Validation of the Crystallography Open Database Using the Crystallographic Information Framework

Overview

Journal J Appl Crystallogr

Date 2021 May 6

PMID 33953659

Citations 19

Authors

Antanas Vaitkus

Andrius Merkys

Saulius Grazulis

Affiliations

Soon will be listed here.

Abstract

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 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.

Citing Articles

3D nanocomposites of β-TCP-HBO-Cu with improved mechanical and biological performances for bone regeneration applications.

Avinashi S, Mishra R, Shweta , Kumar S, Shamsad A, Parveen S Sci Rep. 2025; 15(1):3224.

PMID: 39863796 PMC: 11763077. DOI: 10.1038/s41598-025-87988-4.

Laser Synthesis of Platinum Single-Atom Catalysts for Hydrogen Evolution Reaction.

Guo H, Wang L, Liu X, Mativenga P, Liu Z, Thomas A Nanomaterials (Basel). 2025; 15(1.

PMID: 39791836 PMC: 11723019. DOI: 10.3390/nano15010078.

A high-resolution in situ X-ray diffraction study of mineral transitions due to post-hydration heating in CM chondrite meteorites.

Jenkins L, King A, Lee M, Daly L, Thompson S, Day S Earth Planets Space. 2024; 76(1):172.

PMID: 39735616 PMC: 11669613. DOI: 10.1186/s40623-024-02116-2.

Enhancement of the Photoluminescent Intensity of YVO: Er, Yb UCNPs Using a Simple Coprecipitation Synthesis Method.

Rivera-Enriquez C, Ojeda-Martinez M, Velasquez-Ordonez C, Rodriguez-Betancourtt V J Fluoresc. 2024; .

PMID: 39549189 DOI: 10.1007/s10895-024-04004-0.

Synthesis of Titanium-Based Powders from Titanium Oxy-Sulfate Using Ultrasonic Spray Pyrolysis Method.

Kostic D, Stopic S, Keutmann M, Emil-Kaya E, Husovic T, Perusic M Materials (Basel). 2024; 17(19).

PMID: 39410348 PMC: 11477860. DOI: 10.3390/ma17194779.

References

Grabowski M, Cymborowski M, Porebski P, Osinski T, Shabalin I, Cooper D . The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years. Struct Dyn. 2019; 6(6):064301. PMC: 6874509. DOI: 10.1063/1.5128672. View

Helliwell J . FACT and FAIR with Big Data allows objectivity in science: The view of crystallography. Struct Dyn. 2019; 6(5):054306. PMC: 6816445. DOI: 10.1063/1.5124439. View

Merkys A, Vaitkus A, Butkus J, Okulic-Kazarinas M, Kairys V, Grazulis S . : an error-correcting CIF parser for the Perl language. J Appl Crystallogr. 2016; 49(Pt 1):292-301. PMC: 4762566. DOI: 10.1107/S1600576715022396. View

McMahon B . Applied and implied semantics in crystallographic publishing. J Cheminform. 2012; 4(1):19. PMC: 3497589. DOI: 10.1186/1758-2946-4-19. View

Joosten R, Long F, Murshudov G, Perrakis A . The PDB_REDO server for macromolecular structure model optimization. IUCrJ. 2014; 1(Pt 4):213-20. PMC: 4107921. DOI: 10.1107/S2052252514009324. View

El Mendili Y, Vaitkus A, Merkys A, Grazulis S, Chateigner D, Mathevet F . Raman Open Database: first interconnected Raman-X-ray diffraction open-access resource for material identification. J Appl Crystallogr. 2019; 52(Pt 3):618-625. PMC: 6557180. DOI: 10.1107/S1600576719004229. View

Longo D, Drazen J . Data Sharing. N Engl J Med. 2016; 374(3):276-7. DOI: 10.1056/NEJMe1516564. View

Grazulis S, Chateigner D, Downs R, Yokochi A, Quiros M, Lutterotti L . Crystallography Open Database - an open-access collection of crystal structures. J Appl Crystallogr. 2012; 42(Pt 4):726-729. PMC: 3253730. DOI: 10.1107/S0021889809016690. View

Adams S, de Castro P, Echenique P, Estrada J, Hanwell M, Murray-Rust P . The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age. J Cheminform. 2011; 3:38. PMC: 3206452. DOI: 10.1186/1758-2946-3-38. View

10.

Berman H, Henrick K, Nakamura H . Announcing the worldwide Protein Data Bank. Nat Struct Biol. 2003; 10(12):980. DOI: 10.1038/nsb1203-980. View

11.

Williams A, Ekins S . A quality alert and call for improved curation of public chemistry databases. Drug Discov Today. 2011; 16(17-18):747-50. DOI: 10.1016/j.drudis.2011.07.007. View

12.

Spadaccini N, Castleden I, du Boulay D, Hall S . dREL: a relational expression language for dictionary methods. J Chem Inf Model. 2012; 52(8):1917-25. DOI: 10.1021/ci300076w. View

13.

Spadaccini N, Hall S . DDLm: a new dictionary definition language. J Chem Inf Model. 2012; 52(8):1907-16. DOI: 10.1021/ci300075z. View

14.

Grazulis S, Daskevic A, Merkys A, Chateigner D, Lutterotti L, Quiros M . Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration. Nucleic Acids Res. 2011; 40(Database issue):D420-7. PMC: 3245043. DOI: 10.1093/nar/gkr900. View

15.

Brown I, McMahon B . CIF: the computer language of crystallography. Acta Crystallogr B. 2002; 58(Pt 3 Pt 1):317-24. DOI: 10.1107/s0108768102003464. View