Difference between revisions of "Plant Ontology Citations"

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=2015=
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- Lobet G, Pound MP, Diener J, Pradal C, Draye X, Godin C, Javaux M, Leitner D, Meunier F, Nacry P, et al (2015) Root System Markup Language: Toward a Unified Root Architecture Description Language. Plant Physiology 167: 617–627  [http://www.plantphysiol.org/content/167/3/617.full]
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- Berardini, TZ, L Reiser, D Li, Y Mezheritsky, R Muller.  Genesis, 2015. The Arabidopsis Information Resource: Making and mining the 'gold standard' annotated reference plant genome. [http://onlinelibrary.wiley.com/doi/10.1002/dvg.22877/abstract]
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Abstract: The Arabidopsis Information Resource (TAIR) is a continuously updated, online database of genetic and molecular biology data for the model plant Arabidopsis thaliana that provides a global research community with centralized access to data for over 30,000 ...
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- Takehisa, H., Y Sato, B Antonio, Y Nagamura - Rice, 2015. Coexpression Network Analysis of Macronutrient Deficiency Response Genes in Rice (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4513034/)
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Background: Macronutrients are pivotal elements for proper plant growth and development. Although extensive gene expression profiling revealed a large number of genes differentially expressed under various nutrient deprivation, characterization of these genes ...
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[https://scholar.google.com/scholar?as_ylo=2015&hl=en&as_sdt=5,38&cites=2387136611136667159&scipsc= Google Scholar 2015]
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=2014=
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[https://scholar.google.com/scholar?oi=bibs&hl=en&cites=2387136611136667159&as_sdt=5&as_ylo=2014&as_yhi=2014 Google Scholar 2014 citations "The plant ontology as a tool for comparative plant anatomy and genomic analyses"]
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=2013=
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* Cobb J, DeClerck G, Greenberg A, Clark R, McCouch S. 2013. Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype–phenotype relationships and its relevance to crop improvement. Theoretical and Applied Genetics 126, 867–887. [http://link.springer.com/article/10.1007/s00122-013-2066-0 abstract]
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=2012=
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* Lai L, Liberzon A, Hennessey J, Jiang G, Qi J, Mesirov JP, Ge SX (2012) AraPath: a knowledgebase for pathway analysis in Arabidopsis. Bioinformatics 28: 2291–2292. [http://bioinformatics.oxfordjournals.org/content/28/17/2291.abstract abstract]
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*Deans, Andrew R., Matthew J. Yoder, and James P. Balhoff. “Time to Change How We Describe Biodiversity.” Trends in Ecology & Evolution 27, no. 2 (February 1, 2012): 78–84. [http://www.cell.com/trends/ecology-evolution/fulltext/S0169-5347(11)00330-2 link to full text]
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* McCouch, S. R., McNally, K. L., Wang, W. and Sackville Hamilton, R. (2012). Genomics of gene banks: A case study in rice. Am J of Bot., 99, 407 -423. [http://www.amjbot.org/content/99/2/407.full?sid=43c212cf-bc81-4272-8888-f779555fbd81 Link to full text]
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=2011=
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*Iida K, Kawaguchi S, Kobayashi N, Yoshida Y, Ishii M, Harada E, Hanada K, Matsui A, Okamoto M, Ishida J, et al (2011) ARTADE2DB: Improved Statistical Inferences for Arabidopsis Gene Functions and Structure Predictions by Dynamic Structure-Based Dynamic Expression (DSDE) Analyses. Plant and Cell Physiology 52: 254–264 [http://pcp.oxfordjournals.org/content/52/2/254.full#F6 link]
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*Kumar, T. K. A., Crow, J. A., Wennblom, T. J., Abril, M., Letcher, P. M., Blackwell, M., Roberson, R. W., and McLaughlin, D. J. (2011). An ontology of fungal subcellular traits. American Journal of Botany, 98, 1504 -1510. [http://www.amjbot.org/content/98/9/1504.abstract Kumar et al, 2011]  
 
*Kumar, T. K. A., Crow, J. A., Wennblom, T. J., Abril, M., Letcher, P. M., Blackwell, M., Roberson, R. W., and McLaughlin, D. J. (2011). An ontology of fungal subcellular traits. American Journal of Botany, 98, 1504 -1510. [http://www.amjbot.org/content/98/9/1504.abstract Kumar et al, 2011]  
  
* Qiuling He, Arthur Berg, Yao Li, C. Eduardo Vallejos and Rongling Wu. 2010. Mapping genes for plant structure, development and evolution: functional mapping meets ontology. Trends in Genetics 26(1): 39-46 [http://www.cell.com/trends/genetics/abstract/S0168-9525(09)00232-7 Abstract] [http://dx.doi.org/10.1016/j.tig.2009.11.004 Full Text]
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*Schaeffer, M. L., Harper, L. C., Gardiner, J. M., Andorf, C. M., Campbell, D. A., Cannon, E. K. S., Sen, T. Z., and Lawrence, C. J. (2011). MaizeGDB: curation and outreach go hand-in-hand. Database, 2011.
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*Kobayashi N, Ishii M, Takahashi S, Mochizuki Y, Matsushima A, Toyoda T (2011) Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases. Nucleic Acids Research 39: W533 –W540
  
*Clark, J. I., Brooksbank, C., and Lomax, J. (2005). It's All GO for Plant Scientists. Plant Physiol., 138, 1268-1279. (this does not actually cite the PO)
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=2010=
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*Hong, C. (2010). Competency evaluation of plant character ontologies against domain literature. Journal of the American Society for Information Science & Technology, 61(6), 1144-1165. doi:10.1002/asi.21325
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*Qiuling He, Arthur Berg, Yao Li, C. Eduardo Vallejos and Rongling Wu. 2010. Mapping genes for plant structure, development and evolution: functional mapping meets ontology. Trends in Genetics 26(1): 39-46 [http://www.cell.com/trends/genetics/abstract/S0168-9525(09)00232-7 Abstract] [http://dx.doi.org/10.1016/j.tig.2009.11.004 Full Text]
  
* De Bodt, S., Carvajal, D., Hollunder, J., Van den Cruyce, J., Movahedi, S., and Inze, D. (2010). CORNET: A User-Friendly Tool for Data Mining and Integration. Plant Physiol., 152, 1167-1179.
+
*De Bodt, S., Carvajal, D., Hollunder, J., Van den Cruyce, J., Movahedi, S., and Inze, D. (2010). CORNET: A User-Friendly Tool for Data Mining and Integration. Plant Physiol., 152, 1167-1179.
  
  
*Schaeffer, M. L., Harper, L. C., Gardiner, J. M., Andorf, C. M., Campbell, D. A., Cannon, E. K. S., Sen, T. Z., and Lawrence, C. J. (2011). MaizeGDB: curation and outreach go hand-in-hand. Database, 2011.
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=2009 and earlier=
 +
*Clark, J. I., Brooksbank, C., and Lomax, J. (2005). It's All GO for Plant Scientists. Plant Physiol., 138, 1268-1279. (this does not actually cite the PO)

Latest revision as of 13:06, 28 July 2015

2015

- Lobet G, Pound MP, Diener J, Pradal C, Draye X, Godin C, Javaux M, Leitner D, Meunier F, Nacry P, et al (2015) Root System Markup Language: Toward a Unified Root Architecture Description Language. Plant Physiology 167: 617–627 [1]

- Berardini, TZ, L Reiser, D Li, Y Mezheritsky, R Muller. Genesis, 2015. The Arabidopsis Information Resource: Making and mining the 'gold standard' annotated reference plant genome. [2]

Abstract: The Arabidopsis Information Resource (TAIR) is a continuously updated, online database of genetic and molecular biology data for the model plant Arabidopsis thaliana that provides a global research community with centralized access to data for over 30,000 ...

- Takehisa, H., Y Sato, B Antonio, Y Nagamura - Rice, 2015. Coexpression Network Analysis of Macronutrient Deficiency Response Genes in Rice (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4513034/)

Background: Macronutrients are pivotal elements for proper plant growth and development. Although extensive gene expression profiling revealed a large number of genes differentially expressed under various nutrient deprivation, characterization of these genes ...

Google Scholar 2015

2014

Google Scholar 2014 citations "The plant ontology as a tool for comparative plant anatomy and genomic analyses"

2013

  • Cobb J, DeClerck G, Greenberg A, Clark R, McCouch S. 2013. Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype–phenotype relationships and its relevance to crop improvement. Theoretical and Applied Genetics 126, 867–887. abstract

2012

  • Lai L, Liberzon A, Hennessey J, Jiang G, Qi J, Mesirov JP, Ge SX (2012) AraPath: a knowledgebase for pathway analysis in Arabidopsis. Bioinformatics 28: 2291–2292. abstract
  • Deans, Andrew R., Matthew J. Yoder, and James P. Balhoff. “Time to Change How We Describe Biodiversity.” Trends in Ecology & Evolution 27, no. 2 (February 1, 2012): 78–84. link to full text
  • McCouch, S. R., McNally, K. L., Wang, W. and Sackville Hamilton, R. (2012). Genomics of gene banks: A case study in rice. Am J of Bot., 99, 407 -423. Link to full text

2011

  • Iida K, Kawaguchi S, Kobayashi N, Yoshida Y, Ishii M, Harada E, Hanada K, Matsui A, Okamoto M, Ishida J, et al (2011) ARTADE2DB: Improved Statistical Inferences for Arabidopsis Gene Functions and Structure Predictions by Dynamic Structure-Based Dynamic Expression (DSDE) Analyses. Plant and Cell Physiology 52: 254–264 link
  • Kumar, T. K. A., Crow, J. A., Wennblom, T. J., Abril, M., Letcher, P. M., Blackwell, M., Roberson, R. W., and McLaughlin, D. J. (2011). An ontology of fungal subcellular traits. American Journal of Botany, 98, 1504 -1510. Kumar et al, 2011
  • Schaeffer, M. L., Harper, L. C., Gardiner, J. M., Andorf, C. M., Campbell, D. A., Cannon, E. K. S., Sen, T. Z., and Lawrence, C. J. (2011). MaizeGDB: curation and outreach go hand-in-hand. Database, 2011.
  • Kobayashi N, Ishii M, Takahashi S, Mochizuki Y, Matsushima A, Toyoda T (2011) Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases. Nucleic Acids Research 39: W533 –W540

2010

  • Hong, C. (2010). Competency evaluation of plant character ontologies against domain literature. Journal of the American Society for Information Science & Technology, 61(6), 1144-1165. doi:10.1002/asi.21325
  • Qiuling He, Arthur Berg, Yao Li, C. Eduardo Vallejos and Rongling Wu. 2010. Mapping genes for plant structure, development and evolution: functional mapping meets ontology. Trends in Genetics 26(1): 39-46 Abstract Full Text
  • De Bodt, S., Carvajal, D., Hollunder, J., Van den Cruyce, J., Movahedi, S., and Inze, D. (2010). CORNET: A User-Friendly Tool for Data Mining and Integration. Plant Physiol., 152, 1167-1179.


2009 and earlier

  • Clark, J. I., Brooksbank, C., and Lomax, J. (2005). It's All GO for Plant Scientists. Plant Physiol., 138, 1268-1279. (this does not actually cite the PO)