Toward an Integrated RNA Motif Database
Identifieur interne : 000218 ( Istex/Corpus ); précédent : 000217; suivant : 000219Toward an Integrated RNA Motif Database
Auteurs : L. Wang ; Dongrong Wen ; A. Shapiro ; G. Herbert ; Jing Li ; Kaushik GhoshSource :
- Lecture Notes in Computer Science [ 0302-9743 ] ; 2007.
Abstract
Abstract: In this paper we present the design and implementation of an RNA structural motif database, called RmotifDB. The structural motifs stored in RmotifDB come from three sources: (1) collected manually from biomedical literature; (2) submitted by scientists around the world; and (3) discovered by a wide variety of motif mining methods. We present here a motif mining method in detail. We also describe the interface and search mechanisms provided by RmotifDB as well as techniques used to integrate RmotifDB with the Gene Ontology. The RmotifDB system is fully operational and accessible on the Internet at http://datalab.njit.edu/bioinfo/
Url:
DOI: 10.1007/978-3-540-73255-6_5
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The structural motifs stored in RmotifDB come from three sources: (1) collected manually from biomedical literature; (2) submitted by scientists around the world; and (3) discovered by a wide variety of motif mining methods. We present here a motif mining method in detail. We also describe the interface and search mechanisms provided by RmotifDB as well as techniques used to integrate RmotifDB with the Gene Ontology. The RmotifDB system is fully operational and accessible on the Internet at http://datalab.njit.edu/bioinfo/</Para></Abstract></ChapterHeader><NoBody></NoBody></Chapter></Part></Book></Series></Publisher></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Toward an Integrated RNA Motif Database</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Toward an Integrated RNA Motif Database</title></titleInfo><name type="personal"><namePart type="given">Jason</namePart><namePart type="given">T.</namePart><namePart type="given">L.</namePart><namePart type="family">Wang</namePart><affiliation>Bioinformatics Program and Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Dongrong</namePart><namePart type="family">Wen</namePart><affiliation>Bioinformatics Program and Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Bruce</namePart><namePart type="given">A.</namePart><namePart type="family">Shapiro</namePart><affiliation>Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Katherine</namePart><namePart type="given">G.</namePart><namePart type="family">Herbert</namePart><affiliation>Department of Computer Science, Montclair State University, Montclair, NJ 07043</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Jing</namePart><namePart type="family">Li</namePart><affiliation>Applied Statistics Program and Department of Mathematical Sciences, New Jersey Institute of Technology, Newark, NJ 07102</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Kaushik</namePart><namePart type="family">Ghosh</namePart><affiliation>Applied Statistics Program and Department of Mathematical Sciences, New Jersey Institute of Technology, Newark, NJ 07102</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="conference" displayLabel="OriginalPaper"></genre><originInfo><publisher>Springer Berlin Heidelberg</publisher><place><placeTerm type="text">Berlin, Heidelberg</placeTerm></place><dateIssued encoding="w3cdtf">2007</dateIssued><copyrightDate encoding="w3cdtf">2007</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: In this paper we present the design and implementation of an RNA structural motif database, called RmotifDB. The structural motifs stored in RmotifDB come from three sources: (1) collected manually from biomedical literature; (2) submitted by scientists around the world; and (3) discovered by a wide variety of motif mining methods. We present here a motif mining method in detail. We also describe the interface and search mechanisms provided by RmotifDB as well as techniques used to integrate RmotifDB with the Gene Ontology. The RmotifDB system is fully operational and accessible on the Internet at http://datalab.njit.edu/bioinfo/</abstract><relatedItem type="host"><titleInfo><title>Data Integration in the Life Sciences</title><subTitle>4th International Workshop, DILS 2007, Philadelphia, PA, USA, June 27-29, 2007. Proceedings</subTitle></titleInfo><name type="personal"><namePart type="given">Sarah</namePart><namePart type="family">Cohen-Boulakia</namePart><role><roleTerm type="text">editor</roleTerm></role></name><name type="personal"><namePart type="given">Val</namePart><namePart type="family">Tannen</namePart><role><roleTerm type="text">editor</roleTerm></role></name><genre type="book-series" displayLabel="Proceedings"></genre><originInfo><copyrightDate encoding="w3cdtf">2007</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="H28009">Health Informatics</topic><topic authority="SpringerSubjectCodes" authorityURI="I18024">Database Management</topic><topic authority="SpringerSubjectCodes" authorityURI="I18040">Information Systems Applications (incl.Internet)</topic><topic authority="SpringerSubjectCodes" authorityURI="I23050">Computational Biology/Bioinformatics</topic><topic authority="SpringerSubjectCodes" authorityURI="L17004">Computer Appl. in Life Sciences</topic></subject><identifier type="DOI">10.1007/978-3-540-73255-6</identifier><identifier type="ISBN">978-3-540-73254-9</identifier><identifier type="eISBN">978-3-540-73255-6</identifier><identifier type="ISSN">0302-9743</identifier><identifier type="eISSN">1611-3349</identifier><identifier type="BookTitleID">150710</identifier><identifier type="BookID">978-3-540-73255-6</identifier><identifier type="BookChapterCount">21</identifier><identifier type="BookVolumeNumber">4544</identifier><identifier type="BookSequenceNumber">4544</identifier><identifier type="PartChapterCount">6</identifier><part><date>2007</date><detail type="part"><title>New Architectures and Experience on Using Systems</title></detail><detail type="volume"><number>4544</number><caption>vol.</caption></detail><extent unit="pages"><start>27</start><end>36</end></extent></part><recordInfo><recordOrigin>Springer-Verlag Berlin Heidelberg, 2007</recordOrigin></recordInfo></relatedItem><relatedItem type="series"><titleInfo><title>Lecture Notes in Computer Science</title></titleInfo><originInfo><copyrightDate encoding="w3cdtf">2007</copyrightDate><issuance>serial</issuance></originInfo><relatedItem type="constituent"><titleInfo><title>Lecture Notes in Bioinformatics</title></titleInfo><name type="personal"><namePart type="given">Sorin</namePart><namePart type="family">Istrail</namePart><role><roleTerm type="text">editor</roleTerm></role></name><name type="personal"><namePart type="given">Pavel</namePart><namePart type="family">Pevzner</namePart><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><role><roleTerm type="text">editor</roleTerm></role></name><name type="personal"><namePart type="given">Sarah</namePart><namePart type="family">Cohen-Boulakia</namePart><role><roleTerm type="text">editor</roleTerm></role></name><name type="personal"><namePart type="given">Val</namePart><namePart type="family">Tannen</namePart><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, 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