ISA API: An open platform for interoperable life science experimental metadata

David Johnson; Dominique Batista; Keeva Cochrane; Robert Davey; Anthony Etuk; Alejandra N Gonzalez-Beltran; Kenneth Haug; Massimiliano Izzo; Martin F. Larralde; Thomas N. Lawson; Alice Minotto; Pablo A Moreno; Venkata Chandrasekhar Nainala; Claire O’Donovan; Luca Pireddu; Pierrick Roger; Felix Shaw; Christoph Steinbeck; Ralf J. M. Weber; Susanna‐Assunta Sansone; Philippe Rocca‐Serra

doi:10.1093/gigascience/giab060

BioinformaticsGigaScienceSep 1, 2021

Peer-reviewed journal article

ISA API: An open platform for interoperable life science experimental metadata

David Johnson iD, Dominique Batista iD, Keeva Cochrane iD, Robert Davey iD, Anthony Etuk iD, Alejandra N Gonzalez-Beltran iD, Kenneth Haug iD, Massimiliano Izzo iD, Martin F. Larralde iD, Thomas N. Lawson iD, Alice Minotto iD, Pablo A Moreno iD, Venkata Chandrasekhar Nainala iD, Claire O’Donovan iD, Luca Pireddu iD, Pierrick Roger iD, Felix Shaw iD, Christoph Steinbeck iD, Ralf J. M. Weber iD, Susanna‐Assunta Sansone iD, Philippe Rocca‐Serra iD

Abstract

BackgroundThe Investigation/Study/Assay (ISA) Metadata Framework is an established and widely used set of open-source community specifications and software tools for enabling discovery, exchange and publication of metadata from experiments in the life sciences. The original ISA software suite provided a set of user-facing Java tools for creating and manipulating the information structured in ISA-Tab - a now widely used tabular format. To make the ISA framework more accessible to machines and enable programmatic manipulation of experiment metadata, a JSON serialization ISA-JSON was developed. ResultsIn this work, we present the ISA API, a Python library for the creation, editing, parsing, and validating of ISA-Tab and ISA-JSON formats by using a common data model engineered as Python object classes. We describe the ISA API feature set, early adopters and its growing user community. ConclusionsThe ISA API provides users with rich programmatic metadata handling functionality to support automation, a common interface and an interoperable medium between the two ISA formats, as well as with other life science data formats required for depositing data in public databases.

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