Contents

List of Figures

List of Tables

Title and Copyright Information

Preface

• Audience
• Disclaimer Regarding Third Party Data
• Documentation Accessibility
• Finding Information and Patches on My Oracle Support
• Finding Documentation on Oracle Technology Network
• Related Documents
• Conventions

1 Omics Data Model

• Introduction
  • Reference Data
  • Result Data
• Logical Data Model
• Reference Data Tables
• Result Data Tables

2 Prerequisites for Loading Data

• Setting up a Directory Object
• Setting up Oracle Wallet
• Integration with Oracle Health Sciences Cohort Explorer Data Model or Another External Data Model
  • Specimen and Vendor Number Requirement
• Reference Version Compatibility
• Handling Newline Characters in Input Files

3 Loaders for Reference Data

• Ensembl and SwissProt Loaders (Java)
  • Installing the Loader
  • Files to Load
  • Loading the Data
• HUGO Loader (PLSQL)
• GVF Ensembl Loader (PLSQL)
• Pathway Loader
  • Description
  • Installing and Running the Loader
  • Files and Tables Used in Loading
• Template of Command Line Arguments for Reference Loaders
  • Glossary of Parameter Templates
  • SwissProt
  • EMBL
  • HUGO
  • GVF
  • Pathway

4 Loaders for Result Data

• Prerequisites
• Overview of Result Loaders
• Probe Loader
  • Assumptions for Data File
• Gene Expression Loader
  • Running Gene Expression Loader on Windows
  • Running Gene Expression Loader on Linux
  • Assumptions for Data File
• CGI Sequence Data Loader
  • Files to Load
  • Data Load
• MAF Sequence Data Loader
  • Files to Load
  • Data Load
• VCF Sequence Data Loader
  • Files to Load
  • Data Load
• Typical Errors Associated with Result Loaders (CGI, MAF, VCF, Gene Expression)
• Template of Command Line Arguments for Result Loaders
  • Glossary of Parameter Templates
  • Probe Annotation
  • Gene Expression
  • CGI masterVar
  • MAF
  • VCF

5 Model Dictionary

• System Columns
• Reference Data Tables
• Result Data Tables
• Table Descriptions

6 Use Case Examples

• Use Cases
  • Scenario 1
  • Scenario 2
  • Scenario 3
  • Scenario 4
  • Scenario 5
  • Scenario 6
  • Scenario 7
  • Scenario 8
  • Scenario 9
  • Scenario 10
  • Scenario 11
  • Scenario 12
  • Scenario 13
  • Scenario 14
  • Scenario 15
  • Scenario 16
  • Scenario 17
  • Scenario 18
  • Scenario 19
  • Scenario 20
  • Scenario 21
  • Scenario 22
  • Scenario 23
  • Scenario 24
  • Scenario 25
  • Scenario 26
  • Scenario 27
  • Scenario 28
• Global Temporary Table Creation Code Snippets
  • table query_1
  • table query_2
  • table query_2a
  • table query_4
  • table query_5
  • table query_6
  • table query_7
  • table query_8
  • table query_9
  • table query_10
  • table query_11
  • table query_12
  • table query_15
  • table query_17
  • table query_18
  • table query_19a
  • table query_26a
  • table query_26b
  • table query_26c
  • table query_26d

7 Miscellaneous Topics

• Querying Database Cross-references for Variations
  • Ensembl db_xref Qualifier Issue
  • Swissprot db_xref Qualifier Issue
• Mitochondrial Chromosome Mappings
• Promoter Offset
• CGI End Position

A Additional Result Tables

• Pre-Seeded Tables
• Populated by User or Loader
• Unpopulated Result Entities or Tables

Index