Development and Implementation

Transcription

1 International Presentation Crop Title Information Goes Here System : Development and Implementation presentation subtitle. Graham Mclaren GCP

2 The ICIS Vision Connecting Islands of data o Connecting germplasm to crop improvement o Integrating data across disciplines o Leveraging data sets to understand crop adaptation o Linking phenotype to genetics and genomics :: color, composition, and layout

3 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 :: color, composition, and layout

4 Components of ICIS Crop Data Management o Genealogy Management System (GMS) o Ontology Management System (OMS) o Data Management System (DMS) o Inventory Management System (IMS) o Genetic Resources Information Management System (GRIMS) Genetics/Genomics o Management of Genes, Markers, Alleles (GEMS) o Management of Genotypong data :: color, composition, and layout

5 Dual Database System of ICIS ICIS operated thrpough a dual database system. For each project there is a central database which is chares (physically or via internet) with everyone, and there is a local database which is physically controlled by the project ensuring privacy of data Periodically project managers submit their local database for upload to the central, at which tile all can see that data. :: color, composition, and layout

6 Eg: IRRIGATED RICE BREEDING PBGB DATA MANAGEMENT Cross Definition IRRIGATED RICE BREEDERS Evaluation Data and Pedigree Processing Field Books for HB, F2, PN, OYT, RYT CENTRAL IRIS DATABASE Grain Quality Quality Data IRB LOCAL DATABASE :: color, composition, and layout

7 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 :: color, composition, and layout

8 The GMS Data Model GERMPLASM has progenitors has group has source GENERATIVE GERMPLASM DERIVATIVE AND MAINTENANCE GERMPLASM Developed by METHODS Called NAMES Developed at LOCATIONS Named at Named by Developed by USERS With value of ATTRIBUTES Defined property of USER-DEFINED FIELDS :: color, composition, and layout

9 The GMS Schema

10 GMS Applications Genealogy Display Tools Pedigree Input Tools Breeder s Tools (Set Generation) Breeder s Tools (Field Books) Analysis Tools (Coefficients of Parentage) :: color, composition, and layout

11 ICIS Applications: SetGen

12 The Data Management System (DMS) The DMS is required to manage all characterization and evaluation data from any experimental design or survey for any set of traits and gernplasm Data is annotated by community curated trait ontologies, agreed scales (units), protocols and quality standards the trait dictionary :: color, composition, and layout

13 Data Model of DMS Study Filename: N2000DS.xls Variate Factor Level Observation Unit Datum :: color, composition, and layout

14 Annotation with Ontologies... Factor Variate PROPERTY Fert NITROGEN FERTILIZER Yield GRAIN YIELD SCALE kg/ha t/ha METHOD Total Application Adjusted Yield :: color, composition, and layout

15 Data Model... STUDY FACTOR PROPERTY VARIATE SCALE METHOD LEVEL DATUM OBSERVATION UNIT

16 DMS Schema OMS

17 DMS Applications Workbook Retriever Data Mining Tool Study Mart :: color, composition, and layout

18 DMS Applications: The Workbook I

19 DMS Applications: The Workbook II

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23 GCP-Compliant Molecular Breeding Platform Framework ICIS Windows Apps (*) ICIS Windows DLL ICIS( ) GCP Compliant MS.NET Clients GCP Compliant BioMoby Clients Web Browser Koios Web (JavaScript Client) MBDT/MOSEL/ GenoMedium (Eclipse RCP (Java)) MS.NET Web Services Provider (Java) BioMOBY Web Services Provider (Java) Koios Web (Java Server) Koios Workbench (Belenus/Java) Tomcat Web Application Container Pantheon (Demeter/Ceres/Java) Koios Engine (Java) (connects GCP DataSource(s)) (*) Existing MS Windows ICIS Applications (incl. Excel VB apps) using ICIS DLL ( ) Note that the same ICIS databases can be directly accessed by ICIS applications and wrapped as a GCP DataSource for direct GCP Platform access. Relational Database GCP DS (JPA/ Hibernate) Databases ( ) Web Service GCP DS (BioMoby) Other GCP DS (e.g. File Parsers) e.g. XML

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28 Zeus in action

29 Zeus - CropFinder in action

30 Germplasm pedigree viewer Fully integrated into Zeus but also available as a component for other applications Documentation with many examples: Features: Parental trees, germplasm neighborhood trees Show/Hide the full selection history and number of shown generations Selectable information that is included in the pedigree nodes Exportable to various image formats Customizable look & feel Included links to detailed germplasm sources

31 Partial parental pedigree (without full selection history) for IR 64

32 Partial pedigree of derivative neighborhood for IR 64