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Information on Lines Information on CIMMYT lines imported to Australia can be downloaded in spreadsheet form from the CAGE database imported lines page. All lines have CID and SID identifiers, which together specify the line, rather than the pedigree, which will the same for all progeny of the same cross. Please note, all users should maintain the CID and SID identifier fields in any records or analysis of the lines. To date, CAGE contains all quarantine lists from 1988 onwards, including pedigrees and phenotyping data supplied by CIMMYT, synthetics data, germplasm seed increase results, trial information and breeders’ field data for 2005 and 2006 supplied by AGT, CSIRO, QDPI&F and DAFWA. Background The University of Queensland staff working on management of the CIMMYT-Australian germplasm evaluation (CAGE) data are using an ICIS format, expanding on the Global Wheat Information System (GWIS), which already holds historic Australian wheat pedigrees and reports on trials for numerous varieties. ICIS (International Crop Information System) is a database incorporating a set of modules, which can be used with the accumulated international data, or used as a shell to input the breeders’ own data. It is open source (i.e free to download) and in its current form, runs as a stand-alone system on the user’s desktop. Existing (open-source) ICIS functionalities include: Genealogy Management User Access Management List Management Data Management Inventory Management Gene Management Genetic Resources Information Management Location Management Advances from ICIS Development Workshops 2006 and 2007 At the ICIS Development Workshop, 15–19 May 2006 at CIMMYT El Batan, Mexico, ICIS partners from CIMMYT, Nunhems, ICARDA, UQ, CIP, AAFC, University of Agricultural Sciences Bangalore and IRRI reported on progress to existing ICIS modules and formed work groups to coordinate future work. Among the notable developments reported at the workshop were the molecular marker module, system integrity and data validation tools from IRRI, high function multidimensional / OLAP developments including DataMart - Mondrian and DIVA_GIS integration with ICIS, and CIPPEX, a molecular LIMS, by Edwin Rojas at CIP (Peru), and the Data Comparison Tool, a very user-friendly web interface front end for breeders to set up click-select multi-variable queries without the need for training in ICIS, developed by Shawn Yates at the Semiarid Prairie Agricultural Research Centre at Swift Current, Saskatchewan. Data is input via Excel templates designed to allow direct uploading of data to the ICIS database back end. The ICIS Developer group was also interested in integrating the Gramene-derived ontologies feature from RGMIMS reported by Leakha Henry, CSIRO, into the ICIS suite. Richard Trethowan’s presentation focussed on the need to handle the range of phenotyping data generated by breeders, coupled with molecular marker data, and the trade-off between yield and quality. Clare Johnson followed with a discussion of the DArT® diversity marker philosophy for co-selection of yield with quality, the volume of data generated per sample and the absolute requirement for correlation with phenotype. She made the case for an ICIS module with this data mining capability, potentially based on a multidimensional database architecture for speed with complex queries. It became clear from other presentations in the session that the relevant components had already been developed and it was a question of integrating them and tailoring them to handle DArT® data and phenotype correlations. A fuller summary of the ICIS Developers’ Workshops 2006 and 2007, including many of the presentations, can be found on ICISWiki. Development of Web-delivered ICIS CAGE The Australian web-implementation of ICIS for the CAGE suite is being developed for an expected launch in March 2008. Through the Coordination Project, a collaboration has been set up with CIMMYT’s Crop Research Informatics Laboratory (CRIL) and IRRI, who will integrate upgraded modules developed over the last year to make use of these functionalities, with differential security to separate public and private data. This will include the capacity to handle high throughput molecular marker data and DArT® profiles, and the development of queries, visualisation and analytical techniques using CRIL’s expertise. Web-delivered ICIS CAGE will: deliver all lists of CIMMYT introduced germplasm; deliver all data: CIMMYT International Nursery data; CIMMYT breeder data; quarantine data; preliminary field data; field yield data; add a "study" query for downloading full data on selected studies - this adds to the existing germplasm query (show me all data from all studies on a line) and trait query (what studies have these traits) handle high throughput molecular marker and DArT® data; be password protected; customise queries. be supported by a help-desk for users. The order of development is: store and make data available including marker and DArT® data, develop queries including visualisations from CRIL, move to analytical methods. Data migration from CIMMYT's IWIS database to ICIS was completed in 2006. This will enable direct transfer to the CAGE project of data on CIMMYT lines imported to Australia, avoiding any potential data entry errors. Working Party Workshop 19-23 March 2007 The development team got together to workshop the development of the database and web interface in March 2007. The minutes are recorded on ICIS Wiki under the following headings: Summary of requirements for the project Basic queries for genotype, phenotype and characterization data Visualisation tools for genotype and phenotype data Use of DArT® data in selection and breeding Storing DArT® data in ICIS DArT® : Row data production and processing Pre-structuring of data for data warehousing to increase performance on data querying Query design and user interface refinement By trait By germplasm Occurrence table Features required Recap of decisions taken so far Molecular selection Discussion with UQ IT staff UQ and IRRI staff are working towards these goals and completion is expected in June 2008.

Coordinators:
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Information on Lines

Information on CIMMYT lines imported to Australia can be downloaded in spreadsheet form from the CAGE database imported lines page. All lines have CID and SID identifiers, which together specify the line, rather than the pedigree, which will the same for all progeny of the same cross. Please note, all users should maintain the CID and SID identifier fields in any records or analysis of the lines.

To date, CAGE contains all quarantine lists from 1988 onwards, including pedigrees and phenotyping data supplied by CIMMYT, synthetics data, germplasm seed increase results, trial information and breeders’ field data for 2005 and 2006 supplied by AGT, CSIRO, QDPI&F and DAFWA.

Background

The University of Queensland staff working on management of the CIMMYT-Australian germplasm evaluation (CAGE) data are using an ICIS format, expanding on the Global Wheat Information System (GWIS), which already holds historic Australian wheat pedigrees and reports on trials for numerous varieties.

ICIS (International Crop Information System) is a database incorporating a set of modules, which can be used with the accumulated international data, or used as a shell to input the breeders’ own data. It is open source (i.e free to download) and in its current form, runs as a stand-alone system on the user’s desktop.

Existing (open-source) ICIS functionalities include:

Genealogy Management
User Access Management
List Management
Data Management
Inventory Management
Gene Management
Genetic Resources Information Management
Location Management

Advances from ICIS Development Workshops 2006 and 2007

At the ICIS Development Workshop, 15–19 May 2006 at CIMMYT El Batan, Mexico, ICIS partners from CIMMYT, Nunhems, ICARDA, UQ, CIP, AAFC, University of Agricultural Sciences Bangalore and IRRI reported on progress to existing ICIS modules and formed work groups to coordinate future work.

Among the notable developments reported at the workshop were the molecular marker module, system integrity and data validation tools from IRRI, high function multidimensional / OLAP developments including DataMart - Mondrian and DIVA_GIS integration with ICIS, and CIPPEX, a molecular LIMS, by Edwin Rojas at CIP (Peru), and the Data Comparison Tool, a very user-friendly web interface front end for breeders to set up click-select multi-variable queries without the need for training in ICIS, developed by Shawn Yates at the Semiarid Prairie Agricultural Research Centre at Swift Current, Saskatchewan. Data is input via Excel templates designed to allow direct uploading of data to the ICIS database back end. The ICIS Developer group was also interested in integrating the Gramene-derived ontologies feature from RGMIMS reported by Leakha Henry, CSIRO, into the ICIS suite.

Richard Trethowan’s presentation focussed on the need to handle the range of phenotyping data generated by breeders, coupled with molecular marker data, and the trade-off between yield and quality. Clare Johnson followed with a discussion of the DArT® diversity marker philosophy for co-selection of yield with quality, the volume of data generated per sample and the absolute requirement for correlation with phenotype. She made the case for an ICIS module with this data mining capability, potentially based on a multidimensional database architecture for speed with complex queries. It became clear from other presentations in the session that the relevant components had already been developed and it was a question of integrating them and tailoring them to handle DArT® data and phenotype correlations.

A fuller summary of the ICIS Developers’ Workshops 2006 and 2007, including many of the presentations, can be found on ICISWiki.

Development of Web-delivered ICIS CAGE

The Australian web-implementation of ICIS for the CAGE suite is being developed for an expected launch in March 2008. Through the Coordination Project, a collaboration has been set up with CIMMYT’s Crop Research Informatics Laboratory (CRIL) and IRRI, who will integrate upgraded modules developed over the last year to make use of these functionalities, with differential security to separate public and private data. This will include the capacity to handle high throughput molecular marker data and DArT® profiles, and the development of queries, visualisation and analytical techniques using CRIL’s expertise.

Web-delivered ICIS CAGE will:

deliver all lists of CIMMYT introduced germplasm;
deliver all data: CIMMYT International Nursery data; CIMMYT breeder data; quarantine data; preliminary field data; field yield data;
add a "study" query for downloading full data on selected studies - this adds to the existing germplasm query (show me all data from all studies on a line) and trait query (what studies have these traits)
handle high throughput molecular marker and DArT® data;
be password protected;
customise queries.
be supported by a help-desk for users.

The order of development is:

store and make data available including marker and DArT® data,
develop queries including visualisations from CRIL,
move to analytical methods.

Data migration from CIMMYT's IWIS database to ICIS was completed in 2006. This will enable direct transfer to the CAGE project of data on CIMMYT lines imported to Australia, avoiding any potential data entry errors.

Working Party Workshop 19-23 March 2007

The development team got together to workshop the development of the database and web interface in March 2007. The minutes are recorded on ICIS Wiki under the following headings:

Summary of requirements for the project
Basic queries for genotype, phenotype and characterization data
Visualisation tools for genotype and phenotype data
Use of DArT® data in selection and breeding
Storing DArT® data in ICIS
DArT® : Row data production and processing
Pre-structuring of data for data warehousing to increase performance on data querying
Query design and user interface refinement
By trait
By germplasm
Occurrence table
Features required
Recap of decisions taken so far
Molecular selection
Discussion with UQ IT staff

UQ and IRRI staff are working towards these goals and completion is expected in June 2008.

Global Wheat Information System

Information on Lines

Background

Advances from ICIS Development Workshops 2006 and 2007

Development of Web-delivered ICIS CAGE

Working Party Workshop 19-23 March 2007

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