Difference between revisions of "Related Publications"

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==2013==
 
==2013==
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Cooper L, Walls RL, Elser J, Gandolfo MA, Stevenson DW, Smith B, Preece J, Athreya B, Mungall CJ, Rensing S, et al (2013) The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses. Plant and Cell Physiology 54: e1–e1
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* 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
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==2012==
 
==2012==
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*
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* 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.
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*'''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).
 
  
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*'''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.
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* 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.
  
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* Lens, F., L. Cooper, M.A. Gandolfo, A. Groover, P. Jaiswal, B. Lachenbruch, R. Spicer, et al. 2012. An extension of the Plant Ontology project supporting wood anatomy and development research. IAWA Journal 33: 113–117.
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* 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
  
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* Arnaud E, Cooper L, Shrestha R, Menda N, Nelson RT, Matteis L, Skofic M, Bastow R, Jaiswal P, Mueller L, 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
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* 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==
 
==2008==
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*'''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]
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*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]
  
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*'''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
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*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==
 
==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]]
 
*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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*'''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 />
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*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==
 
==2006==
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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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*'''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
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*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==
 
==2005==

Latest revision as of 00:43, 13 July 2014

2013

2012

  • Lens et al. 2012. An extension of the Plant Ontology project supporting wood anatomy and development research. IAWA Journal 33: 113–117.
  • 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

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

2005

  • Relations in Biomedical Ontologies”, Genome Biology (2005), 6 (5), R46. [Smith etal, 2005]

2004

2003

  • 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.

  • 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]
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