Plant Structure Ontology, a unified vocabulary of anatomy and morphology of a flowering plant. [[http://www.plantphysiol.org/cgi/content/abstract/143/2/587 Abstract]] [[http://www.plantphysiol.org/cgi/content/full/143/2/587 Full Text]]<br />[http://www.plantphysiol.org/ Plant Physiology], 2007, 143: 587-599 <br />
 
−
 
−
*Whole-plant growth stage ontology for angiosperms and its application in plant biology. [[http://www.plantphysiol.org/cgi/content/abstract/142/2/414 Abstract]] [[http://www.plantphysiol.org/cgi/content/full/142/2/414 Full Text]]<br />[http://www.plantphysiol.org/ Plant Physiology], 2006, 142: 414-428
 
−
 
−
*Plant Ontology (PO): a controlled vocabulary of plant structures and growth stages. [[http://www.hindawi.com/GetArticle.aspx?doi=10.1002/cfg.496&e=CTA Abstract]] [[http://www.hindawi.com/GetPDF.aspx?doi=10.1002/cfg.496 Full Text]]<br />[http://www3.interscience.wiley.com/cgi-bin/jhome/77002016 Comparative and Functional Genomics], 2005, Volume 6(7-8), 388 - 397
 
−
 
−
*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.
 
*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.

Revision as of 04:39, 19 July 2011


2006

  • Ontologies for data and knowledge sharing in biology: plant ROS signaling as a case study. [Abstract] [Full Text]
    Bioessays, 2006, Vol28(2): 199-210.


2008

  • The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration”, Nature Biotechnology,25 (11), November 2007, 1251 -1255. [Smith et al, 2007]
  • Relations in Biomedical Ontologies”, Genome Biology (2005), 6 (5), R46. [Smith etal, 2005]
  • Plant Structure Ontology (PSO) - A morphological and anatomical ontology of flowering plants. In Anatomy Ontologies for Bioinformatics, Springer, 2008, p 27-42. [Book]
  • The Plant Ontology Database: a community resource for plant structure and development stages controlled vocabulary and annotations. [Abstract] [Full Text]
    Nucleic Acid Research, 2008, 36(Database issue):D449-D454


2005

2004

2003

2002

  • Extension and Integration of the Gene Ontology (GO): Combining GO Vocabularies With External Vocabularies. [Abstract] [Full Text]
    Genome research 2002,12: 1982-1991.
  • Surrounding Space: On the Ontology of Organism-Environment Relations. Theory in Biosciences 120:2 (2002), 139–162 [Smith and Varzi, 2002]

2001

2000 and Older

  • On the representation of gene function in genetic databases. by Michael Ashburner, ISMB 1998. [HTML]


  • Zea mays ontology – a database of international terms
    Trends in Plant Science, 2003, 8(11): 517-520 [Abstract]
  • Extension and Integration of the Gene Ontology (GO): Combining GO Vocabularies With External Vocabularies. [Abstract] [Full Text]
    Genome research 2002,12: 1982-1991.
  • On the representation of gene function in genetic databases. by Michael Ashburner, ISMB 1998. [HTML]

Publications

Plant Structure Ontology (PSO) - A morphological and anatomical ontology of flowering plants. In Anatomy Ontologies for Bioinformatics, Springer, 2008, p 27-42. [Book]

The Plant Ontology Database: a community resource for plant structure and development stages controlled vocabulary and annotations. [Abstract] [Full Text] Nucleic Acid Research, 2008, 36(Database issue):D449-D454

The Plant Structure Ontology, a unified vocabulary of anatomy and morphology of a flowering plant. [Abstract] [Full Text] Plant Physiology, 2007, 143: 587-599

Whole-plant growth stage ontology for angiosperms and its application in plant biology. [Abstract] [Full Text] Plant Physiology, 2006, 142: 414-428

Plant Ontology (PO): a controlled vocabulary of plant structures and growth stages. [Abstract] [Full Text] Comparative and Functional Genomics, 2005, Volume 6(7-8), 388 - 397

The Gene Ontology (GO) database and informatics resource. [Abstract] [Full Text] Nucleic Acids Research, 2004, Vol 32: D258-D261.

Bio-ontologies-fast and furious. [Full Text] Nature Biotechnology, 2004, Vol 22(6): 773-774.

Functional annotation of the Arabidopsis genome using controlled vocabularies. [Abstract] [Full Text] Plant Physiology, 2004, Vol 135(2): 745-755.

Ontologies in biology: design, applications and future challenges. [Abstract] [Full Text] Nature Reviews Genetics 2004, Vol 5(3): 213-222.

Zea mays ontology – a database of international terms Trends in Plant Science, 2003, 8(11): 517-520 [Abstract]

Ontologies: Formalising biological knowledge for bioinformatics. [Abstract] [Full Text] Bioessays, 2003, Vol 25(5): 501-506.

Extension and Integration of the Gene Ontology (GO): Combining GO Vocabularies With External Vocabularies. [Abstract] [Full Text] Genome research 2002,12: 1982-1991.

The Plant OntologyTM Consortium and Plant Ontologies [Abstract] [Full Text] Comparative and Functional Genomics, 2002, Vol 3(2), 137-142

Gramene: development and integration of trait and gene ontologies for rice [Abstract] [Full Text] Comparative and Functional Genomics, 2002, Vol 3(2), 132-136

Creating the gene ontology resource: design and implementation. [Abstract] [Full Text] Genome Research, 2001, Vol 11(8), 1425-1433

Gene Ontology: tool for the unification of biology. [Abstract] [Full Text] Nature Genetics, 2000, 25: 25-29

On the representation of gene function in genetic databases. by Michael Ashburner, ISMB 1998. [HTML]

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