Data integration in biological research: an overview
Identifieur interne : 000666 ( Ncbi/Merge ); précédent : 000665; suivant : 000667Data integration in biological research: an overview
Auteurs : Vasileios Lapatas [Grèce] ; Michalis Stefanidakis [Grèce] ; Rafael C. Jimenez ; Allegra Via [Italie] ; Maria Victoria SchneiderSource :
- Journal of Biological Research [ 1790-045X ] ; 2015.
Abstract
Data sharing, integration and annotation are essential to ensure the reproducibility of the analysis and interpretation of the experimental findings. Often these activities are perceived as a role that bioinformaticians and computer scientists have to take with no or little input from the experimental biologist. On the contrary, biological researchers, being the producers and often the end users of such data, have a big role in enabling biological data integration. The quality and usefulness of data integration depend on the existence and adoption of standards, shared formats, and mechanisms that are suitable for biological researchers to submit and annotate the data, so it can be easily searchable, conveniently linked and consequently used for further biological analysis and discovery. Here, we provide background on what is data integration from a computational science point of view, how it has been applied to biological research, which key aspects contributed to its success and future directions.
Url:
DOI: 10.1186/s40709-015-0032-5
PubMed: 26336651
PubMed Central: 4557916
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PMC:4557916Le document en format XML
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<front><div type="abstract" xml:lang="en"><p>Data sharing, integration and annotation are essential to ensure the reproducibility of the analysis and interpretation of the experimental findings. Often these activities are perceived as a role that bioinformaticians and computer scientists have to take with no or little input from the experimental biologist. On the contrary, biological researchers, being the producers and often the end users of such data, have a big role in enabling biological data integration. The quality and usefulness of data integration depend on the existence and adoption of standards, shared formats, and mechanisms that are suitable for biological researchers to submit and annotate the data, so it can be easily searchable, conveniently linked and consequently used for further biological analysis and discovery. Here, we provide background on what is data integration from a computational science point of view, how it has been applied to biological research, which key aspects contributed to its success and future directions.</p>
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</TEI>
<pmc article-type="review-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">J Biol Res (Thessalon)</journal-id>
<journal-id journal-id-type="iso-abbrev">J Biol Res (Thessalon)</journal-id>
<journal-title-group><journal-title>Journal of Biological Research</journal-title>
</journal-title-group>
<issn pub-type="ppub">1790-045X</issn>
<issn pub-type="epub">2241-5793</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
<publisher-loc>London</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">26336651</article-id>
<article-id pub-id-type="pmc">4557916</article-id>
<article-id pub-id-type="publisher-id">32</article-id>
<article-id pub-id-type="doi">10.1186/s40709-015-0032-5</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Review</subject>
</subj-group>
</article-categories>
<title-group><article-title>Data integration in biological research: an overview</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Lapatas</surname>
<given-names>Vasileios</given-names>
</name>
<address><email>piar301@gmail.com</email>
</address>
<xref ref-type="aff" rid="Aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Stefanidakis</surname>
<given-names>Michalis</given-names>
</name>
<address><email>mistral@ionio.gr</email>
</address>
<xref ref-type="aff" rid="Aff1"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Jimenez</surname>
<given-names>Rafael C.</given-names>
</name>
<address><email>Rafael.Jimenez@elixir-europe.org</email>
</address>
<xref ref-type="aff" rid="Aff2"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Via</surname>
<given-names>Allegra</given-names>
</name>
<address><email>allegra.via@uniroma1.it</email>
</address>
<xref ref-type="aff" rid="Aff3"></xref>
</contrib>
<contrib contrib-type="author" corresp="yes"><name><surname>Schneider</surname>
<given-names>Maria Victoria</given-names>
</name>
<address><email>Vicky.Schneider@tgac.ac.uk</email>
</address>
<xref ref-type="aff" rid="Aff4"></xref>
</contrib>
<aff id="Aff1"><label></label>
Department of Informatics, Ionian University, 7 Tsirigoti Square, Corfu, 49100 Greece</aff>
<aff id="Aff2"><label></label>
ELIXIR, Wellcome Trust Genome Campus, Hinxton, CB10 1SD UK</aff>
<aff id="Aff3"><label></label>
Biocomputing Group, Sapienza University, Piazzale Aldo Moro 5, Rome, 00185 Italy</aff>
<aff id="Aff4"><label></label>
361° Division, The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH UK</aff>
</contrib-group>
<pub-date pub-type="epub"><day>2</day>
<month>9</month>
<year>2015</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>2</day>
<month>9</month>
<year>2015</year>
</pub-date>
<pub-date pub-type="collection"><month>12</month>
<year>2015</year>
</pub-date>
<volume>22</volume>
<issue>1</issue>
<elocation-id>9</elocation-id>
<history><date date-type="received"><day>20</day>
<month>4</month>
<year>2015</year>
</date>
<date date-type="accepted"><day>10</day>
<month>8</month>
<year>2015</year>
</date>
</history>
<permissions><copyright-statement>© Lapatas et al. 2015</copyright-statement>
<license license-type="OpenAccess"><license-p><bold>Open Access</bold>
This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>
) applies to the data made available in this article, unless otherwise stated.</license-p>
</license>
</permissions>
<abstract id="Abs1"><p>Data sharing, integration and annotation are essential to ensure the reproducibility of the analysis and interpretation of the experimental findings. Often these activities are perceived as a role that bioinformaticians and computer scientists have to take with no or little input from the experimental biologist. On the contrary, biological researchers, being the producers and often the end users of such data, have a big role in enabling biological data integration. The quality and usefulness of data integration depend on the existence and adoption of standards, shared formats, and mechanisms that are suitable for biological researchers to submit and annotate the data, so it can be easily searchable, conveniently linked and consequently used for further biological analysis and discovery. Here, we provide background on what is data integration from a computational science point of view, how it has been applied to biological research, which key aspects contributed to its success and future directions.</p>
</abstract>
<kwd-group xml:lang="en"><title>Keywords</title>
<kwd>Data integration</kwd>
<kwd>Standards</kwd>
<kwd>Bioinformatics</kwd>
<kwd>Data driven</kwd>
<kwd>Open sciences</kwd>
</kwd-group>
<custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name>
<meta-value>© The Author(s) 2015</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>Grèce</li>
<li>Italie</li>
</country>
<region><li>Latium</li>
</region>
<settlement><li>Rome</li>
</settlement>
</list>
<tree><noCountry><name sortKey="Jimenez, Rafael C" sort="Jimenez, Rafael C" uniqKey="Jimenez R" first="Rafael C." last="Jimenez">Rafael C. Jimenez</name>
<name sortKey="Schneider, Maria Victoria" sort="Schneider, Maria Victoria" uniqKey="Schneider M" first="Maria Victoria" last="Schneider">Maria Victoria Schneider</name>
</noCountry>
<country name="Grèce"><noRegion><name sortKey="Lapatas, Vasileios" sort="Lapatas, Vasileios" uniqKey="Lapatas V" first="Vasileios" last="Lapatas">Vasileios Lapatas</name>
</noRegion>
<name sortKey="Stefanidakis, Michalis" sort="Stefanidakis, Michalis" uniqKey="Stefanidakis M" first="Michalis" last="Stefanidakis">Michalis Stefanidakis</name>
</country>
<country name="Italie"><region name="Latium"><name sortKey="Via, Allegra" sort="Via, Allegra" uniqKey="Via A" first="Allegra" last="Via">Allegra Via</name>
</region>
</country>
</tree>
</affiliations>
</record>
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