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<%@ page language="java"%>
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<%@page import="java.util.List"%>
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<%@page import="org.ecoinformatics.sms.SMS"%>
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<%@page import="org.ecoinformatics.sms.ontology.OntologyClass"%>
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<%
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/**
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*
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* '$RCSfile$'
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* Copyright: 2008 Regents of the University of California and the
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* National Center for Ecological Analysis and Synthesis
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* '$Author$'
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* '$Date$'
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* '$Revision$'
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*
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* This program is free software; you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation; either version 2 of the License, or
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* (at your option) any later version.
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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* You should have received a copy of the GNU General Public License
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* along with this program; if not, write to the Free Software
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* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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*/
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%>
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<%
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// construct the selection fields for existing annotations
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// Entity
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StringBuffer entityOptions = new StringBuffer();
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List<OntologyClass> entities = SMS.getInstance().getAnnotationManager().getActiveEntities();
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for (OntologyClass oc: entities) {
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entityOptions.append("<option ");
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entityOptions.append("title='");
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entityOptions.append(oc.getURI());
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entityOptions.append("' ");
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entityOptions.append("value='");
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entityOptions.append(oc.getURI());
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entityOptions.append("'");
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entityOptions.append(">");
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entityOptions.append(oc.getName());
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entityOptions.append("</option>");
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}
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// Characteristic
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StringBuffer characteristicOptions = new StringBuffer();
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List<OntologyClass> characteristics = SMS.getInstance().getAnnotationManager().getActiveCharacteristics();
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for (OntologyClass oc: characteristics) {
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characteristicOptions.append("<option ");
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characteristicOptions.append("title='");
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characteristicOptions.append(oc.getURI());
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characteristicOptions.append("' ");
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characteristicOptions.append("value='");
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characteristicOptions.append(oc.getURI());
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characteristicOptions.append("'");
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characteristicOptions.append(">");
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characteristicOptions.append(oc.getName());
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characteristicOptions.append("</option>");
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}
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// Standard
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StringBuffer standardOptions = new StringBuffer();
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List<OntologyClass> standards = SMS.getInstance().getAnnotationManager().getActiveStandards();
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for (OntologyClass oc: standards) {
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standardOptions.append("<option ");
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standardOptions.append("title='");
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standardOptions.append(oc.getURI());
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standardOptions.append("' ");
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standardOptions.append("value='");
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standardOptions.append(oc.getURI());
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standardOptions.append("'");
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standardOptions.append(">");
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standardOptions.append(oc.getName());
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standardOptions.append("</option>");
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}
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// Protocol
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StringBuffer protocolOptions = new StringBuffer();
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List<OntologyClass> protocols = SMS.getInstance().getAnnotationManager().getActiveProtocols();
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for (OntologyClass oc: protocols) {
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protocolOptions.append("<option ");
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protocolOptions.append("title='");
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protocolOptions.append(oc.getURI());
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protocolOptions.append("' ");
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protocolOptions.append("value='");
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protocolOptions.append(oc.getURI());
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protocolOptions.append("'");
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protocolOptions.append(">");
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protocolOptions.append(oc.getName());
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protocolOptions.append("</option>");
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}
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// Measurement
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StringBuffer measurementOptions = new StringBuffer();
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List<OntologyClass> measurements = SMS.getInstance().getAnnotationManager().getActiveMeasurements();
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for (OntologyClass oc: measurements) {
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measurementOptions.append("<option ");
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measurementOptions.append("title='");
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measurementOptions.append(oc.getURI());
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measurementOptions.append("' ");
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measurementOptions.append("value='");
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measurementOptions.append(oc.getURI());
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measurementOptions.append("'");
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measurementOptions.append(">");
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measurementOptions.append(oc.getName());
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measurementOptions.append("</option>");
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}
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%>
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<%@ include file="../../common/common-settings.jsp"%>
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<%@ include file="../../common/configure-check.jsp"%>
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<html>
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<head>
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<title>Semantic search</title>
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<link rel="stylesheet" type="text/css" href="<%=STYLE_SKINS_URL%>/semtools/semtools.css">
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<script type="text/javascript"
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src="<%=STYLE_SKINS_URL%>/semtools/search.js"></script>
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<script type="text/javascript">
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// Set defaults for this installation
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//var BP_SEARCH_SERVER = "http://oor-01.cim3.net";
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//var BP_SITE = "Sandbox";
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//var BP_ORG = "OOR";
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</script>
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<script language="Javascript" type="text/JavaScript"
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src="<%=STYLE_SKINS_URL%>/semtools/bioportal/form_complete.js">
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</script>
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<script language="javascript" type="text/javascript" src="<%=STYLE_SKINS_URL%>/semtools/semtools.js"></script>
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<script language="javascript" type="text/javascript" src="<%=STYLE_COMMON_URL%>/branding.js"></script>
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</head>
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<body>
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<script language="javascript">
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insertTemplateOpening("<%=CONTEXT_URL%>");
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</script>
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<div id="content_wrapper">
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<h2>Annotation-based search</h2>
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<form method="POST" action="<%=SERVLET_URL%>" target="_top" id="searchForm" name="searchForm" onSubmit="return checkSearch(this)">
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<input name="query" type="hidden" />
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<input name="qformat" value="semtools" type="hidden" />
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<input name="action" value="semquery" type="hidden" />
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<table class="group group_border">
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<tr>
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<th colspan="5">
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<p>
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Locate <b>data packages</b> that have been semantically annotated within the observation model by
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selecting concepts from
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<br/>
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(a) existing semantic annotations
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<br/>
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(b) registered OBOE extension ontologies
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</p>
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</th>
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</tr>
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<tr>
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<td>
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<table class="subGroup subGroup_border">
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<tr>
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<th colspan="1">
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Entity
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</th>
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</tr>
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<tr>
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<td>Find observations of</td>
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</tr>
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<tr>
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<td>
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(a)
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<select name="dynamicValue" id="dynamicValue" multiple="multiple" size="5" style="width: 216px">
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<%=entityOptions %>
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</select>
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<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Entity"/>
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</td>
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</tr>
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<tr>
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<td colspan="1">
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(b)
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<input type="text" name="dynamicValue" id="dynamicValue" class="bp_form_complete-all-uri" size="30" />
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<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Entity"/>
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</td>
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</tr>
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</table>
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</td>
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<td>
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<table class="subGroup subGroup_border">
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<tr>
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<th colspan="1">
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Characteristic
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</th>
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</tr>
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<tr>
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<td>where measurements of</td>
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</tr>
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<tr>
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<td>
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<select name="dynamicValue" id="dynamicValue" multiple="multiple" size="5" style="width: 216px">
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<%=characteristicOptions %>
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</select>
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<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Characteristic"/>
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</td>
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</tr>
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<tr>
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<td colspan="1">
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<input type="text" name="dynamicValue" id="dynamicValue" class="bp_form_complete-all-uri" size="30" />
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<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Characteristic"/>
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</td>
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</tr>
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</table>
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</td>
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<td>
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<table class="subGroup subGroup_border">
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<tr>
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<th colspan="1">
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Standard
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</th>
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</tr>
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<tr>
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<td>were recorded in units of</td>
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</tr>
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<tr>
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<td>
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<select name="dynamicValue" id="dynamicValue" multiple="multiple" size="5" style="width: 216px">
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<%=standardOptions %>
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</select>
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<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Standard"/>
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</td>
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</tr>
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<tr>
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<td colspan="1">
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<input type="text" name="dynamicValue" id="dynamicValue" class="bp_form_complete-all-uri" size="30" />
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| 236 |
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<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Standard"/>
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| 237 |
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</td>
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| 238 |
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</tr>
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| 239 |
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</table>
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</td>
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<td>
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<table class="subGroup subGroup_border">
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| 243 |
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<tr>
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| 244 |
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<th colspan="1">
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Protocol
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| 246 |
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</th>
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| 247 |
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</tr>
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| 248 |
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<tr>
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| 249 |
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<td>following procedures outlined by</td>
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| 250 |
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</tr>
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| 251 |
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<tr>
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| 252 |
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<td>
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| 253 |
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<select name="dynamicValue" id="dynamicValue" multiple="multiple" size="5" style="width: 216px">
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| 254 |
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<%=protocolOptions %>
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| 255 |
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</select>
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| 256 |
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<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Protocol"/>
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| 257 |
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</td>
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| 258 |
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</tr>
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| 259 |
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<tr>
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| 260 |
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<td colspan="1">
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| 261 |
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<input type="text" name="dynamicValue" id="dynamicValue" class="bp_form_complete-all-uri" size="30" />
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| 262 |
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<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Protocol"/>
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| 263 |
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</td>
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| 264 |
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</tr>
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| 265 |
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</table>
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| 266 |
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</td>
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| 267 |
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<td>
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| 268 |
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<table class="subGroup subGroup_border">
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| 269 |
|
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<tr>
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| 270 |
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<th colspan="2">
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| 271 |
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Measurement
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| 272 |
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</th>
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| 273 |
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</tr>
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| 274 |
|
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<tr>
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| 275 |
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<td>typically defined as</td>
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| 276 |
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</tr>
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| 277 |
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<tr>
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| 278 |
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<td>
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| 279 |
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<select name="dynamicValue" id="dynamicValue" multiple="multiple" size="5" style="width: 216px">
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| 280 |
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<%=measurementOptions %>
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| 281 |
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</select>
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| 282 |
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<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Measurement"/>
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| 283 |
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</td>
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| 284 |
|
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</tr>
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| 285 |
|
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<tr>
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| 286 |
|
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<td colspan="1">
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| 287 |
|
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<input type="text" name="dynamicValue" id="dynamicValue" class="bp_form_complete-all-uri" size="30" />
|
| 288 |
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<input type="hidden" name="dynamicClass" id="dynamicClass" value="http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Measurement"/>
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| 289 |
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</td>
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| 290 |
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</tr>
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| 291 |
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</table>
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| 292 |
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</td>
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| 293 |
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</tr>
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| 294 |
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<tr>
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| 295 |
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<td colspan="5">Match All? <input type="checkbox" name="matchAll" checked="checked"/></td>
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| 296 |
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</tr>
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| 297 |
|
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<tr>
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| 298 |
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<td colspan="5">From same Observation? <input type="checkbox" name="strict"/></td>
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| 299 |
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</tr>
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| 300 |
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<tr>
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| 301 |
5602
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<td colspan="5"><input type="submit" value="Search"/></td>
|
| 302 |
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</tr>
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| 303 |
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</table>
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| 304 |
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<!--
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| 305 |
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<tr>
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| 306 |
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<td>Entity: (SBC only)</td>
|
| 307 |
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<td><input type="text" name="entity" class="bp_form_complete-1523-uri" size="100" /></td>
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| 308 |
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</tr>
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| 309 |
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-->
|
| 310 |
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</form>
|
| 311 |
|
|
|
| 312 |
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<!--
|
| 313 |
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<h2>Ontology search</h2>
|
| 314 |
|
|
<div id="bp_quick_jump"></div>
|
| 315 |
|
|
<script type="text/javascript">
|
| 316 |
|
|
var BP_ontology_id = "all";
|
| 317 |
|
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</script>
|
| 318 |
|
|
<script src="<%=STYLE_SKINS_URL%>/semtools/bioportal/quick_jump.js" type="text/javascript" charset="utf-8">
|
| 319 |
|
|
</script>
|
| 320 |
|
|
|
| 321 |
|
|
<h2>Tree browser</h2>
|
| 322 |
|
|
|
| 323 |
|
|
<object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000"
|
| 324 |
|
|
id="OntologyTree" width="300" height="100%"
|
| 325 |
|
|
codebase="http://fpdownload.macromedia.com/get/flashplayer/current/swflash.cab">
|
| 326 |
|
|
<param name="movie" value="http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf" />
|
| 327 |
|
|
<param name="quality" value="high" />
|
| 328 |
|
|
<param name="bgcolor" value="#ffffff" />
|
| 329 |
|
|
<param name="allowScriptAccess" value="always" />
|
| 330 |
|
|
<param name="flashVars" value="ontology=1523&alerterrors=false&canchangeontology=false&virtual=true" />
|
| 331 |
|
|
<embed src="http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf" quality="high" bgcolor="#ffffff"
|
| 332 |
|
|
width="300" height="100%" name="OntologyTree" align="middle"
|
| 333 |
|
|
play="true"
|
| 334 |
|
|
loop="false"
|
| 335 |
|
|
allowScriptAccess="always"
|
| 336 |
|
|
type="application/x-shockwave-flash"
|
| 337 |
|
|
flashVars="ontology=1523&alerterrors=false&canchangeontology=false&virtual=true"
|
| 338 |
|
|
pluginspage="http://www.adobe.com/go/getflashplayer">
|
| 339 |
|
|
</embed>
|
| 340 |
|
|
</object>
|
| 341 |
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-->
|
| 342 |
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|
|
| 343 |
|
|
<!-- Included default search/login -->
|
| 344 |
|
|
<% if ( PropertyService.getProperty("spatial.runSpatialOption").equals("true") ) { %>
|
| 345 |
|
|
<script language="javascript">
|
| 346 |
|
|
insertMap("<%=CONTEXT_URL%>");
|
| 347 |
|
|
</script>
|
| 348 |
|
|
<br/>
|
| 349 |
|
|
<% } %>
|
| 350 |
|
|
|
| 351 |
|
|
<script language="javascript">
|
| 352 |
|
|
insertSearchBox("<%=CONTEXT_URL%>");
|
| 353 |
|
|
insertLoginBox("<%=CONTEXT_URL%>");
|
| 354 |
|
|
</script>
|
| 355 |
|
|
|
| 356 |
5574
|
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|
</div>
|
| 357 |
|
|
|
| 358 |
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|
<script language="javascript">
|
| 359 |
|
|
insertTemplateClosing("<%=CONTEXT_URL%>");
|
| 360 |
|
|
</script>
|
| 361 |
|
|
|
| 362 |
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|
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|
</body>
|
| 363 |
|
|
</html>
|