Merge branch 'tux02-master'

3 files changed, 44 insertions, 33 deletions

diff --git a/templates/about.html b/templates/about.html
index bdf52f7..3cdefc5 100644
--- a/templates/about.html
+++ b/templates/about.html
@@ -7,25 +7,25 @@
         <h3> About GeneCup </h3>
         <hr>
 
-        <p>GeneCup searches PubMed to find abstracts containing genes of interest and keywords in the custom ontologies. 
-            The title and abstracts corresponding to the PMIDs are then retrieved from a 
-            <a href="https://dataguide.nlm.nih.gov/edirect/archive.html">local archive of the PubMed</a>. 
-            No limit on the date of publication is set. Each abstract is then broken down into sentences, 
-            which are then filtered by gene names and keywords. We also parse the GWAS catalog to obtain 
+        <p>GeneCup searches PubMed to find abstracts containing genes of interest and keywords in the custom ontologies.
+            The title and abstracts corresponding to the PMIDs are then retrieved from a
+            <a href="https://dataguide.nlm.nih.gov/edirect/archive.html">local archive of the PubMed</a>.
+            No limit on the date of publication is set. Each abstract is then broken down into sentences,
+            which are then filtered by gene names and keywords. We also parse the GWAS catalog to obtain
             genetics associations with the keywords of the custom ontology.
 
-        <p>A list of curated <a href="/ontology">addiction-related keywords</a> can be used to search 
-            addiction-related genes. We compiled the most studied 100 addiction related genes 
-            by searching 29,761 human genes against addiction related keywords. 
-            To ensure comprehensive coverage, gene alias obtained from NCBI gene database were included in the search. 
-            The results were extensively curated to remove over 900 alias that matched words 
-            that were not gene name or wrong genes. Some incorrect results remained because the same name 
-            also produced correct results. The resulting 61,000 sentences are archived localy and can be accessed 
-            via the <a href="/allTopGenes">Addiction Genes</a> link.  We also archived  5.3 million PMIDs 
-            associated with these gene for efficient search of query gene to addiction gene relations. 
-            We obtain 23,000 genetics associations with the addiction and psychiatric phenotypes from GWAS catalog. 
+        <p>A list of curated <a href="/ontology">addiction-related keywords</a> can be used to search
+            addiction-related genes. We compiled the most studied 100 addiction related genes
+            by searching 29,761 human genes against addiction related keywords.
+            To ensure comprehensive coverage, gene alias obtained from NCBI gene database were included in the search.
+            The results were extensively curated to remove over 900 alias that matched words
+            that were not gene name or wrong genes. Some incorrect results remained because the same name
+            also produced correct results. The resulting 61,000 sentences are archived localy and can be accessed
+            via the <a href="/allTopGenes">Addiction Genes</a> link.  We also archived  5.3 million PMIDs
+            associated with these gene for efficient search of query gene to addiction gene relations.
+            We obtain 23,000 genetics associations with the addiction and psychiatric phenotypes from GWAS catalog.
             These results are included in the search by default.
-            
+
         <p> We plan to update the local PubMed archive daily and the EBI GWAS catalog quarterly.
 
     </div>
@@ -37,9 +37,7 @@
 
 Cite: Gunturkun MH, Flashner E, Wang T, Mulligan MK, Williams RW, Prins P, Chen H. <a href="https://academic.oup.com/g3journal/article/12/5/jkac059/6548160" target=_new>GeneCup: mining PubMed and GWAS catalog for gene-keyword relationships.</a> G3 (Bethesda). 2022 May 6;12(5):jkac059. doi: 10.1093/g3journal/jkac059. PMID: 35285473; PMCID: PMC9073678.
 
-<p> <a href="https://github.com/chen42/ratspub"> Source code </a>
+<p> <a href="https://git.genenetwork.org/genecup/">Source code </a>
 
 
 {% endblock %}
-
-
diff --git a/templates/index.html b/templates/index.html
index 526820b..d098324 100644
--- a/templates/index.html
+++ b/templates/index.html
@@ -6,24 +6,23 @@
 
 <div class="row">
 	<div class="col-md-9">
-		<p>GeneCup is a tool to efficiently and comprehensively answer the question <b>"What do we know about these genes and the topic I study?".  
+		<p>GeneCup is a tool to answer the question <b>"What do we know about these genes and the topic I study?".  
 		</b> GeneCup answers this question by searching PubMed to find <i>sentences</i> containing gene symbols and a custom list of keywords. 
-		These keywords are organized into a user defined ontology, which groups related keywords together for better organization of the results.  
+		<!-- These keywords are organized into a user defined ontology, which groups related keywords together for better organization of the results. -->
 		Human GWAS findings from <a href="https://www.ebi.ac.uk/gwas/">NHGRI-EBI GWAS catalog </a>are also included in the search.
-		These gene-keyword relationships are presented as an interactive graph and a table. 
+		These gene-keyword relationships are presented as a graph or a table. 
 		<!--Gene alias often include non-specific words and are thus not included in the initial search. 
 			However, a list of alias can be found by clicking on the gene symbol in the results section. 
 			These alias then can be searched with a single click. --> 
-		As an example, we present a curated ontology for drug addiction with over <a href="/ontology"> 300 keywords organized into seven categories.</a> 
-		Furthermore, <b>deep learning </b> is used to distinguish automatically the sentences describing systemic stress from those describing cellular stress. 
-		A user account (free) is needed to create custom ontologies and save the search results.
+		Here we present a curated ontology for drug addiction with over <a href="/ontology"> 300 keywords organized into seven categories.</a> 
+		<b>Deep learning </b> is used to distinguish, for example, the sentences describing systemic stress from those describing cellular stress. 
+		A user account (free) is needed to create custom ontologies and save the search results. We do not track you.
 		</p>
 
 		<p>Example: </b><a href=/progress?type=GWAS&type=addiction&type=drug&type=brain&type=stress&type=psychiatric&type=cell&type=function&query=Rgma+Penk>Rgma Penk</a>.</p>
 		
 		{%if ("name" not in session) %}
 			By default, the <a href="/ontology">addiction</a> ontology is used. Custom ontologies can be created in user accounts. 
-			Please choose keyword categories to be included in the search. 
 
 			<form action="/progress">
 				<div id="check_selection"></div>
diff --git a/templates/layout.html b/templates/layout.html
index 20dbcbe..1c73fd9 100644
--- a/templates/layout.html
+++ b/templates/layout.html
@@ -4,7 +4,7 @@
     <meta charset="utf-8">
     <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
     <meta http-equiv="X-UA-Compatible" content="ie=edge">
-	 
+
     <!-- Bootstrap CSS -->
     <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous">
     <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/js/bootstrap.min.js" integrity="sha384-wfSDF2E50Y2D1uUdj0O3uMBJnjuUD4Ih7YwaYd1iqfktj0Uod8GCExl3Og8ifwB6" crossorigin="anonymous"></script>
@@ -16,11 +16,11 @@
 <body>
 
 <!-- Navigation bar -->
-<nav class="navbar navbar-expand-lg navbar-dark bg-dark">
+<nav class="navbar navbar-expand-lg navbar-dark">
   <div class="col-1">
 		<a href="/"><div class='img'><img src="/static/white_logo.png" class="img-fluid", style="width:60%"></div></a>
 	</div>
-  
+
   <a class="navbar-brand" href="/">GeneCup</a>
   <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation">
     <span class="navbar-toggler-icon"></span>
@@ -90,15 +90,29 @@
     {% endif %}
   {% endwith %}
 </div>
-<br>
-<div class="container">
+<div class="container main">
 	{% block content %}{% endblock %}
 </div>
 
+{% if not no_footer %}
+ <footer class="footer footer-dark">
+        <div class="container">
+            <div class="row">
+                <div class="col-md-6">
+                  GeneCup {{ version }}: PubMed + GWAS catalog deep learning.
+                  Cite <a href="https://academic.oup.com/g3journal/article/12/5/jkac059/6548160">GeneCup.</a>
+                </div>
+                <div class="col-md-6" align="right">
+                  <a href="https://git.genenetwork.org/genecup/">Code</a>
+                  powered by <a href="https://www.tensorflow.org/">Tensorflow</a> on <a href="https://genenetwork.org/">GeneNetwork.org</a>
+                </div>
+            </div>
+        </div>
+ </footer>
+{% endif %}
+
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 </body>
-
-