RKB: a Semantic Web knowledge base for RNA View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2010-06

AUTHORS

Jose Cruz-Toledo, Michel Dumontier, Marc Parisien, François Major

ABSTRACT

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. More... »

PAGES

s2

References to SciGraph publications

  • 2006. FaCT++ Description Logic Reasoner: System Description in AUTOMATED REASONING
  • 2005-05. Relations in biomedical ontologies in GENOME BIOLOGY
  • 2009-08-10. MIREOT: the Minimum Information to Reference an External Ontology Term in NATURE PRECEDINGS
  • 2008. Chemical Knowledge for the Semantic Web in DATA INTEGRATION IN THE LIFE SCIENCES
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/2041-1480-1-s1-s2

    DOI

    http://dx.doi.org/10.1186/2041-1480-1-s1-s2

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1017025248

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/20626922


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