Cargando…

RKB: a Semantic Web knowledge base for RNA

Increasingly sophisticated knowledge about RNA structure and function requires an inclusive knowledge representation that facilitates the integration of independently –generated information arising from such efforts as genome sequencing projects, microarray analyses, structure determination and RNA...

Descripción completa

Detalles Bibliográficos
Autores principales: Cruz-Toledo, Jose, Dumontier, Michel, Parisien, Marc, Major, François
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2903721/
https://www.ncbi.nlm.nih.gov/pubmed/20626922
http://dx.doi.org/10.1186/2041-1480-1-S1-S2
_version_ 1782183840479969280
author Cruz-Toledo, Jose
Dumontier, Michel
Parisien, Marc
Major, François
author_facet Cruz-Toledo, Jose
Dumontier, Michel
Parisien, Marc
Major, François
author_sort Cruz-Toledo, Jose
collection PubMed
description Increasingly sophisticated knowledge about RNA structure and function requires an inclusive knowledge representation that facilitates the integration of independently –generated information arising from such efforts as genome sequencing projects, microarray analyses, structure determination and RNA SELEX experiments. While RNAML, an XML-based representation, has been proposed as an exchange format for a select subset of information, it lacks domain-specific semantics that are essential for answering questions that require expert knowledge. Here, we describe an RNA knowledge base (RKB) for structure-based knowledge using RDF/OWL Semantic Web technologies. RKB extends a number of ontologies and contains basic terminology for nucleic acid composition along with context/model-specific structural features such as sugar conformations, base pairings and base stackings. RKB (available at http://semanticscience.org/projects/rkb) is populated with PDB entries and MC-Annotate structural annotation. We show queries to the RKB using description logic reasoning, thus opening the door to question answering over independently-published RNA knowledge using Semantic Web technologies.
format Text
id pubmed-2903721
institution National Center for Biotechnology Information
language English
publishDate 2010
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-29037212010-07-14 RKB: a Semantic Web knowledge base for RNA Cruz-Toledo, Jose Dumontier, Michel Parisien, Marc Major, François J Biomed Semantics Proceedings Increasingly sophisticated knowledge about RNA structure and function requires an inclusive knowledge representation that facilitates the integration of independently –generated information arising from such efforts as genome sequencing projects, microarray analyses, structure determination and RNA SELEX experiments. While RNAML, an XML-based representation, has been proposed as an exchange format for a select subset of information, it lacks domain-specific semantics that are essential for answering questions that require expert knowledge. Here, we describe an RNA knowledge base (RKB) for structure-based knowledge using RDF/OWL Semantic Web technologies. RKB extends a number of ontologies and contains basic terminology for nucleic acid composition along with context/model-specific structural features such as sugar conformations, base pairings and base stackings. RKB (available at http://semanticscience.org/projects/rkb) is populated with PDB entries and MC-Annotate structural annotation. We show queries to the RKB using description logic reasoning, thus opening the door to question answering over independently-published RNA knowledge using Semantic Web technologies. BioMed Central 2010-06-22 /pmc/articles/PMC2903721/ /pubmed/20626922 http://dx.doi.org/10.1186/2041-1480-1-S1-S2 Text en Copyright ©2010 Dumontier et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Proceedings
Cruz-Toledo, Jose
Dumontier, Michel
Parisien, Marc
Major, François
RKB: a Semantic Web knowledge base for RNA
title RKB: a Semantic Web knowledge base for RNA
title_full RKB: a Semantic Web knowledge base for RNA
title_fullStr RKB: a Semantic Web knowledge base for RNA
title_full_unstemmed RKB: a Semantic Web knowledge base for RNA
title_short RKB: a Semantic Web knowledge base for RNA
title_sort rkb: a semantic web knowledge base for rna
topic Proceedings
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2903721/
https://www.ncbi.nlm.nih.gov/pubmed/20626922
http://dx.doi.org/10.1186/2041-1480-1-S1-S2
work_keys_str_mv AT cruztoledojose rkbasemanticwebknowledgebaseforrna
AT dumontiermichel rkbasemanticwebknowledgebaseforrna
AT parisienmarc rkbasemanticwebknowledgebaseforrna
AT majorfrancois rkbasemanticwebknowledgebaseforrna