Utopia documents: linking scholarly literature with research data
Identifieur interne : 000540 ( Pmc/Checkpoint ); précédent : 000539; suivant : 000541Utopia documents: linking scholarly literature with research data
Auteurs : T. K. Attwood ; D. B. Kell [Royaume-Uni] ; P. Mcdermott ; J. Marsh ; S. R. Pettifer ; D. ThorneSource :
- Bioinformatics [ 1367-4803 ] ; 2010.
Abstract
Url:
DOI: 10.1093/bioinformatics/btq383
PubMed: 20823323
PubMed Central: 2935404
Affiliations:
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Utopia documents: linking scholarly literature with research data</title>
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<series><title level="j">Bioinformatics</title>
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<front><div type="abstract" xml:lang="en"><p><bold>Motivation:</bold>
In recent years, the gulf between the mass of accumulating-research data and the massive literature describing and analyzing those data has widened. The need for intelligent tools to bridge this gap, to rescue the knowledge being systematically isolated in literature and data silos, is now widely acknowledged.</p>
<p><bold>Results:</bold>
To this end, we have developed Utopia Documents, a novel PDF reader that semantically integrates visualization and data-analysis tools with published research articles. In a successful pilot with editors of the <italic>Biochemical Journal</italic>
(<italic>BJ</italic>
), the system has been used to transform static document features into objects that can be linked, annotated, visualized and analyzed interactively (<ext-link ext-link-type="uri" xlink:href="http://www.biochemj.org/bj/424/3/">http://www.biochemj.org/bj/424/3/</ext-link>
). Utopia Documents is now used routinely by <italic>BJ</italic>
editors to mark up article content prior to publication. Recent additions include integration of various text-mining and biodatabase plugins, demonstrating the system's ability to seamlessly integrate on-line content with PDF articles.</p>
<p><bold>Availability:</bold>
<ext-link ext-link-type="uri" xlink:href="http://getutopia.com">http://getutopia.com</ext-link>
</p>
<p><bold>Contact:</bold>
<email>teresa.k.attwood@manchester.ac.uk</email>
</p>
</div>
</front>
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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">Bioinformatics</journal-id>
<journal-id journal-id-type="publisher-id">bioinformatics</journal-id>
<journal-id journal-id-type="hwp">bioinfo</journal-id>
<journal-title-group><journal-title>Bioinformatics</journal-title>
</journal-title-group>
<issn pub-type="ppub">1367-4803</issn>
<issn pub-type="epub">1367-4811</issn>
<publisher><publisher-name>Oxford University Press</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">20823323</article-id>
<article-id pub-id-type="pmc">2935404</article-id>
<article-id pub-id-type="doi">10.1093/bioinformatics/btq383</article-id>
<article-id pub-id-type="publisher-id">btq383</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Eccb 2010 Conference Proceedings September 26 to September 29, 2010, Ghent, Belgium</subject>
<subj-group><subject>Original Papers</subject>
<subj-group><subject>Text Mining, Ontologies and Databases</subject>
</subj-group>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title>Utopia documents: linking scholarly literature with research data</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Attwood</surname>
<given-names>T. K.</given-names>
</name>
<xref ref-type="aff" rid="AFF1"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="AFF1"><sup>2</sup>
</xref>
<xref ref-type="corresp" rid="COR1">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Kell</surname>
<given-names>D. B.</given-names>
</name>
<xref ref-type="aff" rid="AFF1"><sup>3</sup>
</xref>
<xref ref-type="aff" rid="AFF1"><sup>4</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>McDermott</surname>
<given-names>P.</given-names>
</name>
<xref ref-type="aff" rid="AFF1"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="AFF1"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Marsh</surname>
<given-names>J.</given-names>
</name>
<xref ref-type="aff" rid="AFF1"><sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Pettifer</surname>
<given-names>S. R.</given-names>
</name>
<xref ref-type="aff" rid="AFF1"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Thorne</surname>
<given-names>D.</given-names>
</name>
<xref ref-type="aff" rid="AFF1"><sup>3</sup>
</xref>
</contrib>
</contrib-group>
<aff id="AFF1"><sup>1</sup>
School of Computer Science,<sup>2</sup>
Faculty of Life Sciences,<sup>3</sup>
School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL and<sup>4</sup>
Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, UK</aff>
<author-notes><corresp id="COR1">* To whom correspondence should be addressed.</corresp>
</author-notes>
<pub-date pub-type="ppub"><day>15</day>
<month>9</month>
<year>2010</year>
</pub-date>
<pub-date pub-type="epub"><day>4</day>
<month>9</month>
<year>2010</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>4</day>
<month>9</month>
<year>2010</year>
</pub-date>
<pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
. </pmc-comment>
<volume>26</volume>
<issue>18</issue>
<fpage>i568</fpage>
<lpage>i574</lpage>
<permissions><copyright-statement>© The Author(s) 2010. Published by Oxford University Press.</copyright-statement>
<copyright-year>2010</copyright-year>
<license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/2.0/uk/"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/2.5">http://creativecommons.org/licenses/by-nc/2.5</ext-link>
), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<abstract><p><bold>Motivation:</bold>
In recent years, the gulf between the mass of accumulating-research data and the massive literature describing and analyzing those data has widened. The need for intelligent tools to bridge this gap, to rescue the knowledge being systematically isolated in literature and data silos, is now widely acknowledged.</p>
<p><bold>Results:</bold>
To this end, we have developed Utopia Documents, a novel PDF reader that semantically integrates visualization and data-analysis tools with published research articles. In a successful pilot with editors of the <italic>Biochemical Journal</italic>
(<italic>BJ</italic>
), the system has been used to transform static document features into objects that can be linked, annotated, visualized and analyzed interactively (<ext-link ext-link-type="uri" xlink:href="http://www.biochemj.org/bj/424/3/">http://www.biochemj.org/bj/424/3/</ext-link>
). Utopia Documents is now used routinely by <italic>BJ</italic>
editors to mark up article content prior to publication. Recent additions include integration of various text-mining and biodatabase plugins, demonstrating the system's ability to seamlessly integrate on-line content with PDF articles.</p>
<p><bold>Availability:</bold>
<ext-link ext-link-type="uri" xlink:href="http://getutopia.com">http://getutopia.com</ext-link>
</p>
<p><bold>Contact:</bold>
<email>teresa.k.attwood@manchester.ac.uk</email>
</p>
</abstract>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>Royaume-Uni</li>
</country>
</list>
<tree><noCountry><name sortKey="Attwood, T K" sort="Attwood, T K" uniqKey="Attwood T" first="T. K." last="Attwood">T. K. Attwood</name>
<name sortKey="Marsh, J" sort="Marsh, J" uniqKey="Marsh J" first="J." last="Marsh">J. Marsh</name>
<name sortKey="Mcdermott, P" sort="Mcdermott, P" uniqKey="Mcdermott P" first="P." last="Mcdermott">P. Mcdermott</name>
<name sortKey="Pettifer, S R" sort="Pettifer, S R" uniqKey="Pettifer S" first="S. R." last="Pettifer">S. R. Pettifer</name>
<name sortKey="Thorne, D" sort="Thorne, D" uniqKey="Thorne D" first="D." last="Thorne">D. Thorne</name>
</noCountry>
<country name="Royaume-Uni"><noRegion><name sortKey="Kell, D B" sort="Kell, D B" uniqKey="Kell D" first="D. B." last="Kell">D. B. Kell</name>
</noRegion>
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</tree>
</affiliations>
</record>
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