1/9

Contents

Title and Copyright Information

Preface

• Documentation Accessibility
• Finding more information
• Related documents

1 What can I do with Oracle Healthcare Translational Research?

2 Modify criteria for queries using the Cohort Query

• Before you begin building your query
• Build a cohort query
  • Patient Information
    • Demographics
    • Consent
  • Clinical Data
    • Diagnosis
    • Clinical Encounter
    • Procedure
    • Medication
    • Patient History
    • Test or Observation
    • Specimen
    • Study
    • Relative Time Events
  • Genomic Data
    • Sequence Variants
    • Copy Number Variation
    • Microarray Expression
    • RNA-seq Expression
    • Metadata Filters
• Combine inclusion and exclusion criteria
  • Modify details of an existing criteria statement
  • Understand the logic behind Inclusion and Exclusion criteria
• View Patient or Subject Count and data
• View Specimen Count
• Save a query
• Load a saved query

3 View and maintain cohorts

• View cohort lists
  • Filter data in cohort lists
  • Display reference range values
• View cohort timelines
  • Select patients or subjects
  • Filter data in cohort timelines
  • Display patient or subject data
  • Select the Timeline Mode
• Align data by Patient or Subject Event
• View cohort reports
  • View demographic reports
    • Handle unknown data
  • View clinical reports
    • Handle Unknown Data
  • View genomic reports
    • View genomic data presence reports
    • View Genomic Reports - SNP, Indel, CNV
      • Mutated Gene Frequency and Gene Expression
      • Copy Number Variation Frequency and Gene Expression
      • Mutated Gene vs Sample Matrix
      • Variant vs Sample Reports
    • Structural Variations
      • Structural Variations in Genes
      • Structural Variations in Gene Pairs
• Export genomic data
  • Select results to export
  • Set the location
  • Select file type
    • Mutation - VCF
      • Handle Non-variant and No-call Data
      • Handle Duplicate Genetic Information Exports
    • Copy Number Variation - SEG
    • Gene Expression - RES
    • Gene Expression Dual Channel - GCT
  • Specify the export options

4 View data of a single patient or subject

• View records
  • Navigate through selected patients or subjects
  • View genomic data
    • Specimen with Genomic Results
    • Derived Files
    • File Lineage
    • Variants Found
  • Select the Assembly Version
  • Use the Dalliance Browser
• View circular genomic data
  • Select data to plot
    • Microarray Expression
    • Sequencing-Variant Density
    • RNA-Seq Expression
    • Copy Number Variation
    • Dual Channel Microarray Expression

5 Search genomic results with the Genomic Query

• Search for genes
• Search for variants
  • Perform a search by Variant ID
  • Perform a search by Variant Attributes

6 Manage queries, gene sets and jobs in My Workspace

• What can I do in My Workspace?
  • My recent items
  • My queries
  • Queries or lists shared with me
  • My cohort lists
  • Queries or lists shared with all
  • My gene sets
• Manage queries
  • Search for queries
  • Modify queries
• Manage cohort lists
  • Search and view your cohort lists
  • Modify cohort lists
• Manage gene sets
  • Create a new gene set
  • Edit a gene set
  • Manage a gene set
• Administrate user groups
  • Create a user group
  • Assign users to a group
  • Remove users from a group
  • Manage user groups
• Schedule and monitor genomic data export jobs
  • Manage jobs
  • View job inputs
  • View and download job outputs
• Switch between Patient and Subject context