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

Dataset type: Metadata, Software, Bioinformatics
Data released on June 11, 2021

Johnson D; Batista D; Cochrane K; Davey RP; Etuk A; Gonzalez-Beltran AN; Haug K; Izzo M; Larralde M; Lawson TN; Minotto A; Moreno P; Nainala VC; O’Donovan C; Pireddu L; Roger P; Shaw F; Steinbeck C; Weber RJM; Sansone SA; Rocca-Serra P (2021): Supporting data for "ISA API: An open platform for interoperable life science experimental metadata" GigaScience Database. http://dx.doi.org/10.5524/100907

DOI10.5524/100907

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.
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.
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.

Additional details

Read the peer-reviewed publication(s):

(PubMed: 34528664)

Github links:

http://github.com/ISA-tools/isa-api/

Additional information:

https://doi.org/10.24433/CO.8813991.v2

https://anaconda.org/bioconda/isatools/

https://pypi.org/project/isatools/





File NameSample IDData TypeFile FormatSizeRelease Date 
GitHub archivezip12.19 MB2021-08-13
ReadmeTEXT2.54 KB2021-05-15
Displaying 1-2 of 2 File(s).
Funding body Awardee Award ID Comments
Horizon 2020 Christoph Steinbeck/Claire o'Donovan EC654241
Biotechnology and Biological Sciences Research Council Robert Davey BB/L021390/1 BB/L024055/1 BB/L024071/1 BB/L024101/1
Natural Environment Research Council Pr Mark Viant NE/L002493/1 Awardee not listed as an author due to work being carried out by Ralf Weber and Thomas Lawson
Biotechnology and Biological Sciences Research Council Susanna Assunta Sansone BB/M027635/1
Biotechnology and Biological Sciences Research Council Susanna Assunta Sansone BB/J020265/1

Code Ocean:

Date Action
June 10, 2021 Dataset publish
July 22, 2021 readme_100907.txt: additional file attribute added
July 22, 2021 File readme_100907.txt updated
August 13, 2021 File isa-api-master.zip updated, repo was updated just prior to manuscript publication after this dataset was first released, so we have updated the dataset with the corrected github repo snapshot.
August 13, 2021 Author added : Batista, Dominique
August 23, 2021 Manuscript Link added : 10.1093/gigascience/giab060
November 8, 2021 Manuscript Link updated : 10.1093/gigascience/giab060