Review of ICIS for Molecular Breeding

From ICISWiki

Contents 1 Review of DMS and GEMS 6.0 schema and implementation of ICIS Data Source use cases for Molecular Breeding 1.1 Scope of Review 1.2 Final outcomes of Review 1.3 Working Documents 1.4 Supporting Documents

Review of DMS and GEMS 6.0 schema and implementation of ICIS Data Source use cases for Molecular Breeding

Here you will find all information required for the review and implementation. In most cases these are links to existing wiki pages that need to be read and in some cases updated during the review. By only maintaining links here these pages can be used as a resource after the review has finished.

Scope of Review

The review is restricted to following areas:

1. Development of query, visualisation and analysis user requirements for genotyping studies for molecular breeding
2. Formalized query use cases for these user requirements
3. Review of GEMS version 6.0 schema in respect to these use cases
4. Implementation of use cases in the GCP ICIS Data Source
5. Implementation of ICIS tools for uploading gneotyping data
   
6. Implementation of GUI in Zeus and GenoMedium for these use cases
   1. GenoMedium query wizards or Zeus 'forms' for gathering user parameters for these use cases
   2. Development of new visualisation or integration of existing visualisation for genotyping studies

Final outcomes of Review

• Proposed changes in ICIS 6.0
• Four Types of Database Storage for Study Data

Working Documents

• Workflows for molecular breeding projects
• User requirements for molecular breeding informatics
• Proposed GEMS 6.0 schema
• Managing Marker Lists
• Sample Tracking with IMS
• ICIS Version 6.0
• ICIS Known Genes
• IRRI-CRIL MBP Consultation with IRRI Breeders February 9 - 2009
• ICIS Workbook Study types

Supporting Documents

• ICIS
  • Current support for storage of molecular data in ICIS DMS
  • Current GEMS 5.4 schema
• Review of existing SNP Data Management projects
• Domain Model
  • Domain Model (Demeter) Java API
  • Germplasm Genotype Model
• Formalised use cases
  • Genomic Feature Detectors (Markers)
  • Retrieve Detected Variants (Allele)
  • Retrieve Tabular Data
    • Retrieve Genotype Study as TabularData
      • Retrieve Genotype Study as TabularData for Dominant Markers
      • Retrieve Genotype Study as TabularData for Codominant Markers
      • Retrieve Genotype Study as TabularData with Frequency

Zeus is the new name for Koios Web (release 3). Please note Koios now only refers to the search engine.