ELIXIR biovalidator for semantic validation of life science metadata

Isuru Liyanage; Tony Burdett; Bert Droesbeke; Karoly Erdos; Rolando Fernandez; Alasdair Gray; Muhammad Haseeb; Flavia Penim; Cyril Pommier; Philippe Rocca-Serra; Mélanie Courtot; Frederik Coppens

doi:10.1093/bioinformatics/btac195

ELIXIR biovalidator for semantic validation of life science metadata

Isuru Liyanage, Tony Burdett, Bert Droesbeke, Karoly Erdos, Rolando Fernandez, Alasdair Gray, Muhammad Haseeb, Flavia Penim, Cyril Pommier, Philippe Rocca-Serra, Mélanie Courtot, Frederik Coppens

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Abstract

SUMMARY: To advance biomedical research, increasingly large amounts of complex data need to be discovered and integrated. This requires syntactic and semantic validation to ensure shared understanding of relevant entities. This article describes the ELIXIR biovalidator, which extends the syntactic validation of the widely used AJV library with ontology-based validation of JSON documents.

AVAILABILITY AND IMPLEMENTATION: Source code: https://github.com/elixir-europe/biovalidator, Release: v1.9.1, License: Apache License 2.0, Deployed at: https://www.ebi.ac.uk/biosamples/schema/validator/validate.

Original language	English
Journal	Bioinformatics
Early online date	5 Apr 2022
DOIs	https://doi.org/10.1093/bioinformatics/btac195
Publication status	E-pub ahead of print - 5 Apr 2022

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@article{dbdb4203ee214f0bac8691e89a15c049,

title = "ELIXIR biovalidator for semantic validation of life science metadata",

abstract = "SUMMARY: To advance biomedical research, increasingly large amounts of complex data need to be discovered and integrated. This requires syntactic and semantic validation to ensure shared understanding of relevant entities. This article describes the ELIXIR biovalidator, which extends the syntactic validation of the widely used AJV library with ontology-based validation of JSON documents.AVAILABILITY AND IMPLEMENTATION: Source code: https://github.com/elixir-europe/biovalidator, Release: v1.9.1, License: Apache License 2.0, Deployed at: https://www.ebi.ac.uk/biosamples/schema/validator/validate.",

author = "Isuru Liyanage and Tony Burdett and Bert Droesbeke and Karoly Erdos and Rolando Fernandez and Alasdair Gray and Muhammad Haseeb and Flavia Penim and Cyril Pommier and Philippe Rocca-Serra and M{\'e}lanie Courtot and Frederik Coppens",

note = "{\textcopyright} The Author(s) 2022. Published by Oxford University Press.",

year = "2022",

month = apr,

day = "5",

doi = "10.1093/bioinformatics/btac195",

language = "English",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

}

ELIXIR biovalidator for semantic validation of life science metadata. / Liyanage, Isuru; Burdett, Tony; Droesbeke, Bert; Erdos, Karoly; Fernandez, Rolando; Gray, Alasdair; Haseeb, Muhammad; Penim, Flavia; Pommier, Cyril; Rocca-Serra, Philippe; Courtot, Mélanie; Coppens, Frederik.

In: Bioinformatics, 05.04.2022.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - ELIXIR biovalidator for semantic validation of life science metadata

AU - Liyanage, Isuru

AU - Burdett, Tony

AU - Droesbeke, Bert

AU - Erdos, Karoly

AU - Fernandez, Rolando

AU - Gray, Alasdair

AU - Haseeb, Muhammad

AU - Penim, Flavia

AU - Pommier, Cyril

AU - Rocca-Serra, Philippe

AU - Courtot, Mélanie

AU - Coppens, Frederik

PY - 2022/4/5

Y1 - 2022/4/5

N2 - SUMMARY: To advance biomedical research, increasingly large amounts of complex data need to be discovered and integrated. This requires syntactic and semantic validation to ensure shared understanding of relevant entities. This article describes the ELIXIR biovalidator, which extends the syntactic validation of the widely used AJV library with ontology-based validation of JSON documents.AVAILABILITY AND IMPLEMENTATION: Source code: https://github.com/elixir-europe/biovalidator, Release: v1.9.1, License: Apache License 2.0, Deployed at: https://www.ebi.ac.uk/biosamples/schema/validator/validate.

AB - SUMMARY: To advance biomedical research, increasingly large amounts of complex data need to be discovered and integrated. This requires syntactic and semantic validation to ensure shared understanding of relevant entities. This article describes the ELIXIR biovalidator, which extends the syntactic validation of the widely used AJV library with ontology-based validation of JSON documents.AVAILABILITY AND IMPLEMENTATION: Source code: https://github.com/elixir-europe/biovalidator, Release: v1.9.1, License: Apache License 2.0, Deployed at: https://www.ebi.ac.uk/biosamples/schema/validator/validate.

U2 - 10.1093/bioinformatics/btac195

DO - 10.1093/bioinformatics/btac195

M3 - Article

C2 - 35380605

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

ER -

ELIXIR biovalidator for semantic validation of life science metadata

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