Dataset Details - RDF Portal

PolyInfo BDG_S, ID definition

Website

NIMS polymer database PoLyInfo-Bio Linkage Project, Definition of biodegradation IDs and linking schemas for synthetic polymers.

Dataset specifications

Tags	Drug/Chemical
Provenance	Original
Registration	Submitted
Data provider	National Institute for Materials Science
Creator	Masashi IshiiNational Institute for Materials Science
Issued	2020-02-06
Licenses	Creative Commons BY 4.0 International (CC BY 4.0) link CC BY 4.0 by National Institute for Materials Science (NIMS), Japan
Version	0.2
Download	https://rdfportal.org/download/polyinfo
SPARQL Endpoint	https://rdfportal.org/primary/sparql

Dataset statistics

Triples: 5446

Subjects: 1329

Properties: 14

Objects: 3293

Classes: 14

SPARQL example queries

Example 1

Run on Endpoint

# (1) "poly(prop-1-ene)"を生分解分解する菌種名、および"poly(prop-1-ene)"の化学式＋SMILES

prefix biodg: <http://dice.nims.go.jp/ontology/polymer-bio-ont/Biodeg#>
prefix cu: <http://dice.nims.go.jp/ontology/PoLyInfo-ont/polyinfo-rdf/ConstitutionalUnit#>
prefix dc: <http://purl.org/dc/elements/1.1/>
prefix taxddbj: <http://ddbj.nig.ac.jp/ontologies/taxonomy/>
prefix homo: <http://dice.nims.go.jp/ontology/PoLyInfo-ont/polyinfo-rdf/Homopolymer#>
prefix obo: <http://purl.obolibrary.org/obo/>
prefix pli: <http://dice.nims.go.jp/ontology/PoLyInfo-ont/Schema#>
prefix prism: <http://prismstandard.org/namespaces/basic/2.0/>
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix ref: <http://dice.nims.go.jp/ontology/polymer-bio-ont/Reference/>
prefix sio: <http://semanticscience.org/resource/>
prefix taxonomy: <http://identifiers.org/taxonomy/>
prefix wdt: <http://dice.nims.go.jp/ontology/polymer-bio-ont/Property#>
prefix xsd: <http://www.w3.org/2001/XMLSchema#>

SELECT distinct ?mf_val ?smiles_val ?deg_label ?tax_name
WHERE {
  ?poly rdfs:label "poly(prop-1-ene)"@en ;
    sio:SIO_000008 ?cu .
  ?cu a pli:ConstitutionalUnit ;
    obo:BFO_0000051 ?mf .
  ?mf a pli:MolecularFormula ;
    sio:SIO_000300 ?mf_val .
  ?cu obo:BFO_0000051 ?smiles .
  ?smiles a pli:Smiles ;
    sio:SIO_000300 ?smiles_val .
  ?deg obo:RO_0000057 ?poly;
    rdfs:label ?deg_label ;
    obo:RO_0000057 ?tax .
  SERVICE <https://rdfportal.org/ddbj/sparql>{
    ?tax a taxddbj:Taxon ;
    taxddbj:scientificName ?tax_name .
  }
}

Example 2

Run on Endpoint

# (2)"Pseudomonas putida"が生分解するポリマーの構造基礎名と分子量

prefix biodg: <http://dice.nims.go.jp/ontology/polymer-bio-ont/Biodeg#>
prefix cu: <http://dice.nims.go.jp/ontology/PoLyInfo-ont/polyinfo-rdf/ConstitutionalUnit#>
prefix dc: <http://purl.org/dc/elements/1.1/>
prefix taxddbj: <http://ddbj.nig.ac.jp/ontologies/taxonomy/>
prefix homo: <http://dice.nims.go.jp/ontology/PoLyInfo-ont/polyinfo-rdf/Homopolymer#>
prefix obo: <http://purl.obolibrary.org/obo/>
prefix pli: <http://dice.nims.go.jp/ontology/PoLyInfo-ont/Schema#>
prefix prism: <http://prismstandard.org/namespaces/basic/2.0/>
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix ref: <http://dice.nims.go.jp/ontology/polymer-bio-ont/Reference/>
prefix sio: <http://semanticscience.org/resource/>
prefix taxonomy: <http://identifiers.org/taxonomy/>
prefix wdt: <http://dice.nims.go.jp/ontology/polymer-bio-ont/Property#>
prefix xsd: <http://www.w3.org/2001/XMLSchema#>

SELECT distinct ?tax ?sname ?mw_val
WHERE {
  SERVICE <https://rdfportal.org/ddbj/sparql>{
  ?tax taxddbj:scientificName "Pseudomonas putida" ;
    a taxddbj:Taxon .
  }
  ?deg obo:RO_0000057 ?tax;
    obo:RO_0000057 ?poly .
  ?poly a pli:Homopolymer ;
    sio:SIO_000008 ?name .
  ?name a pli:StructureBasedName ;
    sio:SIO_000300 ?sname .
  ?poly sio:SIO_000008 ?cu .
  ?cu a pli:ConstitutionalUnit ;
    obo:BFO_0000051 ?mw .
  ?mw  a pli:MolecularWeight ;
    sio:SIO_000300 ?mw_val .
}

Example 3

Run on Endpoint

# (3)菌種taxonomy:69781とポリマーhomo:P370120の組み合わせによる生分解に関する参考文献

prefix biodg: <http://dice.nims.go.jp/ontology/polymer-bio-ont/Biodeg#>
prefix cu: <http://dice.nims.go.jp/ontology/PoLyInfo-ont/polyinfo-rdf/ConstitutionalUnit#>
prefix dc: <http://purl.org/dc/elements/1.1/>
prefix taxddbj: <http://ddbj.nig.ac.jp/ontologies/taxonomy/>
prefix homo: <http://dice.nims.go.jp/ontology/PoLyInfo-ont/polyinfo-rdf/Homopolymer#>
prefix obo: <http://purl.obolibrary.org/obo/>
prefix pli: <http://dice.nims.go.jp/ontology/PoLyInfo-ont/Schema#>
prefix prism: <http://prismstandard.org/namespaces/basic/2.0/>
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix ref: <http://dice.nims.go.jp/ontology/polymer-bio-ont/Reference/>
prefix sio: <http://semanticscience.org/resource/>
prefix taxonomy: <http://identifiers.org/taxonomy/>
prefix wdt: <http://dice.nims.go.jp/ontology/polymer-bio-ont/Property#>
prefix xsd: <http://www.w3.org/2001/XMLSchema#>

SELECT distinct ?deg_label ?ref ?doi ?author ?year
WHERE {
  ?deg obo:RO_0000057 taxonomy:69781 ;
    obo:RO_0000057 homo:P370120 ;
    rdfs:label ?deg_label ;
    dcterms:referecens ?ref .
OPTIONAL {
  ?ref prism:doi ?doi .
}
OPTIONAL {
  ?ref  dc:creator ?author ;
  prism:publicationDate ?year .
}
}

Example 4

Run on Endpoint

# (4)ポリマーP00001（Polyehene）の生分解一覧とその参考文献

prefix biodg: <http://dice.nims.go.jp/ontology/polymer-bio-ont/Biodeg#>
prefix cu: <http://dice.nims.go.jp/ontology/PoLyInfo-ont/polyinfo-rdf/ConstitutionalUnit#>
prefix dc: <http://purl.org/dc/elements/1.1/>
prefix taxddbj: <http://ddbj.nig.ac.jp/ontologies/taxonomy/>
prefix homo: <http://dice.nims.go.jp/ontology/PoLyInfo-ont/polyinfo-rdf/Homopolymer#>
prefix obo: <http://purl.obolibrary.org/obo/>
prefix pli: <http://dice.nims.go.jp/ontology/PoLyInfo-ont/Schema#>
prefix prism: <http://prismstandard.org/namespaces/basic/2.0/>
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix ref: <http://dice.nims.go.jp/ontology/polymer-bio-ont/Reference/>
prefix sio: <http://semanticscience.org/resource/>
prefix taxonomy: <http://identifiers.org/taxonomy/>
prefix wdt: <http://dice.nims.go.jp/ontology/polymer-bio-ont/Property#>
prefix xsd: <http://www.w3.org/2001/XMLSchema#>

SELECT distinct ?deg_label ?ref ?doi ?author ?year
WHERE {
  ?deg obo:RO_0000057 homo:P010001 ;
    rdfs:label ?deg_label ;
    dcterms:referecens ?ref .
OPTIONAL {
  ?ref prism:doi ?doi .
}
OPTIONAL {
  ?ref  dcterms:creator ?author ;
  prism:publicationDate ?year .
}
}
order by ?ref

Datasets

PolyInfo BDG_S, ID definition

Dataset specifications

Dataset statistics

SPARQL example queries

Example 1

Example 2

Example 3

Example 4

Schema diagram