4. Software toolsΒΆ

The ISA Model Specification has two Reference Implementations as data formats (ISA-Tab and ISA-JSON) with supporting software tools. Below is a summary list of tools and supported formats.

  • Active: In active development and fully supported.
  • Maintenance mode: No new features are being developed or planned, and only basic support and bug fixes will be supported.
  • Unsupported: Not in development and no support available.

Software tools supported by the ISA Team

Tool Description Format Development Status Platform
ISA API Python API for ISA conversions, validation and content creation ISA-Tab, ISA-JSON Active (pre-release) Python 3+
ISA Explorer Visualization and search over collections of ISA-Tabs (browser) ISA-Tab, ISA-JSON Not released - see preview Python 3+
linkedISA Convert ISA-Tab to OWL ISA-Tab Active Java 1.6
OntoMaton Annotation of ISA-Tab spreadsheets ISA-Tab Active Google Spreadsheets Add-on
rISA Parse ISA-Tab into R data structures ISA-Tab Active R/Bioconductor
biopy-isatab Python Parser for ISA-Tab ISA-Tab Active Python 2.7+
ISA creator Used for creating ISA-Tab files ISA-Tab Maintenance mode Java 1.6
ISA-Tab Viewer Visualizer for ISA-Tabs (browser) ISA-Tab Maintenance mode JavaScript / HTML / CSS
ISA configurator Used with ISAcreator to develop ISA-Tab XML Configurations that are used as ISA-Tab templates and used for validating against domain-specific requirements ISA-Tab Maintenance mode Java 1.6
ISA validator Used with ISA XML Configurations to validate ISA-Tab files against domain-specific requirements ISA-Tab Maintenance mode Java 1.6
ISA converter Convert ISA-Tab files into other formats ISA-Tab Maintenance mode Java 1.6
BII (Bio Investigation Index) Web application and DB ISA-Tab Maintenance mode Java 1.6
MAGE to ISA converter Converter which can pull from ArrayExpress (by an accession number) or read local files and convert them to ISAtab. ISA-Tab Unsupported Java 1.6

To find these tools please visit http://www.isa-tools.org and http://www.github.com/ISA-tools

Other software tools

Tool Description Format Maintaned by Platform
ISA to RDF Convert from ISA-Tab to RDF ISA-Tab ToxBank project Java 1.6
Bio-Parser-ISATab PERL Parser for ISA-Tab ISA-Tab Unknown PERL

If you are a developer, user, or are aware of other software tools that implement ISA formats that you think should be listed here, please contact the ISA Team.