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

David Johnson (1) , Dominique Batista (1) , Keeva Cochrane (2) , Robert Davey (3) , Anthony Etuk (3) , Alejandra Gonzalez-Beltran (4) , Kenneth Haug (2) , Massimiliano Izzo (1) , Martin Larralde (2) , Thomas Lawson (5) , Alice Minotto (3) , Pablo Moreno (2) , Venkata Chandrasekhar Nainala (2) , Claire O'Donovan (2) , Luca Pireddu (6) , Pierrick Roger Mele (7) , Felix Shaw (3) , Christoph Steinbeck (8) , Ralf Weber (5) , Susanna-Assunta Sansone (1) , Philippe Rocca-Serra (1)

1 Oxford e-Research Centre [Oxford]
2 EMBL - European Molecular Biology Laboratory
3 Earlham Institute [Norwich]
4 RAL - STFC Rutherford Appleton Laboratory
5 University of Birmingham [Birmingham]
6 CRS4 - Center for Advanced Studies, Research and Development in Sardinia
7 LI3A (CEA, LIST) - Intelligence Artificielle et Apprentissage Automatique (CEA, LIST)
8 Institute for Environmental Analytical Chemistry

Background The 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, the JSON serialization ISA-JSON was developed. Results In 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. Conclusions The ISA API provides users with rich programmatic metadata-handling functionality to support automation, a common interface, and an interoperable medium between the 2 ISA formats, as well as with other life science data formats required for depositing data in public databases.

Mots clés: Metadata Framework; open source community; experiment metadata; ISA software suite; user-facing Java tools; ISA-Tab; ISA framework; JSON serialization; Python library; Python object class; ISA API; metadata-handling functionality; interoperability

Domaines: Bio-informatique [q-bio.QM]; Architectures Matérielles [cs.AR]; Algorithme et structure de données [cs.DS]; Interface homme-machine [cs.HC]

David Johnson, Dominique Batista, Keeva Cochrane, Robert Davey, Anthony Etuk, et al.. ISA API: An open platform for interoperable life science experimental metadata. GigaScience, 2021, 10 (9), ⟨10.1093/gigascience/giab060⟩. ⟨hal-04562617⟩