diff options
| -rwxr-xr-x | ratspub.py | 6 | ||||
| -rwxr-xr-x | server.py | 12 | ||||
| -rw-r--r-- | templates/cytoscape.html | 3 | ||||
| -rw-r--r-- | templates/index.html | 20 | ||||
| -rw-r--r-- | templates/layout.html | 6 |
5 files changed, 29 insertions, 18 deletions
diff --git a/ratspub.py b/ratspub.py index cc52591..345146e 100755 --- a/ratspub.py +++ b/ratspub.py @@ -2,10 +2,6 @@ from nltk.tokenize import sent_tokenize import os import re -import codecs -import sys - -#gene=sys.argv[1] ## turn dictionary (synonyms) to regular expression def undic(dic): @@ -94,8 +90,6 @@ def generate_edges(data): json0+="{ data: { id: \'" + edgeID + "\', source: \'" + source + "\', target: '" + target + "\', sentCnt: '" + str(edgeCnts[edgeID]) + "', url:'/sentences?edgeID=" + edgeID + "' } },\n" return(json0) - - addiction_d = {"reward":"reward|hedonic|incentive|intracranial self stimulation|ICSS|reinforcement|conditioned place preference|CPP|self administration|self administered|drug reinforced|operant|instrumental response", "aversion":"aversion|aversive|CTA|withdrawal|conditioned taste aversion", "relapse":"relapse|reinstatement|craving|drug seeking|seeking", diff --git a/server.py b/server.py index c9009d0..0f3d94b 100755 --- a/server.py +++ b/server.py @@ -1,6 +1,5 @@ #!/bin/env python3 from flask import Flask, render_template, request, redirect -import simplejson as json from ratspub import * app=Flask(__name__) @@ -18,6 +17,8 @@ def search(): genes=genes.replace(",", " ") genes=genes.replace(";", " ") genes=genes.split() + if len(genes)>=6: + return render_template('index.html') nodes=default_nodes edges=str() for gene in genes: @@ -30,9 +31,9 @@ def search(): e2=generate_edges(sent2) edges+=e0+e1+e2 all_sentences+=sent0+sent1+sent2 - f=open("all_sentences.tab","w") - f.write(all_sentences) - f.close() + #f=open("all_sentences.tab","w") + #f.write(all_sentences) + #f.close() return render_template('cytoscape.html', elements=nodes+edges) @app.route("/sentences") @@ -42,12 +43,11 @@ def sentences(): print (gene0 + cat0) out="<h3>"+gene0 + " and " + cat0 + "</h3>\n" for sent in all_sentences.split("\n"): - #print (sent) if len(sent.strip())!=0: (gene,nouse,cat, pmid, text)=sent.split("\t") if (gene == gene0 and cat == cat0) : out+= "<li> "+ text + " <a href=\"https://www.ncbi.nlm.nih.gov/pubmed/?term=" + pmid +"\" target=_new>PMID:"+pmid+"<br></a>" - return render_template('sentences.html', sentences=out+"<p>") + return render_template('sentences.html', sentences="<ol>"+out+"</ol><p>") if __name__ == '__main__': app.run(debug=True) diff --git a/templates/cytoscape.html b/templates/cytoscape.html index 749b042..fd2000e 100644 --- a/templates/cytoscape.html +++ b/templates/cytoscape.html @@ -1,7 +1,8 @@ {% extends "layout.html" %} {% block content %} -<script type="text/javascript" src="{{ url_for('static', filename='cytoscape.min.js') }}"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.6.0/cytoscape.min.js" integrity="sha256-uZV2wRlscgr52q3Wb3Oew0rKCPsM3g4aBTv46sF4qzg=" crossorigin="anonymous"></script> + <div id="cy"></div> <script> var cy = cytoscape({ diff --git a/templates/index.html b/templates/index.html index 27455fb..ba18e0c 100644 --- a/templates/index.html +++ b/templates/index.html @@ -2,10 +2,26 @@ {% block content %} <p> - <form class="form-inline my-2 my-lg-0" action="/search"> - <input name="query" class="form-control mr-sm-2" type="search" placeholder="Rgma Nrxn3" aria-label="search" value="Rgma Nrxn3"> + <form action="/search"> + <input name="query" class="form-control form-control-lg" type="search" placeholder="e.g., Rgma Nrxn3, up to 5 terms are allowed" aria-label="search" value=""> <button class="btn btn-outline-success my-2 my-sm-0" type="submit">Search</button> </form> + <br> + This app searches PubMed to find <u>sentences</u> that contain the query terms (e.g., gene symbols) and a drug addiction related keyword. <a href="https://github.com/chen42/RatsPub/blob/master/ratspub.py#L95-L129">These keywords</a> belong to the following categories: +<ul> +<li> names of abused drugs, e.g., opioids</li> +<li> terms describing addiction, e.g., relapse </li> +<li> key brain regions implicated in addiction, e.g., ventral striatum </li> +<li> neurotrasmission, e.g., dopaminergic </li> +<li> synaptic plasticity, e.g., long term potentiation </li> +<li> intracellular signaling, e.g., phosphorylation </li> +</ul> + +<br> +Live searches are conducted through PubMed to get relevant PMIDs, which are then used to retrieve the abstracts from a <a href="https://dataguide.nlm.nih.gov/edirect/archive.html">local archive</a>. The relationships are presented as an interactive <a href="https://js.cytoscape.org" >cytoscape</a> graph. The nodes can be moved around to better reveal the connections. Clicking on the links will bring up the corresponding sentences in a new browser window. +<p> +<hr> +<a href="https://github.com/chen42/ratspub"> Source code </a> {% endblock %} diff --git a/templates/layout.html b/templates/layout.html index 0d3021e..d64b331 100644 --- a/templates/layout.html +++ b/templates/layout.html @@ -9,14 +9,13 @@ <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"> <link rel=stylesheet type=text/css href="{{ url_for('static', filename='style.css') }}"> - <title>RatsPub: Relationship with Addiction Through Searches of PubMed</title> </head> <body> -<nav class="navbar navbar-expand-lg navbar-light bg-light"> + <nav class="navbar navbar-expand-lg navbar-light bg-light"> <a class="navbar-brand" href="/">RatsPub:</br> <span style="font-size:small"> <u>R</u>elationship with <u>A</u>ddiction <u>T</u>hrough <u>S</u>earches of <u>Pub</u>Med </span></a> - <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation"> + <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> </button> </nav> @@ -27,6 +26,7 @@ <script src="https://code.jquery.com/jquery-3.3.1.slim.min.js" integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo" crossorigin="anonymous"></script> <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/js/bootstrap.min.js" integrity="sha384-JjSmVgyd0p3pXB1rRibZUAYoIIy6OrQ6VrjIEaFf/nJGzIxFDsf4x0xIM+B07jRM" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.6.0/cytoscape.min.js" integrity="sha256-uZV2wRlscgr52q3Wb3Oew0rKCPsM3g4aBTv46sF4qzg=" crossorigin="anonymous"></script> </body> |