Integrated Data Management for Integrated Data Management for Agricultural Research Agricultural Research Diganta Nath, Intern Diganta Nath, Intern Dr. Rosemary Renaut, Committee Chair Dr. Rosemary Renaut, Committee Chair • • Director, Computational Biosciences PSM Director, Computational Biosciences PSM Dr. Jeffrey W. White, Internship Advisor Dr. Jeffrey W. White, Internship Advisor • • ALARC, USDA ALARC, USDA - - ARC, Maricopa, AZ ARC, Maricopa, AZ Dr. Hasan Davulcu, Committee Member Dr. Hasan Davulcu, Committee Member • • Dept of Computer Science & Dept of Computer Science & Engg Engg . .
31
Embed
Integrated Data Management for Agricultural Researchcbs/projects/2006_presentation...Integrated Data Management for Agricultural Research Diganta Nath, Intern Dr. Rosemary Renaut,
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
Integrated Data Management forIntegrated Data Management for
Agricultural ResearchAgricultural Research
�� Diganta Nath, InternDiganta Nath, Intern
�� Dr. Rosemary Renaut, Committee ChairDr. Rosemary Renaut, Committee Chair
•• Extracts climate data set for collection Extracts climate data set for collection
pointspoints
•• Computes mean and standard deviation Computes mean and standard deviation
from mean for each climatic variablefrom mean for each climatic variable
•• Builds an envelope identifying similar Builds an envelope identifying similar
areas based on percentile.areas based on percentile.
Algorithms contd.Algorithms contd.
�� DOMAINDOMAIN•• Based on GOWER distance Based on GOWER distance –– Relative measure Relative measure of similarity (Absolute distance/maximum of similarity (Absolute distance/maximum distance)distance)
•• Calculates GOWER distance between collection Calculates GOWER distance between collection points and each cellpoints and each cell
•• Generates a map based on similarityGenerates a map based on similarity
�� Used the same codeUsed the same code--base and base and
processprocess
�� Hosted on the same web server and Hosted on the same web server and
database serverdatabase server
VernIS web demoVernIS web demo
�� Vernonia Information SystemVernonia Information System
Excel workbook for data collection Excel workbook for data collection
and data interchangeand data interchange
�� Preformatted workbook for collecting data Preformatted workbook for collecting data of field experimentsof field experiments•• Not all workers need or want a complex Not all workers need or want a complex system like ICISsystem like ICIS
�� Functionalities to import/export dataFunctionalities to import/export data
�� XML outputXML output
�� ICASA standardsICASA standards
Workbook demoWorkbook demo
Conclusion and Future directionConclusion and Future direction
�� DIVADIVA
�� LesquIS and VernISLesquIS and VernIS
�� ICASAICASA
Special ThanksSpecial Thanks
�� Dr. Rosemary RenautDr. Rosemary Renaut
�� Dr. Jeffery W. WhiteDr. Jeffery W. White
�� Dr. Hasan DavulcuDr. Hasan Davulcu
�� Dr. Dave DierigDr. Dave Dierig
�� Pernell TomasiPernell Tomasi
�� Dr. Andrew SalywonDr. Andrew Salywon
ReferencesReferences�� Anonymous 2003. Vascular Plant Herbarium, Arizona State UniversiAnonymous 2003. Vascular Plant Herbarium, Arizona State University. ty.
Ma.TMa.T., ., SallanSallan, M.A.B., , M.A.B., UlatUlat, V.J.M., Wang, X., McNally, K.L., Sackville Hamilton, R., Mc, V.J.M., Wang, X., McNally, K.L., Sackville Hamilton, R., McLaren, C.G. 2003. Linking genotype to phenotype: the Laren, C.G. 2003. Linking genotype to phenotype: the International Rice Information System (IRIS). Bioinformatics 19:International Rice Information System (IRIS). Bioinformatics 19: 6363--65.65.
�� Busby, J.R. 1991. BIOCLIM Busby, J.R. 1991. BIOCLIM -- a bioclimatic analysis and prediction system. Pp. 64a bioclimatic analysis and prediction system. Pp. 64--6868
in in MargulesMargules, C.R. and Austin, M.P. (, C.R. and Austin, M.P. (edseds) Nature Conservation: Cost Effective Biological Surveys and dat) Nature Conservation: Cost Effective Biological Surveys and data Analysis. Melbourne: CSIROa Analysis. Melbourne: CSIRO
�� Carpenter, G., Carpenter, G., GillisonGillison, A.N. and Winter, J. 1993. DOMAIN: a flexible , A.N. and Winter, J. 1993. DOMAIN: a flexible modellingmodelling
procedure for mapping potential distributions of plants and animprocedure for mapping potential distributions of plants and animals. Biodiversity and Conservation 2:667als. Biodiversity and Conservation 2:667--680.680.�� DeLacyDeLacy, I.H., McLaren, C.G., Fox, P.N., White, J.W. and , I.H., McLaren, C.G., Fox, P.N., White, J.W. and TrethowanTrethowan, R. The , R. The
Genealogy Management System Genealogy Management System http://www.icis.cgiar.org:8080/TDM/Docs/ICIS02G_GMS_Overview.DOChttp://www.icis.cgiar.org:8080/TDM/Docs/ICIS02G_GMS_Overview.DOC (verified Nov. 20, 2006)(verified Nov. 20, 2006)�� DelacyDelacy, I., and , I., and MicallefMicallef, S. Global Wheat Information System, S. Global Wheat Information System
Breeding strategies for improvement of lesquerella fendleri (Breeding strategies for improvement of lesquerella fendleri (brassicaceaebrassicaceae). pp 689). pp 689--697.697.�� ElithElith, J., H. Graham, Catherine, R. P. Anderson, M. , J., H. Graham, Catherine, R. P. Anderson, M. DudikDudik, S. Ferrier, A. , S. Ferrier, A. GuisanGuisan, R. J., R. J.,,
Hijmans, F. Hijmans, F. HuettmannHuettmann, J. R. , J. R. LeathwickLeathwick, A. Lehmann, J. Li, L. G. , A. Lehmann, J. Li, L. G. LohmannLohmann, B. A. , B. A. LoiselleLoiselle, G. , G. ManionManion, C. Moritz, M. Nakamura, Y. , C. Moritz, M. Nakamura, Y. NakazawaNakazawa, J. , J. McCMcC. . M. Overton, A. Townsend Peterson, S. J. Phillips, K. Richardson,M. Overton, A. Townsend Peterson, S. J. Phillips, K. Richardson, R. R. ScachettiScachetti--Pereira, R. E. Pereira, R. E. SchapireSchapire, J. , J. SoberonSoberon, S. Williams, M. S. , S. Williams, M. S. WiszWisz, and N. E. , and N. E. Zimmermann. 2006. Novel methods improve prediction of species' dZimmermann. 2006. Novel methods improve prediction of species' distributions from occurrence data. istributions from occurrence data. EcographyEcography 29:12929:129--151.151.
�� Fox, P.N., McLaren, C.G. and White, J.W. The International Crop Fox, P.N., McLaren, C.G. and White, J.W. The International Crop
Information System: Reflects the Information System: Reflects the InforamtionInforamtion--Intensive Nature of Modern Crop Research. Intensive Nature of Modern Crop Research. http://www.icis.cgiar.org:8080/TDM/Docs/ICIS01k_Introduction.DOChttp://www.icis.cgiar.org:8080/TDM/Docs/ICIS01k_Introduction.DOC (verified Nov. 20, 2006)(verified Nov. 20, 2006)
�� Franco, J., Crossa, J., Warburton, M.L., and Franco, J., Crossa, J., Warburton, M.L., and TabaTaba, S. 2006. Sampling Strategies for Conserving Maize Diversity Wh, S. 2006. Sampling Strategies for Conserving Maize Diversity When Forming Core Subsets Using en Forming Core Subsets Using Genetic Markers. Crop Sci 46: 854Genetic Markers. Crop Sci 46: 854--864.864.
�� Hijmans, R. J., Hijmans, R. J., SchreuderSchreuder, M., De la Cruz, J. and , M., De la Cruz, J. and GuarinoGuarino, L.. 1999. Using GIS to check, L.. 1999. Using GIS to check
coco--ordinates of ordinates of genebankgenebank accessions. Genetic Resources and Crop Evolution 46:291accessions. Genetic Resources and Crop Evolution 46:291--296.296.�� Hijmans, R.J., Hijmans, R.J., GuarinoGuarino, L., Jarvis, A., O'Brien, R., , L., Jarvis, A., O'Brien, R., MathurMathur P., C. P., C. BussinkBussink, M. Cruz, I. , M. Cruz, I.
BarrantesBarrantes and Rojas, E. 2005. DIVAand Rojas, E. 2005. DIVA--GIS, version 5.2. Manual. GIS, version 5.2. Manual. http://www.divahttp://www.diva--gis.org/DIVAgis.org/DIVA--GIS5_manual.pdfGIS5_manual.pdf
�� Hijmans, R.J. & D.M. Spooner, 2001. Geographic distribution of wHijmans, R.J. & D.M. Spooner, 2001. Geographic distribution of wild potato species.ild potato species.
AmerAmer J J BotBot 88: 210188: 2101––2112.2112.�� Hijmans, R.J., Cameron, S., and Hijmans, R.J., Cameron, S., and ParraParra, J., 2004. DIVA, J., 2004. DIVA--GIS Climate data from GIS Climate data from WorldclimWorldclim, http://, http://www.worldclim.orgwww.worldclim.org/, version 1.3, October 2004/, version 1.3, October 2004�� Hunt, L.A., White, J.W., Hoogenboom, G., 2001. Agronomic data: aHunt, L.A., White, J.W., Hoogenboom, G., 2001. Agronomic data: advances in dvances in
documentation and protocols for exchange and use. Agricultural Sdocumentation and protocols for exchange and use. Agricultural Systems 70, 477ystems 70, 477--492.492.
�� Hunt, L.A., G. Hoogenboom, J.W. Jones, J.W. White, 2006. ICASA VHunt, L.A., G. Hoogenboom, J.W. Jones, J.W. White, 2006. ICASA Version 1.0 Data ersion 1.0 Data
Standards for Agricultural Research and Decision Support. Standards for Agricultural Research and Decision Support. www.icasa.netwww.icasa.net/standards (verified Nov. 20, 2006)./standards (verified Nov. 20, 2006).�� McLaren, G., Bruskiewich, R., Metz, T. INTERNATIONAL RICE INFORMMcLaren, G., Bruskiewich, R., Metz, T. INTERNATIONAL RICE INFORMATION ATION
SYSTEM web. SYSTEM web. http://http://www.iris.irri.orgwww.iris.irri.org/(Verified/(Verified Nov. 20, 2006)Nov. 20, 2006)�� ReyesReyes--UlatUlat, M.T., Bruskiewich, R., , M.T., Bruskiewich, R., CosicoCosico, A. ICIS WEB INTERFACE (, A. ICIS WEB INTERFACE (ICISWebICISWeb))
http://www.icis.cgiar.org:8080/TDM/Docs/ICIS16A_ICIS_Web.dochttp://www.icis.cgiar.org:8080/TDM/Docs/ICIS16A_ICIS_Web.doc (verified Nov. 20, 2006)(verified Nov. 20, 2006)�� Thompson, A.E., D.A., Dierig, E.R. Johnson, G.H. Thompson, A.E., D.A., Dierig, E.R. Johnson, G.H. DahlquistDahlquist, and R. , and R. KleimanKleiman. 1994a.. 1994a.
Germplasm development of Vernonia galamensis as a new industrialGermplasm development of Vernonia galamensis as a new industrial oilseed crop.oilseed crop.