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 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.
Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan kawano@dbcls.rois.ac.jp.
Shin
S
Kawano
CrossEdge Systems Inc., 2-14-42 Higashi Yamada, Tsuzuki-ku, Yokohama, Kanagawa 224-0023, Japan.
Tsutomu
T
Watanabe
Department of Tumor Genetics and Biology, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, Kumamoto 860-8556, Japan.
Sohei
S
Mizuguchi
Department of Tumor Genetics and Biology, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, Kumamoto 860-8556, Japan.
Norie
N
Araki
Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan.
Toshiaki
T
Katayama
Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan.
Atsuko
A
Yamaguchi
D016208:Databases, Factual; D030541:Databases, Genetic; D020407:Internet; D058977:Molecular Sequence Annotation; D012984:Software