NBDC NikkajiRDF
2016/11/09Web Site: http://doi.org/10.15079/NIKKAJI
FTP Site: ftp://ftp.biosciencedbc.jp/archive/nikkaji/
RDF data of Japan Chemical Substance Dictionary (Nikkaji) described by standard ontologies.
README Content
1. Database Component
- README
- Basic Information
- InChI and InChIKey
- Canonical SMILES
- Links to J-GLOBAL
- Molecular Formula and Molecular Weight
- Links to Other DBs (based on UniChem)
- Links to Other DBs (based on PubChem)
- Core
2. Data Description
2.1 README
| Data name | README |
|---|---|
| Description of data contents | HTML file to describe "NBDC NikkajiRDF" data. |
| File | README_e.html (English) |
2.2 Basic Information
| Data name | Basic Information |
|---|---|
| Description of data contents | This RDF data includes the basic information of 3.4 million or more chemical substances, such as NIkkaji Number, molecular formula, molecular weight, English/Japanese name, and MOLfiles. |
| File | NBDC_NikkajiRDF_main.tar.gz (995 MB) |
2.3 InChI and InChIKey
| Data name | InChI and InChIKey |
|---|---|
| Description of data contents | This RDF data includes InChI and InChIKey of chemical substances registered in Nikkaji by using CHEMINF, SIO and other ontologies. We recommend to use this RDF together with the Core RDF. |
| File | NBDC_NikkajiRDF_InChI.tar.gz (398 MB) |
2.4 Canonical SMILES
| Data name | Canonical SMILES |
|---|---|
| Description of data contents | This RDF data includes Canonical SMILES of chemical substances registered in Nikkaji by using CHEMINF, SIO and other ontologies. We recommend to use this RDF together with the Core RDF. |
| File | NBDC_NikkajiRDF_SMILES.tar.gz (89.0 MB) |
2.5 Links to J-GLOBAL
| Data name | Links to J-GLOBAL |
|---|---|
| Description of data contents | This RDF data includes information of links to other databases, such as J-GLOBAL which contains information of chemical substances, genes, researchers, literature, patents, and other scientific and technologies information (http://jglobal.jst.go.jp/). |
| File | NBDC_NikkajiRDF_link2JGLOBAL.ttl.gz (1.8 MB) |
2.6 Molecular Formula and Molecular Weight
| Data name | Molecular Formula and Molecular Weight |
|---|---|
| Description of data contents | This RDF data includes molecular formula and molecular weight of chemical substances registered in Nikkaji by using CHEMINF, SIO and other ontologies. |
| File | NBDC_NikkajiRDF_MFMW.tar.gz (404 MB) |
2.7 Links to Other DBs (based on UniChem)
| Data name | Links to Other DBs (based on UniChem) |
|---|---|
| Description of data contents | This RDF data includes information of links between Nikkaji substances and chemical substances registered in other databases* by using skos:closeMatch. This is based on a work at https://www.ebi.ac.uk/unichem/ . *: ChEMBL, DrugBank, PDB, Guide to Pharmacology, KEGG, ChEBI, ZINC, Gene Expression Atlas, PharmGKB, Human Metabolome Database (HMDB), PubChem, NMRShiftDB, Aggregated Computational Toxicology Resource (ACToR), BindingDB, and KNApSAcK. |
| File | NBDC_NikkajiRDF_link2OtherDBs_basedOnUniChem.gz (56 MB) |
2.8 Links to Other DBs (based on PubChem)
| Data name | Links to Other DBs (based on PubChem) |
|---|---|
| Description of data contents | This RDF data includes information of links between Nikkaji substances and PubChem substances, compounds and GlyTouCan (https://glytoucan.org/) by using skos:exactMatch and skos:closeMatch. This is a result of BioHackathon 2015 (http://2015.biohackathon.org/hackathon). |
| File | NBDC_NikkajiRDF_link2OtherDBs_basedOnPubChem.gz (104 MB) |
2.9 Core
| Data name | Core |
|---|---|
| Description of data contents | This RDF data includes the core information of chemical substances such as NIkkaji Number, English/Japanese label, Type, Chemical structure diagram, and same object which were extracted extracted from the Basic Information RDF. We recommend to use this RDF together with the 'InChI and InChIKey' or 'Canonical SMILES' RDF. |
| File | NBDC_NikkajiRDF_core.tar.gz (277 MB) |
3. License
You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.
The license for this database is specified in the Creative Commons Attribution 2.1 Japan.
If you use data from this database, please be sure attribute this database as follows: "NBDC NikkajiRDF © Japan Science and Technology Agency licensed under CC Attribution 2.1 Japan".
The summary of the Creative Commons Attribution 2.1 Japan is found here.
With regard to this database, you are licensed to:
- freely access part or whole of this database, and acquire data;
- freely redistribute part or whole of the data from this database; and
- freely create and distribute database and other derivative works based on part or whole of the data from this database,
under the license, as long as you comply with the following conditions:
- You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any derivative work.
- You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.
E-mail: support[at]biosciencedbc[dot]jp
About Providing Links to This Database
You can freely provide links to all contents in this database. But, contents might be changed without notice.
4. Update History
| Date | Update contents |
|---|---|
| 2016/11/09 |
|
| 2016/03/10 |
|
| 2015/10/23 |
|
| 2015/08/31 | NBDC NikkajiRDF English archive site is opened. |
| 2005/03/31 | NikkajiWeb (http://nikkajiweb.jst.go.jp/) is opened. |
5. Literature
Takahiro KIMURA, Tatsuya KUSHIDAOpenness of Nikkaji RDF data and integration of chemical information by Nikkaji acting as a hub. (written in Japanese)
Journal of Information Processing and Management Vol. 58 (2015) No. 3 p. 204-212. (http://doi.org/10.1241/johokanri.58.204)
6. Contact address
When you have any question about "NBDC NikkajiRDF", contact the following:Email: support[at]biosciencedbc[dot]jp