| Oracle® Health Sciences Omics Data Bank Release Content Document Release 1.0.1 Part Number E27537-02 |
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| View PDF |
| Oracle® Health Sciences Omics Data Bank Release Content Document Release 1.0.1 Part Number E27537-02 |
|
| View PDF |
Release Content Document
Release 1.0.1
E27537-02
April 2012
The Release Content Document (RCD) communicates information about Oracle Health Sciences Omics Data Bank.
Oracle Health Sciences Omics Data Bank (ODB) is a new product from Oracle Health Sciences. ODB 1.0.1 is a cross-platform data model for omics information. It enables users to ask biologically meaningful questions. Moreover, it is fully integrated with the Oracle Health Sciences Cohort Explorer (OHSCE), bringing both phenotypic and genotypic data to researchers and clinicians.
The data model supports reference omics information and annotation, as well as result data from each individual sample. ODB 1.0.1 is packaged with a set of data loaders for reference and result data, thereby reducing your adoption barrier. It also includes Oracle SecureFile as an optional file storage mechanism.
ODB 1.0.1 includes the following components:
Reference tables for biological context
Results tables for individual sample data
Multiple omics datatypes
Simple variation including SNV, insertion, and deletion
Gene expression
Copy number variation
Reference data loaders for
Ensembl (for example, genome definition, annotations from dbSNP and COSMIC, and so on)
Swiss-Prot
HUGO
Pathwaycommons
Result data loaders for
Variant call format (VCF v4.1)
Complete Genomics variant format (MasterVar)
Tab-delimited format for expression data
Mutation annotation format (MAF)
Oracle SecureFile as an option for all data files that should be kept in a secure environment
Cross-Platform Omics Data Model
ODB supports omics data management and analysis regardless of the scientific approach (for example, next generation sequencing, gene expression, and so on) and technology platform (for example, Illumina, CompleteGenomics, and so on).
ODB can model reference DNA, gene, and protein information from multiple species.
Cross Reference Omics Information
ODB can handle cross reference information for DNA source, gene, gene component, variant, protein, and protein component.
Integration with Clinical Data
ODB is fully compatible with the Cohort Data Mart (part of OHSCE v1.0.0.1) to let end users integrate both clinical and omics information in their cohort selection.
Easy-to-use command line data loaders with comprehensive instructions.
ODB differentiates no-call regions from those that are identical to the reference genome in the result data.
Links with Original Result Files
ODB links derived genomic results with their corresponding files either through Oracle SecureFile or a regular file directory.
Result tables are partitioned by study, and several reference tables are partitioned by DNA_SOURCE.
| Term | Definition |
|---|---|
|
COSMIC |
Catalogue of Somatic Mutations in Cancer |
|
HUGO |
HUGO Gene Nomenclature Committee |
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MAF |
Mutation Annotation Format |
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ODB |
Omics Data Bank |
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OHSCE |
Oracle Health Sciences Cohort Explorer |
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SNV |
Single-nucleotide Variation |
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TRC |
Translation Research Center |
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VCF |
Variant Call Format |
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Oracle Health Sciences Omics Data Bank Release Content Document, Release 1.0.1
E27537-02
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