ICIS - The International Crop Information System - A Workshop Report

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ICIS - The International Crop Information System
- A Workshop Report

• Jörn Vorwald
• Institute of Plant Genetics and Crop Plant
  Research Gatersleben
• Corrensstraße 3, D-06466 Gatersleben,
  http//www.ipk-gatersleben.de, vorwald_at_ipk-gatersl
  eben.de

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Outline
What is ICIS?

• What is ICIS?

What is new in ICIS?
What is new in ICIS?
What is ICIS?
What is ICIS?
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• What is ICIS?

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What is ICIS?
International
Crop
Information
System

• Graham McLaren, IRRI
• Its a community an alliance of partners
  collaborating on development and deployment of
  crop information systems
• The goal is to pool intellectual and physical
  resources to create a generic crop information
  platform

Jörn Vorwald ICIS Workshop 2005 report - What is
ICIS?
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What is ICIS and what it is not (yet)?

• ICIS homepage
• a database system for management and integration
  of global information on genetic resources and
  crop improvement
• allows ambiguous germplasm identification,
  tracing pedigree information, integration
  between genetic resources, breeding,
  characterisation, evaluation, and utilisation of
  data
• being developed by genetic resource specialists,
  crop scientists, and information technicians
• implemented separately for each crop

• It is not
• A gene bank information system
• A plant data warehouse

Jörn Vorwald ICIS Workshop 2005 report - What is
ICIS?
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ICIS partners (by G. McLaren)

• Developers
• CIMMYT, ICARDA, IRRI
• Grain Biotech Australia
• VIDA
• SPARC
• Nunhems
• University of Queensland

• Users
• MARDI
• East West Seed Co.
• Bayer Cropscience/Bioscience
• University of Agricultural Sciences, Bangalore
• Philrice, Philipines
• CNRRI, China
• Ubon RRC, Thailand
• SARSBN
• CIAT
• IITA
• ...

• Alliances
• The Generation Challenge Program
• SINGER
• Germinate
• Gramene
• Phenotype Ontology Consortium
• IRFGC

Jörn Vorwald ICIS Workshop 2005 report - What is
ICIS?
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Where is IPK?

• First contact in 2002 visit at the developers
  workshop
• Is ICIS a useful tool for IPK gene bank?
• Decision in summer 2002 after test installation
  It is not.
• Pros
• International developer community
• Successful implementations around the world
• Flexible and easy CE data input and access
• Contras
• No gene bank module
• Focused on single crops
• Redundant data management
• Problems with installation
• Today Was it the wrong decision?
• Virtual enlargement of development capacities
• Open source project with flexible database layer
• Gene bank module is coming up

Jörn Vorwald ICIS Workshop 2005 report - What is
ICIS?
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• What is new in ICIS?

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Software development of ICIS (by A. Cosico A.
Portugal, IRRI)

• Enhancement of existing ICIS Applications
• SetGen
• Workbook
• Browse
• GMSSearch
• Retriever
• ICISForms
• Implementation of the Invetory Tracker
• Initial implementation of Genetic
  Resource Information Management System
• Porting of the ICIS32.dll in .NET
  to interoperate with web services

Jörn Vorwald ICIS Workshop 2005 report - What is
new in ICIS?
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New Platform (by A. Cosico A. Portugal, IRRI)

• ICIS4 ? ICIS5/Java
• Reimplementation of some major components
• Moving core ICIS APIs (GMS/DMS) from client to
  server
• Integrating a high-performance object-oriented
  persistence framework
• Implementing web services (SOAP/XML) for
  programming language-agnostic access to core
  APIs and integration with existing Delphi, VB,
  FORTRAN, etc. front ends
• Developing a Web-based portal for browser access
• Code management using GForge/CVS

Jörn Vorwald ICIS Workshop 2005 report - What is
new in ICIS?
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New modules

• ICISForms (by M. A. Sallan, IRRI)
• creates a GUI on the fly
• GEMS (by T. Metz, IRRI)
• manages genotype data
• SQL code generator for queries on the fly
• towards data warehouse functionality
• Marker Assisted Selection (by F. Clarke, SPARC)
• more a need a tool for support
• ICIS QU-GENE Link (by I. DeLacy, UQ)
• just another need integrating ICIS with
  analysis tools

Jörn Vorwald ICIS Workshop 2005 report - What is
new in ICIS?
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Other reports I

• Location data quality in ICIS (by I. Mukema,
  IRRI)
• data quality dimensions modeled
• IRGCIS migration to ICIS (by R. Herrera, IRRI)
• IRRIs GBIS with new functions
• Replacing Oracle based system by open source due
  to costs
• DIVA-GIS (by R. Simon, CIP)
• Tool for PGR management introducing
  GIS functionality
• ICIS connectivity planned for 2005
• Data abstraction I (by J. Vorwald, IPK)
• introducing object-oriented approach to RDBMS

Jörn Vorwald ICIS Workshop 2005 report - What is
new in ICIS?
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Other reports II

• Data abstraction II (by J. Vorwald, IPK)
• towards a PGR ontology
• Managing pedigrees (by S. Micallef, UQ / S.
  Yates, SPARC / G. McLaren, IRRI)
• problems with data update
• Database platform experiences (by A. Portugal,
  IRRI / C. aan den Boom J. Heber, Nunhems / T.
  Metz, IRRI)
• MS-Access, MySQL, Oracle, PostgreSQL
• Data abstraction III (by R. Bruskievich, IRRI
  / I. DeLacy, UQ)
• data management concepts global identifiers,
  ontology domain models
• ontology of plant genealogy

Jörn Vorwald ICIS Workshop 2005 report - What is
new in ICIS?
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• What is ICIS?

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What ICIS is and what will it be?

• An open source community and project
• A gene bank information system
• A plant data warehouse

Jörn Vorwald ICIS Workshop 2005 report - What is
ICIS?
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Why should we deal with ICIS?

• IPK as part of plant resource research
  community
• A lot of benefits from collaboration
• developments and solutions
• virtual enlargement of development capacities
  
• A little bit to give
• visualisation and database representation of
  graphs? for pedigrees (represented as trees, but
  real graphs)
• query builder database and Java implementation
• a lot of theory contributions to ontologies and
  data quality
• experiences data migration, 3-tier-software- ar
  chitecture

Jörn Vorwald ICIS Workshop 2005 report - Summary
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ICIS http//www.icis.cgiar.org http//cropwiki.ir
ri.org/icis/index.php/Main_Page http//cropforge.i
rri.org/
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• Thank you

End