The EcoData Retriever: Improving Access to Existing Ecological Data
Identifieur interne : 000621 ( Pmc/Curation ); précédent : 000620; suivant : 000622The EcoData Retriever: Improving Access to Existing Ecological Data
Auteurs : Benjamin D. Morris ; Ethan P. WhiteSource :
- PLoS ONE [ 1932-6203 ] ; 2013.
Abstract
Ecological research relies increasingly on the use of previously collected data. Use of existing datasets allows questions to be addressed more quickly, more generally, and at larger scales than would otherwise be possible. As a result of large-scale data collection efforts, and an increasing emphasis on data publication by journals and funding agencies, a large and ever-increasing amount of ecological data is now publicly available via the internet. Most ecological datasets do not adhere to any agreed-upon standards in format, data structure or method of access. Some may be broken up across multiple files, stored in compressed archives, and violate basic principles of data structure. As a result acquiring and utilizing available datasets can be a time consuming and error prone process. The EcoData Retriever is an extensible software framework which automates the tasks of discovering, downloading, and reformatting ecological data files for storage in a local data file or relational database. The automation of these tasks saves significant time for researchers and substantially reduces the likelihood of errors resulting from manual data manipulation and unfamiliarity with the complexities of individual datasets.
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DOI: 10.1371/journal.pone.0065848
PubMed: 23785456
PubMed Central: 3681786
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The EcoData Retriever: Improving Access to Existing Ecological Data</title><author><name sortKey="Morris, Benjamin D" sort="Morris, Benjamin D" uniqKey="Morris B" first="Benjamin D." last="Morris">Benjamin D. Morris</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="White, Ethan P" sort="White, Ethan P" uniqKey="White E" first="Ethan P." last="White">Ethan P. White</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23785456</idno><idno type="pmc">3681786</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3681786</idno><idno type="RBID">PMC:3681786</idno><idno type="doi">10.1371/journal.pone.0065848</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000621</idno><idno type="wicri:Area/Pmc/Curation">000621</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The EcoData Retriever: Improving Access to Existing Ecological Data</title><author><name sortKey="Morris, Benjamin D" sort="Morris, Benjamin D" uniqKey="Morris B" first="Benjamin D." last="Morris">Benjamin D. Morris</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="White, Ethan P" sort="White, Ethan P" uniqKey="White E" first="Ethan P." last="White">Ethan P. White</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Ecological research relies increasingly on the use of previously collected data. Use of existing datasets allows questions to be addressed more quickly, more generally, and at larger scales than would otherwise be possible. As a result of large-scale data collection efforts, and an increasing emphasis on data publication by journals and funding agencies, a large and ever-increasing amount of ecological data is now publicly available via the internet. Most ecological datasets do not adhere to any agreed-upon standards in format, data structure or method of access. Some may be broken up across multiple files, stored in compressed archives, and violate basic principles of data structure. As a result acquiring and utilizing available datasets can be a time consuming and error prone process. The EcoData Retriever is an extensible software framework which automates the tasks of discovering, downloading, and reformatting ecological data files for storage in a local data file or relational database. The automation of these tasks saves significant time for researchers and substantially reduces the likelihood of errors resulting from manual data manipulation and unfamiliarity with the complexities of individual datasets.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Brown, Jh" uniqKey="Brown J">JH Brown</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sauer, Jr" uniqKey="Sauer J">JR Sauer</name></author><author><name sortKey="Hines, Je" uniqKey="Hines J">JE Hines</name></author><author><name sortKey="Fallon, J" uniqKey="Fallon J">J Fallon</name></author><author><name sortKey="Pardieck, Kl" uniqKey="Pardieck K">KL Pardieck</name></author><author><name sortKey="Ziolkowski, Dj Jr" uniqKey="Ziolkowski D">DJ Jr Ziolkowski</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Lislevand, T" uniqKey="Lislevand T">T 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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">23785456</article-id><article-id pub-id-type="pmc">3681786</article-id><article-id pub-id-type="publisher-id">PONE-D-12-15668</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0065848</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>The EcoData Retriever: Improving Access to Existing Ecological Data</article-title><alt-title alt-title-type="running-head">The EcoData Retriever</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Morris</surname><given-names>Benjamin D.</given-names></name><xref ref-type="corresp" rid="cor1">*</xref><xref ref-type="aff" rid="aff1"></xref></contrib><contrib contrib-type="author"><name><surname>White</surname><given-names>Ethan P.</given-names></name><xref ref-type="aff" rid="aff1"></xref></contrib></contrib-group><aff id="aff1"><addr-line>Department of Biology and The Ecology Center, Utah State University, Logan, Utah, United States of America</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Swenson</surname><given-names>Nathan G.</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>Michigan State University, United States of America</addr-line></aff><author-notes><corresp id="cor1">* E-mail: <email>ben@bendmorris.com</email></corresp><fn fn-type="conflict"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con"><p>Conceived and designed the experiments: BDM EPW. Performed the experiments: BDM EPW. Wrote the manuscript: BDM EPW. </p></fn></author-notes><pub-date pub-type="collection"><year>2013</year></pub-date><pub-date pub-type="epub"><day>13</day><month>6</month><year>2013</year></pub-date><volume>8</volume><issue>6</issue><elocation-id>e65848</elocation-id><history><date date-type="received"><day>24</day><month>5</month><year>2012</year></date><date date-type="accepted"><day>04</day><month>5</month><year>2013</year></date></history><permissions><copyright-year>2013</copyright-year><copyright-holder>Morris et al</copyright-holder><license><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p></license></permissions><abstract><p>Ecological research relies increasingly on the use of previously collected data. Use of existing datasets allows questions to be addressed more quickly, more generally, and at larger scales than would otherwise be possible. As a result of large-scale data collection efforts, and an increasing emphasis on data publication by journals and funding agencies, a large and ever-increasing amount of ecological data is now publicly available via the internet. Most ecological datasets do not adhere to any agreed-upon standards in format, data structure or method of access. Some may be broken up across multiple files, stored in compressed archives, and violate basic principles of data structure. As a result acquiring and utilizing available datasets can be a time consuming and error prone process. The EcoData Retriever is an extensible software framework which automates the tasks of discovering, downloading, and reformatting ecological data files for storage in a local data file or relational database. The automation of these tasks saves significant time for researchers and substantially reduces the likelihood of errors resulting from manual data manipulation and unfamiliarity with the complexities of individual datasets.</p></abstract><funding-group><funding-statement>This work was funded by the National Science Foundation as part of a CAREER award to Ethan White(DEB-0953694). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement></funding-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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