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

Johnson, David (author)
Uppsala universitet,Institutionen för informatik och media,Univ Oxford, Oxford E Res Ctr, Dept Engn Sci, 7 Keble Rd, Oxford OX1 3QG, England
Batista, Dominique (author)
Univ Oxford, Oxford E Res Ctr, Dept Engn Sci, 7 Keble Rd, Oxford OX1 3QG, England
Cochrane, Keeva (author)
European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Genome Campus, Cambridge CB10 1SD, England
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Davey, Robert P. (author)
Earlham Inst, Data Infrastruct & Algorithms, Norwich Res Pk, Norwich NR4 7UZ, Norfolk, England
Etuk, Anthony (author)
Earlham Inst, Data Infrastruct & Algorithms, Norwich Res Pk, Norwich NR4 7UZ, Norfolk, England
Gonzalez-Beltran, Alejandra (author)
Univ Oxford, Oxford E Res Ctr, Dept Engn Sci, 7 Keble Rd, Oxford OX1 3QG, England; Rutherford Appleton Lab, Sci Comp Dept, Sci & Technol Facil Council, Harwell Campus, Didcot OX11 0QX, Oxon, England
Haug, Kenneth (author)
European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Genome Campus, Cambridge CB10 1SD, England; Genome Res Ltd, Wellcome Sanger Inst, Wellcome Trust Genome Campus, Saffron Walden CB10 1RQ, Essex, England
Izzo, Massimiliano (author)
Univ Oxford, Oxford E Res Ctr, Dept Engn Sci, 7 Keble Rd, Oxford OX1 3QG, England
Larralde, Martin (author)
European Mol Biol Lab EMBL, Struct & Computat Biol Unit, Meyerhofstr 1, D-69117 Heidelberg, Germany
Lawson, Thomas N. (author)
Univ Birmingham, Sch Biosci, Birmingham B15 2TT, W Midlands, England
Minotto, Alice (author)
Earlham Inst, Data Infrastruct & Algorithms, Norwich Res Pk, Norwich NR4 7UZ, Norfolk, England
Moreno, Pablo (author)
European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Genome Campus, Cambridge CB10 1SD, England
Nainala, Venkata Chandrasekhar (author)
European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Genome Campus, Cambridge CB10 1SD, England
O'Donovan, Claire (author)
European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Genome Campus, Cambridge CB10 1SD, England
Pireddu, Luca (author)
CRS4 Ctr Adv Studies Res & Dev Sardinia, Distributed Comp Grp, I-09050 Pula, Italy
Roger, Pierrick (author)
CEA, LIST, Lab Data Anal & Syst Intelligence, MetaboHUB, F-91191 Gif Sur Yvette, France
Shaw, Felix (author)
Earlham Inst, Data Infrastruct & Algorithms, Norwich Res Pk, Norwich NR4 7UZ, Norfolk, England
Steinbeck, Christoph (author)
Inst Analyt Chem, Cheminformat & Computat Metabol, Lessingstr 8, D-07743 Jena, Germany
Weber, Ralf J. M. (author)
Univ Birmingham, Sch Biosci, Birmingham B15 2TT, W Midlands, England; Univ Birmingham, Phenome Ctr Birmingham, Birmingham B15 2TT, W Midlands, England
Sansone, Susanna-Assunta (author)
Univ Oxford, Oxford E Res Ctr, Dept Engn Sci, 7 Keble Rd, Oxford OX1 3QG, England
Rocca-Serra, Philippe (author)
Univ Oxford, Oxford E Res Ctr, Dept Engn Sci, 7 Keble Rd, Oxford OX1 3QG, England
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 (creator_code:org_t)
2021-09-16
2021
English.
In: GigaScience. - : Oxford University Press. - 2047-217X. ; 10:9
Related links:
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https://uu.diva-port... (primary) (Raw object)
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  • Journal article (peer-reviewed)
Abstract Subject headings
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  • 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.

Subject headings

NATURVETENSKAP  -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
NATURAL SCIENCES  -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
NATURVETENSKAP  -- Data- och informationsvetenskap -- Datavetenskap (hsv//swe)
NATURAL SCIENCES  -- Computer and Information Sciences -- Computer Sciences (hsv//eng)

Keyword

metadata
standards
reproducibility
open-source software
life science
API

Publication and Content Type

ref (subject category)
art (subject category)

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