pISA-tree

pISA-tree creates standardized nested directory trees and associated metadata files for life science research data management based on the ISA model.

Key Features:

• Hierarchical directory structure: Generates on-the-fly nested directory trees at four levels (project/Investigation/Study/Assay) using consecutive batch files.
• Metadata generation: Produces templates-based metadata at each level with Description files containing meta-information about research, protocols, samples, and features.
• Standards compliance: Aligns with the ISA-tab framework and supports standards such as MIQE, MIAMI, and MIRIAM for particular assays.
• R package integration: pisar facilitates integration of pISA-tree datasets into bioinformatic pipelines and generation of ISA-Tab exports.
• Repository synchronization: seekr enables synchronisation with the FAIRDOMHub repository via the SEEK API.

Scientific Applications:

• Research data organization: Supports structured storage of life science project-associated research data and metadata for small to moderate size projects.
• Reproducible research: Enables reproducibility of data analyses and reports through structured organization of data augmented with sufficient metadata for future re-use.
• FAIR data principles: Supports findable, accessible, interoperable and reusable research in accordance with the Open Science initiative.
• Multi-partner projects: Demonstrated applicability in national and international collaborative research projects.
• Data exchange: Allows exchange of data with other data management services including the FAIRdom platform and digital notebooks such as SciNote.

Methodology:

The system generates directory trees on the fly using batch files on Windows platform, with three batch files (makeInvestigation, makeStudy, and makeAssay) creating new hierarchical levels and generating necessary folders and meta-data template files.