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
