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