<?php
header('Content-type: application/rdf+xml');
?>
<?php
include 'vars.php';
include 'namespaces.php';
include 'functions.php';
include 'to.php';
# classifications
foreach ($array as $code => $array2) {
$higher = $array2["higher"];
$uri = $array2["uri"];
$desc = $array2["label"];
$example = $array2["classification"];
echo triple($uri, $RDF . "type", $SKOS . "Concept");
echo triple($uri, $RDFS . "subClassOf", $higher);
echo triple($higher, $SKOS . "narrower", $uri);
echo data_triple($uri, $SKOS . "prefLabel", $desc);
echo data_triple($uri, $SKOS . "scopeNote", $code);
echo data_triple($uri, $SKOS . "example", $example);
}
$current_date = gmDate("Y-m-d\\TH:i:s");
echo triple($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'];
$chemblChemInfRes = $assay . "/chemblid";
echo triple($assay, $CHEMINF . "CHEMINF_000200", $chemblChemInfRes);
echo triple($chemblChemInfRes, $RDF . "type", $CHEMINF . "CHEMINF_000412");
echo data_triple($chemblChemInfRes, $CHEMINF . "SIO_000300", $row['chembl_id']);
if ($row['assay_organism']) {
echo data_triple($assay, $ONTO . "organism", $row['assay_organism']);
}
if ($row['assay_tax_id']) {
echo triple($assay, $ONTO . "hasTaxonomy", "http://bio2rdf.org/taxonomy:" . $row['assay_tax_id']);
}
if ($row['description']) {
# clean up description
$description = $row['description'];
$description = str_replace("\\", "\\\\", $description);
$description = str_replace("\"", "\\\"", $description);
echo data_triple($assay, $ONTO . "hasDescription", $description);
}
if ($row['doc_id']) {
$docProps = mysqli_query($con, "SELECT DISTINCT chembl_id FROM docs WHERE doc_id = " . $row['doc_id']);
while ($docProp = mysqli_fetch_assoc($docProps)) {
echo triple($assay, $CITO . "citesAsDataSource", $CHEMBL . $docProp['chembl_id']);
}
}
$props = mysqli_query($con, "SELECT DISTINCT * FROM assay2target WHERE assay_id = " . $row['assay_id']);
while ($prop = mysqli_fetch_assoc($props)) {
if ($prop['tid']) {
$targetURI = $TRG . "t" . $prop['tid'];
if ($prop['confidence_score']) {
$targetScore = $assay . "/score/t" . $prop['tid'];
echo triple($assay, $ONTO . "hasTargetScore", $targetScore);
echo triple($targetScore, $ONTO . "forTarget", $targetURI);
$hier = "";
if ($classRow['l1']) {
$hier = appendTo($hier, $classRow['l1']);
}
if ($classRow['l2']) {
$hier = appendTo($hier, $classRow['l2']);
}
if ($classRow['l3']) {
$hier = appendTo($hier, $classRow['l3']);
}
if ($classRow['l4']) {
$hier = appendTo($hier, $classRow['l4']);
}
if ($classRow['l5']) {
$hier = appendTo($hier, $classRow['l5']);
}
if ($classRow['l6']) {
$hier = appendTo($hier, $classRow['l6']);
}
if ($classRow['l7']) {
$hier = appendTo($hier, $classRow['l7']);
}
if ($classRow['l8']) {
$hier = appendTo($hier, $classRow['l8']);
}
echo triple($target, $ONTO . "targetClass", $array[$hier]["uri"]);
}
if ($row['pref_name']) {
echo data_triple($target, $DC . "title", $row['pref_name']);
}
}
$masterset = $mastervoid . "ChEMBLRDF";
$thisset = $mastervoid . "ChEMBLDocs";
$thisSetTitle = "ChEMBL Documents";
$thisSetDescription = "Document 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", $ini["license"]);
echo "\n";
while ($row = mysqli_fetch_assoc($allIDs)) {
$resource = $CHEMBL . $row['chembl_id'];
echo triple($resource, $RDF . "type", $BIBO . "Article");
if ($row['doi']) {
echo data_triple($resource, $BIBO . "doi", $row['doi']);
}
if ($row['pubmed_id']) {
echo data_triple($resource, $BIBO . "pmid", $row['pubmed_id']);
}
echo data_triple($resource, $DC . "date", $row['year']);
echo data_triple($resource, $BIBO . "volume", $row['volume']);
echo data_triple($resource, $BIBO . "issue", $row['issue']);
echo data_triple($resource, $BIBO . "pageStart", $row['first_page']);
echo data_triple($resource, $BIBO . "pageEnd", $row['last_page']);
echo triple($resource, $DC . "isPartOf", $JRN . "j" . md5($row['journal']));
}
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);
}
}
}
