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Contents

List of Figures

List of Tables

Title and Copyright Information

Preface

• Audience
• Documentation Accessibility
• Related Documents
• Conventions

1 Getting Started with Oracle Health Sciences Translational Research Center

• 1.1 Overview
  • 1.1.1 What You Can Do Using Oracle Health Sciences Translational Research Center
• 1.2 Architecture
• 1.3 Regulatory Compliance
  • 1.3.1 Tracking Data
  • 1.3.2 Managing ETL Versions
  • 1.3.3 Security
  • 1.3.4 Disclaimer Regarding Third Party Data or Software
    • 1.3.4.1 Public Domain Data
    • 1.3.4.2 Software

2 Logging in to Oracle Health Sciences Cohort Explorer

• 2.1 User Account
• 2.2 Roles and Permissions
• 2.3 Patient vs Subject Context
• 2.4 Navigator
  • 2.4.1 Cohort Explorer
  • 2.4.2 Manage User Groups

3 Cohort Explorer

• 3.1 Home
  • 3.1.1 My Workspace
    • 3.1.1.1 My Recent Items
    • 3.1.1.2 My Queries
    • 3.1.1.3 My Cohort List
    • 3.1.1.4 Queries or Lists Shared with Me
    • 3.1.1.5 Queries or Lists Shared with All
  • 3.1.2 Manage Queries
    • 3.1.2.1 My Queries
    • 3.1.2.2 Sharing Queries
  • 3.1.3 Manage Cohort Lists
    • 3.1.3.1 My Cohort Lists
    • 3.1.3.2 Sharing Cohort Lists
  • 3.1.4 Manage Gene Sets
    • 3.1.4.1 Create New or Edit Gene Set
    • 3.1.4.2 Manage Gene Set
  • 3.1.5 Jobs
    • 3.1.5.1 Job Details
    • 3.1.5.2 Job Inputs
    • 3.1.5.3 Job Outputs

4 Cohort Query

• 4.1 Overview
• 4.2 Cohort Criteria Selection
  • 4.2.1 Required Fields for Criteria
  • 4.2.2 Patient Information or Subject Information
    • 4.2.2.1 Demographics
    • 4.2.2.2 Consent
  • 4.2.3 Clinical Data
    • 4.2.3.1 Diagnosis
    • 4.2.3.2 Clinical Encounter
    • 4.2.3.3 Procedure
    • 4.2.3.4 Medication
    • 4.2.3.5 Patient History
    • 4.2.3.6 Test or Observation
    • 4.2.3.7 Specimen
    • 4.2.3.8 Study
    • 4.2.3.9 Relative Time Events
  • 4.2.4 Genomic Data
    • 4.2.4.1 Microarray Expression
    • 4.2.4.2 Sequence Variants
    • 4.2.4.3 Copy Number Variation
    • 4.2.4.4 RNA-seq Expression
    • 4.2.4.5 Metadata Filters
• 4.3 Patient or Subject Count
• 4.4 Inclusion and Exclusion Criteria
• 4.5 Final Patient or Specimen Count
• 4.6 Query Library
  • 4.6.1 Load Query
  • 4.6.2 Save Query

5 Cohort Viewer

• 5.1 Cohort Viewer
• 5.2 Cohort List Viewer
  • 5.2.1 Patients
  • 5.2.2 Patient or Subject Data
• 5.3 Cohort Timelines Viewer
  • 5.3.1 Selecting Patients or Subjects
  • 5.3.2 Selecting Data
  • 5.3.3 Display of Patient or Subject Data
  • 5.3.4 Align Data by Patient or Subject Event
• 5.4 Cohort Reports
  • 5.4.1 Demographic Reports
  • 5.4.2 Clinical Reports
  • 5.4.3 Genomic Reports
    • 5.4.3.1 Sequence Variants
    • 5.4.3.2 Copy Number Variation
    • 5.4.3.3 Structural Variations in Genes
    • 5.4.3.4 Structural Variations in Gene Pairs
• 5.5 Genomic Data Export
  • 5.5.1 Selecting Patients or Subjects
  • 5.5.2 Selecting Results to Export
  • 5.5.3 Selecting Location
    • 5.5.3.1 In Genes From
    • 5.5.3.2 At Genomic Region
    • 5.5.3.3 All Data
  • 5.5.4 Selecting File Type
    • 5.5.4.1 Mutation - VCF
    • 5.5.4.2 Copy Number Variation - SEG
    • 5.5.4.3 Gene Expression - RES
    • 5.5.4.4 Gene Expression Dual Channel - GCT
    • 5.5.4.5 Export Options

6 Single Patient or Subject Viewer

• 6.1 View Records
  • 6.1.1 Clinical Data
  • 6.1.2 Genomic Data
    • 6.1.2.1 Variants Found
• 6.2 Circular Genomics Viewer
  • 6.2.1 Selecting Data to Plot
    • 6.2.1.1 Microarray Expression
    • 6.2.1.2 Sequencing-Variant Density
    • 6.2.1.3 RNA-Seq Expression
    • 6.2.1.4 Copy Number Variation
    • 6.2.1.5 Dual Channel Microarray Expression
  • 6.2.2 Circular Representation

7 Dashboard

• 7.1 Standard Reports
  • 7.1.1 Selection of Date Range Using Statistics from and to Prompt
  • 7.1.2 Patients Diagnosed and Treated (TRC-CER-001,TRC-SD-P004)
  • 7.1.3 Number of Treatments Performed (TRC-CER-005)
  • 7.1.4 Ethnicity or Race of Newly Diagnosed Patients (TRC-CER-002)
  • 7.1.5 Age or Gender of Newly Diagnosed Patients (TRC-CER-003)
  • 7.1.6 Biospecimen Samples Status (TRC-CER-006)
  • 7.1.7 Detailed Information on Each Report and Prompt Set
    • 7.1.7.1 Statistics from-to (Prompt Set TRC-CEP-001)
    • 7.1.7.2 Patients Diagnosed and Treated (Report TRC-CER-001)
    • 7.1.7.3 Number of Treatments Performed (Report TRC-CER-003)
    • 7.1.7.4 Ethnicity or Race of Newly Diagnosed Patients (Report TRC-CER-004)
    • 7.1.7.5 Age or Gender of Newly Diagnosed Patients (Report TRC-CER-005)
    • 7.1.7.6 Biospecimen Samples Status (Report TRC-CER-006)

8 Genomic Query

• 8.1 Omics Data Bank
  • 8.1.1 Genomic Query

9 Benefits of Cohort Explorer and Omics Data Bank if Purchased Together

• 9.1 Benefits

Index