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A posteriori metadata from automated provenance tracking: integration of AiiDA and TCOD

In order to make results of computational scientific research findable, accessible, interoperable and re-usable, it is necessary to decorate them with standardised metadata. However, there are a number of technical and practical challenges that make this process difficult to achieve in practice. Her...

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Autores principales: Merkys, Andrius, Mounet, Nicolas, Cepellotti, Andrea, Marzari, Nicola, Gražulis, Saulius, Pizzi, Giovanni
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5686034/
https://www.ncbi.nlm.nih.gov/pubmed/29138947
http://dx.doi.org/10.1186/s13321-017-0242-y
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author Merkys, Andrius
Mounet, Nicolas
Cepellotti, Andrea
Marzari, Nicola
Gražulis, Saulius
Pizzi, Giovanni
author_facet Merkys, Andrius
Mounet, Nicolas
Cepellotti, Andrea
Marzari, Nicola
Gražulis, Saulius
Pizzi, Giovanni
author_sort Merkys, Andrius
collection PubMed
description In order to make results of computational scientific research findable, accessible, interoperable and re-usable, it is necessary to decorate them with standardised metadata. However, there are a number of technical and practical challenges that make this process difficult to achieve in practice. Here the implementation of a protocol is presented to tag crystal structures with their computed properties, without the need of human intervention to curate the data. This protocol leverages the capabilities of AiiDA, an open-source platform to manage and automate scientific computational workflows, and the TCOD, an open-access database storing computed materials properties using a well-defined and exhaustive ontology. Based on these, the complete procedure to deposit computed data in the TCOD database is automated. All relevant metadata are extracted from the full provenance information that AiiDA tracks and stores automatically while managing the calculations. Such a protocol also enables reproducibility of scientific data in the field of computational materials science. As a proof of concept, the AiiDA–TCOD interface is used to deposit 170 theoretical structures together with their computed properties and their full provenance graphs, consisting in over 4600 AiiDA nodes.
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spelling pubmed-56860342017-12-01 A posteriori metadata from automated provenance tracking: integration of AiiDA and TCOD Merkys, Andrius Mounet, Nicolas Cepellotti, Andrea Marzari, Nicola Gražulis, Saulius Pizzi, Giovanni J Cheminform Research Article In order to make results of computational scientific research findable, accessible, interoperable and re-usable, it is necessary to decorate them with standardised metadata. However, there are a number of technical and practical challenges that make this process difficult to achieve in practice. Here the implementation of a protocol is presented to tag crystal structures with their computed properties, without the need of human intervention to curate the data. This protocol leverages the capabilities of AiiDA, an open-source platform to manage and automate scientific computational workflows, and the TCOD, an open-access database storing computed materials properties using a well-defined and exhaustive ontology. Based on these, the complete procedure to deposit computed data in the TCOD database is automated. All relevant metadata are extracted from the full provenance information that AiiDA tracks and stores automatically while managing the calculations. Such a protocol also enables reproducibility of scientific data in the field of computational materials science. As a proof of concept, the AiiDA–TCOD interface is used to deposit 170 theoretical structures together with their computed properties and their full provenance graphs, consisting in over 4600 AiiDA nodes. Springer International Publishing 2017-11-14 /pmc/articles/PMC5686034/ /pubmed/29138947 http://dx.doi.org/10.1186/s13321-017-0242-y Text en © The Author(s) 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Merkys, Andrius
Mounet, Nicolas
Cepellotti, Andrea
Marzari, Nicola
Gražulis, Saulius
Pizzi, Giovanni
A posteriori metadata from automated provenance tracking: integration of AiiDA and TCOD
title A posteriori metadata from automated provenance tracking: integration of AiiDA and TCOD
title_full A posteriori metadata from automated provenance tracking: integration of AiiDA and TCOD
title_fullStr A posteriori metadata from automated provenance tracking: integration of AiiDA and TCOD
title_full_unstemmed A posteriori metadata from automated provenance tracking: integration of AiiDA and TCOD
title_short A posteriori metadata from automated provenance tracking: integration of AiiDA and TCOD
title_sort posteriori metadata from automated provenance tracking: integration of aiida and tcod
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5686034/
https://www.ncbi.nlm.nih.gov/pubmed/29138947
http://dx.doi.org/10.1186/s13321-017-0242-y
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