ELIXIR biovalidator for semantic validation of life science metadata

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 v...

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Autores principales: Liyanage, Isuru, Burdett, Tony, Droesbeke, Bert, Erdos, Karoly, Fernandez, Rolando, Gray, Alasdair, Haseeb, Muhammad, Jupp, Simon, Penim, Flavia, Pommier, Cyril, Rocca-Serra, Philippe, Courtot, Mélanie, Coppens, Frederik
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9154242/
https://www.ncbi.nlm.nih.gov/pubmed/35380605
http://dx.doi.org/10.1093/bioinformatics/btac195
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author Liyanage, Isuru
Burdett, Tony
Droesbeke, Bert
Erdos, Karoly
Fernandez, Rolando
Gray, Alasdair
Haseeb, Muhammad
Jupp, Simon
Penim, Flavia
Pommier, Cyril
Rocca-Serra, Philippe
Courtot, Mélanie
Coppens, Frederik
author_facet Liyanage, Isuru
Burdett, Tony
Droesbeke, Bert
Erdos, Karoly
Fernandez, Rolando
Gray, Alasdair
Haseeb, Muhammad
Jupp, Simon
Penim, Flavia
Pommier, Cyril
Rocca-Serra, Philippe
Courtot, Mélanie
Coppens, Frederik
author_sort Liyanage, Isuru
collection PubMed
description 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. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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spelling pubmed-91542422022-06-04 ELIXIR biovalidator for semantic validation of life science metadata Liyanage, Isuru Burdett, Tony Droesbeke, Bert Erdos, Karoly Fernandez, Rolando Gray, Alasdair Haseeb, Muhammad Jupp, Simon Penim, Flavia Pommier, Cyril Rocca-Serra, Philippe Courtot, Mélanie Coppens, Frederik Bioinformatics Applications Notes 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. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2022-04-05 /pmc/articles/PMC9154242/ /pubmed/35380605 http://dx.doi.org/10.1093/bioinformatics/btac195 Text en © The Author(s) 2022. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Liyanage, Isuru
Burdett, Tony
Droesbeke, Bert
Erdos, Karoly
Fernandez, Rolando
Gray, Alasdair
Haseeb, Muhammad
Jupp, Simon
Penim, Flavia
Pommier, Cyril
Rocca-Serra, Philippe
Courtot, Mélanie
Coppens, Frederik
ELIXIR biovalidator for semantic validation of life science metadata
title ELIXIR biovalidator for semantic validation of life science metadata
title_full ELIXIR biovalidator for semantic validation of life science metadata
title_fullStr ELIXIR biovalidator for semantic validation of life science metadata
title_full_unstemmed ELIXIR biovalidator for semantic validation of life science metadata
title_short ELIXIR biovalidator for semantic validation of life science metadata
title_sort elixir biovalidator for semantic validation of life science metadata
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9154242/
https://www.ncbi.nlm.nih.gov/pubmed/35380605
http://dx.doi.org/10.1093/bioinformatics/btac195
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