A paper "TogoGenome/TogoStanza: modularized Semantic Web genome database" was published in the Database journal.
2019. 01. 18 /
A paper “TogoGenome/TogoStanza: modularized Semantic Web genome database” was published in the Database journal.
Project Associate Professor Shinobu Okamoto and Project Assistant Professors Toshiaki Katayama, Shuichi Kawashima, Yuki Moriya, Hirokazu Chiba and Yuki Naito in DBCLS contributed to this work.
The full paper can be found online at: https://doi.org/10.1093/database/bay132, PubMed
TogoGenome is a genome database that is purely based on the Semantic Web technology, which enables the integration of heterogeneous data and flexible semantic searches. All the information is stored as Resource Description Framework (RDF) data, and the reporting web pages are generated on the fly using SPARQL Protocol and RDF Query Language (SPARQL) queries. TogoGenome provides a semantic-faceted search system by gene functional annotation, taxonomy, phenotypes and environment based on the relevant ontologies. TogoGenome also serves as an interface to conduct semantic comparative genomics by which a user can observe pan-organism or organism-specific genes based on the functional aspect of gene annotations and the combinations of organisms from different taxa. The TogoGenome database exhibits a modularized structure, and each module in the report pages is separately served as TogoStanza, which is a generic framework for rendering an information block as IFRAME/Web Components, which can, unlike several other monolithic databases, also be reused to construct other databases.
Toshiaki Katayama, Shuichi Kawashima, Shinobu Okamoto, Yuki Moriya, Hirokazu Chiba, Yuki Naito, Takatomo Fujisawa, Hiroshi Mori, and Toshihisa Takagi, TogoGenome/TogoStanza: modularized Semantic Web genome database, Database (Oxford), 2019, 1–11.