The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age
Identifieur interne : 000267 ( Ncbi/Merge ); précédent : 000266; suivant : 000268The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age
Auteurs : Sam Adams [Royaume-Uni] ; Pablo De Castro ; Pablo Echenique [Espagne] ; Jorge Estrada [Espagne] ; Marcus D. Hanwell [États-Unis] ; Peter Murray-Rust [Royaume-Uni] ; Paul Sherwood [Royaume-Uni] ; Jens Thomas [Royaume-Uni] ; Joe Townsend [Royaume-Uni]Source :
- Journal of Cheminformatics [ 1758-2946 ] ; 2011.
Abstract
Computational Quantum Chemistry has developed into a powerful, efficient, reliable and increasingly routine tool for exploring the structure and properties of small to medium sized molecules. Many thousands of calculations are performed every day, some offering results which approach experimental accuracy. However, in contrast to other disciplines, such as crystallography, or bioinformatics, where standard formats and well-known, unified databases exist, this QC data is generally destined to remain locally held in files which are not designed to be machine-readable. Only a very small subset of these results will become accessible to the wider community through publication.
In this paper we describe how the Quixote Project is developing the infrastructure required to convert output from a number of different molecular quantum chemistry packages to a common semantically rich, machine-readable format and to build respositories of QC results. Such an infrastructure offers benefits at many levels. The standardised representation of the results will facilitate software interoperability, for example making it easier for analysis tools to take data from different QC packages, and will also help with archival and deposition of results. The repository infrastructure, which is lightweight and built using Open software components, can be implemented at individual researcher, project, organisation or community level, offering the exciting possibility that in future many of these QC results can be made publically available, to be searched and interpreted just as crystallography and bioinformatics results are today.
Although we believe that quantum chemists will appreciate the contribution the Quixote infrastructure can make to the organisation and and exchange of their results, we anticipate that greater rewards will come from enabling their results to be consumed by a wider community. As the respositories grow they will become a valuable source of chemical data for use by other disciplines in both research and education.
The Quixote project is unconventional in that the infrastructure is being implemented in advance of a full definition of the data model which will eventually underpin it. We believe that a working system which offers real value to researchers based on tools and shared, searchable repositories will encourage early participation from a broader community, including both producers and consumers of data. In the early stages, searching and indexing can be performed on the chemical subject of the calculations, and well defined calculation meta-data. The process of defining more specific quantum chemical definitions, adding them to dictionaries and extracting them consistently from the results of the various software packages can then proceed in an incremental manner, adding additional value at each stage.
Not only will these results help to change the data management model in the field of Quantum Chemistry, but the methodology can be applied to other pressing problems related to data in computational and experimental science.
Url:
DOI: 10.1186/1758-2946-3-38
PubMed: 21999363
PubMed Central: 3206452
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<front><div type="abstract" xml:lang="en"><p>Computational Quantum Chemistry has developed into a powerful, efficient, reliable and increasingly routine tool for exploring the structure and properties of small to medium sized molecules. Many thousands of calculations are performed every day, some offering results which approach experimental accuracy. However, in contrast to other disciplines, such as crystallography, or bioinformatics, where standard formats and well-known, unified databases exist, this QC data is generally destined to remain locally held in files which are not designed to be machine-readable. Only a very small subset of these results will become accessible to the wider community through publication.</p>
<p>In this paper we describe how the Quixote Project is developing the infrastructure required to convert output from a number of different molecular quantum chemistry packages to a common semantically rich, machine-readable format and to build respositories of QC results. Such an infrastructure offers benefits at many levels. The standardised representation of the results will facilitate software interoperability, for example making it easier for analysis tools to take data from different QC packages, and will also help with archival and deposition of results. The repository infrastructure, which is lightweight and built using Open software components, can be implemented at individual researcher, project, organisation or community level, offering the exciting possibility that in future many of these QC results can be made publically available, to be searched and interpreted just as crystallography and bioinformatics results are today.</p>
<p>Although we believe that quantum chemists will appreciate the contribution the Quixote infrastructure can make to the organisation and and exchange of their results, we anticipate that greater rewards will come from enabling their results to be consumed by a wider community. As the respositories grow they will become a valuable source of chemical data for use by other disciplines in both research and education.</p>
<p>The Quixote project is unconventional in that the infrastructure is being implemented in advance of a full definition of the data model which will eventually underpin it. We believe that a working system which offers real value to researchers based on tools and shared, searchable repositories will encourage early participation from a broader community, including both producers and consumers of data. In the early stages, searching and indexing can be performed on the chemical subject of the calculations, and well defined calculation meta-data. The process of defining more specific quantum chemical definitions, adding them to dictionaries and extracting them consistently from the results of the various software packages can then proceed in an incremental manner, adding additional value at each stage.</p>
<p>Not only will these results help to change the data management model in the field of Quantum Chemistry, but the methodology can be applied to other pressing problems related to data in computational and experimental science.</p>
</div>
</front>
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<author><name sortKey="Murray Rust, P" uniqKey="Murray Rust P">P Murray-Rust</name>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">J Cheminform</journal-id>
<journal-title-group><journal-title>Journal of Cheminformatics</journal-title>
</journal-title-group>
<issn pub-type="epub">1758-2946</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">21999363</article-id>
<article-id pub-id-type="pmc">3206452</article-id>
<article-id pub-id-type="publisher-id">1758-2946-3-38</article-id>
<article-id pub-id-type="doi">10.1186/1758-2946-3-38</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" id="A1"><name><surname>Adams</surname>
<given-names>Sam</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>s.e.adams@gmail.com</email>
</contrib>
<contrib contrib-type="author" id="A2"><name><surname>de Castro</surname>
<given-names>Pablo</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>pcastro@db.uc3m.es</email>
</contrib>
<contrib contrib-type="author" id="A3"><name><surname>Echenique</surname>
<given-names>Pablo</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
<xref ref-type="aff" rid="I4">4</xref>
<xref ref-type="aff" rid="I5">5</xref>
<email>echenique.p@gmail.com</email>
</contrib>
<contrib contrib-type="author" id="A4"><name><surname>Estrada</surname>
<given-names>Jorge</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
<xref ref-type="aff" rid="I4">4</xref>
<xref ref-type="aff" rid="I6">6</xref>
<email>jorge.estrada@unizar.es</email>
</contrib>
<contrib contrib-type="author" id="A5"><name><surname>Hanwell</surname>
<given-names>Marcus D</given-names>
</name>
<xref ref-type="aff" rid="I7">7</xref>
<email>marcus.hanwell@kitware.com</email>
</contrib>
<contrib contrib-type="author" corresp="yes" id="A6"><name><surname>Murray-Rust</surname>
<given-names>Peter</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>pm286@cam.ac.uk</email>
</contrib>
<contrib contrib-type="author" id="A7"><name><surname>Sherwood</surname>
<given-names>Paul</given-names>
</name>
<xref ref-type="aff" rid="I8">8</xref>
<email>paul.sherwood@stfc.ac.uk</email>
</contrib>
<contrib contrib-type="author" id="A8"><name><surname>Thomas</surname>
<given-names>Jens</given-names>
</name>
<xref ref-type="aff" rid="I8">8</xref>
<email>j.m.h.thomas@stfc.ac.uk</email>
</contrib>
<contrib contrib-type="author" id="A9"><name><surname>Townsend</surname>
<given-names>Joe</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>jat45@jatownsend.net</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK</aff>
<aff id="I2"><label>2</label>
SONEX Workgroup for Scholarly Output Notification and Exchange, http://sonexworkgroup.blogspot.com</aff>
<aff id="I3"><label>3</label>
Instituto de Química Física "Rocasolano", CSIC, Serrano 119, E-28006 Madrid, Spain</aff>
<aff id="I4"><label>4</label>
Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Mariano Esquillor s/n, Edificio I+D, E-50018 Zaragoza, Spain</aff>
<aff id="I5"><label>5</label>
Departamento de Física Teórica, Universidad de Zaragoza, Pedro Cerbuna 12, E-50009 Zaragoza, Spain</aff>
<aff id="I6"><label>6</label>
Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Pedro Cerbuna 12, E-50009 Zaragoza, Spain</aff>
<aff id="I7"><label>7</label>
Kitware, Inc., 28 Corporate Drive, Clifton Park, NY 12065, USA</aff>
<aff id="I8"><label>8</label>
STFC Daresbury Laboratory, Daresbury Science and Innovation Campus, Warrington WA4 4AD, UK</aff>
<pub-date pub-type="collection"><year>2011</year>
</pub-date>
<pub-date pub-type="epub"><day>14</day>
<month>10</month>
<year>2011</year>
</pub-date>
<volume>3</volume>
<fpage>38</fpage>
<lpage>38</lpage>
<history><date date-type="received"><day>1</day>
<month>7</month>
<year>2011</year>
</date>
<date date-type="accepted"><day>14</day>
<month>10</month>
<year>2011</year>
</date>
</history>
<permissions><copyright-statement>Copyright ©2011 Adams et al; licensee Chemistry Central Ltd.</copyright-statement>
<copyright-year>2011</copyright-year>
<copyright-holder>Adams et al; licensee Chemistry Central Ltd.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<self-uri xlink:href="http://www.jcheminf.com/content/3/1/38"></self-uri>
<abstract><p>Computational Quantum Chemistry has developed into a powerful, efficient, reliable and increasingly routine tool for exploring the structure and properties of small to medium sized molecules. Many thousands of calculations are performed every day, some offering results which approach experimental accuracy. However, in contrast to other disciplines, such as crystallography, or bioinformatics, where standard formats and well-known, unified databases exist, this QC data is generally destined to remain locally held in files which are not designed to be machine-readable. Only a very small subset of these results will become accessible to the wider community through publication.</p>
<p>In this paper we describe how the Quixote Project is developing the infrastructure required to convert output from a number of different molecular quantum chemistry packages to a common semantically rich, machine-readable format and to build respositories of QC results. Such an infrastructure offers benefits at many levels. The standardised representation of the results will facilitate software interoperability, for example making it easier for analysis tools to take data from different QC packages, and will also help with archival and deposition of results. The repository infrastructure, which is lightweight and built using Open software components, can be implemented at individual researcher, project, organisation or community level, offering the exciting possibility that in future many of these QC results can be made publically available, to be searched and interpreted just as crystallography and bioinformatics results are today.</p>
<p>Although we believe that quantum chemists will appreciate the contribution the Quixote infrastructure can make to the organisation and and exchange of their results, we anticipate that greater rewards will come from enabling their results to be consumed by a wider community. As the respositories grow they will become a valuable source of chemical data for use by other disciplines in both research and education.</p>
<p>The Quixote project is unconventional in that the infrastructure is being implemented in advance of a full definition of the data model which will eventually underpin it. We believe that a working system which offers real value to researchers based on tools and shared, searchable repositories will encourage early participation from a broader community, including both producers and consumers of data. In the early stages, searching and indexing can be performed on the chemical subject of the calculations, and well defined calculation meta-data. The process of defining more specific quantum chemical definitions, adding them to dictionaries and extracting them consistently from the results of the various software packages can then proceed in an incremental manner, adding additional value at each stage.</p>
<p>Not only will these results help to change the data management model in the field of Quantum Chemistry, but the methodology can be applied to other pressing problems related to data in computational and experimental science.</p>
</abstract>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>Espagne</li>
<li>Royaume-Uni</li>
<li>États-Unis</li>
</country>
<region><li>Aragon</li>
<li>Communauté de Madrid</li>
<li>État de New York</li>
</region>
<settlement><li>Saragosse</li>
</settlement>
<orgName><li>Université de Saragosse</li>
</orgName>
</list>
<tree><noCountry><name sortKey="De Castro, Pablo" sort="De Castro, Pablo" uniqKey="De Castro P" first="Pablo" last="De Castro">Pablo De Castro</name>
</noCountry>
<country name="Royaume-Uni"><noRegion><name sortKey="Adams, Sam" sort="Adams, Sam" uniqKey="Adams S" first="Sam" last="Adams">Sam Adams</name>
</noRegion>
<name sortKey="Murray Rust, Peter" sort="Murray Rust, Peter" uniqKey="Murray Rust P" first="Peter" last="Murray-Rust">Peter Murray-Rust</name>
<name sortKey="Sherwood, Paul" sort="Sherwood, Paul" uniqKey="Sherwood P" first="Paul" last="Sherwood">Paul Sherwood</name>
<name sortKey="Thomas, Jens" sort="Thomas, Jens" uniqKey="Thomas J" first="Jens" last="Thomas">Jens Thomas</name>
<name sortKey="Townsend, Joe" sort="Townsend, Joe" uniqKey="Townsend J" first="Joe" last="Townsend">Joe Townsend</name>
</country>
<country name="Espagne"><region name="Communauté de Madrid"><name sortKey="Echenique, Pablo" sort="Echenique, Pablo" uniqKey="Echenique P" first="Pablo" last="Echenique">Pablo Echenique</name>
</region>
<name sortKey="Echenique, Pablo" sort="Echenique, Pablo" uniqKey="Echenique P" first="Pablo" last="Echenique">Pablo Echenique</name>
<name sortKey="Echenique, Pablo" sort="Echenique, Pablo" uniqKey="Echenique P" first="Pablo" last="Echenique">Pablo Echenique</name>
<name sortKey="Estrada, Jorge" sort="Estrada, Jorge" uniqKey="Estrada J" first="Jorge" last="Estrada">Jorge Estrada</name>
<name sortKey="Estrada, Jorge" sort="Estrada, Jorge" uniqKey="Estrada J" first="Jorge" last="Estrada">Jorge Estrada</name>
<name sortKey="Estrada, Jorge" sort="Estrada, Jorge" uniqKey="Estrada J" first="Jorge" last="Estrada">Jorge Estrada</name>
</country>
<country name="États-Unis"><region name="État de New York"><name sortKey="Hanwell, Marcus D" sort="Hanwell, Marcus D" uniqKey="Hanwell M" first="Marcus D" last="Hanwell">Marcus D. Hanwell</name>
</region>
</country>
</tree>
</affiliations>
</record>
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