Table 3

Comparing InSilico DB with other databases

InSilico DB functionality

Description

GEO comparison

Expression Atlas


Data sources

Public repositories

Support main platforms of GEO, SRA and notable public datasets

All platforms supported, limited to submissions

Support for Array-Express

Grouping

New datasets created by subsetting and combining datasets

Biocuration

Collaborative

Commonalizing biocuration effort through collaborative platform

Vocabulary

User-defined tabular structured text

Free text

Ontologies & free text

Versioning

Multiple, user-contributed, batch submissions from biocuration projects, and in-house biocurator

In-house biocuration

In-house biocuration

Augment

Enrich curation with analysis results

Data management

Processing raw data with latest algorithms, for example, fRMA for microarrays, TopHat+Cufflinks for RNA-Seq

Datasets can be shared at progressive levels, including groups, and published to the InSilico DB public repository

Data export

Raw data

Raw data are available for download

Raw data are available for download

Through ArrayExpress links

Output Format

Multiple ready-to-use analysis-tool-compatible format (GenePattern, R/Bioconductor and IGV compatible)

GEO-defined SOFT and text formats

Programmatic access

InSilico Db R/Bioconductor package

Through third-party GEOquery R/Bioconductor package


SRA, Short Read Archive.

Coletta et al. Genome Biology 2012 13:R104   doi:10.1186/gb-2012-13-11-r104

Open Data