From 472e2f6ee34c508312b5f0e7b3ca2d1728de192c Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 6 Oct 2016 14:47:56 +0000
Subject: URLs: update GO database URL and removed opening new browser pages

---
 wqflask/wqflask/templates/index_page.html | 39 +++++++++++++++----------------
 1 file changed, 19 insertions(+), 20 deletions(-)

diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index dc7e058c..47181a4c 100644
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -72,7 +72,7 @@
                                 </div>
 
                                 <!--  USER HELP   -->
-                                <!--<p >Databases marked with <b>**</b>-->
+                                <!--<p>Databases marked with <b>**</b>-->
                                 <!--      suffix are not public yet.<br>-->
                                 <!--     Access requires <a href="/account.html" target=-->
                                 <!--      "_blank" class="fs14">user login</a>.</p>-->
@@ -140,27 +140,26 @@
                         chromosome 1 between 25 and 30 Mb.</li>
 
                         <li><b>MEAN=(15 16) LRS=(23 46)</b> in the <b>Combined</b> field finds
-                        highly expressed genes (15 to 16 log2 units) AND with peak <a href="http://www.genenetwork.org/glossary.html#L" target="_blank">LRS</a>
+                        highly expressed genes (15 to 16 log2 units) AND with peak <a href="http://www.genenetwork.org/glossary.html#L">LRS</a>
                         linkage between 23 and 46.</li>
 
-                        <li><b>RIF=mitochondrial</b> searches RNA databases for <a href="https://en.wikipedia.org/wiki/GeneRIF" target="_blank">
+                        <li><b>RIF=mitochondrial</b> searches RNA databases for <a href="https://en.wikipedia.org/wiki/GeneRIF">
                         GeneRIF</a> links.</li>
 
-                        <li><b>WIKI=nicotine</b> searches <a href="http://www.genenetwork.org/webqtl/main.py?FormID=geneWiki" target="_blank">
+                        <li><b>WIKI=nicotine</b> searches <a href="http://www.genenetwork.org/webqtl/main.py?FormID=geneWiki">
                         GeneWiki</a> for genes that you or other users have annotated
                         with the word <i>nicotine</i>.</li>
 
                         <li><b>GO:0045202</b> searches for synapse-associated genes listed in the
-                        <a href="http://www.godatabase.org/cgi-bin/amigo/go.cgi" target="_blank">
-                            Gene Ontology</a>.</li>
+                        <a href="http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0045202">Gene Ontology</a>.</li>
 
                         <li><b>GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)</b>
-                        finds synapse-associated genes with <a href="http://www.genenetwork.org/glossary.html#E" target="_blank">
+                        finds synapse-associated genes with <a href="http://www.genenetwork.org/glossary.html#E">
                         cis eQTL</a> on Chr 4 from 122 and 155 Mb with LRS scores
                         between 9 and 999.</li>
 
                         <li><b>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</b>
-                        finds diabetes-associated transcripts with peak <a href="http://www.genenetwork.org/glossary.html#E" target="_blank">
+                        finds diabetes-associated transcripts with peak <a href="http://www.genenetwork.org/glossary.html#E">
                         trans eQTLs</a> on Chr 2 between 100 and 105 Mb with LRS
                         scores between 9 and 999.</li>
                       </ul>
@@ -176,7 +175,7 @@
                     <h3>Thirty minute tour</h3>
                     <p>
                       Take the 30 minute
-                      GeneNetwork <a href="http://www.genenetwork.org/tutorial/WebQTLTour/" target="_blank" class="fs14">tour</a> that includes screen shots and
+                      GeneNetwork <a href="http://www.genenetwork.org/tutorial/WebQTLTour/"  class="fs14">tour</a> that includes screen shots and
                       typical steps in the analysis.
                     </p>
 
@@ -187,8 +186,8 @@
                       and Database fields above.
                     </p>
 
-                      <p>The <a href="/conditionsofUse.html" target="_blank">conditions</a>
-                      and <a href="/statusandContact.html" target="_blank">contact
+                      <p>The <a href="/conditionsofUse.html">conditions</a>
+                      and <a href="/statusandContact.html">contact
                       </a> pages have information on the status of data sets
                       and advice on their use and citation.</p>
 
@@ -201,25 +200,25 @@
                     </div>
                     <h3>Websites affiliated with GeneNetwork</h3>
                     <ul>
-                        <li><a href="http://ucscbrowser.genenetwork.org/" target="_blank">Genome
+                        <li><a href="http://ucscbrowser.genenetwork.org/">Genome
                         browser</a> at UTHSC</li>
 
-                        <li><a href="http://galaxy.genenetwork.org/" target="_blank">Galaxy</a> at
+                        <li><a href="http://galaxy.genenetwork.org/">Galaxy</a> at
                         UTHSC</li>
 
-                        <li>GeneNetwork 1 at <a href="http://ec2.genenetwork.org/" target="_blank">Amazon
+                        <li>GeneNetwork 1 at <a href="http://ec2.genenetwork.org/">Amazon
                         Cloud (EC2)</a></li>
 
-                        <li>GeneNetwork 1 Source Code at <a href="http://sourceforge.net/projects/genenetwork/" target="_blank">SourceForge</a></li>
+                        <li>GeneNetwork 1 Source Code at <a href="http://sourceforge.net/projects/genenetwork/">SourceForge</a></li>
 
-                        <li>GeneNetwork 2 Source Code at <a href="https://github.com/genenetwork/genenetwork2" target="_blank">GitHub</a></li>
+                        <li>GeneNetwork 2 Source Code at <a href="https://github.com/genenetwork/genenetwork2">GitHub</a></li>
                     </ul>
                     <h3>GN1 Mirror and development sites</h3>
 
                     <ul>
-                        <li><a href="http://www.genenetwork.org/" target="_blank">Main GN1 site at UTHSC</a> (main site)</li>
-                        <li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank">Germany at the HZI</a></li>
-                        <li><a href="http://genenetwork.memphis.edu/" target="_blank">Memphis at the U of M</a></li>
+                        <li><a href="http://www.genenetwork.org/">Main GN1 site at UTHSC</a> (main site)</li>
+                        <li><a href="http://genenetwork.helmholtz-hzi.de/">Germany at the HZI</a></li>
+                        <li><a href="http://genenetwork.memphis.edu/">Memphis at the U of M</a></li>
                     </ul>
                 </section>
 
@@ -256,7 +255,7 @@
 
                 <h3>User Guide</h3>
                 <h5>Read the
-                <a href="http://www.genenetwork.org/index4.html" target="_blank">
+                <a href="http://www.genenetwork.org/index4.html">
                     user guide</a>.</h5>
 
                 </section>-->
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