BMRBj - Examples

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

rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
rdfs: <http://www.w3.org/2000/01/rdf-schema#>
owl: <http://www.w3.org/2002/07/owl#>

Reference Ontorogies

BMRB/OWL: BMRB/RDF ontology
PDB/OWL: PDB/RDF ontology
VRPT/OWL: VRPT/RDF ontology

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.

Category holders

Select all category holders of datablock class of BMRB entry 15400:
Select all category holders of datablock class of Metabolomics entry bmse000400:

Entry statistics

Count entries per submission year and experimental method (subtype):

Assembly descriptions

Select all assembly names, asym IDs, entity IDs, polymer types, formula weights and functions in a assembly:

Entity descriptions

Select all entity names and sequences of polymer entities expressed using one-letter code:
Select all original source information of molecular entities and external links to NCBI Taxonomy:
Select all biological systems to produce molecular entities and external links to NCBI Taxonomy:

Citation information

Select citation information of all entries together with external links to PubMed and DOI, if available:
Count the number of primary publications cited from BMRB entries per year:

Related databases

Select all NMR structures and its PDB IDs together with external RDF resources:
Select all related entries of other biological databases and BLAST alignment information between BMRB entity and related one:
Select all PubChem substance IDs in Metabolomics database together with external RDF resources:

Sample conditions

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:

Software applied

Select all applied software and its roles:

NMR spectrometers

Select all NMR spectrometers used to collect experimental data:

Assigned chemical shifts

Select all assigned chemical shifts of alpha carbon:
Select all assigned chemical shifts of alpha carbon and beta carbon (optional):
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:
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:
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:
Select all assigned chemical shifts of alpha carbon with sample conditions; pH value is lower than 5.5:
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:

Structural annotations

Select all SCOP annotations:
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:
Select all Protein Block annotations about the first model of NMR structures:

Chemical shift validation report

Select all chemical shift offset values estimated by LACS program:
Select all anomalous chemical shifts judged by LACS program:

Completeness of assigned chemical shifts

Select all information about completeness of assigned chemical shifts:

Federated SPARQL queries

Select all RDF resources in UniProt SPARQL endpoint from a RDF link of BMRB entry 15154:
Select all RDF resources in PDB SPARQL endpoint (stored locally) from a RDF link of BMRB entry 15154: