Toward an integrated RNA motif database

Jason T.L. Wang; Dongrong Wen; Bruce A. Shapiro; Katherine G. Herbert; Jing Li; Kaushik Ghosh

doi:10.1007/978-3-540-73255-6_5

Toward an integrated RNA motif database

Jason T.L. Wang, Dongrong Wen, Bruce A. Shapiro, Katherine G. Herbert, Jing Li, Kaushik Ghosh

Computer Science

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

1 Scopus citations

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/

Original language	English
Title of host publication	Data Integration in the Life Sciences - 4th International Workshop, DILS 2007, Proceedings
Publisher	Springer Verlag
Pages	27-36
Number of pages	10
ISBN (Print)	3540732543, 9783540732549
DOIs	https://doi.org/10.1007/978-3-540-73255-6_5
State	Published - 2007
Event	4th International Workshop on Data Integration in the Life Sciences, DILS 2007 - Philadelphia, PA, United States Duration: 27 Jun 2007 → 29 Jun 2007

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	4544 LNBI
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Other

Other	4th International Workshop on Data Integration in the Life Sciences, DILS 2007
Country/Territory	United States
City	Philadelphia, PA
Period	27/06/07 → 29/06/07

Access to Document

10.1007/978-3-540-73255-6_5

Cite this

Wang, J. T. L., Wen, D., Shapiro, B. A., Herbert, K. G., Li, J., & Ghosh, K. (2007). Toward an integrated RNA motif database. In Data Integration in the Life Sciences - 4th International Workshop, DILS 2007, Proceedings (pp. 27-36). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4544 LNBI). Springer Verlag. https://doi.org/10.1007/978-3-540-73255-6_5

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title = "Toward an integrated RNA motif database",

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/",

author = "Wang, {Jason T.L.} and Dongrong Wen and Shapiro, {Bruce A.} and Herbert, {Katherine G.} and Jing Li and Kaushik Ghosh",

year = "2007",

doi = "10.1007/978-3-540-73255-6_5",

language = "English",

isbn = "3540732543",

series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

publisher = "Springer Verlag",

pages = "27--36",

booktitle = "Data Integration in the Life Sciences - 4th International Workshop, DILS 2007, Proceedings",

note = "4th International Workshop on Data Integration in the Life Sciences, DILS 2007 ; Conference date: 27-06-2007 Through 29-06-2007",

}

Wang, JTL, Wen, D, Shapiro, BA, Herbert, KG, Li, J & Ghosh, K 2007, Toward an integrated RNA motif database. in Data Integration in the Life Sciences - 4th International Workshop, DILS 2007, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 4544 LNBI, Springer Verlag, pp. 27-36, 4th International Workshop on Data Integration in the Life Sciences, DILS 2007, Philadelphia, PA, United States, 27/06/07. https://doi.org/10.1007/978-3-540-73255-6_5

Toward an integrated RNA motif database. / Wang, Jason T.L.; Wen, Dongrong; Shapiro, Bruce A. et al.
Data Integration in the Life Sciences - 4th International Workshop, DILS 2007, Proceedings. Springer Verlag, 2007. p. 27-36 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4544 LNBI).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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AB - 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/

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Wang JTL, Wen D, Shapiro BA, Herbert KG, Li J, Ghosh K. Toward an integrated RNA motif database. In Data Integration in the Life Sciences - 4th International Workshop, DILS 2007, Proceedings. Springer Verlag. 2007. p. 27-36. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-540-73255-6_5

Toward an integrated RNA motif database

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