PDBj-BMRB Data Server:

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

Graph URIs
  • https://bmrbpub.pdbj.org/rdf/bmr (for BMRB entries)
  • https://bmrbpub.pdbj.org/rdf/bms (for Metabolomics entries)
  • https://rdf.wwpdb.org/pdb (for PDB entries)
  • https://rdf.wwpdb.org/pdb-validation (for wwPDB validation reports)
  • https://rdf.wwpdb.org/sifts (for PDBj-SIFTS)
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, respectivery.

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/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/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)