compounds_ls_ebi.php

<?php header('Content-type: text/n3');

include 'namespaces.php';
include 'functions.php';

$ini = parse_ini_file("vars.properties");
$rooturi = $ini["rooturi"];
$importedBy = $ini["importedBy"];
$db = $ini["dbprefix"] . $ini["version"];

$con = mysqli_connect(ini_get("mysqli.default_host"), ini_get("mysqli.default_user"), ini_get("mysqli.default_pw"), $db);
if (mysqli_connect_errno($con)) die(mysqli_connect_errno($con));

# VOID
$mastervoid = $rooturi . "void.ttl#";
$masterset = $mastervoid . "ChEMBLRDF";
$thisset = $mastervoid . "ChEMBLChEBIMapping";
$thisSetTitle = "ChEMBL - ChEBI OWL mappings";
$thisSetDescription = "Mappings between ChEMBL compounds and the ChEBI ontology.";
$sourceSet = $mastervoid . "ChEMBLCompound";
$sourceSpace = $CHEMBL;
$targetSet = $mastervoid . "ChEBI";
$targetSpace = "http://purl.obolibrary.org/obo/";
$linkPredicate = $SKOS . "exactMatch";
$expresses = $CHEMINF . "CHEMINF_000407";

$current_date = gmDate("Y-m-d\TH:i:s");
echo triple( $thisset , $PAV . "createdBy",  $importedBy );
echo typeddata_triple( $thisset, $PAV . "createdOn", $current_date,  $XSD . "dateTime" );
echo triple( $thisset , $PAV . "authoredBy",  $importedBy );
echo typeddata_triple( $thisset, $PAV . "authoredOn", $current_date,  $XSD . "dateTime" );
echo triple( $thisset, $RDF . "type", $VOID . "Linkset" );
echo triple( $masterset, $VOID . "subset" , $thisset );

# echo triple( $molset, $RDF . "type", $VOID . "Dataset" );
echo data_triple( $sourceSet, $VOID . "uriSpace", $sourceSpace );
echo triple( $masterset, $VOID . "subset" , $sourceSet );

# echo triple( $chebiset, $RDF . "type", $VOID . "Dataset" );
echo data_triple( $targetSet, $VOID . "uriSpace", $targetSpace );

echo triple( $masterset, $VOID . "subset" , $thisset );
echo "\n";
echo data_triple( $thisset, $DCT . "title", $thisSetTitle ) ;
echo data_triple( $thisset, $DCT . "description", $thisSetDescription ) ;
echo triple( $thisset, $VOID . "subjectsTarget", $sourceSet) ;
echo triple( $thisset, $VOID . "objectsTarget", $targetSet);
echo triple( $thisset, $VOID . "linkPredicate", $linkPredicate );
echo triple( $thisset, $DCT . "license", $ini["license"] ) ;
echo triple( $thisset, $DUL . "expresses", $expresses);
echo "\n";

# DATA
$allIDs = mysqli_query($con,
  "SELECT DISTINCT molregno, chembl_id FROM molecule_dictionary " . $ini["limit"]
);

while ($row = mysqli_fetch_assoc($allIDs)) {
  $molregno = $row['molregno'];
  $molecule = $CHEMBL . $row['chembl_id'];

  # get the compound type, ChEBI, and ChEMBL identifiers
  $chebi = mysqli_query($con, "SELECT DISTINCT chebi_par_id FROM molecule_dictionary WHERE molregno = $molregno");
  if ($chebiRow = mysqli_fetch_assoc($chebi)) {
    $chebiid = $chebiRow['chebi_par_id'];
    if ($chebiid) {
      echo triple( $molecule, $SKOS . "exactMatch", $chebiSpace . "CHEBI_" . $chebiid );
    }
  }

}

?>