/
bioP_Medline.php
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/
bioP_Medline.php
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<?php
include 'dbstuff.php';
//DB STUFF
// Create connection
$conn = new mysqli($servername, $username, $password, $dbname);
// Check connection
if ($conn->connect_error) {
die("Connection failed: " . $conn->connect_error);
}
// PDO migration
$db_pdo = new PDO('mysql:host=localhost;dbname=drugsafetyportal;charset=utf8mb4', 'root', '');
//DB STUFF - done
//MEDLINE Querying stuff
$proxy_name = '';
$proxy_port = '';
$proxy_username = '';
$proxy_password = '';
$curl_site_url = '';
function query_pmid($pmid, $compact = false)
{
$XML = pubmed_efetch($pmid);
return parse($XML, $compact);
}
// Returns an XML object
function pubmed_efetch($pmid)
{
// Setup the URL for efetch
$params = array(
'db' => 'pubmed',
'retmode' => 'xml',
'retmax' => 25,
'id' => (string) $pmid
);
$efetch = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?';
$q = array();
foreach ($params as $key => $value) { $q[] = $key . '=' . $value; }
$httpquery = implode('&',$q);
$url = $efetch . $httpquery;
$XML = proxy_simplexml_load_file($url);
return $XML;
}
function parse($xml, $compact = false)
{
$data = array();
foreach ($xml->PubmedArticle as $art) {
if ($compact) {
// Compact
$data[] = array(
'pmid' => (string) $art->MedlineCitation->PMID,
'volume' => (string)$art->MedlineCitation->Article->Journal->JournalIssue->Volume,
'issue' => (string)$art->MedlineCitation->Article->Journal->JournalIssue->Issue,
'year' => (string)$art->MedlineCitation->Article->Journal->JournalIssue->PubDate->Year,
'month' => (string)$art->MedlineCitation->Article->Journal->JournalIssue->PubDate->Month,
'journal' => (string) $art->MedlineCitation->Article->Journal->Title,
'journalabbrev' => (string) $art->MedlineCitation->Article->Journal->ISOAbbreviation,
'title' => (string) $art->MedlineCitation->Article->ArticleTitle,
);
} else {
// Full metadata
// Authors array contains concatendated LAST NAME + INITIALS
$authors = array();
if (isset($art->MedlineCitation->Article->AuthorList->Author)) {
try {
foreach ($art->MedlineCitation->Article->AuthorList->Author as $k => $a) {
$authors[] = (string)$a->LastName .' '. (string)$a->Initials;
}
} catch (Exception $e) {
$a = $art->MedlineCitation->Article->AuthorList->Author;
$authors[] = (string)$a->LastName .' '. (string)$a->Initials;
}
}
// Keywords array
$keywords = array();
if (isset($art->MedlineCitation->MeshHeadingList->MeshHeading)) {
foreach ($art->MedlineCitation->MeshHeadingList->MeshHeading as $k => $m) {
$keywords[] = (string)$m->DescriptorName;
if (isset($m->QualifierName)) {
if (is_array($m->QualifierName)) {
$keywords = array_merge($keywords,$m->QualifierName);
} else {
$keywords[] = (string)$m->QualifierName;
}
}
}
}
// Article IDs array
$articleid = array();
if (isset($art->PubmedData->ArticleIdList)) {
foreach ($art->PubmedData->ArticleIdList->ArticleId as $id) {
$articleid[] = $id;
}
}
$data[] = array(
'pmid' => (string) $art->MedlineCitation->PMID,
'volume' => (string)$art->MedlineCitation->Article->Journal->JournalIssue->Volume,
'issue' => (string)$art->MedlineCitation->Article->Journal->JournalIssue->Issue,
'year' => (string)$art->MedlineCitation->Article->Journal->JournalIssue->PubDate->Year,
'month' => (string)$art->MedlineCitation->Article->Journal->JournalIssue->PubDate->Month,
'pages' => (string) $art->MedlineCitation->Article->Pagination->MedlinePgn,
'issn' => (string)$art->MedlineCitation->Article->Journal->ISSN,
'journal' => (string) $art->MedlineCitation->Article->Journal->Title,
'journalabbrev' => (string) $art->MedlineCitation->Article->Journal->ISOAbbreviation,
'title' => (string) $art->MedlineCitation->Article->ArticleTitle,
'abstract' => (string) $art->MedlineCitation->Article->Abstract->AbstractText,
'affiliation' => (string) $art->MedlineCitation->Article->Affiliation,
'authors' => $authors,
'articleid' => implode(',',$articleid),
'keywords' => $keywords
);
}
}
return $data;
}
function proxy_simplexml_load_file($url)
{
$xml_string = '';
ini_set('user_agent', $_SERVER['HTTP_USER_AGENT']);
$xml = load_xml_from_url($url);
#JSTOR hack
if (empty($xml) && strpos($url, 'jstor') !== false) {
$xml = new XMLReader();
$xml->open($url);
}
return $xml;
}
function load_file_from_url($url)
{
$curl = curl_init();
curl_setopt($curl, CURLOPT_URL, $url);
curl_setopt($curl, CURLOPT_RETURNTRANSFER, true);
curl_setopt($curl, CURLOPT_REFERER, $curl_site_url);
$str = curl_exec($curl);
curl_close($curl);
return $str;
}
function load_xml_from_url($url)
{
return simplexml_load_string(load_file_from_url($url));
}
//END OF MEDLINE STUFF
// Query Recording
if ($_SERVER['HTTP_CLIENT_IP']!="") {
$ip = $_SERVER['HTTP_CLIENT_IP'];
} elseif ($_SERVER['HTTP_X_FORWARDED_FOR']!="") {
$ip = $_SERVER['HTTP_X_FORWARDED_FOR'];
}
else {
$ip = $_SERVER['REMOTE_ADDR'];
}
$stmt = $db_pdo->prepare("INSERT INTO query_hist (user,query) VALUES(:usr,:qry)");
$stmt->execute(array(':usr' => $ip, ':qry' => urldecode($_POST['bioMedline'])));
$term = stripslashes(urldecode($_POST['bioMedline']));
$ch = curl_init();
$request_headers = array();
$request_headers[] = 'Authorization: apikey token=cc4e9843-de6c-4234-8ccf-2579c4750bb0';
curl_setopt($ch, CURLOPT_HTTPHEADER, $request_headers);
//$test_query=rawurlencode('ritalin adderall');
$test_query=rawurlencode($term);
$url = 'http://data.bioontology.org/annotator?ontologies=MESH&text='.$test_query;
curl_setopt($ch, CURLOPT_URL, $url);
curl_setopt($ch, CURLOPT_RETURNTRANSFER, true);
$results= curl_exec($ch);
curl_close($ch);
$results_drugs=rawurldecode($results);
//echo $results_drugs;
//Get the identifiers for each drug found in the string
$needle = '"annotatedClass":{"@id"';
$lastPos = 0;
$positions = array();
$mesh_drug_names=array();
$mesh_drug_codes=array();
while (($lastPos = strpos($results_drugs, $needle, $lastPos))!== false) {
$positions[] = $lastPos;
$lastPos = $lastPos + strlen($needle);
}
echo "<html>";
echo "<head>";
echo '
<style type="text/css" media="screen">
body{font-family:"Helvetica Neue",Helvetica,sans-serif;font-size:14px;line-height:19px;}
h1 a{color:#A00;}h1 a:hover{text-decoration:none;}
pre,code{font-family:Monaco,monospace;font-size:12px;}pre{padding:20px;background:#EEE;}
a{color:#00a;text-decoration:none;}a:hover{color:#000;text-decoration:underline;}
table{width:100%;}
th{text-align:left;border-bottom:1px solid #CCC;padding:5px;}
td{vertical-align:top;padding:5px;}
#wrap{width:960px;margin:0 auto;}
input[type=text]{width:300px;font-size:inherit;font-family:inherit;border:1px solid #BBB;padding:5px;}
</style></head>';
echo "<body>";
// Displays 3 and 10
foreach ($positions as $value) {
//echo $value+23+2;
//echo "<h3>".substr($results_drugs, $value+23+2 + 42, 7) . "</h3>"; //49
$mesh_drug_codes[]=substr($results_drugs, $value+23+2 + 42, 7);
$temp=file_get_contents('http://id.nlm.nih.gov/mesh/'.substr($results_drugs, $value+23+2 + 42, 7).'.json');
//Get the
$jsonIterator = new RecursiveIteratorIterator(
new RecursiveArrayIterator(json_decode($temp, TRUE)),
RecursiveIteratorIterator::SELF_FIRST);
foreach ($jsonIterator as $key => $val) {
if(is_array($val)) {
//echo "$key:<br>";
$key_m=$key;
} else {
//echo "$key => $val<br>";
if ($key_m == 'label' && $key=='@value') {
$mesh_drug_names[] = $val;
//echo '<h1>'.$val.'</h1>';
}
}
}
}
//var_dump($mesh_drug_names);
$cnt=0;
foreach ($mesh_drug_codes as $mesh_item) {
echo "Drug name: <a href='http://mesh.bio2rdf.org/describe/?url=http%3A%2F%2Fbio2rdf.org%2Fmesh%3A".$mesh_item."' target='_blank'>".$mesh_drug_names[$cnt]."</a> <br>";
//Interactions found in the DB
$fetch_stuff = mysqli_query($conn, "SELECT count(ddi_id)/2 as countTT FROM ddi WHERE (drug1mesh = '".$mesh_item."' OR drug2mesh = '".$mesh_item."') AND (EHR+FAERS+INDI+MEDLINE+VILAR+TWOSIDES)>0");
//$row_res= mysqli_fetch_row($fetch_stuff);
if($results->num_rows == 0) {
echo '<h3> No interactions found in research datasets </h3>';
} else {
$row_res = mysqli_fetch_row($fetch_stuff);
echo '<h3> Interactions found in research datasets: '.floor($row_res[0]).', <a href="paginate.php?drug='.$mesh_item.'">check here to see them</a></h3>';
$ddi=$ddi+1;
}
//mysql_close($conn);
echo '<div id="medline_results"> ';
//Lets look for the medline results for each drug
$term = $mesh_drug_names[$cnt];
$ADR_query='"adverse effects"[Subheading] AND "chemically induced"[Subheading] AND "Chemicals and Drugs Category"[Mesh]';
//$query_string=urlencode('"Chemicals and Drugs Category/adverse effects"[Mesh] AND "chemically induced"[Subheading] AND "Drug interactions"[Mesh]');
$query_string=$ADR_query. ' AND "'.$term.'"[Mesh]';
//echo '<p>'.$query_string.'</p>';
$result = file_get_contents('http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retmax=5&term='.urlencode($query_string).'&retmode=xml');
$xml = simplexml_load_string($result);
//
$total_hits=$xml->Count;
if ($total_hits == 0) {
echo '<p> No results found for '.$term.'<p>';
} else {
$results = array();
if (isset($xml->IdList->Id) && !empty($xml->IdList->Id)) {
$ids = array();
foreach ($xml->IdList->children() as $id) {
$ids[] = (string)$id;
}
$results = query_pmid(implode(',',$ids), $compact);
}
$tr_results=$xml->Count;
if ($tr_results < 5) {
$recent=$tr_results;
} else {
$recent=5;
}
echo "<p>Search results for <strong>".urldecode($query_string)."</strong> (".$tr_results." results, showing the most recent ".$recent.")</p>";
//echo "<p>Search results for <strong>".urldecode($query_string)."</strong> (".$xml->Count." results, showing the most recent 5)</p>";
echo '<table border="0" cellspacing="0" cellpadding="0">';
echo " <tr>";
echo " <th>PMID</th>";
echo " <th>Title</th>";
echo " <th>Authors</th>";
echo " <th>Journal</th>";
echo " <th>Year</th>";
echo " </tr>";
foreach ($results as $resultMD) {
echo " <tr>";
echo " <td>".$resultMD['pmid']."</td>";
echo ' <td><a href="http://www.ncbi.nlm.nih.gov/pubmed/'.$resultMD['pmid'].'" target="_blank">'.$resultMD['title']."</a></td>";
echo ' <td>'.implode(", ",$resultMD['authors']).'</td>';
echo ' <td>'.$resultMD['journalabbrev'].'</td>';
echo ' <td>'.$resultMD['year'].'</td>';
echo ' </tr>';
}
echo '</table>';
echo '</div>';
}
$cnt++;
echo '<br> <br>';
}
echo "<br>";
//echo "<h1> count: " .count($mesh_drug_codes).'</h1>';
if (count($mesh_drug_codes) > 1) {
// Let's look at the interactions between multiple drugs
echo "<h3> Adverse event literature featuring all drugs (not necesarily a complementary interaction): ";
$drugs_total=0;
$medline_query=$ADR_query.' AND "';
foreach ($mesh_drug_codes as $mesh_item) {
if ($drugs_total >0 ){
echo ", ";
}
if ($drugs_total>=1) {
$medline_query=$medline_query. ' AND "';
}
echo "<a href='http://mesh.bio2rdf.org/describe/?url=http%3A%2F%2Fbio2rdf.org%2Fmesh%3A".$mesh_item."'>".$mesh_drug_names[$drugs_total]."</a>";
$medline_query=$medline_query.$mesh_drug_names[$drugs_total].'"[Mesh]';
$drugs_total=$drugs_total+1;
}
echo "</h3>";
echo '<div id="medline_results"> ';
//Lets look for the medline results for each drug
//$term = $mesh_drug_names[$cnt];
//$ADR_query='"adverse effects"[Subheading] AND "chemically induced"[Subheading] AND "Chemicals and Drugs Category"[Mesh]';
//$query_string=urlencode('"Chemicals and Drugs Category/adverse effects"[Mesh] AND "chemically induced"[Subheading] AND "Drug interactions"[Mesh]');
$query_string=$medline_query;
//echo '<p>'.$query_string.'</p>';
$result = file_get_contents('http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retmax=5&term='.urlencode($query_string).'&retmode=xml');
$xml = simplexml_load_string($result);
//
$total_hits=$xml->Count;
if ($total_hits == 0) {
echo '<p> No results found for '.$medline_query.'<p>';
} else {
$results = array();
if (isset($xml->IdList->Id) && !empty($xml->IdList->Id)) {
$ids = array();
foreach ($xml->IdList->children() as $id) {
$ids[] = (string)$id;
}
$results = query_pmid(implode(',',$ids), $compact);
}
$tr_results=$xml->Count;
if ($tr_results < 5) {
$recent=$tr_results;
} else {
$recent=5;
}
echo "<p>Search results for <strong>".urldecode($query_string)."</strong> (".$tr_results." results, showing the most recent ".$recent.")</p>";
echo '<table border="0" cellspacing="0" cellpadding="0">';
echo " <tr>";
echo " <th>PMID</th>";
echo " <th>Title</th>";
echo " <th>Authors</th>";
echo " <th>Journal</th>";
echo " <th>Year</th>";
echo " </tr>";
foreach ($results as $resultMD) {
echo " <tr>";
echo " <td>".$resultMD['pmid']."</td>";
echo ' <td><a href="http://www.ncbi.nlm.nih.gov/pubmed/'.$resultMD['pmid'].'" target="_blank">'.$resultMD['title']."</a></td>";
echo ' <td>'.implode(", ",$resultMD['authors']).'</td>';
echo ' <td>'.$resultMD['journalabbrev'].'</td>';
echo ' <td>'.$resultMD['year'].'</td>';
echo ' </tr>';
}
echo '</table>';
}
echo '</div>';
}
echo "<br>";
echo "<br>";
echo "</body>";
echo "</html>";
?>