Datasets

PubCaseFinder RDF

Website

PubCaseFinder (PCF) is a Human Phenotype Ontology (HPO)-based clinical decision support system for rare and genetic diseases, always up-to-date.

Dataset specifications

Tags
Rare Disease Genetic Disease Human Phenotype Ontology Phenotype Disease Search
Provenance Original
Registration Submitted
Data provider
  • Database Center for Life Science
Creator
  • Jaemoon ShinDatabase Center for Life Science
  • Atsuko YamaguchiDatabase Center for Life Science
  • Shuichi KawashimaDatabase Center for Life Science
  • Toyofumi FujiwaraDatabase Center for Life Science
Issued 2021-05-18
Licenses
  • Attribution 4.0 International (CC BY 4.0) Database Center for Life Science
Version 1.3.0
Download https://rdfportal.org/download/pubcasefinder
SPARQL Endpoint https://rdfportal.org/primary/sparql

Dataset statistics

Triples
16367389
Subjects
2128002
Properties
6
Objects
2176841
Classes
7

SPARQL example queries

Example 1

Run on Endpoint 
# 1. Retrieve a list of phenotypes which are associated with a disease with OMIM ID 100050.

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX oa: <http://www.w3.org/ns/oa#>
PREFIX mim: <http://identifiers.org/mim/>
 
SELECT distinct ?hpo FROM <https://pubcasefinder.dbcls.jp/rdf> WHERE{
  ?an rdf:type oa:Annotation ;
      oa:hasTarget mim:100050 ;
      oa:hasBody ?hpo.
}

Example 2

Run on Endpoint 
# 3. Retrieve a list of phenotypes which are associated with a gene with Entrez Gene ID 6710.

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX oa: <http://www.w3.org/ns/oa#>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX ncit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
PREFIX ncbigene: <http://identifiers.org/ncbigene/>
 
SELECT distinct ?hpo FROM <https://pubcasefinder.dbcls.jp/rdf> WHERE{
  ?an oa:hasTarget ?disease ;
      oa:hasBody ?hpo .
  ?as rdf:type sio:SIO_000983 ;
      sio:SIO_000628 ?disease ;
      sio:SIO_000628 ncbigene:6710 .
  ?gene rdf:type ncit:C16612.
}

Example 3

Run on Endpoint 
# 2. Retrieve a list of genes which are associated with a disease with OMIM ID 616645.
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX ncit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
PREFIX mim: <http://identifiers.org/mim/>
 
SELECT distinct ?gene FROM <https://pubcasefinder.dbcls.jp/rdf> WHERE{
  ?as sio:SIO_000628 mim:616645 ;
      sio:SIO_000628 ?gene .
  ?gene rdf:type ncit:C16612 .
}

Example 4

Run on Endpoint 
# 4. Retrieve a list of PMIDs whose papers include a disease with Orphanet ID 822 and a phenotype with HPO ID 0001744.

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX oa: <http://www.w3.org/ns/oa#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX ordo: <http://www.orpha.net/ORDO/>
PREFIX bibo: <http://purl.org/ontology/bibo/>

SELECT distinct ?pubmed  FROM <https://pubcasefinder.dbcls.jp/rdf> WHERE{
  ?an rdf:type oa:Annotation ;
      oa:hasTarget ordo:Orphanet_822 ;
      oa:hasBody obo:HP_0001744 ;
      dcterms:source [      
          dcterms:references ?paper
      ] .
  ?paper rdf:type bibo:Article ;
         rdfs:seeAlso ?pubmed .  
}