Validation of the Crystallography Open Database using the Crystallographic Information Framework

Data curation practices of the Crystallography Open Database (COD) are described with additional focus being placed on the formal validation using the Crystallographic Information Framework (CIF). The cif_validate program, capable of validating CIF files against both the DDL1 and the DDLm dictionari...

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Autores principales: Vaitkus, Antanas, Merkys, Andrius, Gražulis, Saulius
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2021
Materias:
CIF applications
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8056762/
https://www.ncbi.nlm.nih.gov/pubmed/33953659
http://dx.doi.org/10.1107/S1600576720016532
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author Vaitkus, Antanas
Merkys, Andrius
Gražulis, Saulius
author_facet Vaitkus, Antanas
Merkys, Andrius
Gražulis, Saulius
author_sort Vaitkus, Antanas
collection PubMed
description Data curation practices of the Crystallography Open Database (COD) are described with additional focus being placed on the formal validation using the Crystallographic Information Framework (CIF). The cif_validate program, capable of validating CIF files against both the DDL1 and the DDLm dictionaries, is presented and used to process the entirety of the COD. Validation results collected from over 450 000 CIF files are demonstrated to be a useful resource in the data maintenance process as well as the development of the underlying ontologies. A set of programs intended to aid in the dictionary migration from DDL1 to DDLm is also presented.
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spelling pubmed-80567622021-05-04 Validation of the Crystallography Open Database using the Crystallographic Information Framework Vaitkus, Antanas Merkys, Andrius Gražulis, Saulius J Appl Crystallogr CIF applications Data curation practices of the Crystallography Open Database (COD) are described with additional focus being placed on the formal validation using the Crystallographic Information Framework (CIF). The cif_validate program, capable of validating CIF files against both the DDL1 and the DDLm dictionaries, is presented and used to process the entirety of the COD. Validation results collected from over 450 000 CIF files are demonstrated to be a useful resource in the data maintenance process as well as the development of the underlying ontologies. A set of programs intended to aid in the dictionary migration from DDL1 to DDLm is also presented. International Union of Crystallography 2021-02-14 /pmc/articles/PMC8056762/ /pubmed/33953659 http://dx.doi.org/10.1107/S1600576720016532 Text en © Antanas Vaitkus et al. 2021 https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
spellingShingle CIF applications
Vaitkus, Antanas
Merkys, Andrius
Gražulis, Saulius
Validation of the Crystallography Open Database using the Crystallographic Information Framework
title Validation of the Crystallography Open Database using the Crystallographic Information Framework
title_full Validation of the Crystallography Open Database using the Crystallographic Information Framework
title_fullStr Validation of the Crystallography Open Database using the Crystallographic Information Framework
title_full_unstemmed Validation of the Crystallography Open Database using the Crystallographic Information Framework
title_short Validation of the Crystallography Open Database using the Crystallographic Information Framework
title_sort validation of the crystallography open database using the crystallographic information framework
topic CIF applications
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8056762/
https://www.ncbi.nlm.nih.gov/pubmed/33953659
http://dx.doi.org/10.1107/S1600576720016532
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AT merkysandrius validationofthecrystallographyopendatabaseusingthecrystallographicinformationframework
AT grazulissaulius validationofthecrystallographyopendatabaseusingthecrystallographicinformationframework

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