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{% 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>
<script>
function toggle(source) {
type = document.getElementsByName('type');
for(var i=0, n=type.length;i<n;i++) {
type[i].checked = source.checked;
}
}
var newdiv = document.createElement('div');
var checkbox = '';
{%for ky in dict_onto.keys()%}
checkbox += '<strong><input type="checkbox" name="type" value="{{ky}}" checked> {{ky}}    </strong>';
{% endfor %}
checkbox += '<strong><input type="checkbox" onClick="toggle(this)"/> (Un)select all'
newdiv.innerHTML = "<inout name='type' id='onto'> "+checkbox + " </input> ";
document.getElementById('check_selection').appendChild(newdiv);
</script>
{%if "name" in session %}
<script>
var newdiv = document.createElement('div');
var i=0
var options = '<option>addiction</option>';
{%for i in range(0,onto_len_dir)%}
options += " <option>{{onto_list[i]}}</option>";
{% endfor %}
newdiv.innerHTML = "<select name='onto' id='onto'> "+options + " </select> ";
document.getElementById('onto_selection').appendChild(newdiv);
</script>
{% endif %}
{% endblock %}
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