ISAISA-Tab is a general-purpose metadata framework for describing complex experimental workflows in the life sciences. Widely adopted in metabolomics, genomics, proteomics, and environmental studies, it structures experimental metadata into three hierarchical layers -- Investigation, Study, and Assay -- providing a consistent way to capture the design, execution, and measurement details of multi-omics experiments.
Background
The ISA framework was developed to address the challenge of managing an increasingly diverse set of experiments that employ one or a combination of technologies. The ISA-Tab tabular format was first published around 2008, emerging from the needs of the metabolomics and functional genomics communities for a standard way to describe experimental metadata that would enable reproducibility and reuse.
Purpose and Scope
The ISA framework helps researchers to:
- Collect and curate experimental descriptions following community-defined minimum reporting requirements and ontologies
- Store and browse experiments locally or publicly, creating searchable repositories
- Submit reformatted experiments to supported public repositories or directly export to those using ISA formats
- Analyse data using a growing number of well-known analysis systems that ISA formats connect with
- Release and reason over experiments, opening them to the linked data universe or publishing nano-statements of discoveries
- Publish data alongside articles in data journals accepting ISA format submissions
Data Model
The ISA model separates metadata into three layers:
| Layer | Scope |
|---|---|
| Investigation | The project context, including overall goals, contacts, and publications |
| Study | A unit of research, defining the subjects of study and study design |
| Assay | Analytical measurement details, linking samples to data files through protocols |
This hierarchy provides rich description of experimental metadata including sample characteristics, technology and measurement types, and sample-to-data relationships.
Serializations
The ISA framework supports three serialization formats:
- ISA-Tab: The original tabular (TSV) format
- ISA-JSON: A JSON serialization for machine-readable interchange
- ISA-RDF: An RDF representation for linked data integration
Governance and Maintenance
The ISA framework is maintained by the ISA Commons community, with tools and specifications hosted at isa-tools.org. The ISA API (Python) and ISA specifications are developed on GitHub.
Notable Implementations
ISA-Tab is used by major biological data repositories and is supported by metabolomics platforms. The ISA Creator tool (version 1.7.11 as of December 2017) provides a user interface for creating ISA-Tab metadata. The framework has been developed specifically for the metabolomics community among other domains.
Related Standards
- Nanopublication (nanopublication): ISA supports nanopublishing of experimental discoveries