1. Graham McLaren and Arllet M. Portugal Generation Challenge Program
International Crop Information System : Its Development and its Rice & Wheat Implementation
Graham McLaren and Arllet M. Portugal
Generation Challenge Program

2. 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

3. 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

4. Importance of Data Management …
Greater access to research data will lead to:
Better science
Driven by the capacity for
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
Debby Terry

5. The ICIS Vision Connecting Islands of data
Connecting germplasm to crop improvement
Integrating data across disciplines
Leveraging data sets to understand crop adaptation
Linking phenotype to genetics and genomics
Enabling collaboration
Seed exchanged with information
Leveling the information playing field
Developing global information resourcs

6. 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
IVIS
ICHIS
ISCIS
IBIS …
IRIS

7. Components of ICIS Crop Data Management
Genealogy Management System (GMS)
Data Management System (DMS)
Inventory Management System (IMS)
Genetic Resources Information Management System (GRIMS)
Genetics/Genomics (GEMS)

8. 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’

9. AND MAINTENANCE GERMPLASM
The GMS Data Model
has progenitors
Developed by
Called
Developed at
With value of
Named by
METHODS
NAMES
LOCATIONS
USERS
USER-DEFINED FIELDS
ATTRIBUTES
Named at
GERMPLASM
Defined property of
GENERATIVE GERMPLASM
DERIVATIVE
AND MAINTENANCE GERMPLASM
has group
has source

10. 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

11. Data Model of DMS Variate Study Factor Level Observation Unit Datum
Filename: N2000DS.xls
Factor
Level
Observation
Unit
Datum

12. Data Model ... Factor Variate Fert Yield PROPERTY NITROGEN FERTILIZER
GRAIN YIELD
t/ha
SCALE
kg/ha
Adjusted Yield
METHOD
Total Application

13. Data Model .... VARIATE STUDY FACTOR PROPERTY LEVEL DATUM SCALE METHOD
Observed in
STUDY
FACTOR
Applied in
Identified by
PROPERTY
LEVEL
Level of
Expressed in
Measured/Applied by
DATUM
Measurement of
SCALE
METHOD
OBSERVATION
UNIT
Indexed by
Recorded from

14. ICIS Applications: Standalone Tools
SetGen
ICIS Workbook
Inventory Tracker

15. GMS Applications Genealogy Display Tools Pedigree Input Tools
Breeder’s Tools (Set Generation)
Breeder’s Tools (Field Books)
Analysis Tools (Coefficients of Parentage)

16. SETGEN
GMS application for managing lists of germplasm for breeding, characterization or evaluation
genealogy
nomenclature
chronology

17. List Manager – germplam list generator

18. A. Add germplasm record

19. B. Generate a cross

20. C. Generate a Selection

21. D. Create a trial list – Import from Excel

22. ICIS Workbook
It is a macro in Excel that facilitates loading and retrieving evaluation, nursery trial, crop improvement data and even molecular data.

23. Workbook File: Evaluation Data
Sample Workbook file for the Irrigated Breeding Program

24. Browse – pedigree analysis
Mendelgram of Yecora F 70 and Oasis F 86
Released lines
Coefficient of Parentage (COP)

25. IRIS: Linking Islands of Information
BREEDING
PROGRAM
SOIL STRESS DATA
INGER
GRC
SHU
IR64 MUTANT DATABASE
GCP DATA
GAMMA LAB

26. IRRIGATED RICE BREEDING
CENTRAL IRIS
DATABASE
PBGB DATA
MANAGEMENT
Evaluation Data and
Pedigree Processing
Cross Definition
Field Books for HB,
F2, PN, OYT, RYT
IRRIGATED RICE
BREEDERS
IRB LOCAL
DATABASE
Grain Quality
Quality
Data

27. Sample Field book with historical data

28. IRRI Rice Breeding Programs – fully managed in IRIS

29. INGER: International Trials
Trial Details
Field book
Rainfall
Promising entries
Weather
>>

30. SHU and SMTA Portal

31. SMTA Document

32. IWIS3: Managing the Global Wheat Data
International
Nursery Trials
IWIS2
Genebank
Accessions
CIMMYT
Breeding Data
Durum/ Triticale
Irrigated
Rainfed
NARS
Punjab Agricultural University
Directorate of Wheat Research, India
IWIS3
Advanced Research Institute
SPARC-AAFC
Univ. of Sydney UQ
ICARDA
Wheat Breeding

33. IWIS3 websites CIMMYT http://iwis.cimmyt.org/ Search for a germplasm
Trial Study
Pedigree Tree

34. IWIS3 websites Australia- India Wheat Molecular Breeding

35. IWIS3 for Wheat Breeding
Rainfed
Durum
Triticale
Irrigated

36. Generate a cross
IWIS Cross

37. 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

38. Entering data using handheld
FieldLog

39. 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

40. ICIS Development Documentation
Management of the codes and its releases
Feature Request
Error-fixing
Workshops and Training

41. ICIS Development Code management and release of ICIS
Documentation of ICIS

42. 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

43. Acknowledgement ICIS Development Team Zeus Development Team
IBP Development Team
CRIL Staff