BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management.
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 w...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2020-10-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1008247 |
| _version_ | 1819260299283267584 |
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| author | David Sehnal Sebastian Bittrich Sameer Velankar Jaroslav Koča Radka Svobodová Stephen K Burley Alexander S Rose |
| author_facet | David Sehnal Sebastian Bittrich Sameer Velankar Jaroslav Koča Radka Svobodová Stephen K Burley Alexander S Rose |
| author_sort | David Sehnal |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-23T19:23:42Z |
| format | Article |
| id | doaj.art-313803daed7c480ca2e26869858d8f23 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-23T19:23:42Z |
| publishDate | 2020-10-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-313803daed7c480ca2e26869858d8f232022-12-21T17:34:06ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582020-10-011610e100824710.1371/journal.pcbi.1008247BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management.David SehnalSebastian BittrichSameer VelankarJaroslav KočaRadka SvobodováStephen K BurleyAlexander S Rose3D 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.https://doi.org/10.1371/journal.pcbi.1008247 |
| spellingShingle | David Sehnal Sebastian Bittrich Sameer Velankar Jaroslav Koča Radka Svobodová Stephen K Burley Alexander S Rose BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management. PLoS Computational Biology |
| title | BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management. |
| title_full | BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management. |
| title_fullStr | BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management. |
| title_full_unstemmed | BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management. |
| title_short | BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management. |
| title_sort | binarycif and ciftools lightweight efficient and extensible macromolecular data management |
| url | https://doi.org/10.1371/journal.pcbi.1008247 |
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