Difference between revisions of "Related Publications"
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| − | * | + | ==2013== |
| + | * Cooper and Walls et al (2013). '''[http://pcp.oxfordjournals.org/content/54/2/e1.full The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses]'''. Plant and Cell Physiology 54: e1–e1 | ||
| − | * | + | ==2012== |
| + | * Lens et al. 2012. '''An extension of the Plant Ontology project supporting wood anatomy and development research.''' [http://bio.kuleuven.be/sys/iawa/IAWA%20J%20pdf%27s/33.no1-4.2012/IAWA%20J%2033%20%282%29%20113-117.pdf IAWA Journal] 33: 113–117. | ||
| − | * | + | * Walls et al (2012). '''A plant disease extension of the Infectious Disease Ontology.''' In ''[http://ceur-ws.org/Vol-897/ Proceedings 3rd International Conference on Biomedical Ontology]'', Medical University of Graz, Graz, Austria. |
| − | * | + | * Arnaud, et al (2012). '''Towards a Reference Plant Trait Ontology for Modeling Knowledge of Plant Traits and Phenotypes'''. Proceedings of the International Conference on Knowledge Engineering and Ontology Development. Barcelona, Spain, pp 220–225 |
| − | * | + | * Walls et al (2012). '''Ontologies as integrative tools for plant science.''' [http://www.amjbot.org/content/99/8/1263 American Journal of Botany] 99: 1263 –1275 (special invited paper). |
| + | ==2008== | ||
| + | *Ilic et al, 2008. '''Plant Structure Ontology (PSO) - A morphological and anatomical ontology of flowering plants.''' In ''Anatomy Ontologies for Bioinformatics'', Springer, p 27-42. [http://www.springer.com/computer/computational+biology+and+bioinformatics/book/978-1-84628-884-5 Book] | ||
| + | |||
| + | *Avraham et al, 2008.'''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], 36(Database issue):D449-D454 | ||
| + | |||
| + | ==2007== | ||
| + | *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]] | ||
| + | |||
| + | *Ilic et al, 2007.'''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 /> | ||
| + | |||
| + | ==2006== | ||
| + | *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 /> | ||
| + | |||
| + | *Pujar et al, 2006.'''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 | ||
| + | |||
| + | ==2005== | ||
| + | *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 /> | ||
| + | |||
| + | *'''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 | ||
| + | |||
| + | *Relations in Biomedical Ontologies”, Genome Biology (2005), 6 (5), R46. [[http://genomebiology.com/2005/6/5/R46 Smith etal, 2005]] | ||
| + | |||
| + | ==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. | ||
| Line 17: | Line 44: | ||
*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. | ||
| − | *Zea mays ontology | + | ==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 /> | ||
*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. | ||
| + | *Zea mays ontology – a database of international terms<br /> 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]] | ||
| + | |||
| + | ==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. | ||
| − | *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 | + | '''*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 | + | *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. |
| − | * | + | *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]] |
| − | * | + | ==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. | ||
| − | * | + | ==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. | ||
| − | [[ | + | *On the representation of gene function in genetic databases. by Michael Ashburner, ISMB 1998. [[http://www.geneontology.org/doc/gene_ontology_discussion.html HTML]] |
| − | |||
Latest revision as of 17:43, 12 July 2014
2013
- Cooper and Walls et al (2013). The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses. Plant and Cell Physiology 54: e1–e1
2012
- Lens et al. 2012. An extension of the Plant Ontology project supporting wood anatomy and development research. IAWA Journal 33: 113–117.
- Walls et al (2012). A plant disease extension of the Infectious Disease Ontology. In Proceedings 3rd International Conference on Biomedical Ontology, Medical University of Graz, Graz, Austria.
- Arnaud, et al (2012). Towards a Reference Plant Trait Ontology for Modeling Knowledge of Plant Traits and Phenotypes. Proceedings of the International Conference on Knowledge Engineering and Ontology Development. Barcelona, Spain, pp 220–225
- Walls et al (2012). Ontologies as integrative tools for plant science. American Journal of Botany 99: 1263 –1275 (special invited paper).
2008
- Ilic et al, 2008. Plant Structure Ontology (PSO) - A morphological and anatomical ontology of flowering plants. In Anatomy Ontologies for Bioinformatics, Springer, p 27-42. Book
- Avraham et al, 2008.The Plant Ontology Database: a community resource for plant structure and development stages controlled vocabulary and annotations. Abstract Full Text]
Nucleic Acid Research, 36(Database issue):D449-D454
2007
- The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration”, Nature Biotechnology,25 (11), November 2007, 1251 -1255. [Smith et al, 2007]
- Ilic et al, 2007.The Plant Structure Ontology, a unified vocabulary of anatomy and morphology of a flowering plant. [Abstract] [Full Text]
Plant Physiology, 2007, 143: 587-599
2006
- Bioinformatics and its applications in plant biology. [Abstract] [Full Text]
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. [Abstract] [Full Text]
Bioessays, 2006, Vol28(2): 199-210.
- Pujar et al, 2006.Whole-plant growth stage ontology for angiosperms and its application in plant biology. [Abstract] [Full Text]
Plant Physiology, 2006, 142: 414-428
2005
- An ontology for cell types. [Abstract] [Full Text]
Genome Biology, 2005, Vol 6: R21.
- 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
- Relations in Biomedical Ontologies”, Genome Biology (2005), 6 (5), R46. [Smith etal, 2005]
2004
- 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.
2003
- Zea mays ontology - a database of international terms
Trends in Plant Science, 2003, 8(11): 517-520 [Abstract] [Full Text]
- Ontologies: Formalising biological knowledge for bioinformatics. [Abstract] [Full Text]
Bioessays, 2003, Vol 25(5): 501-506.
- Zea mays ontology – a database of international terms
Trends in Plant Science, 2003, 8(11): 517-520 [Abstract]
2002
- 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.
- Surrounding Space: On the Ontology of Organism-Environment Relations. Theory in Biosciences 120:2 (2002), 139–162 [Smith and Varzi, 2002]
2001
- Creating the gene ontology resource: design and implementation. [Abstract] [Full Text]
Genome Research, 2001, Vol 11(8), 1425-1433.
2000 and Older
- 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]
