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<%@ page language="java"%>
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<%@page import="java.util.List"%>
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<%@page import="java.util.ArrayList"%>
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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: leinfelder $'
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* '$Date: 2010-11-08 17:25:11 -0800 (Mon, 08 Nov 2010) $'
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* '$Revision: 5632 $'
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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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//harvest parameters
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String[] entityParam = request.getParameterValues("entity");
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String[] characteristicParam = request.getParameterValues("characteristic");
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String[] standardParam = request.getParameterValues("standard");
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String[] protocolParam = request.getParameterValues("protocol");
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String[] measurementParam = request.getParameterValues("measurement");
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List<OntologyClass> activeEntities = new ArrayList<OntologyClass>();
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List<OntologyClass> activeCharacteristics = new ArrayList<OntologyClass>();
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List<OntologyClass> activeStandards = new ArrayList<OntologyClass>();
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List<OntologyClass> activeProtocols = new ArrayList<OntologyClass>();
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List<OntologyClass> activeMeasurements = new ArrayList<OntologyClass>();
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// Entity
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if (entityParam != null) {
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for (String entityString: entityParam) {
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OntologyClass e = new OntologyClass(entityString);
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activeEntities.add(e);
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}
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}
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// Characteristic
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if (characteristicParam != null) {
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for (String classString: characteristicParam) {
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OntologyClass c = new OntologyClass(classString);
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activeCharacteristics.add(c);
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}
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}
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// Standard
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if (standardParam != null) {
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for (String classString: standardParam) {
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OntologyClass c = new OntologyClass(classString);
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activeStandards.add(c);
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}
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}
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// Protocol
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if (protocolParam != null) {
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for (String classString: protocolParam) {
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OntologyClass c = new OntologyClass(classString);
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activeProtocols.add(c);
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}
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}
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// Measurement
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// TODO: implement measurement expansion
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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(activeCharacteristics, activeStandards);
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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(activeEntities, activeStandards);
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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(activeEntities, activeCharacteristics);
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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 TODO: filtering
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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 TODO: filtering
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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="3">
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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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<!-- measurement -->
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<tr>
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<td colspan="3">
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<table class="subGroup subGroup_border onehundred_percent">
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<tr>
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<th colspan="2">
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Measurement
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</th>
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</tr>
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<tr>
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<td>a template that defines Entity, Characteristic, Standard, and/or Protocol</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: 100%">
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<%=measurementOptions %>
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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#Measurement"/>
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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="60" />
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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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</td>
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</tr>
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</table>
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</td>
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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>with 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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<!-- removing Standard
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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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<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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</table>
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</td>
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-->
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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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Protocol
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</th>
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</tr>
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<tr>
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<td>using procedures outlined by</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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<%=protocolOptions %>
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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#Protocol"/>
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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#Protocol"/>
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</td>
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</tr>
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</table>
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</td>
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345
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</tr>
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<tr>
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<td colspan="3">Match All? <input type="checkbox" name="matchAll" checked="checked"/></td>
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</tr>
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<tr>
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<td colspan="3">From same Observation? <input type="checkbox" name="strict"/></td>
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</tr>
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<tr>
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<td colspan="3"><input type="submit" value="Search"/></td>
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</tr>
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</table>
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<!--
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<tr>
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<td>Entity: (SBC only)</td>
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359
|
<td><input type="text" name="entity" class="bp_form_complete-1523-uri" size="100" /></td>
|
|
360
|
</tr>
|
|
361
|
-->
|
|
362
|
</form>
|
|
363
|
|
|
364
|
<!-- Included default search/login -->
|
|
365
|
<% if ( PropertyService.getProperty("spatial.runSpatialOption").equals("true") ) { %>
|
|
366
|
<script language="javascript">
|
|
367
|
insertMap("<%=CONTEXT_URL%>");
|
|
368
|
</script>
|
|
369
|
<br/>
|
|
370
|
<% } %>
|
|
371
|
|
|
372
|
<script language="javascript">
|
|
373
|
insertSearchBox("<%=CONTEXT_URL%>");
|
|
374
|
insertLoginBox("<%=CONTEXT_URL%>");
|
|
375
|
</script>
|
|
376
|
|
|
377
|
</div>
|
|
378
|
|
|
379
|
<script language="javascript">
|
|
380
|
insertTemplateClosing("<%=CONTEXT_URL%>");
|
|
381
|
</script>
|
|
382
|
|
|
383
|
</body>
|
|
384
|
</html>
|