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.