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Calling International Rescue: knowledge lost in literature and data landslide!

Identifieur interne : 000648 ( Pmc/Checkpoint ); précédent : 000647; suivant : 000649

Calling International Rescue: knowledge lost in literature and data landslide!

Auteurs : Teresa K. Attwood [Royaume-Uni] ; Douglas B. Kell [Royaume-Uni] ; Philip Mcdermott [Royaume-Uni] ; James Marsh [Royaume-Uni] ; Steve R. Pettifer [Royaume-Uni] ; David Thorne [Royaume-Uni]

Source :

RBID : PMC:2805925

Abstract

We live in interesting times. Portents of impending catastrophe pervade the literature, calling us to action in the face of unmanageable volumes of scientific data. But it isn't so much data generation per se, but the systematic burial of the knowledge embodied in those data that poses the problem: there is so much information available that we simply no longer know what we know, and finding what we want is hard – too hard. The knowledge we seek is often fragmentary and disconnected, spread thinly across thousands of databases and millions of articles in thousands of journals. The intellectual energy required to search this array of data-archives, and the time and money this wastes, has led several researchers to challenge the methods by which we traditionally commit newly acquired facts and knowledge to the scientific record. We present some of these initiatives here – a whirlwind tour of recent projects to transform scholarly publishing paradigms, culminating in Utopia and the Semantic Biochemical Journal experiment. With their promises to provide new ways of interacting with the literature, and new and more powerful tools to access and extract the knowledge sequestered within it, we ask what advances they make and what obstacles to progress still exist? We explore these questions, and, as you read on, we invite you to engage in an experiment with us, a real-time test of a new technology to rescue data from the dormant pages of published documents. We ask you, please, to read the instructions carefully. The time has come: you may turn over your papers…


Url:
DOI: 10.1042/BJ20091474
PubMed: 19929850
PubMed Central: 2805925


Affiliations:


Links toward previous steps (curation, corpus...)


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PMC:2805925

Le document en format XML

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<p>We live in interesting times. Portents of impending catastrophe pervade the literature, calling us to action in the face of unmanageable volumes of scientific data. But it isn't so much data generation
<italic>per se</italic>
, but the systematic burial of the knowledge embodied in those data that poses the problem: there is so much information available that we simply no longer know what we know, and finding what we want is hard – too hard. The knowledge we seek is often fragmentary and disconnected, spread thinly across thousands of databases and millions of articles in thousands of journals. The intellectual energy required to search this array of data-archives, and the time and money this wastes, has led several researchers to challenge the methods by which we traditionally commit newly acquired facts and knowledge to the scientific record. We present some of these initiatives here – a whirlwind tour of recent projects to transform scholarly publishing paradigms, culminating in Utopia and the Semantic
<italic>Biochemical Journal</italic>
experiment. With their promises to provide new ways of interacting with the literature, and new and more powerful tools to access and extract the knowledge sequestered within it, we ask what advances they make and what obstacles to progress still exist? We explore these questions, and, as you read on, we invite you to engage in an experiment with us, a real-time test of a new technology to rescue data from the dormant pages of published documents. We ask you, please, to read the instructions carefully. The time has come: you may turn over your papers…</p>
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</div1>
</back>
</TEI>
<pmc article-type="review-article">
<pmc-dir>properties open_access</pmc-dir>
<front>
<journal-meta>
<journal-id journal-id-type="nlm-ta">Biochem J</journal-id>
<journal-id journal-id-type="pmc">bic</journal-id>
<journal-id journal-id-type="publisher-id">BJ</journal-id>
<journal-title-group>
<journal-title>Biochemical Journal</journal-title>
</journal-title-group>
<issn pub-type="ppub">0264-6021</issn>
<issn pub-type="epub">1470-8728</issn>
<publisher>
<publisher-name>Portland Press Ltd.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="pmid">19929850</article-id>
<article-id pub-id-type="pmc">2805925</article-id>
<article-id pub-id-type="publisher-id">bj4240317</article-id>
<article-id pub-id-type="doi">10.1042/BJ20091474</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Review Article</subject>
</subj-group>
</article-categories>
<title-group>
<article-title>Calling International Rescue: knowledge lost in literature and data landslide!</article-title>
<alt-title alt-title-type="right-running-head">Rescuing knowledge lost in literature and data</alt-title>
<alt-title alt-title-type="left-running-head">T. K. Attwood and others</alt-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Attwood</surname>
<given-names>Teresa K.</given-names>
</name>
<xref ref-type="aff" rid="A1">*</xref>
<xref ref-type="aff" rid="A2"></xref>
<xref ref-type="corresp" rid="COR1">
<sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Kell</surname>
<given-names>Douglas B.</given-names>
</name>
<xref ref-type="aff" rid="A3"></xref>
<xref ref-type="aff" rid="A4">§</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>McDermott</surname>
<given-names>Philip</given-names>
</name>
<xref ref-type="aff" rid="A1">*</xref>
<xref ref-type="aff" rid="A2"></xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Marsh</surname>
<given-names>James</given-names>
</name>
<xref ref-type="aff" rid="A3"></xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Pettifer</surname>
<given-names>Steve R.</given-names>
</name>
<xref ref-type="aff" rid="A1">*</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Thorne</surname>
<given-names>David</given-names>
</name>
<xref ref-type="aff" rid="A3"></xref>
</contrib>
<aff id="A1">*School of Computer Science, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.</aff>
<aff id="A2">†Faculty of Life Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.</aff>
<aff id="A3">‡School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.</aff>
<aff id="A4">§Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, U.K.</aff>
</contrib-group>
<author-notes>
<fn>
<p>T.K.A., S.R.P. and Portland Press Limited declare competing interests in that part of the work invested in Utopia Documents was funded by Portland Press Limited.</p>
</fn>
<corresp id="COR1">
<sup>1</sup>
To whom correspondence should be addressed (email
<email>teresa.k.attwood@manchester.ac.uk</email>
).</corresp>
</author-notes>
<pub-date pub-type="epub">
<day>10</day>
<month>12</month>
<year>2009</year>
</pub-date>
<pub-date pub-type="ppub">
<day>15</day>
<month>12</month>
<year>2009</year>
</pub-date>
<volume>424</volume>
<issue>Pt 3</issue>
<fpage>317</fpage>
<lpage>333</lpage>
<history>
<date date-type="received">
<day>21</day>
<month>9</month>
<year>2009</year>
</date>
<date date-type="accepted">
<day>29</day>
<month>9</month>
<year>2009</year>
</date>
</history>
<permissions>
<copyright-statement>© 2009 The Author(s) The author(s) has paid for this article to be freely available under the terms of the Creative Commons Attribution Non-Commercial Licence (http://creativecommons.org/licenses/by-nc/2.5/) which permits unrestricted non-commercial use, distribution and reproduction in any medium, provided the original work is properly cited.</copyright-statement>
<copyright-year>2009</copyright-year>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by-nc/2.5/">
<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 work is properly cited.</license-p>
</license>
</permissions>
<abstract>
<p>We live in interesting times. Portents of impending catastrophe pervade the literature, calling us to action in the face of unmanageable volumes of scientific data. But it isn't so much data generation
<italic>per se</italic>
, but the systematic burial of the knowledge embodied in those data that poses the problem: there is so much information available that we simply no longer know what we know, and finding what we want is hard – too hard. The knowledge we seek is often fragmentary and disconnected, spread thinly across thousands of databases and millions of articles in thousands of journals. The intellectual energy required to search this array of data-archives, and the time and money this wastes, has led several researchers to challenge the methods by which we traditionally commit newly acquired facts and knowledge to the scientific record. We present some of these initiatives here – a whirlwind tour of recent projects to transform scholarly publishing paradigms, culminating in Utopia and the Semantic
<italic>Biochemical Journal</italic>
experiment. With their promises to provide new ways of interacting with the literature, and new and more powerful tools to access and extract the knowledge sequestered within it, we ask what advances they make and what obstacles to progress still exist? We explore these questions, and, as you read on, we invite you to engage in an experiment with us, a real-time test of a new technology to rescue data from the dormant pages of published documents. We ask you, please, to read the instructions carefully. The time has come: you may turn over your papers…</p>
</abstract>
<kwd-group kwd-group-type="kwd">
<kwd>dynamic document content</kwd>
<kwd>interactive PDF</kwd>
<kwd>linking documents with research data</kwd>
<kwd>manuscript mark-up</kwd>
<kwd>mark-up standards</kwd>
<kwd>semantic publishing</kwd>
</kwd-group>
<kwd-group kwd-group-type="abbr">
<kwd>
<italic>BJ</italic>
,
<italic>Biochemical Journal</italic>
</kwd>
<kwd>COHSE, Conceptual Open Hypermedia Services Environment</kwd>
<kwd>DOI, Digital Object Identifier</kwd>
<kwd>GO, Gene Ontology</kwd>
<kwd>GPCR, G protein-coupled receptor</kwd>
<kwd>HTML, HyperText Mark-up Language</kwd>
<kwd>IUPAC, International Union of Pure and Applied Chemistry</kwd>
<kwd>
<italic>NTD</italic>
,
<italic>Neglected Tropical Diseases</italic>
</kwd>
<kwd>OBO, Open Biomedical Ontologies</kwd>
<kwd>PDB, Protein Data Bank</kwd>
<kwd>PDF, Portable Document Format</kwd>
<kwd>PLoS, Public Library of Science</kwd>
<kwd>PMC, PubMed Central</kwd>
<kwd>PTM, post-translational modification</kwd>
<kwd>RSC, Royal Society of Chemistry</kwd>
<kwd>SDA, Structured Digital Abstract</kwd>
<kwd>STM, Scientific, Technical and Medical</kwd>
<kwd>UD, Utopia Documents</kwd>
<kwd>XML, eXtensible Mark-up Language</kwd>
<kwd>XMP, eXtensible Metadata Platform</kwd>
</kwd-group>
<counts>
<fig-count count="13"></fig-count>
<ref-count count="82"></ref-count>
<page-count count="17"></page-count>
</counts>
</article-meta>
</front>
</pmc>
<affiliations>
<list>
<country>
<li>Royaume-Uni</li>
</country>
<region>
<li>Angleterre</li>
<li>Grand Manchester</li>
</region>
<settlement>
<li>Manchester</li>
</settlement>
<orgName>
<li>Université de Manchester</li>
</orgName>
</list>
<tree>
<country name="Royaume-Uni">
<region name="Angleterre">
<name sortKey="Attwood, Teresa K" sort="Attwood, Teresa K" uniqKey="Attwood T" first="Teresa K." last="Attwood">Teresa K. Attwood</name>
</region>
<name sortKey="Attwood, Teresa K" sort="Attwood, Teresa K" uniqKey="Attwood T" first="Teresa K." last="Attwood">Teresa K. Attwood</name>
<name sortKey="Kell, Douglas B" sort="Kell, Douglas B" uniqKey="Kell D" first="Douglas B." last="Kell">Douglas B. Kell</name>
<name sortKey="Kell, Douglas B" sort="Kell, Douglas B" uniqKey="Kell D" first="Douglas B." last="Kell">Douglas B. Kell</name>
<name sortKey="Marsh, James" sort="Marsh, James" uniqKey="Marsh J" first="James" last="Marsh">James Marsh</name>
<name sortKey="Mcdermott, Philip" sort="Mcdermott, Philip" uniqKey="Mcdermott P" first="Philip" last="Mcdermott">Philip Mcdermott</name>
<name sortKey="Mcdermott, Philip" sort="Mcdermott, Philip" uniqKey="Mcdermott P" first="Philip" last="Mcdermott">Philip Mcdermott</name>
<name sortKey="Pettifer, Steve R" sort="Pettifer, Steve R" uniqKey="Pettifer S" first="Steve R." last="Pettifer">Steve R. Pettifer</name>
<name sortKey="Thorne, David" sort="Thorne, David" uniqKey="Thorne D" first="David" last="Thorne">David Thorne</name>
</country>
</tree>
</affiliations>
</record>

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