ISA API: An open platform for interoperable life science experimental metadata-Reference-Cited by-同舟云学术

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

Published:2021-09 Issue:9 Volume:10 Page:
ISSN:2047-217X
Container-title:GigaScience
language:en
Short-container-title:

Author:

Johnson David¹²^ORCID,Batista Dominique¹^ORCID,Cochrane Keeva³^ORCID,Davey Robert P⁴^ORCID,Etuk Anthony⁴^ORCID,Gonzalez-Beltran Alejandra¹⁵^ORCID,Haug Kenneth³⁶^ORCID,Izzo Massimiliano¹^ORCID,Larralde Martin⁷^ORCID,Lawson Thomas N⁸^ORCID,Minotto Alice⁴^ORCID,Moreno Pablo³^ORCID,Nainala Venkata Chandrasekhar³^ORCID,O'Donovan Claire³^ORCID,Pireddu Luca⁹^ORCID,Roger Pierrick¹⁰^ORCID,Shaw Felix⁴^ORCID,Steinbeck Christoph¹¹^ORCID,Weber Ralf J M⁸¹²^ORCID,Sansone Susanna-Assunta¹^ORCID,Rocca-Serra Philippe¹^ORCID

Affiliation:

1. Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK

2. Department of Informatics and Media, Uppsala University, Box 513, 75120 Uppsala, Sweden

3. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

4. Earlham Institute, Data infrastructure and algorithms, Norwich Research Park, Norwich NR4 7UZ, UK

5. Science and Technology Facilities Council, Scientific Computing Department, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0QX, UK

6. Genome Research Limited, Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Saffron Walden, CB10 1RQ, UK

7. Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany

8. School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK

9. Distributed Computing Group, CRS4: Center for Advanced Studies, Research & Development in Sardinia, Pula 09050, Italy

10. CEA, LIST, Laboratory for Data Analysis and Systems’ Intelligence, MetaboHUB, Gif-Sur-Yvette F-91191, France

11. Cheminformatics and Computational Metabolomics, Institute for Analytical Chemistry, Lessingstr. 8, 07743 Jena, Germany

12. Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK

Abstract

Abstract 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.

Funder

Horizon 2020 Framework Programme

Biotechnology and Biological Sciences Research Council

Wellcome Trust

National Eye Research Centre

Publisher

Oxford University Press (OUP)

Subject

Computer Science Applications,Health Informatics

Link

http://academic.oup.com/gigascience/article-pdf/10/9/giab060/40394485/giab060.pdf

Reference84 articles.