{% extends "layout.html" %}
{% block content %}
{{ message | safe }}

<h3> Mining PubMed for Gene Relationships using Custom Ontologies </h3>

<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?".  
		</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.  
		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. 
		<!--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.
		</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>
					Up to 200 gene symbols can be entered in the box below. Gene symbols can be separated by a space, a comma or a semicolon. <br>	
				<textarea name="query" class="form-control form-control-lg" type="search" rows="4" e="100%" id="searchform"></textarea>
				<button type="submit" class="btn btn-primary">Search</button>
			</form>

		{% else %}	
			Welcome back, <b> {{session['name']}}</b>. Your <a href="/userarchive"> previous searches </a> 
			and <a href="/ontoarchive"> custom ontologies </a> are available from the links.
			<br>
			Please select an ontology to use for the new search
			<form action="/index_ontology">
				<table><td>
					<div id="onto_selection"></div>
				</td><td>
					<button type="submit" class="btn btn-secondary btn-sm">Select</button>
				</td></table>
			</form>
			<br>
			The <font size="5em" color="tomato"> <strong>{{ontol}}</strong> </font> ontology is selected. Please choose categories to be included in the search. 
			Expect a longer wait time when you include <b>GWAS</b> category.

			<form action="/progress">
				<div id="check_selection"></div>
				Up to 200 gene symbols can be entered in the box below. Gene symbols can be separated by a space, a comma or a semicolon.   <br>	
				<textarea name="query" class="form-control form-control-lg" type="search" rows="4" e="100%" id="searchform"></textarea>
				<button type="submit" class="btn btn-primary">Search</button>
			</form>
		{% endif %}
	</div>

	<div class="col-md-3">
		<div class='img'><img src="/static/cytos.png" class="img-fluid"></div>
	</div>
</div>

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