Informatics and Standards for Nanomedicine Technology
Identifieur interne : 000241 ( Ncbi/Merge ); précédent : 000240; suivant : 000242Informatics and Standards for Nanomedicine Technology
Auteurs : Dennis G. Thomas ; Fred Klaessig ; Stacey L. Harper ; Martin Fritts ; Mark D. Hoover ; Sharon Gaheen ; Todd H. Stokes ; Rebecca Reznik-Zellen ; Elaine T. Freund ; Juli D. Klemm ; David S. Paik ; Nathan A. Baker [États-Unis]Source :
- Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology [ 1939-5116 ] ; 2011.
Abstract
There are several issues to be addressed concerning the management and effective use of information (or data), generated from nanotechnology studies in biomedical research and medicine. These data are large in volume, diverse in content, and are beset with gaps and ambiguities in the description and characterization of nanomaterials. In this work, we have reviewed three areas of nanomedicine informatics: information resources; taxonomies, controlled vocabularies, and ontologies; and information standards. Informatics methods and standards in each of these areas are critical for enabling collaboration, data sharing, unambiguous representation and interpretation of data, semantic (meaningful) search and integration of data; and for ensuring data quality, reliability, and reproducibility. In particular, we have considered four types of information standards in this review, which are standard characterization protocols, common terminology standards, minimum information standards, and standard data communication (exchange) formats. Currently, due to gaps and ambiguities in the data, it is also difficult to apply computational methods and machine learning techniques to analyze, interpret and recognize patterns in data that are high dimensional in nature, and also to relate variations in nanomaterial properties to variations in their chemical composition, synthesis, characterization protocols, etc. Progress towards resolving the issues of information management in nanomedicine using informatics methods and standards discussed in this review will be essential to the rapidly growing field of nanomedicine informatics.
Url:
DOI: 10.1002/wnan.152
PubMed: 21721140
PubMed Central: 3189420
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Informatics and Standards for Nanomedicine Technology</title><author><name sortKey="Thomas, Dennis G" sort="Thomas, Dennis G" uniqKey="Thomas D" first="Dennis G." last="Thomas">Dennis G. Thomas</name><affiliation><nlm:aff id="A1">Knowledge Discovery and Informatics Group, Pacific Northwest National Laboratory.<email>dennis.thomas@pnl.gov</email></nlm:aff></affiliation></author><author><name sortKey="Klaessig, Fred" sort="Klaessig, Fred" uniqKey="Klaessig F" first="Fred" last="Klaessig">Fred Klaessig</name><affiliation><nlm:aff id="A2">Pennsylvania Bio Nano Systems, LLC.<email>fred.klaessig@pabionano.com</email></nlm:aff></affiliation></author><author><name sortKey="Harper, Stacey L" sort="Harper, Stacey L" uniqKey="Harper S" first="Stacey L." last="Harper">Stacey L. Harper</name><affiliation><nlm:aff id="A3">Environmental and Molecular Toxicology & School of Chemical, Biological and Environmental Engineering. Oregon State University.<email>stacey.harper@oregonstate.edu</email></nlm:aff></affiliation></author><author><name sortKey="Fritts, Martin" sort="Fritts, Martin" uniqKey="Fritts M" first="Martin" last="Fritts">Martin Fritts</name><affiliation><nlm:aff id="A4">SAIC-Fredrick, National Cancer Institute.<email>frittsmj@mail.nih.gov</email></nlm:aff></affiliation></author><author><name sortKey="Hoover, Mark D" sort="Hoover, Mark D" uniqKey="Hoover M" first="Mark D." last="Hoover">Mark D. Hoover</name><affiliation><nlm:aff id="A5">National Institute for Occupational Safety and Health.<email>mark.hoover@cdc.hhs.gov</email></nlm:aff></affiliation></author><author><name sortKey="Gaheen, Sharon" sort="Gaheen, Sharon" uniqKey="Gaheen S" first="Sharon" last="Gaheen">Sharon Gaheen</name><affiliation><nlm:aff id="A6">Health Solutions Business Unit, SAIC.<email>gaheens@mail.nih.gov</email></nlm:aff></affiliation></author><author><name sortKey="Stokes, Todd H" sort="Stokes, Todd H" uniqKey="Stokes T" first="Todd H." last="Stokes">Todd H. Stokes</name><affiliation><nlm:aff id="A7">Department of Biomedical Engineering, Emory University and Georgia Tech.<email>thstoke@emory.edu</email></nlm:aff></affiliation></author><author><name sortKey="Reznik Zellen, Rebecca" sort="Reznik Zellen, Rebecca" uniqKey="Reznik Zellen R" first="Rebecca" last="Reznik-Zellen">Rebecca Reznik-Zellen</name><affiliation><nlm:aff id="A8">Center for Hierarchical Manufacturing University of Massachusetts Amherst.<email>rreznikz@library.umass.edu</email></nlm:aff></affiliation></author><author><name sortKey="Freund, Elaine T" sort="Freund, Elaine T" uniqKey="Freund E" first="Elaine T." last="Freund">Elaine T. Freund</name><affiliation><nlm:aff id="A9">3<sup>rd</sup> Millenium, Inc.<email>efreund@3rdmill.com</email></nlm:aff></affiliation></author><author><name sortKey="Klemm, Juli D" sort="Klemm, Juli D" uniqKey="Klemm J" first="Juli D." last="Klemm">Juli D. Klemm</name><affiliation><nlm:aff id="A10">Center for Biomedical Informatics and Information Technology, National Cancer Institute.<email>klemmj@mail.nih.gov</email></nlm:aff></affiliation></author><author><name sortKey="Paik, David S" sort="Paik, David S" uniqKey="Paik D" first="David S." last="Paik">David S. Paik</name><affiliation><nlm:aff id="A11">Radiological Sciences Laboratory, Stanford University.<email>david.paik@stanford.edu</email></nlm:aff></affiliation></author><author><name sortKey="Baker, Nathan A" sort="Baker, Nathan A" uniqKey="Baker N" first="Nathan A." last="Baker">Nathan A. Baker</name><affiliation wicri:level="2"><nlm:aff id="A12">Pacific Northwest National Laboratory, 902 Battelle Blvd. P.O. Box 999, MSIN K7-28, Richland, WA 99352 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Washington (État)</region></placeName><wicri:cityArea>Pacific Northwest National Laboratory, 902 Battelle Blvd. P.O. Box 999, MSIN K7-28, Richland</wicri:cityArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21721140</idno><idno type="pmc">3189420</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3189420</idno><idno type="RBID">PMC:3189420</idno><idno type="doi">10.1002/wnan.152</idno><date when="2011">2011</date><idno type="wicri:Area/Pmc/Corpus">000439</idno><idno type="wicri:Area/Pmc/Curation">000439</idno><idno type="wicri:Area/Pmc/Checkpoint">000504</idno><idno type="wicri:Area/Ncbi/Merge">000241</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Informatics and Standards for Nanomedicine Technology</title><author><name sortKey="Thomas, Dennis G" sort="Thomas, Dennis G" uniqKey="Thomas D" first="Dennis G." last="Thomas">Dennis G. Thomas</name><affiliation><nlm:aff id="A1">Knowledge Discovery and Informatics Group, Pacific Northwest National Laboratory.<email>dennis.thomas@pnl.gov</email></nlm:aff></affiliation></author><author><name sortKey="Klaessig, Fred" sort="Klaessig, Fred" uniqKey="Klaessig F" first="Fred" last="Klaessig">Fred Klaessig</name><affiliation><nlm:aff id="A2">Pennsylvania Bio Nano Systems, LLC.<email>fred.klaessig@pabionano.com</email></nlm:aff></affiliation></author><author><name sortKey="Harper, Stacey L" sort="Harper, Stacey L" uniqKey="Harper S" first="Stacey L." last="Harper">Stacey L. Harper</name><affiliation><nlm:aff id="A3">Environmental and Molecular Toxicology & School of Chemical, Biological and Environmental Engineering. Oregon State University.<email>stacey.harper@oregonstate.edu</email></nlm:aff></affiliation></author><author><name sortKey="Fritts, Martin" sort="Fritts, Martin" uniqKey="Fritts M" first="Martin" last="Fritts">Martin Fritts</name><affiliation><nlm:aff id="A4">SAIC-Fredrick, National Cancer Institute.<email>frittsmj@mail.nih.gov</email></nlm:aff></affiliation></author><author><name sortKey="Hoover, Mark D" sort="Hoover, Mark D" uniqKey="Hoover M" first="Mark D." last="Hoover">Mark D. Hoover</name><affiliation><nlm:aff id="A5">National Institute for Occupational Safety and Health.<email>mark.hoover@cdc.hhs.gov</email></nlm:aff></affiliation></author><author><name sortKey="Gaheen, Sharon" sort="Gaheen, Sharon" uniqKey="Gaheen S" first="Sharon" last="Gaheen">Sharon Gaheen</name><affiliation><nlm:aff id="A6">Health Solutions Business Unit, SAIC.<email>gaheens@mail.nih.gov</email></nlm:aff></affiliation></author><author><name sortKey="Stokes, Todd H" sort="Stokes, Todd H" uniqKey="Stokes T" first="Todd H." last="Stokes">Todd H. Stokes</name><affiliation><nlm:aff id="A7">Department of Biomedical Engineering, Emory University and Georgia Tech.<email>thstoke@emory.edu</email></nlm:aff></affiliation></author><author><name sortKey="Reznik Zellen, Rebecca" sort="Reznik Zellen, Rebecca" uniqKey="Reznik Zellen R" first="Rebecca" last="Reznik-Zellen">Rebecca Reznik-Zellen</name><affiliation><nlm:aff id="A8">Center for Hierarchical Manufacturing University of Massachusetts Amherst.<email>rreznikz@library.umass.edu</email></nlm:aff></affiliation></author><author><name sortKey="Freund, Elaine T" sort="Freund, Elaine T" uniqKey="Freund E" first="Elaine T." last="Freund">Elaine T. Freund</name><affiliation><nlm:aff id="A9">3<sup>rd</sup> Millenium, Inc.<email>efreund@3rdmill.com</email></nlm:aff></affiliation></author><author><name sortKey="Klemm, Juli D" sort="Klemm, Juli D" uniqKey="Klemm J" first="Juli D." last="Klemm">Juli D. Klemm</name><affiliation><nlm:aff id="A10">Center for Biomedical Informatics and Information Technology, National Cancer Institute.<email>klemmj@mail.nih.gov</email></nlm:aff></affiliation></author><author><name sortKey="Paik, David S" sort="Paik, David S" uniqKey="Paik D" first="David S." last="Paik">David S. Paik</name><affiliation><nlm:aff id="A11">Radiological Sciences Laboratory, Stanford University.<email>david.paik@stanford.edu</email></nlm:aff></affiliation></author><author><name sortKey="Baker, Nathan A" sort="Baker, Nathan A" uniqKey="Baker N" first="Nathan A." last="Baker">Nathan A. Baker</name><affiliation wicri:level="2"><nlm:aff id="A12">Pacific Northwest National Laboratory, 902 Battelle Blvd. P.O. Box 999, MSIN K7-28, Richland, WA 99352 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Washington (État)</region></placeName><wicri:cityArea>Pacific Northwest National Laboratory, 902 Battelle Blvd. P.O. Box 999, MSIN K7-28, Richland</wicri:cityArea></affiliation></author></analytic><series><title level="j">Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology</title><idno type="ISSN">1939-5116</idno><idno type="eISSN">1939-0041</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="P1">There are several issues to be addressed concerning the management and effective use of information (or data), generated from nanotechnology studies in biomedical research and medicine. These data are large in volume, diverse in content, and are beset with gaps and ambiguities in the description and characterization of nanomaterials. In this work, we have reviewed three areas of nanomedicine informatics: information resources; taxonomies, controlled vocabularies, and ontologies; and information standards. Informatics methods and standards in each of these areas are critical for enabling collaboration, data sharing, unambiguous representation and interpretation of data, semantic (meaningful) search and integration of data; and for ensuring data quality, reliability, and reproducibility. In particular, we have considered four types of information standards in this review, which are standard characterization protocols, common terminology standards, minimum information standards, and standard data communication (exchange) formats. Currently, due to gaps and ambiguities in the data, it is also difficult to apply computational methods and machine learning techniques to analyze, interpret and recognize patterns in data that are high dimensional in nature, and also to relate variations in nanomaterial properties to variations in their chemical composition, synthesis, characterization protocols, etc. Progress towards resolving the issues of information management in nanomedicine using informatics methods and standards discussed in this review will be essential to the rapidly growing field of nanomedicine informatics.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<pmc-dir>properties manuscript</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-journal-id">101508311</journal-id><journal-id journal-id-type="pubmed-jr-id">36716</journal-id><journal-id journal-id-type="nlm-ta">Wiley Interdiscip Rev Nanomed Nanobiotechnol</journal-id><journal-id journal-id-type="iso-abbrev">Wiley Interdiscip Rev Nanomed Nanobiotechnol</journal-id><journal-title-group><journal-title>Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology</journal-title></journal-title-group><issn pub-type="ppub">1939-5116</issn><issn pub-type="epub">1939-0041</issn></journal-meta><article-meta><article-id pub-id-type="pmid">21721140</article-id><article-id pub-id-type="pmc">3189420</article-id><article-id pub-id-type="doi">10.1002/wnan.152</article-id><article-id pub-id-type="manuscript">NIHMS299401</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Informatics and Standards for Nanomedicine Technology</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Thomas</surname><given-names>Dennis G.</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Klaessig</surname><given-names>Fred</given-names></name><xref ref-type="aff" rid="A2">2</xref></contrib><contrib contrib-type="author"><name><surname>Harper</surname><given-names>Stacey L.</given-names></name><xref ref-type="aff" rid="A3">3</xref></contrib><contrib contrib-type="author"><name><surname>Fritts</surname><given-names>Martin</given-names></name><xref ref-type="aff" rid="A4">4</xref></contrib><contrib contrib-type="author"><name><surname>Hoover</surname><given-names>Mark D.</given-names></name><xref ref-type="aff" rid="A5">5</xref></contrib><contrib contrib-type="author"><name><surname>Gaheen</surname><given-names>Sharon</given-names></name><xref ref-type="aff" rid="A6">6</xref></contrib><contrib contrib-type="author"><name><surname>Stokes</surname><given-names>Todd H.</given-names></name><xref ref-type="aff" rid="A7">7</xref></contrib><contrib contrib-type="author"><name><surname>Reznik-Zellen</surname><given-names>Rebecca</given-names></name><xref ref-type="aff" rid="A8">8</xref></contrib><contrib contrib-type="author"><name><surname>Freund</surname><given-names>Elaine T.</given-names></name><xref ref-type="aff" rid="A9">9</xref></contrib><contrib contrib-type="author"><name><surname>Klemm</surname><given-names>Juli D.</given-names></name><xref ref-type="aff" rid="A10">10</xref></contrib><contrib contrib-type="author"><name><surname>Paik</surname><given-names>David S.</given-names></name><xref ref-type="aff" rid="A11">11</xref></contrib><contrib contrib-type="author"><name><surname>Baker</surname><given-names>Nathan A.</given-names></name><xref ref-type="aff" rid="A12">12</xref></contrib></contrib-group><aff id="A1"><label>1</label>Knowledge Discovery and Informatics Group, Pacific Northwest National Laboratory.<email>dennis.thomas@pnl.gov</email></aff><aff id="A2"><label>2</label>Pennsylvania Bio Nano Systems, LLC.<email>fred.klaessig@pabionano.com</email></aff><aff id="A3"><label>3</label>Environmental and Molecular Toxicology & School of Chemical, Biological and Environmental Engineering. Oregon State University.<email>stacey.harper@oregonstate.edu</email></aff><aff id="A4"><label>4</label>SAIC-Fredrick, National Cancer Institute.<email>frittsmj@mail.nih.gov</email></aff><aff id="A5"><label>5</label>National Institute for Occupational Safety and Health.<email>mark.hoover@cdc.hhs.gov</email></aff><aff id="A6"><label>6</label>Health Solutions Business Unit, SAIC.<email>gaheens@mail.nih.gov</email></aff><aff id="A7"><label>7</label>Department of Biomedical Engineering, Emory University and Georgia Tech.<email>thstoke@emory.edu</email></aff><aff id="A8"><label>8</label>Center for Hierarchical Manufacturing University of Massachusetts Amherst.<email>rreznikz@library.umass.edu</email></aff><aff id="A9"><label>9</label>3<sup>rd</sup> Millenium, Inc.<email>efreund@3rdmill.com</email></aff><aff id="A10"><label>10</label>Center for Biomedical Informatics and Information Technology, National Cancer Institute.<email>klemmj@mail.nih.gov</email></aff><aff id="A11"><label>11</label>Radiological Sciences Laboratory, Stanford University.<email>david.paik@stanford.edu</email></aff><aff id="A12"><label>12</label>Pacific Northwest National Laboratory, 902 Battelle Blvd. P.O. Box 999, MSIN K7-28, Richland, WA 99352 USA</aff><author-notes><corresp id="CR1">To whom correspondence should be addressed. Tel: 509-375-3997. <email>nathan.baker@pnl.gov</email></corresp></author-notes><pub-date pub-type="nihms-submitted"><day>3</day><month>6</month><year>2011</year></pub-date><pub-date pub-type="epub"><day>30</day><month>6</month><year>2011</year></pub-date><pub-date pub-type="ppub"><season>Sep-Oct</season><year>2011</year></pub-date><pub-date pub-type="pmc-release"><day>30</day><month>12</month><year>2012</year></pub-date><volume>3</volume><issue>5</issue><fpage>511</fpage><lpage>532</lpage><pmc-comment>elocation-id from pubmed: 10.1002/wnan.152</pmc-comment>
<abstract><p id="P1">There are several issues to be addressed concerning the management and effective use of information (or data), generated from nanotechnology studies in biomedical research and medicine. These data are large in volume, diverse in content, and are beset with gaps and ambiguities in the description and characterization of nanomaterials. In this work, we have reviewed three areas of nanomedicine informatics: information resources; taxonomies, controlled vocabularies, and ontologies; and information standards. Informatics methods and standards in each of these areas are critical for enabling collaboration, data sharing, unambiguous representation and interpretation of data, semantic (meaningful) search and integration of data; and for ensuring data quality, reliability, and reproducibility. In particular, we have considered four types of information standards in this review, which are standard characterization protocols, common terminology standards, minimum information standards, and standard data communication (exchange) formats. Currently, due to gaps and ambiguities in the data, it is also difficult to apply computational methods and machine learning techniques to analyze, interpret and recognize patterns in data that are high dimensional in nature, and also to relate variations in nanomaterial properties to variations in their chemical composition, synthesis, characterization protocols, etc. Progress towards resolving the issues of information management in nanomedicine using informatics methods and standards discussed in this review will be essential to the rapidly growing field of nanomedicine informatics.</p></abstract></article-meta></front></pmc><affiliations><list><country><li>États-Unis</li></country><region><li>Washington (État)</li></region></list><tree><noCountry><name sortKey="Freund, Elaine T" sort="Freund, Elaine T" uniqKey="Freund E" first="Elaine T." last="Freund">Elaine T. Freund</name><name sortKey="Fritts, Martin" sort="Fritts, Martin" uniqKey="Fritts M" first="Martin" last="Fritts">Martin Fritts</name><name sortKey="Gaheen, Sharon" sort="Gaheen, Sharon" uniqKey="Gaheen S" first="Sharon" last="Gaheen">Sharon Gaheen</name><name sortKey="Harper, Stacey L" sort="Harper, Stacey L" uniqKey="Harper S" first="Stacey L." last="Harper">Stacey L. Harper</name><name sortKey="Hoover, Mark D" sort="Hoover, Mark D" uniqKey="Hoover M" first="Mark D." last="Hoover">Mark D. Hoover</name><name sortKey="Klaessig, Fred" sort="Klaessig, Fred" uniqKey="Klaessig F" first="Fred" last="Klaessig">Fred Klaessig</name><name sortKey="Klemm, Juli D" sort="Klemm, Juli D" uniqKey="Klemm J" first="Juli D." last="Klemm">Juli D. Klemm</name><name sortKey="Paik, David S" sort="Paik, David S" uniqKey="Paik D" first="David S." last="Paik">David S. Paik</name><name sortKey="Reznik Zellen, Rebecca" sort="Reznik Zellen, Rebecca" uniqKey="Reznik Zellen R" first="Rebecca" last="Reznik-Zellen">Rebecca Reznik-Zellen</name><name sortKey="Stokes, Todd H" sort="Stokes, Todd H" uniqKey="Stokes T" first="Todd H." last="Stokes">Todd H. Stokes</name><name sortKey="Thomas, Dennis G" sort="Thomas, Dennis G" uniqKey="Thomas D" first="Dennis G." last="Thomas">Dennis G. Thomas</name></noCountry><country name="États-Unis"><region name="Washington (État)"><name sortKey="Baker, Nathan A" sort="Baker, Nathan A" uniqKey="Baker N" first="Nathan A." last="Baker">Nathan A. Baker</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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