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

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

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

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 http://www.library.uq.edu.au/escholarship/DT_dmp.pdf

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

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

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)

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’

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

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

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

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

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

ICIS Applications: Standalone Tools SetGen ICIS Workbook Inventory Tracker

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

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

List Manager – germplam list generator

A. Add germplasm record

B. Generate a cross

C. Generate a Selection

D. Create a trial list – Import from Excel

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

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

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

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

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

Sample Field book with historical data

IRRI Rice Breeding Programs – fully managed in IRIS

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

SHU and SMTA Portal

SMTA Document

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

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

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/

IWIS3 for Wheat Breeding Rainfed Durum Triticale Irrigated

Generate a cross IWIS Cross

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

Entering data using handheld FieldLog

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

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

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

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

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