AltamISA: a Python API for ISA-Tab files

AltamISA is a Python library for reading, validating, representing and writing the ISA-Tab file format. ISA-Tab is an open, TSV (tab separated values)-based file format for representing the ISA (investigation study assay) tools data model. The ISA tools data model allows for representing life science experiments and annotating the modeled objects and steps with arbitrary meta data. The ISA tools data model and TSV format are used by various life science databases, including MetaboLights.

Shortly, the experimental process from sample extraction from a source (e.g. a donor individual) through processing of the samples to creating read-outs in one or more assays can be represented through DAGs (directed acyclic graphs) consisting of extensively annotatable so-called material and process nodes. Together, the ISA tools data model and ISA-Tab allow for representing most conceivable experiments in life science and to store them into machine-readable files for exchanging information about such experiments. This greatly facilitates the development of data management applications following the FAIR (findable, accessible, interoperable, and reusable) guidelines.