TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model

TogoTable (http://togotable.dbcls.jp/) is a web tool that adds user-specified annotations to a table that a user uploads. Annotations are drawn from several biological databases that use the Resource Description Framework (RDF) data model. TogoTable uses database identifiers (IDs) in the table as a...

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Bibliographic Details
Published in:Nucleic acids research 2014-07, Vol.42 (Web Server issue), p.W442-W448
Main Authors: Kawano, Shin, Watanabe, Tsutomu, Mizuguchi, Sohei, Araki, Norie, Katayama, Toshiaki, Yamaguchi, Atsuko
Format: Article
Language:English
Subjects:
Databases, Factual
Databases, Genetic
Internet
Molecular Sequence Annotation
Software
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Summary:TogoTable (http://togotable.dbcls.jp/) is a web tool that adds user-specified annotations to a table that a user uploads. Annotations are drawn from several biological databases that use the Resource Description Framework (RDF) data model. TogoTable uses database identifiers (IDs) in the table as a query key for searching. RDF data, which form a network called Linked Open Data (LOD), can be searched from SPARQL endpoints using a SPARQL query language. Because TogoTable uses RDF, it can integrate annotations from not only the reference database to which the IDs originally belong, but also externally linked databases via the LOD network. For example, annotations in the Protein Data Bank can be retrieved using GeneID through links provided by the UniProt RDF. Because RDF has been standardized by the World Wide Web Consortium, any database with annotations based on the RDF data model can be easily incorporated into this tool. We believe that TogoTable is a valuable Web tool, particularly for experimental biologists who need to process huge amounts of data such as high-throughput experimental output.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gku403