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Database name DOI Database classification Organism Database description Features and manner of utilization of database Database maintenance site License
Togo Picture Gallery
ImageCollection

Useful images for life science are published without a fee. You can use them as parts of slides or research materials.

Still images provided include model organisms, laboratory instruments, laboratory equipments, schematic drawings, next generation sequencers, cells and microscopes, you can use it for a wide range of materials.
Since it is licensed under Creative Commons attribution 4.0 International (CC BY 4.0), you can use it as long as you describe the credit.

CC BY
TogoTV
Movie Collection

An archive of tutorial videos expounding how to use biological databases and tools

TogoTV (‘Togo’ means ‘integration’ in Japanese; pronunciation symbol is [toɯgoɯ]) that is one of the services in the Database Center for Life Science (DBCLS) in Japan is a portal site of tutorial and lecture videos about bioinformatics resources. Although the original TogoTV site is mostly written in Japanese, there is the English interface for international users. The site contains our original videos. All contents provided by us are distributed under the Creative Commons Attribution 4.0 International (CC-BY-4.0) license and also provided on a YouTube channel. We plan to expand our own English contents so as to enable our service to be used all over the world.

CC BY
SKIP Stemcell Database
(Stemcell Knowledge & Information Portal)
10.18908/lsdba.nbdc01524-000
Human Genes and Diseases
Stemcell
Article
Homo sapiens (9606)

SKIP (Stemcell Knowledge & Information Portal) is the portal site aiming to promote the exchange of information and joint research between researchers by aggregating various information of stem cells (iPS cells, iPS cells derived from patients, etc.) to stimulate research on disease and regenerative medicine using stem cells by enhancing social understanding by providing information on stem cells.

You can one-stop search stemcell information from RIKEN BRC, NIBIO, Coriell, ATCC and many laboratories.

CC BY-SA
PGDBj - Ortholog DB
(Plant Genome Database Japan - Ortholog Database)
10.18908/lsdba.nbdc01194-02-000.V002
Protein sequence databases - Protein domain databases; protein classification
Viridiplantae (33090)
Cyanobacteria (1117)

Orthology is a homologous relationship among genes derived from a common ancestor by speciation. Genes in such a relationship are referred to as orthologs or orthologous genes and provide important clues to clarify the process of genome evolution and to predict the divergence of gene function based on syntenic relationships among species. PGDBj Ortholog DB is a database that provides orthologous relationships of genes that are computationally determined according to similarities between amino acid sequences, and currently consists of 40 species of Viridiplantae (green plants) and 213 species of Cyanobacteria (blue-green algae).

PGDBj Ortholog DB is hierarchically organized to reflect evolutionary relationships among species and taxa. By connecting entries of multiple plant genome databases to this database, PGDBj Ortholog DB can work as a hub database and provide a way to gather and organize the relevant data in the databases. By submitting queries to the PGDBj Ortholog DB with keywords or amino acid sequences, users can obtain the list of the links to the relevant entries of the plant genome databases in relation to the functions and characteristics of genes across various species and taxa including both model plants and crop plants. Following the links obtained, users can retrieve the actual entries from the databases.

Kazusa DNA Research Institute

CC BY-SA
Arabidopsis Phenome Database 10.18908/lsdba.nbdc01509-000
Plant databases - Arabidopsis thaliana
Arabidopsis thaliana (3702)

The Arabidopsis thaliana phenome is the whole set of characteristics expressed in response to genomic, environmental and experimental factors of the most major experimental plant. The huge variety of published data have been accumulated, which is an indispensable resource to improve plant omics studies both on basic and applied research fields. It is also important to link information of bioresources such as mutant lines to the phenome to improve experimental research. Inconstancy among them however has inhibited their effective application. We developed the new Arabidopsis Phenome Database integrating two novel databases. One is the “RIKEN Phenome Integration of Arabidopsis Mutants”, that allows researchers to search mutants developed in RIKEN according to their interests in specified phenotypes to find useful materials for their experimental research. The other, the “Database of Curated Plant Phenome” focusing on the Arabidopsis phenome collected by human curation of published papers, is designed to realize easily both phenotype-to-genome and genome-to-phenotype association studies.

CC BY-SA
Database name DOI Database classification Organism Database description Features and manner of utilization of database Database maintenance site License