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 |