Cyberinfrastructure for the digital brain: spatial standards for integrating rodent brain atlases
Identifieur interne : 000569 ( Ncbi/Merge ); précédent : 000568; suivant : 000570Cyberinfrastructure for the digital brain: spatial standards for integrating rodent brain atlases
Auteurs : Ilya Zaslavsky [États-Unis] ; Richard A. Baldock [Royaume-Uni] ; Jyl Boline [États-Unis]Source :
- Frontiers in Neuroinformatics [ 1662-5196 ] ; 2014.
Abstract
Biomedical research entails capture and analysis of massive data volumes and new discoveries arise from data-integration and mining. This is only possible if data can be mapped onto a common framework such as the genome for genomic data. In neuroscience, the framework is intrinsically spatial and based on a number of paper atlases. This cannot meet today's data-intensive analysis and integration challenges. A scalable and extensible software infrastructure that is standards based but open for novel data and resources, is required for integrating information such as signal distributions, gene-expression, neuronal connectivity, electrophysiology, anatomy, and developmental processes. Therefore, the International Neuroinformatics Coordinating Facility (INCF) initiated the development of a spatial framework for neuroscience data integration with an associated Digital Atlasing Infrastructure (DAI). A prototype implementation of this infrastructure for the rodent brain is reported here. The infrastructure is based on a collection of reference spaces to which data is mapped at the required resolution, such as the Waxholm Space (WHS), a 3D reconstruction of the brain generated using high-resolution, multi-channel microMRI. The core standards of the digital atlasing service-oriented infrastructure include Waxholm Markup Language (WaxML): XML schema expressing a uniform information model for key elements such as coordinate systems, transformations, points of interest (POI)s, labels, and annotations; and Atlas Web Services: interfaces for querying and updating atlas data. The services return WaxML-encoded documents with information about capabilities, spatial reference systems (SRSs) and structures, and execute coordinate transformations and POI-based requests. Key elements of INCF-DAI cyberinfrastructure have been prototyped for both mouse and rat brain atlas sources, including the Allen Mouse Brain Atlas, UCSD Cell-Centered Database, and Edinburgh Mouse Atlas Project.
Url:
DOI: 10.3389/fninf.2014.00074
PubMed: 25309417
PubMed Central: 4162418
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<front><div type="abstract" xml:lang="en"><p>Biomedical research entails capture and analysis of massive data volumes and new discoveries arise from data-integration and mining. This is only possible if data can be mapped onto a common framework such as the genome for genomic data. In neuroscience, the framework is intrinsically spatial and based on a number of paper atlases. This cannot meet today's data-intensive analysis and integration challenges. A scalable and extensible software infrastructure that is standards based but open for novel data and resources, is required for integrating information such as signal distributions, gene-expression, neuronal connectivity, electrophysiology, anatomy, and developmental processes. Therefore, the International Neuroinformatics Coordinating Facility (INCF) initiated the development of a spatial framework for neuroscience data integration with an associated Digital Atlasing Infrastructure (DAI). A prototype implementation of this infrastructure for the rodent brain is reported here. The infrastructure is based on a collection of reference spaces to which data is mapped at the required resolution, such as the Waxholm Space (WHS), a 3D reconstruction of the brain generated using high-resolution, multi-channel microMRI. The core standards of the digital atlasing service-oriented infrastructure include Waxholm Markup Language (WaxML): XML schema expressing a uniform information model for key elements such as coordinate systems, transformations, points of interest (POI)s, labels, and annotations; and Atlas Web Services: interfaces for querying and updating atlas data. The services return WaxML-encoded documents with information about capabilities, spatial reference systems (SRSs) and structures, and execute coordinate transformations and POI-based requests. Key elements of INCF-DAI cyberinfrastructure have been prototyped for both mouse and rat brain atlas sources, including the Allen Mouse Brain Atlas, UCSD Cell-Centered Database, and Edinburgh Mouse Atlas Project.</p>
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</TEI>
<double pmid="25309417"><pmc><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Cyberinfrastructure for the digital brain: spatial standards for integrating rodent brain atlases</title>
<author><name sortKey="Zaslavsky, Ilya" sort="Zaslavsky, Ilya" uniqKey="Zaslavsky I" first="Ilya" last="Zaslavsky">Ilya Zaslavsky</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>San Diego Supercomputer Center, University of California San Diego</institution>
<country>La Jolla, CA, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea></wicri:regionArea>
<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Baldock, Richard A" sort="Baldock, Richard A" uniqKey="Baldock R" first="Richard A." last="Baldock">Richard A. Baldock</name>
<affiliation wicri:level="1"><nlm:aff id="aff2"><institution>MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh</institution>
<country>Edinburgh, UK</country>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea></wicri:regionArea>
<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Boline, Jyl" sort="Boline, Jyl" uniqKey="Boline J" first="Jyl" last="Boline">Jyl Boline</name>
<affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Informed Minds, Wilton Manors</institution>
<country>FL, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea></wicri:regionArea>
<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">25309417</idno>
<idno type="pmc">4162418</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4162418</idno>
<idno type="RBID">PMC:4162418</idno>
<idno type="doi">10.3389/fninf.2014.00074</idno>
<date when="2014">2014</date>
<idno type="wicri:Area/Pmc/Corpus">000540</idno>
<idno type="wicri:Area/Pmc/Curation">000540</idno>
<idno type="wicri:Area/Pmc/Checkpoint">000216</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Cyberinfrastructure for the digital brain: spatial standards for integrating rodent brain atlases</title>
<author><name sortKey="Zaslavsky, Ilya" sort="Zaslavsky, Ilya" uniqKey="Zaslavsky I" first="Ilya" last="Zaslavsky">Ilya Zaslavsky</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>San Diego Supercomputer Center, University of California San Diego</institution>
<country>La Jolla, CA, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea></wicri:regionArea>
<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
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<author><name sortKey="Baldock, Richard A" sort="Baldock, Richard A" uniqKey="Baldock R" first="Richard A." last="Baldock">Richard A. Baldock</name>
<affiliation wicri:level="1"><nlm:aff id="aff2"><institution>MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh</institution>
<country>Edinburgh, UK</country>
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<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea></wicri:regionArea>
<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Boline, Jyl" sort="Boline, Jyl" uniqKey="Boline J" first="Jyl" last="Boline">Jyl Boline</name>
<affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Informed Minds, Wilton Manors</institution>
<country>FL, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea></wicri:regionArea>
<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
</affiliation>
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<series><title level="j">Frontiers in Neuroinformatics</title>
<idno type="eISSN">1662-5196</idno>
<imprint><date when="2014">2014</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p>Biomedical research entails capture and analysis of massive data volumes and new discoveries arise from data-integration and mining. This is only possible if data can be mapped onto a common framework such as the genome for genomic data. In neuroscience, the framework is intrinsically spatial and based on a number of paper atlases. This cannot meet today's data-intensive analysis and integration challenges. A scalable and extensible software infrastructure that is standards based but open for novel data and resources, is required for integrating information such as signal distributions, gene-expression, neuronal connectivity, electrophysiology, anatomy, and developmental processes. Therefore, the International Neuroinformatics Coordinating Facility (INCF) initiated the development of a spatial framework for neuroscience data integration with an associated Digital Atlasing Infrastructure (DAI). A prototype implementation of this infrastructure for the rodent brain is reported here. The infrastructure is based on a collection of reference spaces to which data is mapped at the required resolution, such as the Waxholm Space (WHS), a 3D reconstruction of the brain generated using high-resolution, multi-channel microMRI. The core standards of the digital atlasing service-oriented infrastructure include Waxholm Markup Language (WaxML): XML schema expressing a uniform information model for key elements such as coordinate systems, transformations, points of interest (POI)s, labels, and annotations; and Atlas Web Services: interfaces for querying and updating atlas data. The services return WaxML-encoded documents with information about capabilities, spatial reference systems (SRSs) and structures, and execute coordinate transformations and POI-based requests. Key elements of INCF-DAI cyberinfrastructure have been prototyped for both mouse and rat brain atlas sources, including the Allen Mouse Brain Atlas, UCSD Cell-Centered Database, and Edinburgh Mouse Atlas Project.</p>
</div>
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<pubmed><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Cyberinfrastructure for the digital brain: spatial standards for integrating rodent brain atlases.</title>
<author><name sortKey="Zaslavsky, Ilya" sort="Zaslavsky, Ilya" uniqKey="Zaslavsky I" first="Ilya" last="Zaslavsky">Ilya Zaslavsky</name>
<affiliation wicri:level="2"><nlm:affiliation>San Diego Supercomputer Center, University of California San Diego La Jolla, CA, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>San Diego Supercomputer Center, University of California San Diego La Jolla, CA</wicri:regionArea>
<placeName><region type="state">Californie</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Baldock, Richard A" sort="Baldock, Richard A" uniqKey="Baldock R" first="Richard A" last="Baldock">Richard A. Baldock</name>
<affiliation wicri:level="1"><nlm:affiliation>MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Edinburgh, UK.</nlm:affiliation>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Edinburgh</wicri:regionArea>
<wicri:noRegion>University of Edinburgh Edinburgh</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Boline, Jyl" sort="Boline, Jyl" uniqKey="Boline J" first="Jyl" last="Boline">Jyl Boline</name>
<affiliation wicri:level="1"><nlm:affiliation>Informed Minds, Wilton Manors FL, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Informed Minds, Wilton Manors FL</wicri:regionArea>
<wicri:noRegion>Wilton Manors FL</wicri:noRegion>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2014">2014</date>
<idno type="doi">10.3389/fninf.2014.00074</idno>
<idno type="RBID">pubmed:25309417</idno>
<idno type="pmid">25309417</idno>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">Cyberinfrastructure for the digital brain: spatial standards for integrating rodent brain atlases.</title>
<author><name sortKey="Zaslavsky, Ilya" sort="Zaslavsky, Ilya" uniqKey="Zaslavsky I" first="Ilya" last="Zaslavsky">Ilya Zaslavsky</name>
<affiliation wicri:level="2"><nlm:affiliation>San Diego Supercomputer Center, University of California San Diego La Jolla, CA, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>San Diego Supercomputer Center, University of California San Diego La Jolla, CA</wicri:regionArea>
<placeName><region type="state">Californie</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Baldock, Richard A" sort="Baldock, Richard A" uniqKey="Baldock R" first="Richard A" last="Baldock">Richard A. Baldock</name>
<affiliation wicri:level="1"><nlm:affiliation>MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Edinburgh, UK.</nlm:affiliation>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Edinburgh</wicri:regionArea>
<wicri:noRegion>University of Edinburgh Edinburgh</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Boline, Jyl" sort="Boline, Jyl" uniqKey="Boline J" first="Jyl" last="Boline">Jyl Boline</name>
<affiliation wicri:level="1"><nlm:affiliation>Informed Minds, Wilton Manors FL, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Informed Minds, Wilton Manors FL</wicri:regionArea>
<wicri:noRegion>Wilton Manors FL</wicri:noRegion>
</affiliation>
</author>
</analytic>
<series><title level="j">Frontiers in neuroinformatics</title>
<idno type="eISSN">1662-5196</idno>
<imprint><date when="2014" type="published">2014</date>
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<front><div type="abstract" xml:lang="en">Biomedical research entails capture and analysis of massive data volumes and new discoveries arise from data-integration and mining. This is only possible if data can be mapped onto a common framework such as the genome for genomic data. In neuroscience, the framework is intrinsically spatial and based on a number of paper atlases. This cannot meet today's data-intensive analysis and integration challenges. A scalable and extensible software infrastructure that is standards based but open for novel data and resources, is required for integrating information such as signal distributions, gene-expression, neuronal connectivity, electrophysiology, anatomy, and developmental processes. Therefore, the International Neuroinformatics Coordinating Facility (INCF) initiated the development of a spatial framework for neuroscience data integration with an associated Digital Atlasing Infrastructure (DAI). A prototype implementation of this infrastructure for the rodent brain is reported here. The infrastructure is based on a collection of reference spaces to which data is mapped at the required resolution, such as the Waxholm Space (WHS), a 3D reconstruction of the brain generated using high-resolution, multi-channel microMRI. The core standards of the digital atlasing service-oriented infrastructure include Waxholm Markup Language (WaxML): XML schema expressing a uniform information model for key elements such as coordinate systems, transformations, points of interest (POI)s, labels, and annotations; and Atlas Web Services: interfaces for querying and updating atlas data. The services return WaxML-encoded documents with information about capabilities, spatial reference systems (SRSs) and structures, and execute coordinate transformations and POI-based requests. Key elements of INCF-DAI cyberinfrastructure have been prototyped for both mouse and rat brain atlas sources, including the Allen Mouse Brain Atlas, UCSD Cell-Centered Database, and Edinburgh Mouse Atlas Project.</div>
</front>
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