Table 1 Limitations of existing solutions for the sharing of ‘omics information.
Category | Examples | Limitations |
|---|---|---|
Centralized databases (data upload/download) | NBCI RefSeq95. DiatOmicBase96 ECMDB97 ProPortal55 | Restricted data types Often specific to one type of organism Updates after the initial data deposit can be limited |
Online portals (data upload + online analysis tools) | JGI IMG/M43 KBase98 Galaxy99 PATRIC100 CyVerse101 RAST102 SILVAngs103 BV-BRC104 Phycocosm105 | May not enable sharing of data and results between users Analysis workflows are often black boxes without transparent or changeable parameters Dependence on the platform’s computational resources can hinder high-throughput analyses May not facilitate automation of analysis workflows |
Downloadable tools (local analysis with database snapshots) | Prokka106 KofamScan18 BLAST + 107 GToTree108 Pathway Tools109 DRAM110 | May lack version control and/or easy mechanisms for updating database snapshot Can be difficult to share data/results between users with different local versions of the database snapshot Tool functionality is typically constrained to or tailored towards one kind of analysis |
