Datasets

FAMSBASE GPCR

RDFized reference gene expresson dataset derived from CAGE and GeneChip experiments in the RefEx database.

Dataset specifications

Tags
Protein Structure
Provenance Original
Registration Submitted
Data provider
  • Chuo University
Creator
  • Mitsuo IwadateChuo University
  • Shuichi KawahsimaDatabase Center for Life Science
Issued 2016-03-24
Licenses
  • Attribution 4.0 International (CC BY 4.0) Database Center for Life Science
Version 2016-03-24
Download https://rdfportal.org/download/famsbase
SPARQL Endpoint https://rdfportal.org/primary/sparql

Dataset statistics

Triples
21297786
Subjects
5858909
Properties
24
Objects
6378252
Classes
15

SPARQL example queries

Example 1

Run on Endpoint
#Get predicted protein structures by FAMS with GPCR ( pdb: 3OE8 chain A) as template and a threshold (1.0e-100) for
#the e-value of pairwise sequence alignments between the template and targets.

PREFIX edam: <http://edamontology.org/>
PREFIX pdb: <http://identifiers.org/pdb/>
PREFIX famsbaseo: <http://purl.jp/bio/01/famsbase/ontology/>
PREFIX faldo: <http://biohackathon.org/resource/faldo#>

SELECT  ?entry ?model ?evalue ?uniprot
FROM <http://fams.bio.chuo-u.ac.jp/GPCR/rdf/>
WHERE {
  ?entry famsbaseo:hasModel ?model .
  ?model edam:is_output_of ?bk .
  ?bk edam:hasInput ?template .
  ?template a edam:data_1460 .
  ?template rdfs:seeAlso pdb:3OE8 .
  ?template famsbaseo:chain "A" .
  ?bk edam:hasInput ?in_aln .
  ?in_aln a edam:data_0863 .
  ?in_aln famsbaseo:evalue ?ev .
  ?in_aln famsbaseo:identity ?identity .
  BIND(xsd:double(?ev) AS ?evalue)
  FILTER(?evalue < 1.0e-100)
  ?in_aln edam:is_output_of ?bk2 .
  ?bk2 edam:hasInput ?bk3 .
  ?bk3 rdfs:seeAlso ?uniprot .
  ?uniprot a <http://identifiers.org/uniprot/> .
} LIMIT 100

Schema diagram

Schema diagram for famsbase
Schema diagram for famsbase