1K1RG-Documentations

1K1 Rice Genome Project – Philippines (Overview)

📊 1kRG Activity Plan and Deliverables - IRRI

Table of Contents

1. 🎯 Objectives
2. 📅 Year 1 Targets
   • 📅 Quarter 1
     • 📋 Activities
     • 📅 Sub-Activities
     • 📜 Deliverables
     • 🎯 Tangible Results

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🎯 OBJECTIVES

1. 🔧 Implement SNP-Seek Database Components of PH Rice GDB Portal at UPLB (including server configuration)
2. 🌾 Populate Databases with information relevant to the Philippine TRVs from the public domain
3. 🧬 Implement Bioinformatic Tools that will allow use of the new reference genomes and the re-sequencing data from the Philippine TRVs
4. 📚 Training on Genome Assembly and Annotation
5. 🖥️ Training on Database Development and Curation
6. 🔍 Training on the Use of the PH Rice GDB Database and other associated tools

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📅 Year 1 Targets

• 💻 Software Development and Server Setup on Y1 Q1–Q3
• 🚀 Pilot SNP-Seek Component of PH Rice GDB alpha version released by Y1 Q4
• 📊 Collated and Curated Passport and existing agro-morpho data for TRVs by Y1 Q3–Q4
• 🎓 First Training conducted by Y1 Q3
• 📚 Continuous Training of project staff by the IRRI team from Y1 Q1–Q3
• 👩‍🎓 1st Intake of Students as a special project in UPLB by Q2

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📅 Quarter 1

📋 Activities

• Software Development and Server Setup

📅 Sub-Activities

1. Evaluation and gap analysis of current SNP-Seek database (v3) software for viability for PH Rice GDB
2. Genotyping Data Preparation and Transformation
3. Variety and phenotyping data preparation and transformation

📜 Deliverables

Deliverable 1: Current SNP-Seek DB Evaluation, Gap Analysis, and Development Roadmap

1. Review SNP-Seek v3 Features

• Identify key features and functionalities required by PH Rice GDB
• Confirm feature alignment with user needs (from project team discussions)

2. Set Up Software Development Version Control

• Create a project directory structure
• Organize configurations, components, utilities, and assets
• Identify and design initial API structure, use cases, and endpoints required by PH Rice GDB
• Identify additional use cases not in the current design but important to PH Rice GDB end users

🎯 Tangible Results

1. Feature review document (includes API/Use Case Design Document)
2. Code Repository (Bitbucket or GitHub) with the initial project structure

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Deliverable 2: Data Preparation and Transformation

Genotyping data for subset 3KRG accessions from PH

1. Clean, normalize, and validate data (VCFs)
2. Transform data into a suitable intermediate format (prior to HDF5 creation)
3. Generate HDF5 files for efficient storage and retrieval of structured data
4. Prepare and curate passport and agro-morphological data for 1k1 TRVs
5. Transform variety data for application loading

🎯 Tangible Results

1. Scripts for data validation and transformation, uploaded to repository
2. Transformed data (genotype) in required formats
3. HDF5 files with structured data
4. Raw Data - Sample Raw Data and outputs