PDBj-BMRB Data Server:

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

Graph URIs
  • http://bmrbpub.protein.osaka-u.ac.jp/rdf/bmr (for BMRB entries)
  • http://bmrbpub.protein.osaka-u.ac.jp/rdf/bms (for Metabolomics entries)
  • http://rdf.wwpdb.org/pdb (for PDB 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" http://bmrbpub.protein.osaka-u.ac.jp/search/rdf
% curl -F "query=@QFILE" -F "format=FORMAT" http://bmrbpub.protein.osaka-u.ac.jp/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.
    Category holders
  1. Select all category holders of datablock class of BMRB entry 15400:
  2. Select all category holders of datablock class of Metabolomics entry bmse000400:
  3. Entry statistics
  4. Count entries per submission year and experimental method (subtype):
  5. Assembly descriptions
  6. Select all assembly names, asym IDs, entity IDs, polymer types, formula weights and functions in a assembly:
  7. Entity descriptions
  8. Select all entity names and sequences of polymer entities expressed using one-letter code:
  9. Select all original source information of molecular entities and external links to NCBI Taxonomy:
  10. Select all biological systems to produce molecular entities and external links to NCBI Taxonomy:
  11. Citation information
  12. Select citation information of all entries together with external links to PubMed and DOI, if available:
  13. Count the number of primary publications cited from BMRB entries per year:
  14. Related databases
  15. Select all NMR structures and its PDB IDs together with external RDF resources:
  16. Select all related entries of other biological databases and BLAST alignment information between BMRB entity and related one:
  17. Select all PubChem substance IDs in Metabolomics database together with external RDF resources:
  18. Sample conditions
  19. Select all entries, which fulfill the following sample conditions; no paramagnetic contained, native physical state, chemical shift referencing by internal DSS compound, pH: 4 ~ 10, pressure: 0.5 ~ 10 atm and temperature: 253 ~ 353 K:
  20. Software applied
  21. Select all applied software and its roles:
  22. NMR spectrometers
  23. Select all NMR spectrometers used to collect experimental data:
  24. Assigned chemical shifts
  25. Select all assigned chemical shifts of alpha carbon:
  26. Select all assigned chemical shifts of alpha carbon and beta carbon (optional):
  27. Select all assigned chemical shifts of alpha and beta carbons of reduced CYS residues, which are distinguished by thiol state and data items in bond category:
  28. Select all assigned chemical shifts of alpha and beta carbons of oxidized CYS residues, which are distinguished by thiol state and data items in bond category:
  29. Select all assigned chemical shifts of alpha and beta carbons of oxidized CYS residues by disulfide bonds, which are distinguished by thiol state and data items in bond category:
  30. Select all assigned chemical shifts of alpha carbon with sample conditions; pH value is lower than 5.5:
  31. Select all assigned chemical shifts of backbone atoms; CA, CB, C, N, H and HA, with chemical shift value filters to wipe away anomalous CS values, where CS values of alpha protons, HA2 and HA3, are averaged in a case of GLY residue:
  32. Structural annotations
  33. Select all SCOP annotations:
  34. Select PACSY structural annotations, such as secondary structure, dihedral angles (φ, ψ), hydrophobicity and solvent accessible surface area (SASA), of averaged NMR structure of BMRB entry 4280, residue Ala64 64:
  35. Select all Protein Block annotations about the first model of NMR structures:
  36. Chemical shift validation report
  37. Select all chemical shift offset values estimated by LACS program:
  38. Select all anomalous chemical shifts judged by LACS program:
  39. Completeness of assigned chemical shifts
  40. Select all information about completeness of assigned chemical shifts:
  41. Federated SPARQL queries
  42. Select all RDF resources in UniProt SPARQL endpoint from a RDF link of BMRB entry 15154:
  43. Select all RDF resources in PDB SPARQL endpoint (stored locally) from a RDF link of BMRB entry 15154: