GMOD

Chado Tutorial 2012

This Chado tutorial was presented by Scott Cain as part of the 2012 GMOD Summer School.

To follow along with the tutorial, you will need to use AMI ID: ami-ad2f98c4, name: GMOD 2012 final day, available in the US East (N. Virginia) region. See the GMOD Cloud Tutorial for information on how to get this AMI.

Chado is the database schema of the GMOD project. This session introduces database concepts, and then provides an overview of Chado’s design and architecture, and then goes into detail about how to use a Chado database.

Contents

• 1 Theory
  • 1.1 Introduction
    • 1.1.1 Database Terminology
      • 1.1.1.1 What’s a database?
      • 1.1.1.2 SQL
  • 1.2 Why Chado?
  • 1.3 Chado Architecture: Modules
    • 1.3.1 Extensible
    • 1.3.2 Plus
    • 1.3.3 Module Caveats
  • 1.4 Exploring the schema
    • 1.4.1 Sequence Module
      • 1.4.1.1 Features
    • 1.4.2 CV (Controlled Vocabularies) Module
      • 1.4.2.1 Controlled Vocabularies
      • 1.4.2.2 Ontologies
      • 1.4.2.3 CVs and Ontologies in Chado
        • 1.4.2.3.1 Data Integrity
        • 1.4.2.3.2 Data Portability and Standardization
        • 1.4.2.3.3 Complexity
    • 1.4.3 Opening our sample database
    • 1.4.4 Our first example query
    • 1.4.5 General Module
      • 1.4.5.1 IDs
        • 1.4.5.1.1 Public IDs
        • 1.4.5.1.2 Private IDs
      • 1.4.5.2 IDs in Chado
    • 1.4.6 Properties
      • 1.4.6.1 Relationships
      • 1.4.6.2 Locations
        • 1.4.6.2.1 Interbase Coordinates
        • 1.4.6.2.2 Location Chains
        • 1.4.6.2.3 featureloc Table
      • 1.4.6.3 Example: Gene
      • 1.4.6.4 Example: Computational Analysis
      • 1.4.6.5 Other Feature Annotations
      • 1.4.6.6 Extending Chado: Properties tables and new modules
• 2 Practice
  • 2.1 Prerequisites
    • 2.1.1 PostgreSQL
      • 2.1.1.1 Edit config files
      • 2.1.1.2 Create a gmod user
      • 2.1.1.3 Installing DBIx::DBStag by hand
    • 2.1.2 BioPerl
    • 2.1.3 Let’s Go!
    • 2.1.4 Environment Variables
  • 2.2 Installing GMOD
    • 2.2.1 Saving your progress to this point
    • 2.2.2 A Note about Redos
  • 2.3 Preparing GFF data for loading
    • 2.3.1 Working with Large GFF files
    • 2.3.2 Loading GFF3
    • 2.3.3 Capturing the output to check for problems
    • 2.3.4 Really loading data
      • 2.3.4.1 Adding our organism
      • 2.3.4.2 Try again
  • 2.4 Loading other data
• 3 Chado for Expression, Genotype, Phenotype, and Natural Diversity
  • 3.1 Expression
    • 3.1.1 What defines an expression pattern?
    • 3.1.2 How does Chado deal with this variety?
    • 3.1.3 FlyBase Example
    • 3.1.4 Chado Allows
    • 3.1.5 Table: expression
    • 3.1.6 Table: expression_cvterm
  • 3.2 Genotype
    • 3.2.1 Table: genotype
    • 3.2.2 Table: feature_genotype
  • 3.3 Environment
    • 3.3.1 Table: environment
    • 3.3.2 Table: environment_cvterm
  • 3.4 Phenotype, Natural Diversity and Atlas Support

Theory

Introduction

Database Terminology

Or six years of school in 15 minutes or less.

• A Brief Guide to Databases
• Chado Tables

What’s a database?

• Chado is a schema, a database design - a blueprint for a database containing genomic data
• Distinct from
  • Database Management System (DBMS)
    • Software system for storing databases
    • e.g., Oracle, PostgreSQL, MySQL
  • Database, a very loose term
    • Any set of organized data that is readable by a computer
    • A web site with database driven content, e.g., FlyBase
    • Schema + DBMS + Data

SQL

SQL is a standardized query language for defining and manipulating databases. Chado uses it. SQL is supported by all major DBMSs.

FlyBase Field Mapping Tables shows some example SQL that queries the FlyBase Chado database. (Caveat: FlyBase sometimes uses Chado in ways that no other organizations do.)

Will SQL be on the test?

No, we aren’t going to teach in-depth SQL in this course but we will use it in examples and show how to write queries in Chado.

You can do basics with Chado without knowing SQL. Many common tasks already have scripts written for them. However, as you get more into using Chado, you will find that a working knowledge of SQL is necessary.

Why Chado?

• Integration
  • Supports many types of data, integrates with many tools
• Modular
  • Use only what you need, ignore the rest
• Extensible
  • Write your own modules and properties
• Widely used
  • FlyBase - Chado started here, large diverse dataset and organization

Facts about “Chado Tutorial 2012”

Has topic	Chado +

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• Last updated at 16:26 on 2 September 2018.
• Content is available under a GNU Free Documentation License unless otherwise noted.