BinaryCIF and CIFTools-Lightweight, efficient and extensible
macromolecular data management

J 2020

BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management

SEHNAL, David, Sebastian BITTRICH, Sameer VELANKAR, Jaroslav KOČA, Radka SVOBODOVÁ et. al.

Basic information

Original name

BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management

Authors

SEHNAL, David (203 Czech Republic, belonging to the institution), Sebastian BITTRICH, Sameer VELANKAR, Jaroslav KOČA (203 Czech Republic, guarantor, belonging to the institution), Radka SVOBODOVÁ (203 Czech Republic, belonging to the institution), Stephen K. BURLEY and Alexander S. ROSE

Edition

PLoS Computational Biology, San Francisco, Public Library of Science, 2020, 1553-734X

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 4.475

RIV identification code

RIV/00216224:14740/20:00117701

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1371/journal.pcbi.1008247

UT WoS

000585163600006

Keywords in English

Structural Biology; Molecular Graphics; Data Curation

Abstract

V originále

3D macromolecular structural data is growing ever more complex and plentiful in the wake of substantive advances in experimental and computational structure determination methods including macromolecular crystallography, cryo-electron microscopy, and integrative methods. Efficient means of working with 3D macromolecular structural data for archiving, analyses, and visualization are central to facilitating interoperability and reusability in compliance with the FAIR Principles. We address two challenges posed by growth in data size and complexity. First, data size is reduced by bespoke compression techniques. Second, complexity is managed through improved software tooling and fully leveraging available data dictionary schemas. To this end, we introduce BinaryCIF, a serialization of Crystallographic Information File (CIF) format files that maintains full compatibility to related data schemas, such as PDBx/mmCIF, while reducing file sizes by more than a factor of two versus gzip compressed CIF files. Moreover, for the largest structures, BinaryCIF provides even better compression-factor ten and four versus CIF files and gzipped CIF files, respectively. Herein, we describe CIFTools, a set of libraries in Java and TypeScript for generic and typed handling of CIF and BinaryCIF files. Together, BinaryCIF and CIFTools enable lightweight, efficient, and extensible handling of 3D macromolecular structural data.

Links

EF16_013/0001777, research and development project

Name: ELIXIR-CZ: Budování kapacit

LM2018131, research and development project

Name: Česká národní infrastruktura pro biologická data (Acronym: ELIXIR-CZ)

Investor: Ministry of Education, Youth and Sports of the CR, Czech National Infrastructure for Biological Data

Citovat

SEHNAL, David, Sebastian BITTRICH, Sameer VELANKAR, Jaroslav KOČA, Radka SVOBODOVÁ, Stephen K. BURLEY and Alexander S. ROSE. BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management. PLoS Computational Biology. San Francisco: Public Library of Science, 2020, vol. 16, No 10, p. 1-13. ISSN 1553-734X. Available from: https://dx.doi.org/10.1371/journal.pcbi.1008247.

@article{1726121,
   author = {Sehnal, David and Bittrich, Sebastian and Velankar, Sameer and Koča, Jaroslav and Svobodová, Radka and Burley, Stephen K. and Rose, Alexander S.},
   article_location = {San Francisco},
   article_number = {10},
   doi = {http://dx.doi.org/10.1371/journal.pcbi.1008247},
   keywords = {Structural Biology; Molecular Graphics; Data Curation},
   language = {eng},
   issn = {1553-734X},
   journal = {PLoS Computational Biology},
   title = {BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management},
   url = {https://doi.org/10.1371/journal.pcbi.1008247},
   volume = {16},
   year = {2020}
}

TY  - JOUR
ID  - 1726121
AU  - Sehnal, David - Bittrich, Sebastian - Velankar, Sameer - Koča, Jaroslav - Svobodová, Radka - Burley, Stephen K. - Rose, Alexander S.
PY  - 2020
TI  - BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management
JF  - PLoS Computational Biology
VL  - 16
IS  - 10
SP  - 1-13
EP  - 1-13
PB  - Public Library of Science
SN  - 1553734X
KW  - Structural Biology
KW  - Molecular Graphics
KW  - Data Curation
UR  - https://doi.org/10.1371/journal.pcbi.1008247
L2  - https://doi.org/10.1371/journal.pcbi.1008247
N2  - 3D macromolecular structural data is growing ever more complex and plentiful in the wake of substantive advances in experimental and computational structure determination methods including macromolecular crystallography, cryo-electron microscopy, and integrative methods. Efficient means of working with 3D macromolecular structural data for archiving, analyses, and visualization are central to facilitating interoperability and reusability in compliance with the FAIR Principles. We address two challenges posed by growth in data size and complexity. First, data size is reduced by bespoke compression techniques. Second, complexity is managed through improved software tooling and fully leveraging available data dictionary schemas. To this end, we introduce BinaryCIF, a serialization of Crystallographic Information File (CIF) format files that maintains full compatibility to related data schemas, such as PDBx/mmCIF, while reducing file sizes by more than a factor of two versus gzip compressed CIF files. Moreover, for the largest structures, BinaryCIF provides even better compression-factor ten and four versus CIF files and gzipped CIF files, respectively. Herein, we describe CIFTools, a set of libraries in Java and TypeScript for generic and typed handling of CIF and BinaryCIF files. Together, BinaryCIF and CIFTools enable lightweight, efficient, and extensible handling of 3D macromolecular structural data.
ER  -

SEHNAL, David, Sebastian BITTRICH, Sameer VELANKAR, Jaroslav KOČA, Radka SVOBODOVÁ, Stephen K. BURLEY and Alexander S. ROSE. BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management. \textit{PLoS Computational Biology}. San Francisco: Public Library of Science, 2020, vol.~16, No~10, p.~1-13. ISSN~1553-734X. Available from: https://dx.doi.org/10.1371/journal.pcbi.1008247.

Detailed Information on Publication Record