The RIKEN integrated database of mammals

Abstract

The RIKEN integrated database of mammals (http://scinets.org/db/mammal) is the official undertaking to integrate its mammalian databases produced from multiple large-scale programs that have been promoted by the institute. The database integrates not only RIKEN's original databases, such as FANTOM, the ENU mutagenesis program, the RIKEN Cerebellar Development Transcriptome Database and the Bioresource Database, but also imported data from public databases, such as Ensembl, MGI and biomedical ontologies. Our integrated database has been implemented on the infrastructure of publication medium for databases, termed SciNetS/SciNeS, or the Scientists' Networking System, where the data and metadata are structured as a semantic web and are downloadable in various standardized formats. The top-level ontology-based implementation of mammal-related data directly integrates the representative knowledge and individual data records in existing databases to ensure advanced cross-database searches and reduced unevenness of the data management operations. Through the development of this database, we propose a novel methodology for the development of standardized comprehensive management of heterogeneous data sets in multiple databases to improve the sustainability, accessibility, utility and publicity of the data of biomedical information.

Figure 1.

Schematic diagram showing the concept of SciNetS. SciNetS provides incubation functions from database construction to the integration of databases in computing clouds or a group of large-scale servers, and discloses databases using interfaces compatible with international standards, thus contributing to the establishment of cyber-infrastructure for integrating worldwide databases [reprinted with the courtesy from Tetsuro Toyoda, ‘Synthetic biology—creating biological resources from information resources’ RIKEN RESEARCH 5(10) 13–16, 2010 (http://www.rikenresearch.riken.jp/eng/frontline/6397)].

Figure 2.

The implementation of data in the RIKEN integrated database of mammals to ensure direct integration between ontologies and databases based on the semantic web technology. Individual public and RIKEN databases are imported as individual projects, and their main contents are reviewed to classify them into the lower classes to root the 15 classes of the integrated database, such as gene, transcript, experimental data, strain and so on. The classification follows the top-level ontology and is directly linked to the equivalents of rdfs:subclassOf across projects. Property links also organized with rdfs:subPropertyOf to represent the logical definition of upper classes are inherited to lower classes or instances.

Figure 3.

The instance page to illustrate the graphical representation of detailed semantic links of the RIKEN integrated database of mammals. Explanations are given by open squares with an arrow.

Figure 4.

The representation of filtering (search) result of the RIKEN integrated database of mammals. The number of query hits is represented on each disk or folder icon with red letters.