Datasets

Metadata of JCM resources

A RDF-based meta-database of microbial strains used in various researches such as biology, environment and human health as bioresources. Microbial strains are available from Japan Collection of Microorganisms (JCM) in RIKEN BioResource Center. Please visit data browser at http://metadb.riken.jp/metadb/db/rikenbrc_jcm_microbe

Dataset specifications

Tags
Organism Bioresource
Provenance Original
Registration Submitted
Data provider
  • RIKEN
Creator
  • Terue TakatsukiDatabase Center for Life Science
  • Hiroshi MasuyaRIKEN Bioresource research center
  • Moriya OhkumaMicrobe Division, RIKEN Bioresource research center
Issued 2019-06-04
Licenses
  • Attribution 4.0 International (CC BY 4.0)
Version 2019-06-04
Download https://rdfportal.org/download/jcm
SPARQL Endpoint https://rdfportal.org/primary/sparql

Dataset statistics

Triples
1113740
Subjects
259214
Properties
36
Objects
442635
Classes
13

SPARQL example queries

Example 1

Run on Endpoint
#Retrieves JCM microbial strains whose growth temperature is more than 75 degree Celsius

PREFIX mccv: <http://purl.jp/bio/10/mccv#>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX mpo: <http://purl.jp/bio/10/mpo/>
PREFIX obo: <http://purl.obolibrary.org/obo/>

SELECT ?strain ?qualified_species_name ?v
FROM <https://metadb.riken.jp/metadb/db/rikenbrc_jcm_microbe>
where {
?strain a mccv:MCCV_000001 ;
       mccv:MCCV_000012 ?qualified_species_name ;
       mccv:MCCV_000073 ?cc .
    ?cc sio:SIO_000216 ?t .
    ?t a mpo:MPO_00102 ;
       sio:SIO_000300 ?v ;
       sio:SIO_000211 obo:UO_0000027
    FILTER(?v > 75)
} LIMIT 100

Example 2

Run on Endpoint
# Retrieves JCM microbial strains sampled from oral cavity.
#
PREFIX mccv: <http://purl.jp/bio/10/mccv#>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX mpo: <http://purl.jp/bio/10/mpo#>
PREFIX obo: <http://purl.obolibrary.org/obo/>

SELECT ?strain ?name ?sample_label
FROM <http://metadb.riken.jp/db/xsearch_jcm_brso>
where {
?strain mccv:MCCV_000024/a mccv:MCCV_000001 ;
      mccv:MCCV_000012 ?name ;
      mccv:MCCV_000028 ?sample .
    ?sample a sio:SIO_001050 .
    ?sample rdfs:label ?sample_label .
    FILTER(REGEX(?sample_label, "Oral cavity", "i"))
} LIMIT 100

Schema diagram

Schema diagram for jcm
Schema diagram for jcm