🌾 1000-Genomes Rice Genome Project

Database Curation
& Loading Training

SNP-Seek / Chado / HDF5 — hands-on workshop covering database loading, bioinformatics pipelines, Linux tooling, and scalable genomic data management.

Dates
Venue IRRI, Los Baños
Format Lecture + Hands-on Labs
2 Days
13 Sessions
4 New Topics
6+ Lab Exercises
🌾 1k1RG Project SNP-Seek · Chado · HDF5

About This Training

Background, what to expect, and what you will be able to do after.

The 1k1RG Database Curation and Loading Workshop is a two-day, hands-on technical training for IT personnel responsible for operating and maintaining the SNP-Seek rice genomics platform. SNP-Seek runs on a specialized stack — PostgreSQL with the Chado biological schema, and HDF5 for genotype matrices. This training closes the gap between server administration and the domain-specific knowledge required to independently curate, load, and verify genomic data without constant support from the development team.

Day 1

Schema, Ontologies & Data Loading

  • 1k1RG project overview and the SNP-Seek technology stack
  • Linux essentials and SQL fundamentals for database operations
  • Biological ontologies — controlled vocabularies and how cvterm types every record in Chado
  • Chado schema deep dive — feature, featureloc, stock, variantset, and the PostgreSQL/HDF5 boundary
  • Lab: install PostgreSQL, restore a Chado training database, explore with psql
  • Lab: load a reference genome into Chado using \copy and GFF-based loader scripts
  • Lab: bulk-load a full genomic dataset using uploadDataset.sh
Day 2

HDF5, VCF Pipeline & Open Lab

  • HDF5 — why the genotype matrix lives outside PostgreSQL and how SNP-Seek reads it
  • VCF format — file structure, INFO/FORMAT fields, and what genotype calls represent
  • Full two-step pipeline: VCF → genotype matrix → HDF5 (hands-on run)
  • Open lab — finish unfinished exercises, troubleshoot, and ask questions
  • Closing Q&A and handover

Learning Outcomes

  • Explain how Chado uses cvterm as the semantic type system across all core tables
  • Set up a PostgreSQL Chado database and restore a training dump independently
  • Navigate and query the Chado schema using psql meta-commands and SQL joins
  • Load a reference genome into Chado from a pre-built CSV or a GFF annotation file
  • Run uploadDataset.sh to bulk-load stock, SNP, and variant data into Chado
  • Explain the PostgreSQL/HDF5 boundary — what lives in the database and what does not
  • Execute the full VCF → genotype matrix → HDF5 pipeline and verify the output
  • Diagnose and recover from common loader failures (term-resolution errors, ID conflicts)

Prerequisites

  • Linux command-line comfort — navigation, file operations, running scripts
  • SQL fundamentals — SELECT, JOIN, INSERT, basic relational tables
  • SSH access to the training server (credentials distributed before the session)
⬇
Materials & Downloads Scripts, data files, and slide decks — grouped by session topic
→

Day 1 — Wednesday

9:00 AM – 5:00 PM
Time Session Speaker Type
9:00 – 9:30 01–02 Orientation & 1k1RG Project Overview Arian Jacildo Lecture
9:30 – 10:30 03 Linux Basics — Part 1 NEW Garth Hendrich Lapitan Lab
10:30 – 10:45 ☕ Break
10:45 – 12:00 03 Linux Basics — Part 2 NEW Garth Hendrich Lapitan Lab
12:00 – 1:30 🍱 Lunch Break
1:30 – 2:15 05 Ontology Concepts Jeffrey Detras Lecture
2:15 – 3:00 06 Chado Schema Deep Dive & Ontology Implementation NEW Lord Hendrix Barboza Lecture
3:00 – 3:15 ☕ Break
3:15 – 3:45 07 Setup and Explore Chado Schema Lord Hendrix Barboza Lab
3:45 – 5:00 08 Loading Reference Genome into Chado Lord Hendrix Barboza Lab

Day 2 — Thursday

9:00 AM – 12:15 PM
Time Session Speaker Type
9:00 – 9:30 09 VCF Format & the Two-Step Pipeline Riza Pasco Lecture
9:30 – 10:30 10 Steps 1 & 2: Full Pipeline Run VCF → HDF5 Riza Pasco Lab
10:30 – 10:45 ☕ Break
10:45 – 11:15 11 HDF5 — What It Is and Why SNP-Seek Uses It NEW Lord Hendrix Barboza Lecture
11:15 – 11:30 12 Loading Dataset into Chado Lord Hendrix Barboza Lab
11:30 – 12:00 13 SQL Basics Garth Hendrich Lapitan Lab
12:00 – 12:15 14 Closing, Q&A & Handover All Wrap-up

Session Types

📘 Lecture
🧪 Lab
🛠 Lecture+Lab
🎤 Demo
⚙ Admin
🎯 Wrap-up
🆕 New in 2026

Workshop Topics

  • Chado schema & ontologies
  • Linux bioinformatics workflow
  • PostgreSQL & SQL essentials
  • HDF5 genotype storage
  • VCF → HDF5 pipeline
  • Bulk data loading scripts

Speakers & Facilitators

  • Arian Jacildo — Orientation & 1k1RG Overview (01–02)
  • Garth Hendrich Lapitan — Linux Basics & SQL Fundamentals (03, 13)
  • Jeffrey Detras — Ontology Concepts (05)
  • Lord Hendrix Barboza — Chado Schema, Bulk Loading, HDF5 (06–08, 11–12)
  • Riza Pasco — VCF Format & Pipeline (09–10)

📡 Offline Backup

If Wi-Fi is unavailable, open index.html from the distributed USB drive. All session pages, scripts, and data files work fully offline.