Toward an integrated RNA motif database

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

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 languageEnglish
Title of host publicationData Integration in the Life Sciences - 4th International Workshop, DILS 2007, Proceedings
Pages27-36
Number of pages10
StatePublished - 3 Aug 2007
Event4th International Workshop on Data Integration in the Life Sciences, DILS 2007 - Philadelphia, PA, United States
Duration: 27 Jun 200729 Jun 2007

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4544 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other4th International Workshop on Data Integration in the Life Sciences, DILS 2007
CountryUnited States
CityPhiladelphia, PA
Period27/06/0729/06/07

Fingerprint

RNA
Ontology
Mining
Computer systems
Genes
Internet
Gene Ontology
Integrate
Design

Cite this

Wang, J. T. L., Wen, D., Shapiro, B. A., Herbert, K., 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).
Wang, Jason T.L. ; Wen, Dongrong ; Shapiro, Bruce A. ; Herbert, Katherine ; Li, Jing ; Ghosh, Kaushik. / Toward an integrated RNA motif database. Data Integration in the Life Sciences - 4th International Workshop, DILS 2007, Proceedings. 2007. pp. 27-36 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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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/",
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Wang, JTL, Wen, D, Shapiro, BA, Herbert, K, 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, pp. 27-36, 4th International Workshop on Data Integration in the Life Sciences, DILS 2007, Philadelphia, PA, United States, 27/06/07.

Toward an integrated RNA motif database. / Wang, Jason T.L.; Wen, Dongrong; Shapiro, Bruce A.; Herbert, Katherine; Li, Jing; Ghosh, Kaushik.

Data Integration in the Life Sciences - 4th International Workshop, DILS 2007, Proceedings. 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 proceedingConference contribution

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Wang JTL, Wen D, Shapiro BA, Herbert K, Li J, Ghosh K. Toward an integrated RNA motif database. In Data Integration in the Life Sciences - 4th International Workshop, DILS 2007, Proceedings. 2007. p. 27-36. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).