Difference between revisions of "Plant Ontology Citations"
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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] [doi | + | =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 [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= | ||
| + | [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= | ||
| + | *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] | ||
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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. | ||
| + | |||
| + | *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 [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. | ||
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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 20:06, 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 ...
2014
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)
