The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years
It has been increasingly recognized that preservation and public accessibility of primary experimental data are cornerstones necessary for the reproducibility of empirical sciences. In the field of molecular crystallography, many journals now recommend that authors of manuscripts presenting a new cr...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
AIP Publishing LLC and ACA
2019-11-01
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| Series: | Structural Dynamics |
| Online Access: | http://dx.doi.org/10.1063/1.5128672 |
| _version_ | 1811213753602015232 |
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| author | Marek Grabowski Marcin Cymborowski Przemyslaw J. Porebski Tomasz Osinski Ivan G. Shabalin David R. Cooper Wladek Minor |
| author_facet | Marek Grabowski Marcin Cymborowski Przemyslaw J. Porebski Tomasz Osinski Ivan G. Shabalin David R. Cooper Wladek Minor |
| author_sort | Marek Grabowski |
| collection | DOAJ |
| description | It has been increasingly recognized that preservation and public accessibility of primary experimental data are cornerstones necessary for the reproducibility of empirical sciences. In the field of molecular crystallography, many journals now recommend that authors of manuscripts presenting a new crystal structure should deposit their primary experimental data (X-ray diffraction images) to one of the dedicated resources created in recent years. Here, we describe our experiences developing the Integrated Resource for Reproducibility in Molecular Crystallography (IRRMC) and describe several examples of a crucial role that diffraction data can play in improving previously determined protein structures. In its first four years, several hundred crystallographers have deposited data from over 5200 diffraction experiments performed at over 60 different synchrotron beamlines or home sources all over the world. In addition to improving the resource and curating submitted data, we have been building a pipeline for extraction or, in some cases, reconstruction of the metadata necessary for seamless automated processing. Preliminary analysis indicates that about 95% of the archived data can be automatically reprocessed. A high rate of reprocessing success shows the feasibility of using the automated metadata extraction and automated processing as a validation step for the deposition of raw diffraction images. The IRRMC is guided by the Findable, Accessible, Interoperable, and Reusable data management principles. |
| first_indexed | 2024-04-12T05:51:28Z |
| format | Article |
| id | doaj.art-23695485c52245c699c4702243f7c094 |
| institution | Directory Open Access Journal |
| issn | 2329-7778 |
| language | English |
| last_indexed | 2024-04-12T05:51:28Z |
| publishDate | 2019-11-01 |
| publisher | AIP Publishing LLC and ACA |
| record_format | Article |
| series | Structural Dynamics |
| spelling | doaj.art-23695485c52245c699c4702243f7c0942022-12-22T03:45:17ZengAIP Publishing LLC and ACAStructural Dynamics2329-77782019-11-0166064301064301-810.1063/1.5128672The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four yearsMarek Grabowski0Marcin Cymborowski1Przemyslaw J. Porebski2Tomasz Osinski3Ivan G. Shabalin4David R. Cooper5Wladek Minor6 Department of Molecular Physiology and Biological Physics, University of Virginia, Charottesville, Virginia 22908, USA Department of Molecular Physiology and Biological Physics, University of Virginia, Charottesville, Virginia 22908, USA Department of Molecular Physiology and Biological Physics, University of Virginia, Charottesville, Virginia 22908, USA Department of Molecular Physiology and Biological Physics, University of Virginia, Charottesville, Virginia 22908, USA Department of Molecular Physiology and Biological Physics, University of Virginia, Charottesville, Virginia 22908, USA Department of Molecular Physiology and Biological Physics, University of Virginia, Charottesville, Virginia 22908, USA Department of Molecular Physiology and Biological Physics, University of Virginia, Charottesville, Virginia 22908, USAIt has been increasingly recognized that preservation and public accessibility of primary experimental data are cornerstones necessary for the reproducibility of empirical sciences. In the field of molecular crystallography, many journals now recommend that authors of manuscripts presenting a new crystal structure should deposit their primary experimental data (X-ray diffraction images) to one of the dedicated resources created in recent years. Here, we describe our experiences developing the Integrated Resource for Reproducibility in Molecular Crystallography (IRRMC) and describe several examples of a crucial role that diffraction data can play in improving previously determined protein structures. In its first four years, several hundred crystallographers have deposited data from over 5200 diffraction experiments performed at over 60 different synchrotron beamlines or home sources all over the world. In addition to improving the resource and curating submitted data, we have been building a pipeline for extraction or, in some cases, reconstruction of the metadata necessary for seamless automated processing. Preliminary analysis indicates that about 95% of the archived data can be automatically reprocessed. A high rate of reprocessing success shows the feasibility of using the automated metadata extraction and automated processing as a validation step for the deposition of raw diffraction images. The IRRMC is guided by the Findable, Accessible, Interoperable, and Reusable data management principles.http://dx.doi.org/10.1063/1.5128672 |
| spellingShingle | Marek Grabowski Marcin Cymborowski Przemyslaw J. Porebski Tomasz Osinski Ivan G. Shabalin David R. Cooper Wladek Minor The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years Structural Dynamics |
| title | The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years |
| title_full | The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years |
| title_fullStr | The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years |
| title_full_unstemmed | The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years |
| title_short | The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years |
| title_sort | integrated resource for reproducibility in macromolecular crystallography experiences of the first four years |
| url | http://dx.doi.org/10.1063/1.5128672 |
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