compounds.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 . "ChEMBLCompound";
$thisSetTitle = "ChEMBL Compound";
$thisSetDescription = "Compound information from ChEMBL.";

$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 . "Dataset" );
echo triple( $masterset, $VOID . "subset" , $thisset );

echo data_triple( $thisset, $DCT . "title", $thisSetTitle ) ;
echo data_triple( $thisset, $DCT . "description", $thisSetDescription ) ;
echo triple( $thisset, $DCT . "license", $ini["license"] ) ;
echo "\n";

$allIDs = mysqli_query($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 literature references
  $refs = mysqli_query($con, "SELECT DISTINCT doc_id FROM compound_records WHERE molregno = $molregno");
  while ($refRow = mysqli_fetch_assoc($refs)) {
    if ($refRow['doc_id']) {
      $docProps = mysqli_query($con, "SELECT DISTINCT chembl_id FROM docs WHERE doc_id = " . $refRow['doc_id']);
      while ($docProp = mysqli_fetch_assoc($docProps)) {
        echo triple( $molecule, $CITO . "citesAsDataSource", $CHEMBL . $docProp['chembl_id']);
      }
    }
  }

  # get the compound type, ChEBI, and ChEMBL identifiers
  $chebi = mysqli_query($con, "SELECT DISTINCT * FROM molecule_dictionary WHERE molregno = $molregno");
  if ($chebiRow = mysqli_fetch_assoc($chebi)) {
    // The BFO SNAP MaterialEntity is the closest thing that all these things adhere too...
    // Let's hope this does not conflict with any of the used ontologies... for ChEBI we're safe, I think
    echo triple( $molecule, $RDFS . "subClassOf", $SNAP . "MaterialEntity");
    if ($chebiRow['molecule_type']) {
      if ($chebiRow['molecule_type'] == "Small molecule") {
        echo triple( $molecule, $RDFS . "subClassOf", $CHEMINF . "CHEMINF_000000"); # chemical entity
      } else if ($chebiRow['molecule_type'] == "Protein") {
        echo triple( $molecule, $RDFS . "subClassOf", $PRO . "PR_000000001" );
      } else if ($chebiRow['molecule_type'] == "Cell") {
        echo triple( $molecule, $RDFS . "subClassOf", $CL . "CL_0000000" );
      } else if ($chebiRow['molecule_type'] == "Oligosaccharide") {
        echo triple( $molecule, $RDFS . "subClassOf", $CHEBI . "CHEBI_50699");
      } else if ($chebiRow['molecule_type'] == "Oligonucleotide") {
        echo triple( $molecule, $RDFS . "subClassOf", $CHEBI . "CHEBI_7754");
      } else if ($chebiRow['molecule_type'] == "Antibody") {
        echo triple( $molecule, $OBO . "has_role", $VO . "VO_0000148" ); // Vaccin Ontology: Antibody
        echo triple( $molecule, $RDFS . "subClassOf", $PRO . "PR_000000001" );
      }
    }
    if ($chebiRow['max_phase'] == "4") {
      echo triple( $molecule, $OBO . "has_role", $CHEBI . "CHEBI_23888" ); // Drug
    }

    echo triple( $molecule, $OWL . "equivalentClass", "http://bio2rdf.org/chebi:" . $chebiRow['chebi_id'] );

    echo data_triple( $molecule, $RDFS . "label", $chebiRow['chembl_id'] );
    $chemblChemInfRes = $molecule . "/chemblid";
    echo triple($molecule, $CHEMINF . "CHEMINF_000200", $chemblChemInfRes);
    echo triple($chemblChemInfRes, $RDF . "type", $CHEMINF . "CHEMINF_000412");
    echo data_triple($chemblChemInfRes, $CHEMINF . "SIO_000300", $chebiRow['chembl_id']);
  }

  # get the structure information
  $structs = mysqli_query($con, "SELECT DISTINCT * FROM compound_structures WHERE molregno = $molregno");
  while ($struct = mysqli_fetch_assoc($structs)) {
    if ($struct['molformula']) {
      $molform = $struct['molformula'];
      $molform = str_replace(" ", "", $molform);
      $molformRes = $molecule . "/molform";
      echo triple($molecule, $CHEMINF . "CHEMINF_000200", $molformRes);
      echo triple($molformRes, $RDF . "type", $CHEMINF . "CHEMINF_000042");
      echo data_triple($molformRes, $CHEMINF . "SIO_000300", $molform);
    }
    if ($struct['canonical_smiles']) {
      $smiles = $struct['canonical_smiles'];
      $smiles = str_replace("\\", "\\\\", $smiles);
      $smiles = str_replace("\n", "", $smiles);
      echo data_triple( $molecule, $CHEM . "smiles", $smiles );
      $molsmiles = $molecule . "/smiles";
      echo triple($molecule, $CHEMINF . "CHEMINF_000200", $molsmiles);
      echo triple($molsmiles, $RDF . "type", $CHEMINF . "CHEMINF_000018");
      echo data_triple($molsmiles, $CHEMINF . "SIO_000300", $smiles);
    }
    if ($struct['standard_inchi']) {
      echo data_triple($molecule, $CHEM . "inchi", $struct['standard_inchi']);
      $molsmiles = $molecule . "/inchi";
      echo triple($molecule, $CHEMINF . "CHEMINF_000200", $molsmiles);
      echo triple($molsmiles, $RDF . "type", $CHEMINF . "CHEMINF_000113");
      echo data_triple($molsmiles, $CHEMINF . "SIO_000300", $struct['standard_inchi']);
      if (strlen($struct['standard_inchi']) < 1500) {
        echo triple($molecule, $OWL . "equivalentClass", "http://rdf.openmolecules.net/?" . $struct['standard_inchi']);
      }
    }
    if ($struct['standard_inchi_key']) {
      echo data_triple( $molecule, $CHEM . "inchikey", $struct['standard_inchi_key'] );
      $molsmiles = $molecule . "/inchikey";
      echo triple($molecule, $CHEMINF . "CHEMINF_000200", $molsmiles);
      echo triple($molsmiles, $RDF . "type", $CHEMINF . "CHEMINF_000059");
      echo data_triple($molsmiles, $CHEMINF . "SIO_000300", $struct['standard_inchi_key']);
    }
  }

  # get parent/child information
  $hierarchies = mysqli_query($con, "SELECT DISTINCT * FROM molecule_hierarchy WHERE molregno = $molregno");
  while ($hierarchy = mysqli_fetch_assoc($hierarchies)) {
    if ($hierarchy['parent_molregno'] != $molregno) {
      $parent = $MOL . "m" . $hierarchy['parent_molregno'];
      echo triple( $molecule, $ONTO . "parentCompound", $parent );
    }
    if ($hierarchy['active_molregno'] != $molregno) {
      $child = $MOL . "m" . $hierarchy['active_molregno'];
      echo triple( $molecule, $ONTO . "activeCompound", $child );
    }
  }

}

?>