<?php
/**
* Author: Zuoshuang Xiang
* The University Of Michigan
* He Group
* Date: 2010-03-04
*
* This is the main program for processing user inputs, form queries,
* process query resuslt and output final results.
*/
header("Content-Type: text/plain");
include 'inc/functions.php';
$vali = new Validation($_REQUEST);
$ontology = $vali->getInput('ontology', 'Ontology', 0, 128);
$ontology2 = $vali->getInput('ontology2', 'Your own ontology', 0, 1024);
$ontology = trim($ontology . "\n" . $ontology2);
$term_iris = $vali->getInput('term_iris', 'Lower level term IRIs to be imported', 0, 81920);
$top_term_iris = $vali->getInput('top_term_iris', 'Top level term IRIs to be imported', 0, 8192);
$top_term_iris2 = $vali->getInput('top_term_iris2', 'Top level term IRIs to be imported', 0, 8192);
$retrieval_setting = $vali->getInput('retrieval_setting', 'Source term retrieval setting', 0, 128);
$annotation_iris = $vali->getInput('annotation_iris', 'annotation IRIs to be included', 0, 8192);
$outputURI = $vali->getInput('output_iri', 'URI of the OWL(RDF/XML) output file', 0, 128);
$str_inputs = "[URI of the OWL(RDF/XML) output file]\r\n{$outputURI}\r\n\r\n[Source ontology]\r\n{$ontology}\r\n\r\n[Low level source term URIs]\r\n{$term_iris}\r\n\r\n[Top level source term URIs and target direct superclass URIs]\r\n{$top_term_iris}\r\n\r\n[Source term retrieval setting]\r\n{$retrieval_setting}\r\n\r\n[Branch extractions from source term URIs and target direct superclass URIs]\r\n{$top_term_iris2}\r\n\r\n[Source annotation URIs]\r\n{$annotation_iris}";
print $str_inputs;
Yongqun “Oliver” He - yongqunh@med.umich.edu
Unit for Laboratory Animal Medicine, Center for Computational Medicine & Bioinformatics
University of Michigan, Ann Arbor, MI 48109, USA
He Group: http://www.hegroup.org
*/
/*
Author: Zuoshuang Xiang
The University Of Michigan
He Group
Date: June 2008 - March 2013
Purpose: Ontobee ontology browsing section ontology terms browsing page.
*/
ini_set('memory_limit', '2048M');
include_once '../inc/Classes.php';
$vali = new Validation($_REQUEST);
$o = $vali->getInput('o', 'Ontology', 1, 60, true);
$l = $vali->getInput('l', 'First Letter', 0, 60, true);
$currPage = $vali->getNumber('currPage', 'Current Page', 0, 5);
?>
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html><!-- InstanceBegin template="/Templates/default.dwt.php" codeOutsideHTMLIsLocked="false" -->
<head>
<!-- InstanceBeginEditable name="doctitle" -->
<title>Ontobee: <?php
echo $o;
?>
</title>
<!-- InstanceEndEditable --><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<link rel="shortcut icon" href="/favicon.ico" />
<link href="../css/styleMain.css" rel="stylesheet" type="text/css">
<!-- InstanceBeginEditable name="head" -->
Date: June 2008 - March 2013
Purpose: Ontobee ontology browsing section rdf query page.
*/
$show_html = false;
if (strpos($_SERVER['HTTP_ACCEPT'], 'application/rdf+xml') === false && strpos($_SERVER['HTTP_ACCEPT'], 'application/xml') === false && strpos($_SERVER['HTTP_ACCEPT'], '*/*') === false) {
$show_html = true;
} elseif (strpos($_SERVER['HTTP_USER_AGENT'], 'bot') || strpos($_SERVER['HTTP_USER_AGENT'], 'spider') || strpos($_SERVER['HTTP_USER_AGENT'], 'crawl') || strpos($_SERVER['HTTP_USER_AGENT'], 'search')) {
$show_html = true;
}
if ($show_html) {
include 'about.php';
} else {
$time_start = microtime(true);
include_once '../inc/Classes.php';
$vali = new Validation($_REQUEST);
$o = $vali->getInput('o', 'Ontology', 1, 60, true);
if ($vali->getErrorMsg() == '') {
$settings = getSettings($o);
$num_queries = 0;
if (!isset($settings['ns_main'])) {
$vali->concatError('Invalid ontology specified.');
}
}
if ($vali->getErrorMsg() == '') {
$iri = $vali->getInput('iri', 'Term IRI', 2, 100, true);
if (substr($iri, 0, 7) != 'http://') {
$iri = 'http://purl.obolibrary.org/obo/' . $iri;
}
if ($vali->getErrorMsg() == '') {
$iri = myUrlDecode($iri);
$outputNSs = array();
$settings = getSettings($o);
if (isset($settings['ontology_fullname'])) {
?>
<h3 align="center"><a href="index.php?o=<?php
echo $o;
?>
"> <?php
print $settings['ontology_fullname'];
?>
</a></h3>
<?php
$time_start = microtime(true);
$num_queries = 0;
$vali = new Validation($_REQUEST);
$keywords = $vali->getInput('keywords', 'Kerwords', 0, 60, true);
if ($vali->getErrorMsg() == '') {
$db = ADONewConnection($driver);
$db->Connect($host, $username, $password, $database);
if ($keywords != '') {
$array_property = array();
$array_property[] = 'http://www.w3.org/2000/01/rdf-schema#label';
$array_property[] = 'http://purl.obolibrary.org/obo/IAO_0000111';
$array_property[] = 'http://purl.obolibrary.org/obo/IAO_0000118';
if (preg_match('/[a-zA-Z]+[:_]\\d{7,}/', $keywords)) {
$search_term_url = 'http://purl.obolibrary.org/obo/' . preg_replace('/:/', '_', $keywords);
$querystring = "SELECT distinct ?s ?o\nfrom <{$settings['ns_main']}>\nWHERE{\n?s ?p ?o .\nfilter (?p in (<" . join('>,<', $array_property) . ">)).\nfilter (?s in (<{$search_term_url}>)).\n}\nORDER BY ?o\nlimit 5000\n";
} else {
$querystring = "SELECT distinct ?s ?o\nfrom <{$settings['ns_main']}>\nWHERE{\n?s ?p ?o .\nfilter (?p in (<" . join('>,<', $array_property) . ">)).\nFILTER (isIRI(?s)).\n?o bif:contains \"'{$keywords}*'\" OPTION (score ?sc)\n}\nORDER BY desc(?sc)\nlimit 5000\n";
}
print "<!--{$querystring}-->";
dojo.byId("btnAddterm"+index).disabled=false;
dojo.byId("btnShowterm"+index).disabled=false;
}
}
</script>
<!-- InstanceEndEditable -->
</head>
<body>
<div id="topbanner"><a href="/index.php"><img src="Images/logo.gif" alt="Logo" width="280" height="50" border="0"></a></div>
<div id="topnav"><a href="index.php" class="topnav">Home</a><a href="introduction.php" class="topnav">Introduction</a><a href="tutorial/index.php" class="topnav">Tutorial</a><a href="faqs.php" class="topnav">FAQs</a><a href="references.php" class="topnav">References</a><a href="links.php" class="topnav">Links</a><a href="contactus.php" class="topnav">Contact</a><a href="acknowledge.php" class="topnav">Acknowledge</a></div>
<div id="mainbody">
<!-- InstanceBeginEditable name="Main" -->
<?php
$vali = new Validation($_REQUEST);
$GALAXY_URL = $vali->getInput('GALAXY_URL', 'GALAXY_URL', 0, 100, true);
if ($GALAXY_URL != '') {
if (isset($_SESSION)) {
$_SESSION['GALAXY_URL'] = $GALAXY_URL;
}
}
$db = ADONewConnection($driver);
$db->Connect($host, $username, $password, $database);
$strSql = "select * from ontology where to_list='y' order by ontology_fullname";
$rs = $db->Execute($strSql);
?>
<form action="getExternal.php" method="post" enctype="multipart/form-data" name="formMain" target="_blank" id="formMain">
<table border="0">
<tr>
<td><p><strong>OntoFox</strong> is a web-based system to support ontology reuse. It allows users to input terms, fetch selected properties, annotations, and certain classes of related terms from source ontologies and save the results using the RDF/XML serialization of the OWL. OntoFox follows and expands the <a href="http://obi-ontology.org/page/MIREOT">MIREOT</a> principle. Inspired by existing ontology modularization techniques, OntoFox also develops a new SPARQL-based ontology term extraction algorithym that extracts terms related to a given set of signature terms. In addition, OntoFox provides an option to extract the hierarchy rooted at a specified ontology term. OntoFox is implemented using one of the following three methods, based on how data is input and whether the OntoFox web interface is used:</p>
<p><span class="header_darkred">1. Data input using web forms:</span>
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
</script>
</head>
<body>
<div id="topbanner"><a href="/index.php" style="font-size:36px; color:#111144; text-decoration:none"><img src="../images/logo.gif" alt="Logo" width="280" height="49" border="0"></a></div>
<div id="topnav"><a href="../index.php" class="topnav">Home</a><a href="../introduction.php" class="topnav">Introduction</a><a href="../ontostat/index.php" class="topnav">Statistics</a><a href="../sparql/index.php" class="topnav">SPARQL</a><a href="../ontobeep/index.php" class="topnav">Ontobeep</a><a href="../tutorial/index.php" class="topnav">Tutorial</a><a href="../faqs.php" class="topnav">FAQs</a><a href="../references.php" class="topnav">References</a><a href="../links.php" class="topnav">Links</a><a href="../contactus.php" class="topnav">Contact</a><a href="../acknowledge.php" class="topnav">Acknowledge</a><a href="../news.php" class="topnav">News</a></div>
<div id="mainbody">
<!-- InstanceBeginEditable name="Main" -->
<?php
include_once '../inc/Classes.php';
$vali = new Validation($_REQUEST);
$keywords = $vali->getInput('keywords', 'Keywords', 1, 60, true);
$ontology = $vali->getInput('ontology', 'Ontology', 0, 60, true);
$jason = array('identifier' => 'url', 'label' => 'name', 'items' => array());
$array_property = array();
$array_property[] = 'http://www.w3.org/2000/01/rdf-schema#label';
$array_property[] = 'http://purl.obolibrary.org/obo/IAO_0000111';
$array_property[] = 'http://purl.obolibrary.org/obo/IAO_0000118';
$db = ADONewConnection($driver);
$db->Connect($host, $username, $password, $database);
$strSql = "select * from ontology where loaded='y' order by ontology_fullname";
$rs = $db->Execute($strSql);
$array_ontology = array();
foreach ($rs as $row) {
$array_ontology[$row['ontology_graph_url']] = $row['ontology_abbrv'];
}
?>
<!-- InstanceBeginEditable name="Main" -->
<p><span class="header_darkred">Retrieving Results</span></p>
<?php
/**
* Author: Zuoshuang Xiang
* The University Of Michigan
* He Group
* Date: 2011-10-28
*
* Provide template based on selected ontology
*/
require_once 'inc/Classes.php';
require_once 'inc/PHPExcel.php';
$vali = new Validation($_REQUEST);
$ontology = $vali->getInput('ontology', 'Ontology', 2, 128);
$a_signature_term_type = array();
$a_signature_term_type[] = 'http://www.w3.org/2002/07/owl#ObjectProperty';
$a_signature_term_type[] = 'http://www.w3.org/2002/07/owl#DatatypeProperty';
$a_signature_term_type[] = 'http://www.w3.org/2002/07/owl#TransitiveProperty';
$a_signature_term_type[] = 'http://www.w3.org/2002/07/owl#SymmetricProperty';
$a_signature_term_type[] = 'http://www.w3.org/2002/07/owl#FunctionalProperty';
$a_signature_term_type[] = 'http://www.w3.org/2002/07/owl#InverseFunctionalProperty';
if ($vali->getErrorMsg() == '') {
$strSql = "select * from ontology where ontology_abbrv='{$ontology}'";
$db = ADONewConnection($driver);
$db->Connect($host, $username, $password, $database);
$rs = $db->Execute($strSql);
if (!$rs->EOF) {
$filename = $ontology;
// print(filemtime("userfiles/$filename.xls") - time());
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
</script>
</head>
<body>
<div id="topbanner"><a href="/index.php" style="font-size:36px; color:#111144; text-decoration:none"><img src="../images/logo.gif" alt="Logo" width="280" height="49" border="0"></a></div>
<div id="topnav"><a href="../index.php" class="topnav">Home</a><a href="../introduction.php" class="topnav">Introduction</a><a href="../ontostat/index.php" class="topnav">Statistics</a><a href="../sparql/index.php" class="topnav">SPARQL</a><a href="../ontobeep/index.php" class="topnav">Ontobeep</a><a href="../tutorial/index.php" class="topnav">Tutorial</a><a href="../faqs.php" class="topnav">FAQs</a><a href="../references.php" class="topnav">References</a><a href="../links.php" class="topnav">Links</a><a href="../contactus.php" class="topnav">Contact</a><a href="../acknowledge.php" class="topnav">Acknowledge</a><a href="../news.php" class="topnav">News</a></div>
<div id="mainbody">
<!-- InstanceBeginEditable name="Main" -->
<?php
$vali = new Validation($_REQUEST);
$c_email = $vali->getEmail('c_email', 'Email Address', true);
$c_subject = $vali->getInput('c_subject', 'Subject', 2, 200);
$c_category = $vali->getInput('c_category', 'Category', 2, 45);
$c_body = $vali->getInput('c_body', 'Message body', 2, 6000);
$c_submit_ip = $_SERVER['REMOTE_ADDR'];
$resp = recaptcha_check_answer(RECAPTCHA_PRIVATEKEY, $_SERVER["REMOTE_ADDR"], $_POST["recaptcha_challenge_field"], $_POST["recaptcha_response_field"]);
if (!$resp->is_valid) {
?>
<p align="center"> Something wrong with your input. Please check the following fields:<br />
<font color="red">The reCAPTCHA wasn't entered correctly.</font> <a href="javascript:history.go(-1);">Go back and try again</a>. </p>
<?php
} elseif (strlen($vali->getErrorMsg()) > 0) {
include '../inc/input_error.php';
} else {
<urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9"
xmlns:image="http://www.google.com/schemas/sitemap-image/1.1"
xmlns:video="http://www.google.com/schemas/sitemap-video/1.1">
<?php
/**
* Author: Zuoshuang Xiang
* The University Of Michigan
* He Group
* Date: 2011-10-28
*
* Provide template based on selected ontology
*/
ini_set('memory_limit', '2048M');
require_once 'inc/Classes.php';
$vali = new Validation($_REQUEST);
$o = $vali->getInput('o', 'Ontology', 2, 60, true);
?>
<url><loc>http://www.ontobee.org/browser/index.php?o=<?php
echo $o;
?>
</loc></url>
<?php
$a_signature_term_type = array();
$a_signature_term_type[] = 'http://www.w3.org/2002/07/owl#Class';
$a_signature_term_type[] = 'http://www.w3.org/2002/07/owl#ObjectProperty';
$a_signature_term_type[] = 'http://www.w3.org/2002/07/owl#DatatypeProperty';
$a_signature_term_type[] = 'http://www.w3.org/2002/07/owl#TransitiveProperty';
$a_signature_term_type[] = 'http://www.w3.org/2002/07/owl#SymmetricProperty';
$a_signature_term_type[] = 'http://www.w3.org/2002/07/owl#FunctionalProperty';
$a_signature_term_type[] = 'http://www.w3.org/2002/07/owl#InverseFunctionalProperty';
<!-- InstanceEndEditable --><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<link rel="shortcut icon" href="/favicon.ico" />
<link href="styleMain.css" rel="stylesheet" type="text/css">
<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->
</head>
<body>
<div id="topbanner"><a href="/index.php"><img src="Images/logo.gif" alt="Logo" width="280" height="50" border="0"></a></div>
<div id="topnav"><a href="index.php" class="topnav">Home</a><a href="introduction.php" class="topnav">Introduction</a><a href="tutorial/index.php" class="topnav">Tutorial</a><a href="faqs.php" class="topnav">FAQs</a><a href="references.php" class="topnav">References</a><a href="links.php" class="topnav">Links</a><a href="contactus.php" class="topnav">Contact</a><a href="acknowledge.php" class="topnav">Acknowledge</a></div>
<div id="mainbody">
<!-- InstanceBeginEditable name="Main" -->
<?php
include 'inc/functions.php';
$vali = new Validation($_REQUEST);
$f = $vali->getInput('f', 'F', 0, 128);
if ($f != '') {
$tokens = preg_split('/,/', $f);
foreach ($tokens as $token) {
if (preg_match('/^[a-z0-9]+$/', $token)) {
system("rm -f userfiles/{$token}.*");
}
}
}
?>
<p>Files have been destroyed!</p>
<!-- InstanceEndEditable -->
</div>
<div id="footer">
Unit for Laboratory Animal Medicine, Center for Computational Medicine & Bioinformatics
University of Michigan, Ann Arbor, MI 48109, USA
He Group: http://www.hegroup.org
-->
<!--
Author: Zuoshuang Xiang
The University Of Michigan
He Group
Date: June 2008 - March 2013
Purpose: Web site page redirection.
-->
<?php
include_once 'inc/Classes.php';
$vali = new Validation($_REQUEST);
$short_id = $vali->getInput('shortid', 'Short ID', 10, 20, true);
if (preg_match('/[a-zA-Z]+_\\d{7,}/', $short_id)) {
header('Location: http://purl.obolibrary.org/obo/' . $short_id);
} else {
?>
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html><!-- InstanceBegin template="/Templates/default.dwt.php" codeOutsideHTMLIsLocked="false" -->
<head>
<!-- InstanceBeginEditable name="doctitle" -->
<title>Ontobee</title>
<!-- InstanceEndEditable --><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<link rel="shortcut icon" href="/favicon.ico" />
<link href="css/styleMain.css" rel="stylesheet" type="text/css">
<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->
<script type="text/javascript">
Unit for Laboratory Animal Medicine, Center for Computational Medicine & Bioinformatics
University of Michigan, Ann Arbor, MI 48109, USA
He Group: http://www.hegroup.org
-->
<!--
Author: Zuoshuang Xiang
The University Of Michigan
He Group
Date: June 2008 - March 2013
Purpose: Ontobee Sparql query index page.
-->
<?php
include_once '../inc/Classes.php';
$vali = new Validation($_REQUEST);
$query = $vali->getInput('query', 'query', 0, 1024 * 8, true);
$format = $vali->getInput('format', 'format', 0, 128, true);
$maxrows = $vali->getInput('maxrows', 'maxrows', 0, 128, true);
$go = $vali->getInput('go', 'go', 0, 128, true);
?>
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html><!-- InstanceBegin template="/Templates/default.dwt.php" codeOutsideHTMLIsLocked="false" -->
<head>
<!-- InstanceBeginEditable name="doctitle" -->
<title>Ontobee SPARQL</title>
<!-- InstanceEndEditable --><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<link rel="shortcut icon" href="/favicon.ico" />
<link href="../css/styleMain.css" rel="stylesheet" type="text/css">
<!-- InstanceBeginEditable name="head" -->
<link rel="stylesheet" href="default.css" type="text/css"/>