Combining Semantic Relations and DNA Microarray Data for Novel Hypotheses Generation
Identifieur interne : 001115 ( Main/Corpus ); précédent : 001114; suivant : 001116Combining Semantic Relations and DNA Microarray Data for Novel Hypotheses Generation
Auteurs : Dimitar Hristovski ; Andrej Kastrin ; Borut Peterlin ; C. RindfleschSource :
- Lecture Notes in Computer Science [ 0302-9743 ] ; 2010.
Abstract
Abstract: Although microarray experiments have great potential to support progress in biomedical research, results are not easy to interpret. Information about the functions and relations of relevant genes needs to be extracted from the vast biomedical literature. A potential solution is to use computerized text analysis methods. Our proposal enhances these methods with semantic relations. We describe an application that integrates such relations with microarray results and discuss its benefits in supporting enhanced access to the relevant literature for interpretation of results and novel hypotheses generation. The application is available at http://sembt.mf.uni-lj.si
Url:
DOI: 10.1007/978-3-642-13131-8_7
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ISTEX:FC61C703D43C762B3CFE3E3BCFC4A3F6727E56C9Le document en format XML
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California</OrgName><OrgAddress><City>Berkeley</City><State>CA</State><Country>USA</Country></OrgAddress></Affiliation><Affiliation ID="Aff14"><OrgName>Rice University</OrgName><OrgAddress><City>Houston</City><State>TX</State><Country>USA</Country></OrgAddress></Affiliation><Affiliation ID="Aff15"><OrgName>Max-Planck Institute of Computer Science</OrgName><OrgAddress><City>Saarbrücken</City><Country>Germany</Country></OrgAddress></Affiliation></EditorGroup></SeriesHeader><SubSeries><SubSeriesInfo><SubSeriesID>5381</SubSeriesID><SubSeriesPrintISSN>0302-9743</SubSeriesPrintISSN><SubSeriesElectronicISSN>1611-3349</SubSeriesElectronicISSN><SubSeriesTitle Language="En">Lecture Notes in Bioinformatics</SubSeriesTitle></SubSeriesInfo><SubSeriesHeader><EditorGroup><Editor AffiliationIDS="Aff16"><EditorName DisplayOrder="Western"><GivenName>Sorin</GivenName><FamilyName>Istrail</FamilyName></EditorName></Editor><Editor AffiliationIDS="Aff17"><EditorName 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OutputMedium="All" TocLevels="0"><BookID>978-3-642-13131-8</BookID><BookTitle>Linking Literature, Information, and Knowledge for Biology</BookTitle><BookSubTitle>Workshop of the BioLink Special Interest Group, ISMB/ECCB 2009, Stockholm, June 28-29, 2009, Revised Selected Papers</BookSubTitle><BookVolumeNumber>6004</BookVolumeNumber><BookSequenceNumber>6004</BookSequenceNumber><BookDOI>10.1007/978-3-642-13131-8</BookDOI><BookTitleID>211223</BookTitleID><BookPrintISBN>978-3-642-13130-1</BookPrintISBN><BookElectronicISBN>978-3-642-13131-8</BookElectronicISBN><BookChapterCount>9</BookChapterCount><BookCopyright><CopyrightHolderName>Springer-Verlag Berlin Heidelberg</CopyrightHolderName><CopyrightYear>2010</CopyrightYear></BookCopyright><BookSubjectGroup><BookSubject Code="I" Type="Primary">Computer Science</BookSubject><BookSubject Code="I18030" Priority="1" Type="Secondary">Data Mining and Knowledge Discovery</BookSubject><BookSubject Code="I21017" Priority="2" Type="Secondary">Artificial Intelligence (incl. Robotics)</BookSubject><BookSubject Code="I16021" Priority="3" Type="Secondary">Algorithm Analysis and Problem Complexity</BookSubject><BookSubject Code="I2203X" Priority="4" Type="Secondary">Pattern Recognition</BookSubject><BookSubject Code="I22021" Priority="5" Type="Secondary">Image Processing and Computer Vision</BookSubject><BookSubject Code="I23050" Priority="6" Type="Secondary">Computational Biology/Bioinformatics</BookSubject><SubjectCollection Code="SUCO11645">Computer Science</SubjectCollection></BookSubjectGroup><BookContext><SeriesID>558</SeriesID><SubSeriesID>5381</SubSeriesID></BookContext></BookInfo><BookHeader><EditorGroup><Editor AffiliationIDS="Aff19"><EditorName DisplayOrder="Western"><GivenName>Christian</GivenName><FamilyName>Blaschke</FamilyName></EditorName><Contact><Email>blaschke@bioalma.com</Email></Contact></Editor><Editor AffiliationIDS="Aff20"><EditorName DisplayOrder="Western"><GivenName>Hagit</GivenName><FamilyName>Shatkay</FamilyName></EditorName><Contact><Email>shatkay@cs.queensu.ca</Email></Contact></Editor><Affiliation ID="Aff19"><OrgName>Bioalma</OrgName><OrgAddress><Street>C/Ronda de Poniente, 4, 2-C</Street><Postcode>28760</Postcode><City>Tres Cantos, Madrid</City><Country>Spain</Country></OrgAddress></Affiliation><Affiliation ID="Aff20"><OrgDivision>Computational Biology and Machine Learning Lab, School of Computing</OrgDivision><OrgName>Queen’s University</OrgName><OrgAddress><Postcode>K7L 3N6</Postcode><City>Kingston</City><State>ON</State><Country>Canada</Country></OrgAddress></Affiliation></EditorGroup></BookHeader><Part ID="Part1"><PartInfo TocLevels="0"><PartID>1</PartID><PartSequenceNumber>1</PartSequenceNumber><PartTitle>BioLINK 2009</PartTitle><PartChapterCount>9</PartChapterCount><PartContext><SeriesID>558</SeriesID><BookTitle>Linking Literature, Information, and Knowledge for Biology</BookTitle></PartContext></PartInfo><Chapter ID="Chap7" Language="En"><ChapterInfo ChapterType="OriginalPaper" ContainsESM="No" NumberingDepth="2" NumberingStyle="ContentOnly" TocLevels="0"><ChapterID>7</ChapterID><ChapterDOI>10.1007/978-3-642-13131-8_7</ChapterDOI><ChapterSequenceNumber>7</ChapterSequenceNumber><ChapterTitle Language="En">Combining Semantic Relations and DNA Microarray Data for Novel Hypotheses Generation</ChapterTitle><ChapterFirstPage>53</ChapterFirstPage><ChapterLastPage>61</ChapterLastPage><ChapterCopyright><CopyrightHolderName>Springer-Verlag Berlin Heidelberg</CopyrightHolderName><CopyrightYear>2010</CopyrightYear></ChapterCopyright><ChapterGrants Type="Regular"><MetadataGrant Grant="OpenAccess"></MetadataGrant><AbstractGrant Grant="OpenAccess"></AbstractGrant><BodyPDFGrant Grant="Restricted"></BodyPDFGrant><BodyHTMLGrant Grant="Restricted"></BodyHTMLGrant><BibliographyGrant Grant="Restricted"></BibliographyGrant><ESMGrant Grant="Restricted"></ESMGrant></ChapterGrants><ChapterContext><SeriesID>558</SeriesID><PartID>1</PartID><BookID>978-3-642-13131-8</BookID><BookTitle>Linking Literature, Information, and Knowledge for Biology</BookTitle></ChapterContext></ChapterInfo><ChapterHeader><AuthorGroup><Author AffiliationIDS="Aff21"><AuthorName DisplayOrder="Western"><GivenName>Dimitar</GivenName><FamilyName>Hristovski</FamilyName></AuthorName><Contact><Email>dimitar.hristovski@mf.uni-lj.si</Email></Contact></Author><Author AffiliationIDS="Aff22"><AuthorName DisplayOrder="Western"><GivenName>Andrej</GivenName><FamilyName>Kastrin</FamilyName></AuthorName><Contact><Email>andrej.kastrin@guest.arnes.si</Email></Contact></Author><Author AffiliationIDS="Aff22"><AuthorName DisplayOrder="Western"><GivenName>Borut</GivenName><FamilyName>Peterlin</FamilyName></AuthorName><Contact><Email>borut.peterlin@guest.arnes.si</Email></Contact></Author><Author AffiliationIDS="Aff23"><AuthorName DisplayOrder="Western"><GivenName>Thomas</GivenName><GivenName>C.</GivenName><FamilyName>Rindflesch</FamilyName></AuthorName><Contact><Email>tcr@nlm.nih.gov</Email></Contact></Author><Affiliation ID="Aff21"><OrgDivision>Faculty of Medicine</OrgDivision><OrgName>Institute of Biomedical Informatics</OrgName><OrgAddress><City>Ljubljana</City><Country>Slovenia</Country></OrgAddress></Affiliation><Affiliation ID="Aff22"><OrgDivision>Institute of Medical Genetics</OrgDivision><OrgName>University Medical Centre</OrgName><OrgAddress><City>Ljubljana</City><Country>Slovenia</Country></OrgAddress></Affiliation><Affiliation ID="Aff23"><OrgName>National Library of Medicine, NIH</OrgName><OrgAddress><City>Bethesda</City><State>MD</State><Country>USA</Country></OrgAddress></Affiliation></AuthorGroup><Abstract ID="Abs1" Language="En"><Heading>Abstract</Heading><Para>Although microarray experiments have great potential to support progress in biomedical research, results are not easy to interpret. Information about the functions and relations of relevant genes needs to be extracted from the vast biomedical literature. A potential solution is to use computerized text analysis methods. Our proposal enhances these methods with semantic relations. We describe an application that integrates such relations with microarray results and discuss its benefits in supporting enhanced access to the relevant literature for interpretation of results and novel hypotheses generation. The application is available at http://sembt.mf.uni-lj.si</Para></Abstract><KeywordGroup Language="En"><Heading>Keywords</Heading><Keyword>microarray analysis</Keyword><Keyword>literature-based discovery</Keyword><Keyword>semantic predications</Keyword><Keyword>natural language processing</Keyword></KeywordGroup></ChapterHeader><NoBody></NoBody></Chapter></Part></Book></Series></Publisher></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Combining Semantic Relations and DNA Microarray Data for Novel Hypotheses Generation</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Combining Semantic Relations and DNA Microarray Data for Novel Hypotheses Generation</title></titleInfo><name type="personal"><namePart type="given">Dimitar</namePart><namePart type="family">Hristovski</namePart><affiliation>Faculty of Medicine, Institute of Biomedical Informatics, Ljubljana, Slovenia</affiliation><affiliation>E-mail: dimitar.hristovski@mf.uni-lj.si</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Andrej</namePart><namePart type="family">Kastrin</namePart><affiliation>Institute of Medical Genetics, University Medical Centre, Ljubljana, Slovenia</affiliation><affiliation>E-mail: andrej.kastrin@guest.arnes.si</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Borut</namePart><namePart type="family">Peterlin</namePart><affiliation>Institute of Medical Genetics, University Medical Centre, Ljubljana, Slovenia</affiliation><affiliation>E-mail: borut.peterlin@guest.arnes.si</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Thomas</namePart><namePart type="given">C.</namePart><namePart type="family">Rindflesch</namePart><affiliation>National Library of Medicine, NIH, Bethesda, MD, USA</affiliation><affiliation>E-mail: tcr@nlm.nih.gov</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="conference [research-article]" displayLabel="OriginalPaper"></genre><originInfo><publisher>Springer Berlin Heidelberg</publisher><place><placeTerm type="text">Berlin, Heidelberg</placeTerm></place><dateIssued encoding="w3cdtf">2010</dateIssued><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></physicalDescription><abstract lang="en">Abstract: Although microarray experiments have great potential to support progress in biomedical research, results are not easy to interpret. Information about the functions and relations of relevant genes needs to be extracted from the vast biomedical literature. A potential solution is to use computerized text analysis methods. Our proposal enhances these methods with semantic relations. We describe an application that integrates such relations with microarray results and discuss its benefits in supporting enhanced access to the relevant literature for interpretation of results and novel hypotheses generation. The application is available at http://sembt.mf.uni-lj.si</abstract><relatedItem type="host"><titleInfo><title>Linking Literature, Information, and Knowledge for Biology</title><subTitle>Workshop of the BioLink Special Interest Group, ISMB/ECCB 2009, Stockholm, June 28-29, 2009, Revised Selected Papers</subTitle></titleInfo><name type="personal"><namePart type="given">Christian</namePart><namePart type="family">Blaschke</namePart><affiliation>Bioalma, C/Ronda de Poniente, 4, 2-C, 28760, Tres Cantos, Madrid, Spain</affiliation><affiliation>E-mail: blaschke@bioalma.com</affiliation><role><roleTerm type="text">editor</roleTerm></role></name><name type="personal"><namePart type="given">Hagit</namePart><namePart type="family">Shatkay</namePart><affiliation>Computational Biology and Machine Learning Lab, School of Computing, Queen’s University, K7L 3N6, Kingston, ON, Canada</affiliation><affiliation>E-mail: shatkay@cs.queensu.ca</affiliation><role><roleTerm type="text">editor</roleTerm></role></name><genre type="Book Series" displayLabel="Proceedings"></genre><originInfo><copyrightDate encoding="w3cdtf">2010</copyrightDate><issuance>monographic</issuance></originInfo><subject><genre>Book Subject Collection</genre><topic authority="SpringerSubjectCodes" authorityURI="SUCO11645">Computer Science</topic></subject><subject><genre>Book Subject Group</genre><topic authority="SpringerSubjectCodes" authorityURI="I">Computer Science</topic><topic authority="SpringerSubjectCodes" authorityURI="I18030">Data Mining and Knowledge Discovery</topic><topic authority="SpringerSubjectCodes" authorityURI="I21017">Artificial Intelligence (incl. Robotics)</topic><topic authority="SpringerSubjectCodes" authorityURI="I16021">Algorithm Analysis and Problem Complexity</topic><topic authority="SpringerSubjectCodes" authorityURI="I2203X">Pattern Recognition</topic><topic authority="SpringerSubjectCodes" authorityURI="I22021">Image Processing and Computer Vision</topic><topic authority="SpringerSubjectCodes" authorityURI="I23050">Computational Biology/Bioinformatics</topic></subject><identifier type="DOI">10.1007/978-3-642-13131-8</identifier><identifier type="ISBN">978-3-642-13130-1</identifier><identifier type="eISBN">978-3-642-13131-8</identifier><identifier type="ISSN">0302-9743</identifier><identifier type="eISSN">1611-3349</identifier><identifier type="BookTitleID">211223</identifier><identifier type="BookID">978-3-642-13131-8</identifier><identifier type="BookChapterCount">9</identifier><identifier type="BookVolumeNumber">6004</identifier><identifier type="BookSequenceNumber">6004</identifier><identifier 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type="family">Terzopoulos</namePart><affiliation>University of California, Los Angeles, CA, USA</affiliation><role><roleTerm type="text">editor</roleTerm></role></name><name type="personal"><namePart type="given">Doug</namePart><namePart type="family">Tygar</namePart><affiliation>University of California, Berkeley, CA, USA</affiliation><role><roleTerm type="text">editor</roleTerm></role></name><name type="personal"><namePart type="given">Moshe</namePart><namePart type="given">Y.</namePart><namePart type="family">Vardi</namePart><affiliation>Rice University, Houston, TX, USA</affiliation><role><roleTerm type="text">editor</roleTerm></role></name><name type="personal"><namePart type="given">Gerhard</namePart><namePart type="family">Weikum</namePart><affiliation>Max-Planck Institute of Computer Science, Saarbrücken, Germany</affiliation><role><roleTerm type="text">editor</roleTerm></role></name><name type="personal"><namePart type="given">Sorin</namePart><namePart type="family">Istrail</namePart><affiliation>Brown University, Providence, RI, USA</affiliation><role><roleTerm type="text">editor</roleTerm></role></name><name type="personal"><namePart type="given">Pavel</namePart><namePart type="family">Pevzner</namePart><affiliation>University of California, San Diego, CA, USA</affiliation><role><roleTerm type="text">editor</roleTerm></role></name><name type="personal"><namePart type="given">Michael</namePart><namePart type="given">S.</namePart><namePart type="family">Waterman</namePart><affiliation>University of Southern California, Los Angeles, CA, USA</affiliation><role><roleTerm type="text">editor</roleTerm></role></name><name type="personal"><namePart type="given">Christian</namePart><namePart type="family">Blaschke</namePart><affiliation>Bioalma, C/Ronda de Poniente, 4, 2-C, 28760, Tres Cantos, Madrid, Spain</affiliation><affiliation>E-mail: blaschke@bioalma.com</affiliation><role><roleTerm type="text">editor</roleTerm></role></name><name type="personal"><namePart type="given">Hagit</namePart><namePart type="family">Shatkay</namePart><affiliation>Computational Biology and Machine Learning Lab, School of Computing, Queen’s University, K7L 3N6, Kingston, ON, Canada</affiliation><affiliation>E-mail: shatkay@cs.queensu.ca</affiliation><role><roleTerm type="text">editor</roleTerm></role></name><genre type="Sub-Series"></genre><identifier type="ISSN">0302-9743</identifier><identifier type="eISSN">1611-3349</identifier><identifier type="SubSeriesID">5381</identifier></relatedItem><identifier type="ISSN">0302-9743</identifier><identifier type="eISSN">1611-3349</identifier><identifier type="SeriesID">558</identifier><recordInfo><recordOrigin>Springer-Verlag Berlin Heidelberg, 2010</recordOrigin></recordInfo></relatedItem><identifier type="istex">FC61C703D43C762B3CFE3E3BCFC4A3F6727E56C9</identifier><identifier type="DOI">10.1007/978-3-642-13131-8_7</identifier><identifier type="ChapterID">Chap7</identifier><identifier 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