ISA Usage
ISA can be implemented via different tools. These tools rely on data exchange in one or two exchange formats: ISA-Tab and ISA-JSON.
Data registration
The ISA supporting software documentation list the following table.
Multiple options are available for registering data according to the ISA data model. This project used the ISA Python API.
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 |
Data Exchange formats
Data that is registered by using the ISA data model is stored and exchanged by either ISA-Tab or ISA-JSON.
ISA-Tab is a collection of tab-delimited text files for the investigation, studies and assays. ISA-JSON is standard JSON serialisation of the registered data, following the ISA data model.