Integrated Data Management forIntegrated Data Management for

Agricultural ResearchAgricultural Research

�� Diganta Nath, InternDiganta Nath, Intern

�� Dr. Rosemary Renaut, Committee ChairDr. Rosemary Renaut, Committee Chair

•• Director, Computational Biosciences PSMDirector, Computational Biosciences PSM

�� Dr. Jeffrey W. White, Internship AdvisorDr. Jeffrey W. White, Internship Advisor

•• ALARC, USDAALARC, USDA--ARC, Maricopa, AZARC, Maricopa, AZ

�� Dr. Hasan Davulcu, Committee Member Dr. Hasan Davulcu, Committee Member

•• Dept of Computer Science & Dept of Computer Science & EnggEngg..

Goals of ProjectGoals of Project

�� Improve data management, analysis Improve data management, analysis

and distributionand distribution

•• GIS Analysis of GIS Analysis of Lesquerella fendleriLesquerella fendleri

•• GMS database for Lesquerella (LesquIS)GMS database for Lesquerella (LesquIS)

•• Web interface for LesquISWeb interface for LesquIS

Goals contd.Goals contd.

•• GMS database for Vernonia (VernIS)GMS database for Vernonia (VernIS)

•• Web interface for VernISWeb interface for VernIS

•• Excel workbook as per ICASA standardsExcel workbook as per ICASA standards

The novel crop The novel crop -- LesquerellaLesquerella

•• Contains oil rich in Contains oil rich in hydroxyhydroxy fatty acid fatty acid

(HFA)(HFA)

•• Used in making resins, waxes, motor Used in making resins, waxes, motor

oils etc.oils etc.

Climate Analysis of Climate Analysis of L. fendleriL. fendleri

Distribution using DIVADistribution using DIVA--GISGIS

�� Data obtained from ALARC Data obtained from ALARC

collections, ASU Herbariumcollections, ASU Herbarium

�� Integrated into one database Integrated into one database –– 248 248

collectionscollections

�� Collection locations linked to climate Collection locations linked to climate

variablesvariables

DIVA contd.DIVA contd.

�� Frequency of mean temperature during Frequency of mean temperature during

the wettest quarter for collection sites of the wettest quarter for collection sites of

L. fendleriL. fendleri

DIVA contd.DIVA contd.

�� Frequency for precipitation of driest Frequency for precipitation of driest

quarterquarter

Climate Analysis algorithmsClimate Analysis algorithms

�� BIOCLIMBIOCLIM

•• 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

•• D = (1 D = (1 –– d ) * 100d ) * 100AB

DIVA DIVA -- BIOCLIMBIOCLIM

�� BIOCLIM Analysis BIOCLIM Analysis –– 3 variables3 variables

BIOCLIM contd.BIOCLIM contd.

�� BIOCLIM Analysis BIOCLIM Analysis –– 4 variables4 variables

DIVA DIVA -- DOMAINDOMAIN

�� DOMAIN Analysis DOMAIN Analysis –– 3 variables3 variables

DOMAIN contd.DOMAIN contd.

�� DOMAIN Analysis DOMAIN Analysis –– 4 variables4 variables

DIVA DIVA –– Next stepNext step

�� Collect more distribution dataCollect more distribution data

�� Involve soil chemistryInvolve soil chemistry

�� Assess other niche modeling Assess other niche modeling

methodsmethods

LesquIS GMSLesquIS GMS

�� ICIS databaseICIS database

•• GMSGMS

�� Import data from Excel into Excel Import data from Excel into Excel

spreadsheetspreadsheet

�� Implement standardized processImplement standardized process

has progenitors

(Recursive

Links) has group

has source

Developed by

Called

Developed at

Developed by

With value of

Named by

METHODS

NAMES

LOCATIONS

USERS

USER-

DEFINED

FIELDS

ATTRIBUTES

Named at

Germplasm

Defined property

Assigned at

Assigned by

Generative Germplasm

Derivative Germplasm

GMS database

ER diagram

LesquIS GMS contd.LesquIS GMS contd.

�� Form for Loading new accessionsForm for Loading new accessions

LesquIS GMS contd.LesquIS GMS contd.

�� Form for loading AttributesForm for loading Attributes

LesquIS webLesquIS web

�� Custom web interface to search Custom web interface to search

Lesquerella germplasm recordsLesquerella germplasm records

�� Technology used Technology used ––

•• Microsoft Active Server PagesMicrosoft Active Server Pages

•• MySQL server databaseMySQL server database

�� Hosted on IIS serverHosted on IIS server

LesquIS web contd.LesquIS web contd.

�� MSMS--Access to MySQL conversionAccess to MySQL conversion

�� Custom tool Custom tool –– NavicatNavicat

�� MySQL Enterprise ManagerMySQL Enterprise Manager

LesquIS web demoLesquIS web demo

�� Lesquerella Information SystemLesquerella Information System

VernIS GMSVernIS GMS

�� Vernonia (ironweed)Vernonia (ironweed)

•• Contains oil rich in epoxy fatty acids.Contains oil rich in epoxy fatty acids.

•• Potential use as plasticizers and Potential use as plasticizers and

additives in PVC, drying agent in paints.additives in PVC, drying agent in paints.

•• Research initiated in ALARC in 1990.Research initiated in ALARC in 1990.

VernIS contd.VernIS contd.

�� Collection Information in Excel.Collection Information in Excel.

�� Same methodology and tools used as Same methodology and tools used as in LesquIS.in LesquIS.

�� No changes to tools were necessary.No changes to tools were necessary.

�� VernIS GMS database implementedVernIS GMS database implemented

VernIS WebVernIS Web

�� Similar to LesquIS webSimilar to LesquIS web

�� 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

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Germplasm development of Vernonia galamensis as a new industrialGermplasm development of Vernonia galamensis as a new industrial oilseed crop.oilseed crop.

Indus. Crops Prod. 3:185Indus. Crops Prod. 3:185--200.200.

QuestionsQuestions

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