Download Objectevolution in GBIS I

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,
[email protected]
Outline
What is ICIS?
What is new in ICIS?
What is ICIS?
What is ICIS?
What is ICIS?
International
Crop
Information
System
Graham McLaren, IRRI:
• It’s 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?
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?
ICIS partners
Developers
•
•
•
•
•
•
CIMMYT, ICARDA, IRRI
Grain Biotech Australia
VIDA
SPARC
Nunhems
University of Queensland
Alliances
•
•
•
•
•
•
The Generation Challenge Program
SINGER
Germinate
Gramene
Phenotype Ontology Consortium
IRFGC
Jörn Vorwald: ICIS Workshop 2005 report - What is ICIS?
Users
(by G. McLaren)
• MARDI
• East West Seed Co.
• Bayer Cropscience/Bioscience
• University of Agricultural
Sciences, Bangalore
• Philrice, Philipines
• CNRRI, China
• Ubon RRC, Thailand
• SARSBN
• CIAT
• IITA
• ...
Where is IPK?
• First contact in 2002: visit at the developer’s 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 C+E 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?
What is new in ICIS?
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?
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?
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?
Other reports I
• Location data quality in ICIS
(by I. Mukema, IRRI)
• data quality dimensions modeled
• IRGCIS migration to ICIS
(by R. Herrera, IRRI)
• IRRI‘s 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?
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?
What is ICIS?
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?
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-softwarearchitecture
Jörn Vorwald: ICIS Workshop 2005 report - Summary
ICIS
http://www.icis.cgiar.org
http://cropwiki.irri.org/icis/index.php/Main_Page
http://cropforge.irri.org/
Thank you
End