BMRBj Data Server:

common open representations of BMRB NMR-STAR data in XML, RDF, and JSON formats

Graph URIs
  • http://bmrbpub.pdbj.org/rdf/bmr (for BMRB entries)
  • http://bmrbpub.pdbj.org/rdf/bms (for Metabolomics entries)
  • http://rdf.wwpdb.org/pdb (for PDB entries)
  • http://rdf.wwpdb.org/cc (for chem_comp entries)
  • http://rdf.wwpdb.org/prd (for BIRD_PRD entries)
  • http://rdf.wwpdb.org/fam (for BIRD_FAM entries)
Prefixes Reference Ontorogies How to run SPARQL query via curl command. Please include FROM clause in a query to select Graph URI.
% curl -F "query=QUERY" -F "format=FORMAT" https://bmrbpub.pdbj.org/search/rdf
% curl -F "query=@QFILE" -F "format=FORMAT" https://bmrbpub.pdbj.org/search/rdf
, where QUERY and QFILE stand for actual query strings and query file name, respectively. FORMAT represents MIME type selected from either text/html, application/vnd.ms-excel, application/results-xml, application/results-json, text/plane, application/rdf+xml, text/csv or text/tab-separated-values.
Database names are "bmr" for BMRB and "bms" for Metabolomics, respectively.

The following REST APIs are provided to access BMRB/XML (noatom) and BMRB/RDF archival data, respectively.

BMRB/XML (entry point of REST APIs):

https://bmrbpub.pdbj.org/xml/
BMRB/XML (BMRB):
https://bmrbpub.pdbj.org/xml/bmr/bmr"id"-noatom.xml (e.g. bmr15400)
BMRB/XML (Metabolomics; experimental)
https://bmrbpub.pdbj.org/xml/bms/bmse"id"-noatom.xml (e.g. bmse000400)
BMRB/XML (Metabolomics; theoretical)
https://bmrbpub.pdbj.org/xml/bms/bmst"id"-noatom.xml (e.g. bmst000200)

BMRB/RDF (entry point of REST APIs):

https://bmrbpub.pdbj.org/rdf/
BMRB/RDF (BMRB):
https://bmrbpub.pdbj.org/rdf/bmr"id" (e.g. bmr15400)
BMRB/RDF (Metabolomics; experimental)
https://bmrbpub.pdbj.org/rdf/bmse"id" (e.g. bmse000400)
BMRB/RDF (Metabolomics; theoretical)
https://bmrbpub.pdbj.org/rdf/bmst"id" (e.g. bmst000200)

NBDC RDF Portal is SPARQL endpoints for comprehensive RDF graphs, which contains RDF graphs for BMRB core, PDB core, wwPDB validation reports, and SIFTS datasets, respectively. RDF graph search using SPARQL is possible on the site.