NBDC NikkajiRDF

2023/06/30

Web Site: http://doi.org/10.18908/lsdba.nbdc01530-02-000

RDF data of Japan Chemical Substance Dictionary (Nikkaji) described by standard ontologies.

README Content

  1. Database Component
  2. Data Description
  3. License
  4. Update History
  5. Literature
  6. Contact address

1. Database Component

  1. README
  2. Basic Information
  3. InChI and InChIKey
  4. Canonical SMILES
  5. Links to J-GLOBAL
  6. Molecular Formula and Molecular Weight
  7. Links to Other DBs (based on UniChem)
  8. Links to Other DBs (based on PubChem)
  9. Core
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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)
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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, and English/Japanese name.
File NBDC_NikkajiRDF_main.tar.gz (1.1 GB)
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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 (523 MB)
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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 (153 MB)
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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)
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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 (519 MB)
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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.tar.gz (69 MB)
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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.tar.gz (49 MB)
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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 (308 MB)
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3. License

Last updated : 2023/06/29

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.

 

Creative Commons License

The license for this database is specified in the Creative Commons Attribution 4.0 International.
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 4.0 International".

The summary of the Creative Commons Attribution 4.0 International is found here.

With regard to this database, you are licensed to:

  1. freely access part or whole of this database, and acquire data;
  2. freely redistribute part or whole of the data from this database; and
  3. freely create and distribute database and other adapted materials based on part or whole of the data from this database,

under the license, as long as you comply with the following conditions:

  1. You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any adapted material.
  2. 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.

https://form2.jst.go.jp/s/contact_nbdc

About Providing Links to This Database

You can freely provide links to all contents in this database. But, contents might be changed without notice.

 

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4. Update History

DateUpdate contents
2022/10/04 "Features and manner of utilization of database" in "Database Description" is updated.
2022/02/01 Archive version V9 Released.
  • "Core" data are updated.
2021/11/09 Archive version V9 Released.
2019/05/15 "URL of the original website" in "Database Description" is updated.
2018/05/18 Archive version V8 Released.
2017/02/17 Archive version V7 Released.
2017/01/12 Archive version V6 Released.
2016/11/09 Archive version V5 Released.
2016/03/10 Archive version V4 Released.
2015/10/23 Archive version V3 Released.
2015/08/31 NBDC NikkajiRDF English archive site is opened.
2015/08/06 Archive version V2 Released.
2015/05/29 NBDC NikkajiRDF archive site is opened.
(Archive version V1)
2005/03/31 NikkajiWeb (http://nikkajiweb.jst.go.jp/) is opened.
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5. Literature

Takahiro KIMURA, Tatsuya KUSHIDA
Openness 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)

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6. Contact address

When you have any question about "NBDC NikkajiRDF", contact the following:

https://form2.jst.go.jp/s/contact_nbdc

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