57

rq turtle/ttl

• mapping
• PDB

Map a selection of PDB identifiers plus chains to UniProtKB

Use at

• https://sparql.uniprot.org/sparql/

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX up: <http://purl.uniprot.org/core/>

SELECT
  ?pdbId ?chain ?pdbChain ?uniprot
WHERE
{
  # A space separated list of pairs of PDB identifiers and the chain code.
  VALUES(?pdbId ?pdbChain) { ('6VXC' 'A') ('1BG3' 'B') }

  # Make an IRI out of the pdbId
  BIND(iri(concat('http://rdf.wwpdb.org/pdb/', ?pdbId)) AS ?pdb)

  # Map to UniProt entries
  ?uniprot rdfs:seeAlso ?pdb .
  ?pdb up:database <http://purl.uniprot.org/database/PDB> ;
       up:chainSequenceMapping ?chainSm .
  ?chainSm up:chain ?chainsPlusRange .

  # Extract the list of chains from the text representation.
  BIND(STRBEFORE(?chainsPlusRange, '=') AS ?chain)

  # Filter those that match.
  FILTER(CONTAINS(?chain, ?pdbChain))
}

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v8("?chain"):::projected 
  v6("?chainSm")
  v7("?chainsPlusRange")
  v4("?pdb")
  v4("?pdbChain"):::projected 
  v3("?pdbId"):::projected 
  v5("?uniprot"):::projected 
  c3([http://purl.uniprot.org/database/PDB]):::iri 
  f0[["contains(?chain,?pdbChain)"]]
  f0 --> v8
  f0 --> v4
  bind1[/VALUES ?pdbChain ?pdbId/]
  bind1-->v3
  bind1-->v4
  bind10(["6VXC"])
  bind10 --> bind1
  bind11(["A"])
  bind11 --> bind1
  bind12(["1BG3"])
  bind12 --> bind1
  bind13(["B"])
  bind13 --> bind1
  bind2[/"concat('http://rdf.wwpdb.org/pdb/',?pdbId)"/]
  v3 --o bind2
  bind2 --as--o v4
  v5 --"rdfs:seeAlso"-->  v4
  v4 --"up:database"-->  c3
  v4 --"up:chainSequenceMapping"-->  v6
  v6 --"up:chain"-->  v7
  bind3[/"substring-before(?chainsPlusRange,'=')"/]
  v7 --o bind3
  bind3 --as--o v8