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Presentation Title Goes Here …presentation subtitle.
International Crop Information System :Its Development
and its Rice & Wheat Implementation
Graham McLaren and Arllet M. Portugal
Generation Challenge Program
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Outline
• Importance of Data Management• ICIS Vision• What is ICIS?• Genealogy Management System• Data Management System• IRIS: Linking Islands of Information• IWIS3: Managing the Global Wheat Data• ICIS Development• Future Development through IBP
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Importance of Data Management
• Data that are properly managed are:
more accessible to other researchers more likely to be re-used in another purpose Available to assist in the development of
combined/mutli-methods/across-time data sets More likely to be preserved – important for historically
significant data
Debby Terryhttp://www.library.uq.edu.au/escholarship/DT_dmp.pdf
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Importance of Data Management …
• Greater access to research data will lead to: Better science
o Driven by the capacity for data linkage, sharing, analysis, aggregation & transformation more sophisticated cross-disciplinary and cross-method
research
o Scientific method changes from: “hypothesize, design and run experiment, analyze results” to “hypothesize, look up answer in database”
Enhanced returns from publicly-funded research Benefits afforded by the capacity for national and
global sharing & linkage of dataDebby Terryhttp://www.library.uq.edu.au/escholarship/DT_dmp.pdf
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The ICIS Vision
• Connecting Islands of datao Connecting germplasm to crop improvemento Integrating data across disciplines o Leveraging data sets to understand crop adaptationo Linking phenotype to genetics and genomics
• Enabling collaborationo Seed exchanged with informationo Leveling the information playing field
• Developing global information resourcs
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What is ICIS?• ICIS is a computerized database system for general,
integrated management and utilization of genealogy, nomenclature, evaluation and characterization data for a wide range of crops.
• ICIS is a public open source collaboration involving a number of CGIAR centers and non-CG partners
• ICIS is an empty shell which must be implemented for each crop individually
ICIS
IWIS IMIS IVISICHIS ISCISIBIS …IRIS
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Components of ICIS
• Crop Data Managemento Genealogy Management System (GMS)o Data Management System (DMS)o Inventory Management System (IMS)o Genetic Resources Information Management
System (GRIMS)• Genetics/Genomics (GEMS)
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Genealogy Management System (GMS)
• GMS stores and manages information on genesis, genealogy, nomenclature and chronology of germplasm for a particular crop. It operates on the principle of unique identification of germplasm through system assigned Germplasm IDs
• It separates management of genealogy data from nomenclature so users are free to name germplasm as they like anf the genealogy is always ‘computable’
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The GMS Data Model
has progenitors
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 of
GENERATIVE GERMPLASM
DERIVATIVEAND MAINTENANCE
GERMPLASM has group
has source
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Data Management System (DMS)
• DMS manages environmental data, germplasm characterization data and evaluation data for genetic resources and crop improvement projects.
• It is a data warehouse that accumulates and integrates data from a variety of sources.
• It handles any data structure and facilitates unambiguous annotation and linkage of data across studies via expandable controlled vocabularies
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Data Model of DMS
The Effect of Fertilizer N on the yield of wheatYear: 2000Location: El Batan
Rep Main Plot Sub Plot Variety Fert Yield1 1 1 B 20 10.31 1 2 B 50 12.71 2 1 C 50 18.41 2 2 C 20 13.71 3 1 A 20 12.61 3 2 A 50 16.72 1 1 B 50 19.22 1 2 B 20 12.32 2 1 A 20 17.12 2 2 A 50 14.12 3 1 C 50 16.32 3 2 C 20 12.2
Filename: N2000DS.xlsStudy
Datum
Variate
Factor
Level
Observation
Unit
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Data Model ...
NITROGEN FERTILIZERPROPERTY
SCALE kg/ha
METHOD
Fert
Total Application
VariateFactor
Yield
GRAIN YIELD
t/ha
Adjusted Yield
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Data Model ....
STUDY
FACTOR
Applied inApplied in
LEVEL
Level ofLevel of
OBSERVATION UNIT
Indexed byIndexed byRecorded Recorded fromfrom
DATUM
Measurement ofMeasurement of
VARIATE
Observed inObserved in
PROPERTY
Identified byIdentified by
SCALE
Expressed inExpressed in
METHOD
Measured/Applied byMeasured/Applied by
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ICIS Applications: Standalone Tools
ICIS Workbook
SetGen
Inventory Tracker
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GMS Applications
• Genealogy Display Tools• Pedigree Input Tools• Breeder’s Tools (Set Generation)• Breeder’s Tools (Field Books)• Analysis Tools (Coefficients of Parentage)
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SETGEN
•GMS application for managing lists of germplasm for breeding, characterization or evaluation
o genealogyo nomenclatureo chronology
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ICIS Workbook • It is a macro in Excel that facilitates loading and
retrieving evaluation, nursery trial, crop improvement data and even molecular data.
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Workbook File: Evaluation Data
Sample Workbook file for the Irrigated Breeding Program
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Browse – pedigree analysis
Released lines
Coefficient of Parentage (COP)
Mendelgram of Yecora F 70 and Oasis F 86
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IRIS: Linking Islands of Information
BREEDING
PROGRAM
SOIL STRES
S DATA
INGER
GRC
SHU
IR64 MUTAN
T DATAB
ASEGCP
DATA
GAMMA LAB
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IRRIGATED RICE BREEDING
CENTRAL IRISDATABASE
IRB LOCALDATABASE
IRRIGATED RICEBREEDERS
Grain Quality
PBGB DATAMANAGEMENT
Cross Definition
Quality
Field Books for HB, F2, PN, OYT, RYT
Evaluation Data andPedigree Processing
Data
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Sample Field book with historical data
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IRRI Rice Breeding Programs – fully managed in IRIS
PROJECT SIZE / CYCLE (Crosses, Lines)
IRRIGATED 500, 10000
RAINFED 500, 10000
HYBRID 1000, 2000
WIDE HYBRIDS 1000, 2000
UPLAND 100, 5000
COLD TOL. 100, 5000
PERENNIAL 500, 1000
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INGER: International Trials
>>
Trial Details
Field book
Rainfall
Promising entries
Weather
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SHU and SMTA Portal
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SMTA Document
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IWIS3: Managing the Global Wheat Data
International
Nursery Trials
IWIS2
Genebank
Accessions
ICARDA
Wheat Breeding
IWIS3NARS
Punjab Agricultural University
Directorate of Wheat Research, India
Advanced Research Institute
SPARC-AAFC
Univ. of Sydney
UQ
CIMMYT
Breeding Data
Durum/ Triticale
Irrigated
Rainfed
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IWIS3 websites• CIMMYT http://iwis.cimmyt.org/
Search for a germplasm
Pedigree Tree
Trial Study
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IWIS3 websites• Australia- India Wheat Molecular Breeding
http://iwis.nrcpb.org/
http://icis.camden.usyd.edu.au:81/IWIS/
http://gwis.lafs.uq.edu.au/
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Rainfed
DurumTriticale
IWIS3 for Wheat Breeding
Irrigated
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Generate a cross
IWIS Cross
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Generate a Selection
• Run IWIS Selection• Retrieve the list of entries to
advance to next generation• Fill up the Description sheet of the
template• Enter the number of plants
selected in the NSEL• Enter outstanding trait, if there is
any.• Load the study• Generate the lines using SetGEn
IWIS Selection
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E. Generating Fieldbook Report• Run the IWIS Retriever• Click “Print Labels and
Fieldbooks”• Select Germplas list• Click Generate Fieldbooks• Click the type of the Field
book you wish to generate
Generate Field book for cross
Generate Field book for selection
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ICIS Development
• Documentation• Management of the codes and its releases• Feature Request• Error-fixing• Workshops and Training
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ICIS Development
Documentation of ICIShttp://www.cropinfo.org/icis/index.php/Main_Page
Code management and release of ICIShttp://cropforge.org/projects/iciscomm/
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Future Development through IBP
• Configurable Workflow• Better management of molecular and genotyping
data• Integration of genotyping and phenotyping data• Integration of ontology system• Integration with analysis tools• Not Operating System dependent
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