| Oracle® Health Sciences Omics Data Bank Release Content Document Release 2.5 E41335-01 |
|
| PDF · Mobi · ePub |
| Oracle® Health Sciences Omics Data Bank Release Content Document Release 2.5 E41335-01 |
|
| PDF · Mobi · ePub |
Release Content Document
Release 2.5
E41335-01
June 2013
ODB is a flexible, cross-platform omics data management system that delivers meaningfully biological contents and the extreme performance required by today's translational research studies. 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 2.5 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 2.5 includes the following components with indication of new components added in this release:
Reference and annotation tables for biological context
Reference genome build, genome annotation, and variant annotation from Ensembl
Protein information from Swiss-Prot and UniProt
Gene information from HUGO
Pathway information from Pathwaycommons
SIFT and Polyphone functional annotations
Multi-version reference support (new)
Selected clinical annotations from BIOBASE's GenomeTrax database, including HGMD and Drug Targets annotations (new)
Result tables for individual sample data across multiple omics datatypes
Simple variation including SNV, small insertion, and small deletion
Gene expression including both single-channel and two-channel microarray data
Copy number variation
RNA sequencing data
Full genotype support including both reference and mutant allele (new)
Structural variant including chromosomal re-arrangement, large insertion, and large deletion (new)
Data for experiment and analysis details (new)
Data Loaders
Reference data loaders for
Ensembl (for example, genome definition, sequence variant annotations from dbSNP and COSMIC, and so on)
Swiss-Prot and UniProt
HUGO
Pathwaycommons
SIFT and Polyphen functional annotations
HGMD and Drug Targets from BIOBASE's GenomeTrax (new)
Result data loaders for
VCF v4.1 including both simple sequence variant and large-size structural variant with improved flexibility and usability (new)
GVCF for variant and monomorphic reference genotype (new)
Tab-delimited format for both single-channel and two-channel microarray expression data
Mutation annotation format
Copy number variant format defined in The Cancer Genome Atlas (TCGA) project
RNA-seq format defined in TCGA project
SecureFile (optional)
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, Life Technologies, CompleteGenomics, and so on).
Multiple Species: 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.
Support of Multiple Versions of Reference Genomes: ODB can organize your result data based on the version of reference genome the data was aligned with. This design improves data management efficiently and reduces interpretation error.
Integration with Clinical Data: ODB is fully compatible with the Cohort Data Mart (part of OHSCE v2.0.2.1) to let end users integrate both clinical and omics information in their cohort selection.
Monomorphic Reference Genotype vs. No-call Region: ODB differentiates monomorphic reference genotype from no-call regions to improve genotype characterization.
Annotation Management: Bringing annotation data to the results, ODB efficiently manages ever improving omics annotations.
Scalability: Result tables are partitioned by study or gene based on your data distribution and usage patterns.
Data Loaders: Easy-to-use command line data loaders with comprehensive instructions.
Table 1 lists the terms used in this document.
| Term | Definition |
|---|---|
|
COSMIC |
Catalogue of Somatic Mutations in Cancer |
|
DNA |
Deoxyribonucleic Aid |
|
GVCF |
Genome Variant Call Format |
|
HGMD |
Human Gene Mutation Database |
|
HUGO |
HUGO Gene Nomenclature Committee |
|
MAF |
Mutation Annotation Format |
|
ODB |
Omics Data Bank |
|
OHSCE |
Oracle Health Sciences Cohort Explorer |
|
RNA |
Ribonucleic Acid |
|
SNV |
Single-nucleotide Variation |
|
TRC |
Translation Research Center |
|
VCF |
Variant Call Format |
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Oracle Health Sciences Omics Data Bank Release Content Document, Release 2.5
E41335-01
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