Dataset Details - RDF Portal

LigandBox

Website

LigandBox is a database of small chemical compounds for drug screening on computer docking studies. This database contains 3D molecular structures produced by calculation based on 2D structural data of chemicals those are provided by companies and KEGG databases.

Dataset specifications

Tags	Drug/Chemical Structure
Provenance	Original
Registration	Submitted
Data provider	Technology Research Association for Next generation natural products chemistry
Creator	Yoshifumi FukunishiMolecular Profiling Research Center for Drug Discovery (molprof), The National Institute of Advanced Industrial Science and Technology (AIST) Takeshi KawabataInstitute for Protein Research, Osaka University Yusuke SugiharaFujitsu Kyushu Systems, Ltd Kohta SakaiFujitsu Kyushu Systems, Ltd Hiroshi KusudoHitachi Solutions East Japan, Ltd. Yoshiaki MikamiHitachi Solutions East Japan, Ltd. Tadaaki MashimoIMSBIO Co., Ltd Haruki NakamuraInstitute for Protein Research, Osaka University
Issued	2021-05-25
Licenses	Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0) LigandBox © Technology Research Association for Next generation natural products chemistry licensed under CC Attribution-Share Alike 4.0 International
Version	2021-05-25
Download	https://rdfportal.org/download/ligandbox
SPARQL Endpoint	https://rdfportal.org/primary/sparql

Dataset statistics

Triples: 283928849

Subjects: 92822893

Properties: 7

Objects: 120779192

Classes: 20

SPARQL example queries

Example 1

Run on Endpoint

# エントリーとPDBのリンクの一覧の表示
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX PDBc: <https://rdf.wwpdb.org/cc/>
SELECT DISTINCT ?entry ?pdb_link
WHERE {
  ?entry rdfs:seeAlso ?pdb_link FILTER regex(str(?pdb_link), "rdf.wwpdb.org/cc/", "i"). 
}
LIMIT 25

Example 2

Run on Endpoint

# 分子量が1500以上のエントリーの一覧の取得
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX cheminf: <http://www.semanticweb.org/ontologies/cheminf.owl#>
SELECT DISTINCT ?entry ?molecular_weight
WHERE {
  ?entry sio:SIO_000008 _:b0 .
  _:b0 rdf:type sio:CHEMINF_000216 ;
     sio:SIO_000300 ?molecular_weight FILTER ( ?molecular_weight > 1500.0 ) .
}
LIMIT 25

Example 3

Run on Endpoint

# 分子量が500以上でかつチャージが-1のエントリーの一覧の取得
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX cheminf: <http://www.semanticweb.org/ontologies/cheminf.owl#>
SELECT DISTINCT ?entry ?molecular_weight ?molecular_charge
WHERE {
  ?entry sio:SIO_000008 _:b0 .
  _:b0 rdf:type sio:CHEMINF_000216 ;
       sio:SIO_000300 ?molecular_weight .
  ?entry sio:SIO_000008 _:b1 .
  _:b1 rdf:type sio:CHEMINF_000120 ;
       sio:SIO_000300 ?molecular_charge FILTER ( ?molecular_charge = 1 && ?molecular_weight > 500.0 )
}
LIMIT 25