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

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 su...

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Published in:bioRxiv
Main Authors: Johnson, David, Cochrane, Keeva, Davey, Robert P, Etuk, Anthony, Gonzalez-Beltran, Alejandra, Haug, Kenneth, Izzo, Massimiliano, Larralde, Martin, Lawson, Thomas N, Minotto, Alice, Moreno, Pablo, Venkata Chandrasekhar Nainala, Claire O’donovan, Pireddu, Luca, Pierrick Roger, Shaw, Felix, Steinbeck, Christoph, Weber, Ralf J M, Sansone, Susanna-Assunta, Rocca-Serra, Philippe
Format: Paper
Language:English
Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 29.03.2021
Cold Spring Harbor Laboratory
Edition:1.2
Subjects:
Application programming interface
Automation
Bioinformatics
Biotechnology
Computer graphics
Computer programs
DNA microarrays
Gene expression
JavaScript
Language
Life sciences
Mass spectroscopy
Metadata
NMR
Nuclear magnetic resonance
Phenotyping
Resource Description Framework-RDF
Software
Stem cells
Structured Query Language-SQL
standards
metadata
open-source software
API
life science
reproducibility
ISSN:2692-8205, 2692-8205
Online Access:Get full text
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Summary: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, a 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 two ISA formats, as well as with other life science data formats required for depositing data in public databases. Competing Interest Statement The authors have declared no competing interest. * List of abbreviations API Application Programming Interface BBSRC Biotechnology and Biological Sciences Research Council BrAPI Breeding API COPO Collaborative Open Plant Omics DAG Directed Acyclic Graph EMBL European Molecular Biology Laboratory EMBL-EBI European Bioinformatics Institute GUI Graphical User Interface H2020 Horizon 2020 ISA Investigation, Study, Assay ISA-JSON ISA JavaScript Object Notation format ISA-Tab ISA Tabular format JSON JavaScript Object Notation JSON-LD JavaScript Object Notation for Linked Data MAGE-TAB MicroArray Gene Expression-Tabular format MIAPPE Minimum Information About a Plant Phenotyping Experiment mzML Mass spectrometry Markup Language NASA National Aeronautics and Space Administration NERC Natural Environment Research Council NCBI National Center for Biotechnology Information nmrML Nuclear magnetic resonance Markup Language MDE Model-driven engineering OLS Ontology Lookup Service OO Object-oriented PhenoMeNal Phenome and Metabolome aNalysis PyPI Python Package Index REST Representational state transfer RDF Resource Description Framework SCDE Stem Cell Discovery Engine SQL Structured Query Language SRA-XML Sequence Read Archive-eXtensible Markup Language TDD Test-driven development VRE Virtual Research Environment
Bibliography:SourceType-Working Papers-1
ObjectType-Working Paper/Pre-Print-1
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Competing Interest Statement: The authors have declared no competing interest.
ISSN:2692-8205
2692-8205
DOI:10.1101/2020.11.13.382119