Data Integration for Dynamic and Sustainable Systems Biology Resources: Challenges and Lessons Learned
Identifieur interne : 000095 ( Istex/Corpus ); précédent : 000094; suivant : 000096Data Integration for Dynamic and Sustainable Systems Biology Resources: Challenges and Lessons Learned
Auteurs : Daniel Sullivan ; Joseph Gabbard Jr. ; Maulik Shukla ; Bruno SobralSource :
- Chemistry & Biodiversity [ 1612-1872 ] ; 2010-05.
English descriptors
Abstract
Systems‐biology and infectious‐disease (host–pathogen–environment) research and development is becoming increasingly dependent on integrating data from diverse and dynamic sources. Maintaining integrated resources over long periods of time presents distinct challenges. This review describes experiences and lessons learned from integrating data in two five‐year projects focused on pathosystems biology: the Pathosystems Resource Integration Center (PATRIC, http://patric.vbi.vt.edu/), with a goal of developing bioinformatics resources for the research and countermeasures‐development communities based on genomics data, and the Resource Center for Biodefense Proteomics Research (RCBPR, http://www.proteomicsresource.org/), with a goal of developing resources based on the experiment data such as microarray and proteomics data from diverse sources and technologies. Some challenges include integrating genomic sequence and experiment data, data synchronization, data quality control, and usability engineering. We present examples of a variety of data‐integration problems drawn from our experiences with PATRIC and RBPRC, as well as open research questions related to long‐term sustainability, and describe the next steps to meeting these challenges. Novel contributions of this work include 1) an approach for addressing discrepancies between experiment results and interpreted results, and 2) expanding the range of data‐integration techniques to include usability engineering at the presentation level.
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DOI: 10.1002/cbdv.200900317
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ISTEX:03AD88C6FCB58AA4B0AFA8B1778882149321CC3BLe document en format XML
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Maintaining integrated resources over long periods of time presents distinct challenges. This review describes experiences and lessons learned from integrating data in two five‐year projects focused on pathosystems biology: the Pathosystems Resource Integration Center (PATRIC, http://patric.vbi.vt.edu/), with a goal of developing bioinformatics resources for the research and countermeasures‐development communities based on genomics data, and the Resource Center for Biodefense Proteomics Research (RCBPR, http://www.proteomicsresource.org/), with a goal of developing resources based on the experiment data such as microarray and proteomics data from diverse sources and technologies. Some challenges include integrating genomic sequence and experiment data, data synchronization, data quality control, and usability engineering. We present examples of a variety of data‐integration problems drawn from our experiences with PATRIC and RBPRC, as well as open research questions related to long‐term sustainability, and describe the next steps to meeting these challenges. Novel contributions of this work include 1) an approach for addressing discrepancies between experiment results and interpreted results, and 2) expanding the range of data‐integration techniques to include usability engineering at the presentation level.</div></front></TEI><istex><corpusName>wiley</corpusName><author><json:item><name>Daniel E. Sullivan</name><affiliations><json:string>CyberInfrastructure Section, Virginia Bioinformatics Institute, Washington Street, MC 0477, Virginia Tech, Blacksburg, Virginia 24061, USA (phone: +1‐540‐231‐2100; fax: +1‐540‐231‐2606)</json:string><json:string>E-mail: dsulliva@vbi.vt.edu</json:string></affiliations></json:item><json:item><name>Joseph L. 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We present examples of a variety of data‐integration problems drawn from our experiences with PATRIC and RBPRC, as well as open research questions related to long‐term sustainability, and describe the next steps to meeting these challenges. Novel contributions of this work include 1) an approach for addressing discrepancies between experiment results and interpreted results, and 2) expanding the range of data‐integration techniques to include usability engineering at the presentation level.</p></abstract><abstract xml:lang="en" style="graphical"><p></p></abstract><textClass xml:lang="en"><keywords scheme="keyword"><list><head>keywords</head><item><term>Systems biology</term></item><item><term>Infectious diseases</term></item><item><term>Data integration</term></item><item><term>Bioinformatics</term></item></list></keywords></textClass><textClass><keywords scheme="Journal Subject"><list><head>article-category</head><item><term>Bioengineering</term></item></list></keywords></textClass></profileDesc><revisionDesc><change when="2009-09-01">Received</change><change 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xml:id="kwd4">Bioinformatics</keyword></keywordGroup><abstractGroup><abstract type="main" xml:lang="en"><title type="main">Abstract</title><p>Systems‐biology and infectious‐disease (host–pathogen–environment) research and development is becoming increasingly dependent on integrating data from diverse and dynamic sources. Maintaining integrated resources over long periods of time presents distinct challenges. This review describes experiences and lessons learned from integrating data in two five‐year projects focused on pathosystems biology: the <i>Pathosystems Resource Integration Center</i> (PATRIC, http://patric.vbi.vt.edu/), with a goal of developing bioinformatics resources for the research and countermeasures‐development communities based on genomics data, and the <i>Resource Center for Biodefense Proteomics Research</i> (RCBPR, http://www.proteomicsresource.org/), with a goal of developing resources based on the experiment data such as microarray and proteomics data from diverse sources and technologies. Some challenges include integrating genomic sequence and experiment data, data synchronization, data quality control, and usability engineering. We present examples of a variety of data‐integration problems drawn from our experiences with PATRIC and RBPRC, as well as open research questions related to long‐term sustainability, and describe the next steps to meeting these challenges. Novel contributions of this work include <i>1</i>) an approach for addressing discrepancies between experiment results and interpreted results, and <i>2</i>) expanding the range of data‐integration techniques to include usability engineering at the presentation level.</p></abstract><abstract type="graphical" xml:lang="en"><p><blockFixed type="graphic"><mediaResourceGroup><mediaResource alt="image" eRights="yes" copyright="WILEY-VCH" href="urn:x-wiley:16121872:media:CBDV200900317:content"></mediaResource><mediaResource alt="thumbnail image" rendition="webLoRes" mimeType="image/gif" href=""></mediaResource><mediaResource alt="original image" rendition="webOriginal" mimeType="image/gif" href=""></mediaResource><mediaResource alt="magnified image" rendition="webHiRes" mimeType="image/gif" href=""></mediaResource></mediaResourceGroup></blockFixed></p></abstract></abstractGroup></contentMeta></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Data Integration for Dynamic and Sustainable Systems Biology Resources: Challenges and Lessons Learned</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Data Integration for Dynamic and Sustainable Systems Biology Resources: Challenges and Lessons Learned</title></titleInfo><name type="personal"><namePart type="given">Daniel E.</namePart><namePart type="family">Sullivan</namePart><affiliation>CyberInfrastructure Section, Virginia Bioinformatics Institute, Washington Street, MC 0477, Virginia Tech, Blacksburg, Virginia 24061, USA (phone: +1‐540‐231‐2100; fax: +1‐540‐231‐2606)</affiliation><affiliation>E-mail: dsulliva@vbi.vt.edu</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Joseph L.</namePart><namePart type="family">Gabbard Jr.</namePart><affiliation>Center for Human‐Computer Interaction, 2202 Kraft Drive, Virginia Tech, Blacksburg, Virginia 24060, USA (phone: +1‐540‐231‐3188; fax: +1‐540‐231‐6075)</affiliation><affiliation>E-mail: jgabbard@vt.edu</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Maulik</namePart><namePart type="family">Shukla</namePart><affiliation>CyberInfrastructure Section, Virginia Bioinformatics Institute, Washington Street, MC 0477, Virginia Tech, Blacksburg, Virginia 24061, USA (phone: +1‐540‐231‐2100; fax: +1‐540‐231‐2606)</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Bruno</namePart><namePart type="family">Sobral</namePart><affiliation>CyberInfrastructure Section, Virginia Bioinformatics Institute, Washington Street, MC 0477, Virginia Tech, Blacksburg, Virginia 24061, USA (phone: +1‐540‐231‐2100; fax: +1‐540‐231‐2606)</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="review-article" displayLabel="reviewArticle"></genre><originInfo><publisher>WILEY‐VCH Verlag</publisher><place><placeTerm type="text">Zürich</placeTerm></place><dateIssued encoding="w3cdtf">2010-05</dateIssued><dateCaptured encoding="w3cdtf">2009-09-01</dateCaptured><copyrightDate encoding="w3cdtf">2010</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><physicalDescription><internetMediaType>text/html</internetMediaType><extent unit="references">38</extent></physicalDescription><abstract lang="en">Systems‐biology and infectious‐disease (host–pathogen–environment) research and development is becoming increasingly dependent on integrating data from diverse and dynamic sources. Maintaining integrated resources over long periods of time presents distinct challenges. This review describes experiences and lessons learned from integrating data in two five‐year projects focused on pathosystems biology: the Pathosystems Resource Integration Center (PATRIC, http://patric.vbi.vt.edu/), with a goal of developing bioinformatics resources for the research and countermeasures‐development communities based on genomics data, and the Resource Center for Biodefense Proteomics Research (RCBPR, http://www.proteomicsresource.org/), with a goal of developing resources based on the experiment data such as microarray and proteomics data from diverse sources and technologies. Some challenges include integrating genomic sequence and experiment data, data synchronization, data quality control, and usability engineering. We present examples of a variety of data‐integration problems drawn from our experiences with PATRIC and RBPRC, as well as open research questions related to long‐term sustainability, and describe the next steps to meeting these challenges. Novel contributions of this work include 1) an approach for addressing discrepancies between experiment results and interpreted results, and 2) expanding the range of data‐integration techniques to include usability engineering at the presentation level.</abstract><abstract type="graphical" lang="en"></abstract><subject lang="en"><genre>keywords</genre><topic>Systems biology</topic><topic>Infectious diseases</topic><topic>Data integration</topic><topic>Bioinformatics</topic></subject><relatedItem type="host"><titleInfo><title>Chemistry & Biodiversity</title></titleInfo><titleInfo type="abbreviated"><title>Chemistry & Biodiversity</title></titleInfo><genre type="journal">journal</genre><subject><genre>article-category</genre><topic>Bioengineering</topic></subject><identifier type="ISSN">1612-1872</identifier><identifier type="eISSN">1612-1880</identifier><identifier type="DOI">10.1002/(ISSN)1612-1880</identifier><identifier type="PublisherID">CBDV</identifier><part><date>2010</date><detail type="title"><title>Systems Biology in the Microbial World and Beyond</title></detail><detail type="volume"><caption>vol.</caption><number>7</number></detail><detail type="issue"><caption>no.</caption><number>5</number></detail><extent unit="pages"><start>1124</start><end>1141</end><total>18</total></extent></part></relatedItem><identifier type="istex">03AD88C6FCB58AA4B0AFA8B1778882149321CC3B</identifier><identifier type="DOI">10.1002/cbdv.200900317</identifier><identifier type="ArticleID">CBDV200900317</identifier><accessCondition type="use and reproduction" contentType="copyright">Copyright © 2010 Verlag Helvetica Chimica Acta AG, Zürich</accessCondition><recordInfo><recordContentSource>WILEY</recordContentSource><recordOrigin>WILEY‐VCH Verlag</recordOrigin></recordInfo></mods></metadata><enrichments><json:item><type>multicat</type><uri>https://api.istex.fr/document/03AD88C6FCB58AA4B0AFA8B1778882149321CC3B/enrichments/multicat</uri></json:item></enrichments><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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