International
CropTitle
Information
System :
Presentation
Goes Here
…presentation subtitle. Its Development
and its Rice & Wheat Implementation
Graham McLaren and Arllet M. Portugal
Generation Challenge Program
Outline
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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 Terry
http://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
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data linkage, sharing, analysis, aggregation & transformation
 more sophisticated cross-disciplinary and cross-method
research
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 data
o
Debby Terry
http://www.library.uq.edu.au/escholarship/DT_dmp.pdf
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The ICIS Vision
• Connecting Islands of data
o Connecting germplasm to crop improvement
o Integrating data across disciplines
o Leveraging data sets to understand crop
adaptation
o Linking phenotype to genetics and genomics
• Enabling collaboration
o Seed exchanged with information
o 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
IRIS
IWIS
IBIS
IMIS
ICHIS
IVIS
ISCIS
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Components of ICIS
• Crop Data Management
o 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
GENERATIVE
GERMPLASM
GERMPLASM
has progenitors
DERIVATIVE
AND MAINTENANCE
GERMPLASM
has group
has source
Developed by
METHODS
Called
NAMES
Named at
Developed at
Developed by
With value of
Named by
LOCATIONS
USERS
ATTRIBUTES
USER-DEFINED
FIELDS
Defined
property of
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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
Study
Variate
Filename: N2000DS.xls
The Effect of Fertilizer N on the yield of wheat
Factor
Level
Observation
Unit
Year: 2000
Location: El Batan
Rep
1
1
1
1
1
1
2
2
2
2
2
2
Main Plot Sub Plot
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1
1
2
2
1
2
2
3
1
3
2
1
1
1
2
2
1
2
2
3
1
3
2
Variety
B
B
C
C
A
A
B
B
A
A
C
C
Fert
20
50
50
20
20
50
50
20
20
50
50
20
Yield
10.3
12.7
18.4
13.7
12.6
16.7
19.2
12.3
17.1
14.1
16.3
12.2
Datum
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Data Model ...
Factor
Variate
Fert
Yield
PROPERTY NITROGEN FERTILIZER
GRAIN YIELD
SCALE
kg/ha
t/ha
METHOD
Total Application
Adjusted Yield
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Data Model ....
STUDY
Observed in
Applied in
Identified by
FACTOR
PROPERTY
Expressed in
Level of
SCALE
Measured/Applied by
METHOD
Measurement of
DATUM
LEVEL
Indexed by
VARIATE
OBSERVATION
UNIT
Recorded
from
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ICIS Applications: Standalone
Tools
SetGen
ICIS Workbook
Inventory Tracker
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GMS Applications
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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 genealogy
o nomenclature
o chronology
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List Manager – germplam list generator
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A. Add germplasm record
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B. Generate a cross
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C. Generate a Selection
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D. Create a trial list – Import from
Excel
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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
Mendelgram of Yecora F 70 and Oasis F 86
Released lines
Coefficient of Parentage (COP)
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IRIS: Linking Islands of Information
BREEDING
PROGRAM
SOIL
STRESS
DATA
GRC
SHU
INGER
IR64
MUTANT
DATABAS
E
GAMMA
LAB
GCP DATA
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IRRIGATED RICE BREEDING
CENTRAL IRIS
DATABASE
PBGB DATA
MANAGEMENT
Cross Definition
Evaluation Data and
Pedigree Processing
Field Books for HB,
IRRIGATED RICE F2, PN, OYT, RYT
BREEDERS
Grain Quality
Quality
Data
IRB LOCAL
DATABASE
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Sample Field book with historical data
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IRRI Rice Breeding Programs – fully
managed in IRIS
PROJECT
IRRIGATED
SIZE / CYCLE
(Crosses, Lines)
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
Genebank
Nursery Trials
Accessions
IWIS2
Irrigated
Durum/
Triticale
Rainfed
Punjab
Agricultural
University
IWIS3
Directorate
of Wheat
Research,
India
CIMMYT
NARS
Breeding Data
UQ
ICARDA
Wheat Breeding
Univ. of
Sydney
SPARCAAFC
Advanced Research
Institute
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IWIS3 websites
• CIMMYT http://iwis.cimmyt.org/
Search for a germplasm
Trial Study
Pedigree Tree
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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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IWIS3 for Wheat Breeding
Rainfed
Durum
Triticale
Irrigated
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Generate a cross
IWIS Cross
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Generate a Selection
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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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Entering data using handheld
FieldLog
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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
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Documentation
Management of the codes and its releases
Feature Request
Error-fixing
Workshops and Training
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ICIS Development
Code management and release of ICIS
http://cropforge.org/projects/iciscomm/
Documentation of ICIS
http://www.cropinfo.org/icis/index.php/Main_Page
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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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Acknowledgement
ICIS Development Team
Zeus Development Team
IBP Development Team
CRIL Staff
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