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Database name DOI Database classification Organism Database description Features and manner of utilization of database Database maintenance site License
NBDC Nikkaji RDF
(NBDC Japan Chemical Substance Dictionary (Nikkaji) RDF)
10.18908/lsdba.nbdc01530-02-000.V011
Chemical Database

NBDC NikkajiRDF is RDF data of Japan Chemical Substance Dictionary (Nikkaji), which is one of the largest chemical substance databases in Japan.

NikkajiRDF is described by standard ontologies, such as Chemical Information Ontology (CHEMINF) and Semanticscience Integrated Ontology (SIO). The users can perform SPARQL search by uploading the downloaded RDF into their own triplesore.

CC BY
16S RNA sequence set for metagenomic analysis 10.18908/lsdba.nbdc02583-000
RNA sequence databases
RNA data

16S RNA sequence set for metagenomic analysis using kraken2.

Graduate School of Integrated Sciences for Life, Hiroshima University

CC BY
jPOST database 10.18908/lsdba.nbdc01594-02-000
Proteomics Resources

jPOSTdatabase (Japan ProteOme STandard DataBase) is a database containing re-analysis results with unified criteria for proteome data from jPOSTrepository. It provides viewers showing the frequency of detected post-translational modifications, the co-occurrence of phosphorylation sites on a peptide and peptide sharing among proteoforms.

jPOST team

CC0
LigandBox
(LIGANDs Data Base Open and eXtensible)
10.18908/lsdba.nbdc00551-000.V004
Structure Databases - Small molecules

LigandBox(LIGANDs Data Base Open and eXtensible) is a 'ready-to-dock' database of small chemical compounds, for virtual drug screening on computer docking studies. It contains the 3D molecular structures including full hydrogen atoms with atomic charges for each compounds.
LigandBox has been developed by JBIC, as one component of the molecular simulation system myPresto, supported by NEDO.
3D conformations of compounds were generated from 2D structural data, kindly provided by Namiki Shoji Co.,Ltd. Compounds from Namiki Shoji Co.,Ltd can be ordered to each company through each inquiry web page.
Chemical structures in this database were computationally generated, may not be identical to structures of compounds stored in supplying companies.

The molecular files are in Sybyl mol2 file format for virtual drug screening, protein-compound docking, and chemo-informatics.The partial atomic charges of each compound is calculated by MOPAC AM1-BCC and the users can adopt these charges in the molecular dynamics simulations.Each compound has physical properties such as solubility and partition coefficient. These information is useful to avoid promiscuous compounds.The compound IDs are the vender’s ID to purchase the compounds and the inventory ratio is high.

CC BY-SA
ChemTHEATRE 10.18908/lsdba.nbdc01632-000.V002
Monitoring of chemical substances

Existing data on the environmental concentration of chemical substances has been digitized as academic papers or public institution reports. But most of them are stored as text or excel files. They are never easy to use for modeling and risk analysis. The prediction of global chemical contamination is much delayed compared with the climate change research. It is probably due to the fact that monitoring data as an input of the prediction model and verification material is not prepared. It is a great loss that valuable research results obtained by investing a large amount of research expenses are not fully utilized. In order to make effective use of these valuable information in the future, I think that building a highly versatile database is an essential task. For that reason, we would like to create a database on concentration information on chemical substances in the environment and create a platform (ChemTHEATRE) that stores and view monitoring data on all chemical substances. Utilizing this platform makes it possible to ensure traceability of chemical substances, facilitate prediction of behavior and fate in the environment, and to cooperate with external databases on chemical substance emissions and toxicity information, etc. It ensure ecological risk assessments of highly seasoned chemical substances with high precision and transparency. Also, with advanced visualization technology of information, we can expect the return of monitoring research to society, especially contribution to environmental education and open science.

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