Content area
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.
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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
Details
Computer programs;
Gene expression;
Metadata;
Application programming interface;
Phenotyping;
Language;
Biotechnology;
Bioinformatics;
Life sciences;
Mass spectroscopy;
Computer graphics;
Automation;
Resource Description Framework-RDF;
Stem cells;
Structured Query Language-SQL;
JavaScript;
Nuclear magnetic resonance--NMR;
DNA microarrays