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Oracle® Health Sciences Omics Data Bank Programmer's Guide
Release 1.0.1
Part Number E27509-02
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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