ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format
Identifieur interne : 000316 ( Pmc/Checkpoint ); précédent : 000315; suivant : 000317ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format
Auteurs : Dennis G. Thomas [États-Unis] ; Sharon Gaheen [États-Unis] ; Stacey L. Harper [États-Unis] ; Martin Fritts [États-Unis] ; Fred Klaessig [États-Unis] ; Elizabeth Hahn-Dantona [États-Unis] ; David Paik [États-Unis] ; Sue Pan [États-Unis] ; Grace A. Stafford [États-Unis] ; Elaine T. Freund [États-Unis] ; Juli D. Klemm [États-Unis] ; Nathan A. Baker [États-Unis]Source :
- BMC Biotechnology [ 1472-6750 ] ; 2013.
Abstract
The high-throughput genomics communities have been successfully using standardized spreadsheet-based formats to capture and share data within labs and among public repositories. The nanomedicine community has yet to adopt similar standards to share the diverse and multi-dimensional types of data (including metadata) pertaining to the description and characterization of nanomaterials. Owing to the lack of standardization in representing and sharing nanomaterial data, most of the data currently shared via publications and data resources are incomplete, poorly-integrated, and not suitable for meaningful interpretation and re-use of the data. Specifically, in its current state, data cannot be effectively utilized for the development of predictive models that will inform the rational design of nanomaterials.
We have developed a specification called ISA-TAB-Nano, which comprises four spreadsheet-based file formats for representing and integrating various types of nanomaterial data. Three file formats (Investigation, Study, and Assay files) have been adapted from the established ISA-TAB specification; while the Material file format was developed
The ISA-TAB-Nano file formats provide a general and flexible framework to record and integrate nanomaterial descriptions, assay data (metadata and endpoint measurements) and protocol information. Like ISA-TAB, ISA-TAB-Nano supports the use of ontology terms to promote standardized descriptions and to facilitate search and integration of the data. The ISA-TAB-Nano specification has been submitted as an ASTM work item to obtain community feedback and to provide a nanotechnology data-sharing standard for public development and adoption.
Url:
DOI: 10.1186/1472-6750-13-2
PubMed: 23311978
PubMed Central: 3598649
Affiliations:
Links toward previous steps (curation, corpus...)
Links to Exploration step
PMC:3598649Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format</title>
<author><name sortKey="Thomas, Dennis G" sort="Thomas, Dennis G" uniqKey="Thomas D" first="Dennis G" last="Thomas">Dennis G. Thomas</name>
<affiliation wicri:level="2"><nlm:aff id="I1">Knowledge Discovery and Informatics, Pacific Northwest National Laboratory, Richland, WA 99352, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Knowledge Discovery and Informatics, Pacific Northwest National Laboratory, Richland, WA 99352</wicri:regionArea>
<placeName><region type="state">Washington (État)</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Gaheen, Sharon" sort="Gaheen, Sharon" uniqKey="Gaheen S" first="Sharon" last="Gaheen">Sharon Gaheen</name>
<affiliation wicri:level="2"><nlm:aff id="I2">SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, Information Systems Program, Rockville, MD 20852, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, Information Systems Program, Rockville, MD 20852</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</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 wicri:level="2"><nlm:aff id="I3">Department of Environmental and Molecular Toxicology, School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, OR 97331, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Environmental and Molecular Toxicology, School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, OR 97331</wicri:regionArea>
<placeName><region type="state">Oregon</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Fritts, Martin" sort="Fritts, Martin" uniqKey="Fritts M" first="Martin" last="Fritts">Martin Fritts</name>
<affiliation wicri:level="2"><nlm:aff id="I2">SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, Information Systems Program, Rockville, MD 20852, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, Information Systems Program, Rockville, MD 20852</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Klaessig, Fred" sort="Klaessig, Fred" uniqKey="Klaessig F" first="Fred" last="Klaessig">Fred Klaessig</name>
<affiliation wicri:level="2"><nlm:aff id="I4">Pennsylvania Bio Nano Systems, LLC, Doylestown, PA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Pennsylvania Bio Nano Systems, LLC, Doylestown, PA</wicri:regionArea>
<placeName><region type="state">Pennsylvanie</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Hahn Dantona, Elizabeth" sort="Hahn Dantona, Elizabeth" uniqKey="Hahn Dantona E" first="Elizabeth" last="Hahn-Dantona">Elizabeth Hahn-Dantona</name>
<affiliation wicri:level="2"><nlm:aff id="I5">Lockheed Martin, Rockville, MD 20852, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Lockheed Martin, Rockville, MD 20852</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Paik, David" sort="Paik, David" uniqKey="Paik D" first="David" last="Paik">David Paik</name>
<affiliation wicri:level="2"><nlm:aff id="I6">Department of Radiology, Stanford University, Stanford, CA 94305, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Radiology, Stanford University, Stanford, CA 94305</wicri:regionArea>
<placeName><region type="state">Californie</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Pan, Sue" sort="Pan, Sue" uniqKey="Pan S" first="Sue" last="Pan">Sue Pan</name>
<affiliation wicri:level="2"><nlm:aff id="I2">SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, Information Systems Program, Rockville, MD 20852, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, Information Systems Program, Rockville, MD 20852</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Stafford, Grace A" sort="Stafford, Grace A" uniqKey="Stafford G" first="Grace A" last="Stafford">Grace A. Stafford</name>
<affiliation wicri:level="1"><nlm:aff id="I7">The Jackson Laboratory, Bar Harbor, Maine 04609, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>The Jackson Laboratory, Bar Harbor, Maine 04609</wicri:regionArea>
<wicri:noRegion>Maine 04609</wicri:noRegion>
</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 wicri:level="2"><nlm:aff id="I8">3rd Millennium, Inc, North Smithfield, RI 02896, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>3rd Millennium, Inc, North Smithfield, RI 02896</wicri:regionArea>
<placeName><region type="state">Rhode Island</region>
</placeName>
</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 wicri:level="2"><nlm:aff id="I9">Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD 20852, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD 20852</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</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="I10">Knowledge Discovery and Informatics, Pacific Northwest National Laboratory, PO Box 999, MSID K7-28, Richland, WA 99352, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Knowledge Discovery and Informatics, Pacific Northwest National Laboratory, PO Box 999, MSID K7-28, Richland, WA 99352</wicri:regionArea>
<placeName><region type="state">Washington (État)</region>
</placeName>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">23311978</idno>
<idno type="pmc">3598649</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3598649</idno>
<idno type="RBID">PMC:3598649</idno>
<idno type="doi">10.1186/1472-6750-13-2</idno>
<date when="2013">2013</date>
<idno type="wicri:Area/Pmc/Corpus">000261</idno>
<idno type="wicri:Area/Pmc/Curation">000261</idno>
<idno type="wicri:Area/Pmc/Checkpoint">000316</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format</title>
<author><name sortKey="Thomas, Dennis G" sort="Thomas, Dennis G" uniqKey="Thomas D" first="Dennis G" last="Thomas">Dennis G. Thomas</name>
<affiliation wicri:level="2"><nlm:aff id="I1">Knowledge Discovery and Informatics, Pacific Northwest National Laboratory, Richland, WA 99352, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Knowledge Discovery and Informatics, Pacific Northwest National Laboratory, Richland, WA 99352</wicri:regionArea>
<placeName><region type="state">Washington (État)</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Gaheen, Sharon" sort="Gaheen, Sharon" uniqKey="Gaheen S" first="Sharon" last="Gaheen">Sharon Gaheen</name>
<affiliation wicri:level="2"><nlm:aff id="I2">SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, Information Systems Program, Rockville, MD 20852, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, Information Systems Program, Rockville, MD 20852</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</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 wicri:level="2"><nlm:aff id="I3">Department of Environmental and Molecular Toxicology, School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, OR 97331, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Environmental and Molecular Toxicology, School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, OR 97331</wicri:regionArea>
<placeName><region type="state">Oregon</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Fritts, Martin" sort="Fritts, Martin" uniqKey="Fritts M" first="Martin" last="Fritts">Martin Fritts</name>
<affiliation wicri:level="2"><nlm:aff id="I2">SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, Information Systems Program, Rockville, MD 20852, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, Information Systems Program, Rockville, MD 20852</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Klaessig, Fred" sort="Klaessig, Fred" uniqKey="Klaessig F" first="Fred" last="Klaessig">Fred Klaessig</name>
<affiliation wicri:level="2"><nlm:aff id="I4">Pennsylvania Bio Nano Systems, LLC, Doylestown, PA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Pennsylvania Bio Nano Systems, LLC, Doylestown, PA</wicri:regionArea>
<placeName><region type="state">Pennsylvanie</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Hahn Dantona, Elizabeth" sort="Hahn Dantona, Elizabeth" uniqKey="Hahn Dantona E" first="Elizabeth" last="Hahn-Dantona">Elizabeth Hahn-Dantona</name>
<affiliation wicri:level="2"><nlm:aff id="I5">Lockheed Martin, Rockville, MD 20852, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Lockheed Martin, Rockville, MD 20852</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Paik, David" sort="Paik, David" uniqKey="Paik D" first="David" last="Paik">David Paik</name>
<affiliation wicri:level="2"><nlm:aff id="I6">Department of Radiology, Stanford University, Stanford, CA 94305, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Radiology, Stanford University, Stanford, CA 94305</wicri:regionArea>
<placeName><region type="state">Californie</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Pan, Sue" sort="Pan, Sue" uniqKey="Pan S" first="Sue" last="Pan">Sue Pan</name>
<affiliation wicri:level="2"><nlm:aff id="I2">SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, Information Systems Program, Rockville, MD 20852, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, Information Systems Program, Rockville, MD 20852</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Stafford, Grace A" sort="Stafford, Grace A" uniqKey="Stafford G" first="Grace A" last="Stafford">Grace A. Stafford</name>
<affiliation wicri:level="1"><nlm:aff id="I7">The Jackson Laboratory, Bar Harbor, Maine 04609, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>The Jackson Laboratory, Bar Harbor, Maine 04609</wicri:regionArea>
<wicri:noRegion>Maine 04609</wicri:noRegion>
</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 wicri:level="2"><nlm:aff id="I8">3rd Millennium, Inc, North Smithfield, RI 02896, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>3rd Millennium, Inc, North Smithfield, RI 02896</wicri:regionArea>
<placeName><region type="state">Rhode Island</region>
</placeName>
</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 wicri:level="2"><nlm:aff id="I9">Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD 20852, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD 20852</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</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="I10">Knowledge Discovery and Informatics, Pacific Northwest National Laboratory, PO Box 999, MSID K7-28, Richland, WA 99352, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Knowledge Discovery and Informatics, Pacific Northwest National Laboratory, PO Box 999, MSID K7-28, Richland, WA 99352</wicri:regionArea>
<placeName><region type="state">Washington (État)</region>
</placeName>
</affiliation>
</author>
</analytic>
<series><title level="j">BMC Biotechnology</title>
<idno type="eISSN">1472-6750</idno>
<imprint><date when="2013">2013</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><sec><title>Background and motivation</title>
<p>The high-throughput genomics communities have been successfully using standardized spreadsheet-based formats to capture and share data within labs and among public repositories. The nanomedicine community has yet to adopt similar standards to share the diverse and multi-dimensional types of data (including metadata) pertaining to the description and characterization of nanomaterials. Owing to the lack of standardization in representing and sharing nanomaterial data, most of the data currently shared via publications and data resources are incomplete, poorly-integrated, and not suitable for meaningful interpretation and re-use of the data. Specifically, in its current state, data cannot be effectively utilized for the development of predictive models that will inform the rational design of nanomaterials.</p>
</sec>
<sec><title>Results</title>
<p>We have developed a specification called ISA-TAB-Nano, which comprises four spreadsheet-based file formats for representing and integrating various types of nanomaterial data. Three file formats (Investigation, Study, and Assay files) have been adapted from the established ISA-TAB specification; while the Material file format was developed <italic>de novo</italic>
to more readily describe the complexity of nanomaterials and associated small molecules. In this paper, we have discussed the main features of each file format and how to use them for sharing nanomaterial descriptions and assay metadata.</p>
</sec>
<sec><title>Conclusion</title>
<p>The ISA-TAB-Nano file formats provide a general and flexible framework to record and integrate nanomaterial descriptions, assay data (metadata and endpoint measurements) and protocol information. Like ISA-TAB, ISA-TAB-Nano supports the use of ontology terms to promote standardized descriptions and to facilitate search and integration of the data. The ISA-TAB-Nano specification has been submitted as an ASTM work item to obtain community feedback and to provide a nanotechnology data-sharing standard for public development and adoption.</p>
</sec>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Roco, Mc" uniqKey="Roco M">MC Roco</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Currall, Sc" uniqKey="Currall S">SC Currall</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="De La Iglesia, D" uniqKey="De La Iglesia D">D de la Iglesia</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Thomas, Dg" uniqKey="Thomas D">DG Thomas</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Collins, F" uniqKey="Collins F">F Collins</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Collins, Fs" uniqKey="Collins F">FS Collins</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Poschet, J" uniqKey="Poschet J">J Poschet</name>
</author>
<author><name sortKey="Shalley, E" uniqKey="Shalley E">E Shalley</name>
</author>
<author><name sortKey="Speakman, J" uniqKey="Speakman J">J Speakman</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hesse, Bw" uniqKey="Hesse B">BW Hesse</name>
</author>
<author><name sortKey="Croyle, Rt" uniqKey="Croyle R">RT Croyle</name>
</author>
<author><name sortKey="Buetow, Kh" uniqKey="Buetow K">KH Buetow</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Payne, Pro" uniqKey="Payne P">PRO Payne</name>
</author>
<author><name sortKey="Embi, Pj" uniqKey="Embi P">PJ Embi</name>
</author>
<author><name sortKey="Niland, J" uniqKey="Niland J">J Niland</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Boyd, Lb" uniqKey="Boyd L">LB Boyd</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hucka, M" uniqKey="Hucka M">M Hucka</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Demir, E" uniqKey="Demir E">E Demir</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Spellman, Pt" uniqKey="Spellman P">PT Spellman</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rayner, Tf" uniqKey="Rayner T">TF Rayner</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sansone, S A" uniqKey="Sansone S">S-A Sansone</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rocca Serra, P" uniqKey="Rocca Serra P">P Rocca-Serra</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sansone, S A" uniqKey="Sansone S">S-A Sansone</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Brazma, A" uniqKey="Brazma A">A Brazma</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Parkinson, H" uniqKey="Parkinson H">H Parkinson</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Hubble, J" uniqKey="Hubble J">J Hubble</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Reich, M" uniqKey="Reich M">M Reich</name>
</author>
<author><name sortKey="Reich, M" uniqKey="Reich M">M Reich</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gentleman, Rc" uniqKey="Gentleman R">RC Gentleman</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Roebben, G" uniqKey="Roebben G">G Roebben</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Shick, L" uniqKey="Shick L">L Shick</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Thomas, Dg" uniqKey="Thomas D">DG Thomas</name>
</author>
<author><name sortKey="Pappu, Rv" uniqKey="Pappu R">RV Pappu</name>
</author>
<author><name sortKey="Baker, Na" uniqKey="Baker N">NA Baker</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Thomas, Dg" uniqKey="Thomas D">DG Thomas</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="De Matos, P" uniqKey="De Matos P">P de Matos</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Sioutos, N" uniqKey="Sioutos N">N Sioutos</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
</listBibl>
</div1>
</back>
</TEI>
<pmc article-type="other" xml:lang="en"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Biotechnol</journal-id>
<journal-id journal-id-type="iso-abbrev">BMC Biotechnol</journal-id>
<journal-title-group><journal-title>BMC Biotechnology</journal-title>
</journal-title-group>
<issn pub-type="epub">1472-6750</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">23311978</article-id>
<article-id pub-id-type="pmc">3598649</article-id>
<article-id pub-id-type="publisher-id">1472-6750-13-2</article-id>
<article-id pub-id-type="doi">10.1186/1472-6750-13-2</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Correspondence</subject>
</subj-group>
</article-categories>
<title-group><article-title>ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" id="A1"><name><surname>Thomas</surname>
<given-names>Dennis G</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>dennis.thomas@pnnl.gov</email>
</contrib>
<contrib contrib-type="author" id="A2"><name><surname>Gaheen</surname>
<given-names>Sharon</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>gaheens@mail.nih.gov</email>
</contrib>
<contrib contrib-type="author" id="A3"><name><surname>Harper</surname>
<given-names>Stacey L</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
<email>stacey.harper@oregonstate.edu</email>
</contrib>
<contrib contrib-type="author" id="A4"><name><surname>Fritts</surname>
<given-names>Martin</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>martin.fritts@nist.gov</email>
</contrib>
<contrib contrib-type="author" id="A5"><name><surname>Klaessig</surname>
<given-names>Fred</given-names>
</name>
<xref ref-type="aff" rid="I4">4</xref>
<email>fred.klaessig@verizon.net</email>
</contrib>
<contrib contrib-type="author" id="A6"><name><surname>Hahn-Dantona</surname>
<given-names>Elizabeth</given-names>
</name>
<xref ref-type="aff" rid="I5">5</xref>
<email>hahndane@mail.nih.gov</email>
</contrib>
<contrib contrib-type="author" id="A7"><name><surname>Paik</surname>
<given-names>David</given-names>
</name>
<xref ref-type="aff" rid="I6">6</xref>
<email>david.paik@stanford.edu</email>
</contrib>
<contrib contrib-type="author" id="A8"><name><surname>Pan</surname>
<given-names>Sue</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>pansu@mail.nih.gov</email>
</contrib>
<contrib contrib-type="author" id="A9"><name><surname>Stafford</surname>
<given-names>Grace A</given-names>
</name>
<xref ref-type="aff" rid="I7">7</xref>
<email>grace.stafford@jax.org</email>
</contrib>
<contrib contrib-type="author" id="A10"><name><surname>Freund</surname>
<given-names>Elaine T</given-names>
</name>
<xref ref-type="aff" rid="I8">8</xref>
<email>elainefreund@yahoo.com</email>
</contrib>
<contrib contrib-type="author" id="A11"><name><surname>Klemm</surname>
<given-names>Juli D</given-names>
</name>
<xref ref-type="aff" rid="I9">9</xref>
<email>klemmj@mail.nih.gov</email>
</contrib>
<contrib contrib-type="author" corresp="yes" id="A12"><name><surname>Baker</surname>
<given-names>Nathan A</given-names>
</name>
<xref ref-type="aff" rid="I10">10</xref>
<email>nathan.baker@pnnl.gov</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
Knowledge Discovery and Informatics, Pacific Northwest National Laboratory, Richland, WA 99352, USA</aff>
<aff id="I2"><label>2</label>
SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, Information Systems Program, Rockville, MD 20852, USA</aff>
<aff id="I3"><label>3</label>
Department of Environmental and Molecular Toxicology, School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, OR 97331, USA</aff>
<aff id="I4"><label>4</label>
Pennsylvania Bio Nano Systems, LLC, Doylestown, PA, USA</aff>
<aff id="I5"><label>5</label>
Lockheed Martin, Rockville, MD 20852, USA</aff>
<aff id="I6"><label>6</label>
Department of Radiology, Stanford University, Stanford, CA 94305, USA</aff>
<aff id="I7"><label>7</label>
The Jackson Laboratory, Bar Harbor, Maine 04609, USA</aff>
<aff id="I8"><label>8</label>
3rd Millennium, Inc, North Smithfield, RI 02896, USA</aff>
<aff id="I9"><label>9</label>
Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD 20852, USA</aff>
<aff id="I10"><label>10</label>
Knowledge Discovery and Informatics, Pacific Northwest National Laboratory, PO Box 999, MSID K7-28, Richland, WA 99352, USA</aff>
<pub-date pub-type="collection"><year>2013</year>
</pub-date>
<pub-date pub-type="epub"><day>14</day>
<month>1</month>
<year>2013</year>
</pub-date>
<volume>13</volume>
<fpage>2</fpage>
<lpage>2</lpage>
<history><date date-type="received"><day>12</day>
<month>4</month>
<year>2012</year>
</date>
<date date-type="accepted"><day>11</day>
<month>12</month>
<year>2012</year>
</date>
</history>
<permissions><copyright-statement>Copyright ©2013 Thomas et al; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2013</copyright-year>
<copyright-holder>Thomas et al; licensee BioMed 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.biomedcentral.com/1472-6750/13/2"></self-uri>
<abstract><sec><title>Background and motivation</title>
<p>The high-throughput genomics communities have been successfully using standardized spreadsheet-based formats to capture and share data within labs and among public repositories. The nanomedicine community has yet to adopt similar standards to share the diverse and multi-dimensional types of data (including metadata) pertaining to the description and characterization of nanomaterials. Owing to the lack of standardization in representing and sharing nanomaterial data, most of the data currently shared via publications and data resources are incomplete, poorly-integrated, and not suitable for meaningful interpretation and re-use of the data. Specifically, in its current state, data cannot be effectively utilized for the development of predictive models that will inform the rational design of nanomaterials.</p>
</sec>
<sec><title>Results</title>
<p>We have developed a specification called ISA-TAB-Nano, which comprises four spreadsheet-based file formats for representing and integrating various types of nanomaterial data. Three file formats (Investigation, Study, and Assay files) have been adapted from the established ISA-TAB specification; while the Material file format was developed <italic>de novo</italic>
to more readily describe the complexity of nanomaterials and associated small molecules. In this paper, we have discussed the main features of each file format and how to use them for sharing nanomaterial descriptions and assay metadata.</p>
</sec>
<sec><title>Conclusion</title>
<p>The ISA-TAB-Nano file formats provide a general and flexible framework to record and integrate nanomaterial descriptions, assay data (metadata and endpoint measurements) and protocol information. Like ISA-TAB, ISA-TAB-Nano supports the use of ontology terms to promote standardized descriptions and to facilitate search and integration of the data. The ISA-TAB-Nano specification has been submitted as an ASTM work item to obtain community feedback and to provide a nanotechnology data-sharing standard for public development and adoption.</p>
</sec>
</abstract>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>États-Unis</li>
</country>
<region><li>Californie</li>
<li>Maryland</li>
<li>Oregon</li>
<li>Pennsylvanie</li>
<li>Rhode Island</li>
<li>Washington (État)</li>
</region>
</list>
<tree><country name="États-Unis"><region name="Washington (État)"><name sortKey="Thomas, Dennis G" sort="Thomas, Dennis G" uniqKey="Thomas D" first="Dennis G" last="Thomas">Dennis G. Thomas</name>
</region>
<name sortKey="Baker, Nathan A" sort="Baker, Nathan A" uniqKey="Baker N" first="Nathan A" last="Baker">Nathan A. Baker</name>
<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="Hahn Dantona, Elizabeth" sort="Hahn Dantona, Elizabeth" uniqKey="Hahn Dantona E" first="Elizabeth" last="Hahn-Dantona">Elizabeth Hahn-Dantona</name>
<name sortKey="Harper, Stacey L" sort="Harper, Stacey L" uniqKey="Harper S" first="Stacey L" last="Harper">Stacey L. Harper</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" sort="Paik, David" uniqKey="Paik D" first="David" last="Paik">David Paik</name>
<name sortKey="Pan, Sue" sort="Pan, Sue" uniqKey="Pan S" first="Sue" last="Pan">Sue Pan</name>
<name sortKey="Stafford, Grace A" sort="Stafford, Grace A" uniqKey="Stafford G" first="Grace A" last="Stafford">Grace A. Stafford</name>
</country>
</tree>
</affiliations>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/CyberinfraV1/Data/Pmc/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000316 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Pmc/Checkpoint/biblio.hfd -nk 000316 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Ticri/CIDE |area= CyberinfraV1 |flux= Pmc |étape= Checkpoint |type= RBID |clé= PMC:3598649 |texte= ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Checkpoint/RBID.i -Sk "pubmed:23311978" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Checkpoint/biblio.hfd \ | NlmPubMed2Wicri -a CyberinfraV1
![]() | This area was generated with Dilib version V0.6.25. | ![]() |