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Oracle® Health Sciences Translational Research Center User's Guide
Release 3.1.0.3
E66623-05
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Contents
List of Figures
List of Tables
Title and Copyright Information
Preface
Audience
Documentation Accessibility
Finding Information and Patches on My Oracle Support
Finding Documentation on Oracle Technology Network
Related Documents
Conventions
1
Getting Started
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
1.4
Known Issues
1.5
Disclaimer Regarding Third Party Data or Software
1.5.1
Public Domain Data
1.5.2
Software
2
Logging in to Oracle Health Sciences Translational Research Center
2.1
User Account
2.2
Roles and Permissions
2.3
Patient vs Subject Context
2.4
Landing Page
2.4.1
Manage User Groups
3
Cohort Explorer
3.1
My Workspace
3.1.1
My Recent Items
3.1.2
My Queries
3.1.3
My Cohort List
3.1.4
My Gene Sets
3.1.5
Shortcuts
3.1.6
Queries or Lists Shared with Me
3.1.7
Queries or Lists Shared with All
3.2
Manage Queries
3.2.1
My Queries
3.2.2
Sharing Queries
3.3
Manage Cohort Lists
3.3.1
My Cohort Lists
3.3.2
Sharing Cohort Lists
3.4
Manage Gene Sets
3.4.1
Create New or Edit Gene Set
3.4.2
Manage Gene Set
3.5
Jobs
3.5.1
Job Details
3.5.2
Job Inputs
3.5.3
Job Outputs
3.6
Manage User Groups
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
5.2.3
Displaying Reference Range Values
5.3
Cohort Timelines Viewer
5.3.1
Selecting Patients or Subjects
5.3.2
Selecting Data
5.3.3
Displaying Patient or Subject Data
5.3.3.1
Selecting the Timeline Mode
5.3.4
Align Data by Patient or Subject Event
5.3.5
Including Criteria Used in Query Option
5.4
Cohort Reports
5.4.1
Demographic Reports
5.4.1.1
Handling Unknown Data
5.4.2
Clinical Reports
5.4.2.1
Handling Unknown Data
5.4.3
Genomic Reports
5.4.3.1
Changes in Genomic Reports
5.4.3.2
Data Presence
5.4.3.3
SNP, Indel and CNV
5.4.3.4
Variant Level Reports
5.4.3.5
Structural Variations in Genes
5.4.3.6
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 Position
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
Navigating Through Selected Patients or Subjects
6.1.2
Source
6.1.3
Clinical Data
6.1.4
Genomic Data
6.1.4.1
Variants Found
6.1.4.2
Dalliance Browser
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
8.2
Genomic Query
8.2.1
Gene Search
8.2.2
Variant Search
9
Benefits of Cohort Explorer and Omics Data Bank if Purchased Together
9.1
Benefits
Index