Dataset Details - RDF Portal

BMRB/RDF

Website

BMRB/RDF is a translation of NMR-STAR data into RDF

Dataset specifications

Tags	Protein Other biomolecule Others Sequence Structure
Provenance	Original
Registration	Submitted
Data provider	Institute for Protein Research, Osaka University
Creator	Masashi YokochiInstitute for Protein Research, Osaka University Naohiro KobayashiInstitute for Protein Research, Osaka University Akira KinjoInstitute for Protein Research, Osaka University Takeshi IwataInstitute for Protein Research, Osaka University Haruki NakamuraInstitute for Protein Research, Osaka University Chojiro KojimaInstitute for Protein Research, Osaka University Toshimichi FujiwaraInstitute for Protein Research, Osaka University Eldon L. UlrichDepartment of Biochemistry, University of Wisconsin-Madison John L. MarkleyDepartment of Biochemistry, University of Wisconsin-Madison Yannis E. IoannidisDepartment of Informatics & Telecommunications, University of Athens Miron LivnyDepartment of Computer Sciences, University of Wisconsin-Madison
Issued	2023-04-29
Licenses	Creative Commons Attribution 2.1 Japan (CC BY 2.1 JP) link BMRB/RDF licensed under CC Attribution 2.1 Japan.
Version	2023-04-29
Download	https://rdfportal.org/download/bmrb
SPARQL Endpoint	https://rdfportal.org/pdb/sparql

Dataset statistics

Triples: 658230916

Subjects: 36916894

Properties: 2695

Objects: 39110387

Classes: 419

SPARQL example queries

Example 1

Run on Endpoint

# SHOWS SEQUENCES

PREFIX bmrbo: <http://bmrbpub.pdbj.org/schema/mmcif_nmr-star.owl#>

SELECT ?entry_id ?entity_id ?sequence
FROM <http://bmrbpub.protein.osaka-u.ac.jp/rdf/bmr>
WHERE {
  VALUES ?entry_id { "1000" "1001" "1002" "1003" "1004" }
  ?s_up bmrbo:entity.entry_id ?entry_id ;
        bmrbo:entity.id ?entity_id ;
        bmrbo:entity.polymer_seq_one_letter_code ?sequence .
}

Example 2

Run on Endpoint

# SHOWS UNIPROT ID

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX bmrbo: <http://bmrbpub.pdbj.org/schema/mmcif_nmr-star.owl#>

SELECT DISTINCT ?entry_id ?entity_id ?entity_name ?uniprot_id
FROM <http://bmrbpub.protein.osaka-u.ac.jp/rdf/bmr>
WHERE {
  VALUES ?entry_id { "10004" "10006" "10008" "10010" "10011" }

  ?s_up bmrbo:entity_db_link.entry_id ?entry_id ;
        bmrbo:entity_db_link.entity_id ?entity_id ;
        bmrbo:entity_db_link.database_code "SP" ; # uniprot
        bmrbo:entity_db_link.accession_code ?uniprot_id ;
        rdfs:seeAlso ?s_uniprot .

  ?s_en bmrbo:entity.entry_id ?entry_id ;
        bmrbo:entity.id ?entity_id ;
        bmrbo:entity.name ?entity_name .
} ORDER BY ?entry_id

Example 3

Run on Endpoint

# SHOWS ALPHA CARBON CHEMICAL SHIFTS

PREFIX bmrbo: <http://bmrbpub.pdbj.org/schema/mmcif_nmr-star.owl#>

SELECT ?entry_id ?seq_id ?comp_id ?ca_ppm
FROM <http://bmrbpub.protein.osaka-u.ac.jp/rdf/bmr>
WHERE {
  ?s_ca bmrbo:atom_chem_shift.atom_id "CA" ;
        bmrbo:atom_chem_shift.atom_type "C" ;
        bmrbo:atom_chem_shift.entry_id ?entry_id ;
        bmrbo:atom_chem_shift.seq_id ?seq_id ;
        bmrbo:atom_chem_shift.comp_id ?comp_id ;
        bmrbo:atom_chem_shift.val ?ca_ppm .
} ORDER BY ?entry_id
LIMIT 100

Example 4

Run on Endpoint

# SHOWS ALPHA CARBON CHEMICAL SHIFTS IN ACIDIC CONDITIONS

PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX bmrbo: <http://bmrbpub.pdbj.org/schema/mmcif_nmr-star.owl#>

SELECT ?entry_id ?ph ?seq_id ?comp_id ?ca_ppm
FROM <http://bmrbpub.protein.osaka-u.ac.jp/rdf/bmr>
WHERE {
  ?s_ph bmrbo:sample_condition_variable.type "pH" ;
        bmrbo:sample_condition_variable.val ?ph ;
        bmrbo:sample_condition_variable.entry_id ?entry_id ;
        bmrbo:sample_condition_variable.sample_condition_list_id
?sample_condition_list_id .

  FILTER (xsd:float(?ph) > 0.0 && xsd:float(?ph) <= 5.5)

  ?s_csl bmrbo:assigned_chem_shift_list.entry_id ?entry_id ;
         bmrbo:assigned_chem_shift_list.sample_condition_list_id
?sample_condition_list_id ;
         bmrbo:assigned_chem_shift_list.id ?assigned_chem_shift_list_id .

  ?s_ca bmrbo:atom_chem_shift.atom_id "CA" ;
        bmrbo:atom_chem_shift.atom_type "C" ;
        bmrbo:atom_chem_shift.entry_id ?entry_id ;
        bmrbo:atom_chem_shift.seq_id ?seq_id ;
        bmrbo:atom_chem_shift.comp_id ?comp_id ;
        bmrbo:atom_chem_shift.assigned_chem_shift_list_id
?assigned_chem_shift_list_id ;
        bmrbo:atom_chem_shift.val ?ca_ppm .
} ORDER BY ?entry_id ?seq_id
LIMIT 100

Example 5

Run on Endpoint

# SHOWS CHEMICAL SHIFTS

PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX bmrbo: <http://bmrbpub.pdbj.org/schema/mmcif_nmr-star.owl#>

SELECT ?entry_id ?entity_id ?seq_id ?comp_id ?ca_ppm ?cb_ppm ?c_ppm
?n_ppm ?h_ppm ?ha_ppm
FROM <http://bmrbpub.protein.osaka-u.ac.jp/rdf/bmr>
{
  VALUES ?entry_id { "10002" }
  VALUES ?seq_id { "2" "3" "4" "5" }
  ?s_ca  bmrbo:atom_chem_shift.atom_id "CA" ;
         bmrbo:atom_chem_shift.atom_type "C" ;
         bmrbo:atom_chem_shift.entry_id ?entry_id ;    # fill entry_id.
         bmrbo:atom_chem_shift.entity_id ?entity_id ;  # fill entity_id.
         bmrbo:atom_chem_shift.comp_index_id ?seq_id ; # fill seq_id.
         bmrbo:atom_chem_shift.comp_id ?comp_id ;
         bmrbo:atom_chem_shift.val ?ca_ppm ;
         bmrbo:atom_chem_shift.assigned_chem_shift_list_id
?assigned_chem_shift_list_id .
  FILTER (xsd:float(?ca_ppm) > 35.0 && xsd:float(?ca_ppm) < 85.0)
  OPTIONAL {
    ?s_cb bmrbo:atom_chem_shift.atom_id "CB" ;
          bmrbo:atom_chem_shift.atom_type "C" ;
          bmrbo:atom_chem_shift.entry_id ?entry_id ;    # fill entry_id.
          bmrbo:atom_chem_shift.entity_id ?entity_id ;  # fill entity_id.
          bmrbo:atom_chem_shift.comp_index_id ?seq_id ; # fill seq_id.
          bmrbo:atom_chem_shift.val ?cb_ppm ;
          bmrbo:atom_chem_shift.assigned_chem_shift_list_id
?assigned_chem_shift_list_id .
    FILTER (xsd:float(?cb_ppm) > 5.0 && xsd:float(?cb_ppm) < 85.0)
  }
  OPTIONAL {
    ?s_c  bmrbo:atom_chem_shift.atom_id "C" ;
          bmrbo:atom_chem_shift.atom_type "C" ;
          bmrbo:atom_chem_shift.entry_id ?entry_id ;    # fill entry_id.
          bmrbo:atom_chem_shift.entity_id ?entity_id ;  # fill entity_id.
          bmrbo:atom_chem_shift.comp_index_id ?seq_id ; # fill seq_id.
          bmrbo:atom_chem_shift.val ?c_ppm ;
          bmrbo:atom_chem_shift.assigned_chem_shift_list_id
?assigned_chem_shift_list_id .
    FILTER (xsd:float(?c_ppm) > 150.0 && xsd:float(?c_ppm) < 200.0)
  }
  OPTIONAL {
    ?s_n  bmrbo:atom_chem_shift.atom_id "N" ;
          bmrbo:atom_chem_shift.atom_type "N" ;
          bmrbo:atom_chem_shift.entry_id ?entry_id ;    # fill entry_id.
          bmrbo:atom_chem_shift.entity_id ?entity_id ;  # fill entity_id.
          bmrbo:atom_chem_shift.comp_index_id ?seq_id ; # fill seq_id.
          bmrbo:atom_chem_shift.val ?n_ppm ;
          bmrbo:atom_chem_shift.assigned_chem_shift_list_id
?assigned_chem_shift_list_id .
    FILTER (xsd:float(?n_ppm) > 90.0 && xsd:float(?n_ppm) < 150.0)
  }
  OPTIONAL {
    ?s_h  bmrbo:atom_chem_shift.atom_id "H" ;
          bmrbo:atom_chem_shift.atom_type "H" ;
          bmrbo:atom_chem_shift.entry_id ?entry_id ;    # fill entry_id.
          bmrbo:atom_chem_shift.entity_id ?entity_id ;  # fill entity_id.
          bmrbo:atom_chem_shift.comp_index_id ?seq_id ; # fill seq_id.
          bmrbo:atom_chem_shift.val ?h_ppm ;
          bmrbo:atom_chem_shift.assigned_chem_shift_list_id
?assigned_chem_shift_list_id .
    FILTER (xsd:float(?h_ppm) > 2.0 && xsd:float(?h_ppm) < 13.0)
  }
  OPTIONAL {
    ?s_ha bmrbo:atom_chem_shift.atom_id "HA" ;
          bmrbo:atom_chem_shift.atom_type "H" ;
          bmrbo:atom_chem_shift.entry_id ?entry_id ;    # fill entry_id.
          bmrbo:atom_chem_shift.entity_id ?entity_id ;  # fill entity_id.
          bmrbo:atom_chem_shift.comp_index_id ?seq_id ; # fill seq_id.
          bmrbo:atom_chem_shift.val ?_ha_ppm ;
          bmrbo:atom_chem_shift.assigned_chem_shift_list_id
?assigned_chem_shift_list_id .
    FILTER (xsd:float(?_ha_ppm) > 0.0 && xsd:float(?_ha_ppm) < 7.0)
  }
  OPTIONAL {
    ?s_ha2 bmrbo:atom_chem_shift.atom_id "HA2" ;
          bmrbo:atom_chem_shift.atom_type "H" ;
          bmrbo:atom_chem_shift.entry_id ?entry_id ;    # fill entry_id.
          bmrbo:atom_chem_shift.entity_id ?entity_id ;  # fill entity_id.
          bmrbo:atom_chem_shift.comp_index_id ?seq_id ; # fill seq_id.
          bmrbo:atom_chem_shift.val ?ha2_ppm ;
          bmrbo:atom_chem_shift.assigned_chem_shift_list_id
?assigned_chem_shift_list_id .
    ?s_ha3 bmrbo:atom_chem_shift.atom_id "HA3" ;
          bmrbo:atom_chem_shift.atom_type "H" ;
          bmrbo:atom_chem_shift.entry_id ?entry_id ;    # fill entry_id.
          bmrbo:atom_chem_shift.entity_id ?entity_id ;  # fill entity_id.
          bmrbo:atom_chem_shift.comp_index_id ?seq_id ; # fill seq_id.
          bmrbo:atom_chem_shift.val ?ha3_ppm ;
          bmrbo:atom_chem_shift.assigned_chem_shift_list_id
?assigned_chem_shift_list_id .
    BIND (STR(round((xsd:float(?ha2_ppm) + xsd:float(?ha3_ppm)) / 2.0
* 1000) / 1000) AS ?gly_ha_ppm)
    FILTER (xsd:float(?gly_ha_ppm) > 0.0 && xsd:float(?gly_ha_ppm) < 7.0)
  }
  BIND (COALESCE(?gly_ha_ppm,?_ha_ppm) AS ?ha_ppm)
} ORDER BY ?entity_id ?seq_id LIMIT 10