diff options
| -rw-r--r-- | VERSION | 1 | ||||
| -rwxr-xr-x | server.py | 136 | ||||
| -rw-r--r-- | templates/about.html | 36 | ||||
| -rw-r--r-- | templates/layout.html | 15 |
4 files changed, 102 insertions, 86 deletions
@@ -0,0 +1 @@ +1.8.3 @@ -1,4 +1,7 @@ #!/bin/env python3 +# +# This is the main flask server + from __future__ import print_function import hashlib @@ -50,6 +53,14 @@ app.config['SQLALCHEMY_DATABASE_URI'] = 'sqlite:///'+datadir+'userspub.sqlite' db = SQLAlchemy(app) nltk.data.path.append("./nlp/") +VERSION=None + +def version(): + if not VERSION: + with open("VERSION", 'r') as file: + VERSION = file.read() + return VERSION + # Sqlite database class users(db.Model): __tablename__='user' @@ -63,8 +74,8 @@ class users(db.Model): def clean_doc(doc, vocab): doc = doc.lower() tokens = doc.split() - re_punc = re.compile('[%s]' % re.escape(string.punctuation)) - tokens = [re_punc.sub('' , w) for w in tokens] + re_punc = re.compile('[%s]' % re.escape(string.punctuation)) + tokens = [re_punc.sub('' , w) for w in tokens] tokens = [word for word in tokens if len(word) > 1] stop_words = set(stopwords.words('english')) tokens = [w for w in tokens if not w in stop_words] @@ -109,7 +120,7 @@ def root(): ontoarchive() onto_len_dir = session['onto_len_dir'] onto_list = session['onto_list'] - else: + else: onto_len_dir = 0 onto_list = '' @@ -161,13 +172,13 @@ def signup(): if (found_user and (bcrypt.checkpw(password.encode('utf8'), found_user.password)==False)): flash("Already registered, but wrong password!", "inval") - return render_template('signup.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) + return render_template('signup.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) session['email'] = email session['hashed_email'] = hashlib.md5(session['email'] .encode('utf-8')).hexdigest() session['name'] = name password = bcrypt.hashpw(password.encode('utf8'), bcrypt.gensalt()) - user = users(name=name, email=email, password = password) + user = users(name=name, email=email, password = password) if found_user: session['email'] = found_user.email session['hashed_email'] = hashlib.md5(session['email'] .encode('utf-8')).hexdigest() @@ -219,10 +230,10 @@ def signin(): return render_template('index.html', onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) else: flash("Invalid username or password!", "inval") - return render_template('signup.html') + return render_template('signup.html') return render_template('signin.html') -# change password +# change password @app.route("/<nm_passwd>", methods=["POST", "GET"]) def profile(nm_passwd): try: @@ -259,7 +270,7 @@ def profile(nm_passwd): return render_template("/passwd_change.html", name=user_name) else: return "This url does not exist" - else: + else: return "This url does not exist" except (AttributeError): return "This url does not exist" @@ -276,7 +287,7 @@ def logout(): global user1 if session['name'] != '': user1 = session['name'] - else: + else: user1 = session['email'] flash("You have been logged out, {user1}", "inval") session.pop('email', None) @@ -286,8 +297,7 @@ def logout(): @app.route("/about") def about(): - return render_template('about.html') - + return render_template('about.html',version=version()) # Ontology selection @app.route("/index_ontology", methods=["POST", "GET"]) @@ -376,7 +386,7 @@ def ontology(): keycat = keycat.replace('| ', '|') namecat=re.sub('[^,a-zA-Z0-9 \n]', '', namecat) - # Generate a unique session ID depending on timestamp to track the results + # Generate a unique session ID depending on timestamp to track the results timestamp = datetime.utcnow().replace(microsecond=0) timestamp = timestamp.replace(tzinfo=pytz.utc) timestamp = timestamp.astimezone(pytz.timezone("America/Chicago")) @@ -409,8 +419,8 @@ def ontology(): with open("addiction.onto","r") as f1: with open(session['namecat']+".onto", "w") as f2: for line in f1: - f2.write(line) - else: + f2.write(line) + else: f= open(session['namecat']+".onto","w") dict_onto={} else: @@ -425,8 +435,8 @@ def ontology(): flag_kw=0 if (',' in maincat) or (',' in subcat): flash("Only one word can be added to the category and subcategory at a time.","inval") - elif maincat in dict_onto.keys(): # Layer 2, main category - if subcat in dict_onto[maincat].keys(): # Layer 3, keywords shown in results + elif maincat in dict_onto.keys(): # Layer 2, main category + if subcat in dict_onto[maincat].keys(): # Layer 3, keywords shown in results keycat_ls = keycat.split('|') for kw in str.split(next(iter(dict_onto[maincat][subcat])), '|'): # Layer 4, synonyms for keycat_word in keycat_ls: @@ -462,7 +472,7 @@ def ontology(): flash("You must login to change the addiction ontology.") else: flash("You must login to create a new ontology.") - + if request.form['submit'] == 'remove': if ('email' in session): session['namecat']=namecat @@ -485,8 +495,8 @@ def ontology(): with open("addiction.onto","r") as f1: with open(session['namecat']+".onto", "w") as f2: for line in f1: - f2.write(line) - else: + f2.write(line) + else: f= open(session['namecat']+".onto","w") dict_onto={} @@ -498,10 +508,10 @@ def ontology(): dict_onto={} else: dict_onto=ast.literal_eval(onto_cont) - + flag_kw=0 - if maincat in dict_onto.keys(): # Layer 2, main category - if subcat in dict_onto[maincat].keys(): # Layer 3, keywords shown in results + if maincat in dict_onto.keys(): # Layer 2, main category + if subcat in dict_onto[maincat].keys(): # Layer 3, keywords shown in results for kw in str.split(next(iter(dict_onto[maincat][subcat])), '|'): keycat_ls = keycat.split('|') for keycat_word in keycat_ls: # Layer 4, synonyms @@ -516,11 +526,11 @@ def ontology(): dict_onto[maincat]=re.sub(r'\''+subcat+'\': \'{}\', ', '', str(dict_onto[maincat])) dict_onto[maincat]=re.sub(r'\''+subcat+'\': \'{}\'', '', str(dict_onto[maincat])) if '{}' in dict_onto[maincat]: - dict_onto=re.sub(r', \''+maincat+'\': \'{}\'', '', str(dict_onto)) + dict_onto=re.sub(r', \''+maincat+'\': \'{}\'', '', str(dict_onto)) dict_onto=str(dict_onto).replace('\"{','{') dict_onto=str(dict_onto).replace('}\"','}') dict_onto=str(dict_onto).replace('\'{','{') - dict_onto=str(dict_onto).replace('}\'','}') + dict_onto=str(dict_onto).replace('}\'','}') with open(session['namecat']+'.onto', 'w') as file3: file3.write(str(dict_onto)) if flag_kw==0: @@ -528,12 +538,12 @@ def ontology(): else: flash("\""+subcat+"\" is not a subcategory.","inval") else: - flash("\""+subcat+"\" is not a category.","inval") + flash("\""+subcat+"\" is not a category.","inval") else: if namecat=='addiction': flash("You must login to change the addiction ontology.") else: - flash("You must login to create a new ontology.") + flash("You must login to create a new ontology.") if 'namecat' in session: file2 = open(session['namecat']+".onto","r") @@ -570,7 +580,7 @@ def ontoarchive(): onto_list = '' onto_cont=open("addiction.onto","r").read() dict_onto=ast.literal_eval(onto_cont) - return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) + return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) else: session['user_folder'] = datadir+"/user/"+str(session['hashed_email']) else: @@ -584,10 +594,10 @@ def ontoarchive(): session_id=session['id'] def sorted_alphanumeric(data): convert = lambda text: int(text) if text.isdigit() else text.lower() - alphanum_key = lambda key: [ convert(c) for c in re.split('([0-9]+)', key) ] + alphanum_key = lambda key: [ convert(c) for c in re.split('([0-9]+)', key) ] return sorted(data, key=alphanum_key) - dirlist = sorted_alphanumeric(os.listdir(session['user_folder']+"/ontology/")) + dirlist = sorted_alphanumeric(os.listdir(session['user_folder']+"/ontology/")) onto_folder_list = [] onto_directory_list = [] onto_list=[] @@ -645,26 +655,26 @@ def progress(): if ('email' in session): onto_len_dir = session['onto_len_dir'] onto_list = session['onto_list'] - else: + else: onto_len_dir = 0 onto_list = '' onto_cont=open("addiction.onto","r").read() dict_onto=ast.literal_eval(onto_cont) message="<span class='text-danger'>Up to 200 terms can be searched at a time</span>" return render_template('index.html' ,onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto, message=message) - + if len(genes)==0: if ('email' in session): onto_len_dir = session['onto_len_dir'] onto_list = session['onto_list'] - else: + else: onto_len_dir = 0 onto_list = '' onto_cont=open("addiction.onto","r").read() dict_onto=ast.literal_eval(onto_cont) message="<span class='text-danger'>Please enter a search term </span>" return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto, message=message) - + tf_path=tempfile.gettempdir() genes_for_folder_name ="" if len(genes) == 1: @@ -680,7 +690,7 @@ def progress(): genes_for_folder_name =str(genes[0])+"_"+str(genes[1])+"_"+str(genes[2]) marker="_m" - # Generate a unique session ID depending on timestamp to track the results + # Generate a unique session ID depending on timestamp to track the results timestamp = datetime.utcnow().replace(microsecond=0) timestamp = timestamp.replace(tzinfo=pytz.utc) timestamp = timestamp.astimezone(pytz.timezone("America/Chicago")) @@ -737,7 +747,7 @@ def progress(): session['rnd'] = timeextension+"_0_"+genes_for_folder_name+marker+"_0_"+onto_name_archive rnd = session['rnd'] else: - rnd = "tmp" + ''.join(random.choice(string.ascii_letters) for x in range(6)) + rnd = "tmp" + ''.join(random.choice(string.ascii_letters) for x in range(6)) session['path']=tf_path+ "/" + rnd os.makedirs(session['path']) search_type = request.args.getlist('type') @@ -778,7 +788,7 @@ def search(): search_type = session['search_type'] temp_nodes = "" json_nodes = "{\"data\":[" - + n_num=0 d={} nodecolor={} @@ -817,7 +827,7 @@ def search(): nodes_list.append(nd) json_nodes += generate_nodes_json(dictionary[ky],str(ky),nodecolor[ky]) d["nj{0}".format(n_num)]='' - + json_nodes = json_nodes[:-2] json_nodes =json_nodes+"]}" def generate(genes, tf_name): @@ -828,7 +838,7 @@ def search(): progress=0 searchCnt=0 nodesToHide=str() - json_edges = str() + json_edges = str() #genes_or = ' [tiab] or '.join(genes) all_d='' @@ -864,7 +874,7 @@ def search(): sent_tok = pmid + ' ' + sent_tok sentences_ls.append(sent_tok) gene=gene.replace("-"," ") - + geneEdges = "" if namecat_flag==1: @@ -890,7 +900,7 @@ def search(): if namecat_flag==1: onto_cont = open(ses_namecat+".onto","r").read() dict_onto=ast.literal_eval(onto_cont) - #ky_d=undic(list(dict_onto[ky].values())) + #ky_d=undic(list(dict_onto[ky].values())) sent=gene_category(gene,ky,str(ky), sentences_ls, addiction_flag,dict_onto) else: #ky_d=undic(list(dict_onto[ky].values())) @@ -898,9 +908,9 @@ def search(): sent=gene_category(gene,ky,str(ky), sentences_ls, addiction_flag,dict_onto) #print(sent) yield "data:"+str(progress)+"\n\n" - + geneEdges += generate_edges(sent, tf_name) - json_edges += generate_edges_json(sent, tf_name) + json_edges += generate_edges_json(sent, tf_name) sentences+=sent if ("GWAS" in search_type): gwas_sent=[] @@ -909,7 +919,7 @@ def search(): | (datf["REPORTED GENE(S)"].str.contains('(?:\s|^)'+gene+'(?:\s|$)', flags=re.IGNORECASE))] print (datf_sub1) for nd2 in dict_onto['GWAS'].keys(): - for nd1 in dict_onto['GWAS'][nd2]: + for nd1 in dict_onto['GWAS'][nd2]: for nd in nd1.split('|'): gwas_text='' datf_sub = datf_sub1[datf_sub1['DISEASE/TRAIT'].str.contains('(?:\s|^)'+nd+'(?:\s|$)', flags=re.IGNORECASE)] @@ -925,11 +935,11 @@ def search(): with open(path_user+"gwas_results.tab", "a") as gwas_edges: gwas_edges.write(sn_file) geneEdges += cys - json_edges += gwas_json + json_edges += gwas_json # report progress immediately progress+=percent yield "data:"+str(progress)+"\n\n" - + if len(geneEdges) >0: edges+=geneEdges nodes+="{ data: { id: '" + gene + "', nodecolor:'#E74C3C', fontweight:700, url:'/synonyms?node="+gene+"'} },\n" @@ -941,7 +951,7 @@ def search(): progress=100 sntdata.write(sentences) sntdata.close() - cysdata.write(nodes+edges) + cysdata.write(nodes+edges) cysdata.close() zeroLinkNode.write(nodesToHide) zeroLinkNode.close() @@ -954,7 +964,7 @@ def search(): # Write edges to txt file in json format also in user folder with open(path_user+"edges.json", "w") as temp_file_edges: - temp_file_edges.write(json_edges) + temp_file_edges.write(json_edges) with open(path_user+"nodes.json", "w") as temp_file_nodes: temp_file_nodes.write(json_nodes) return Response(generate(genes, snt_file), mimetype='text/event-stream') @@ -987,7 +997,7 @@ def tableview(): for line in file_edges.readlines(): if ':' not in line: nodata_temp = 1 - else: + else: nodata_temp = 0 with open(datadir+gene_url_tmp +"/edges.json") as edgesjsonfile: jedges = json.load(edgesjsonfile) @@ -1010,7 +1020,7 @@ def tableview(): for line in file_edges.readlines(): if ':' not in line: nodata_temp = 1 - else: + else: nodata_temp = 0 with open(gene_url_tmp +"/edges.json") as edgesjsonfile: jedges = json.load(edgesjsonfile) @@ -1058,7 +1068,7 @@ def tableview0(): for line in file_edges.readlines(): if ':' not in line: nodata_temp = 1 - else: + else: nodata_temp = 0 with open(datadir+gene_url_tmp+"/edges.json") as edgesjsonfile: jedges = json.load(edgesjsonfile) @@ -1082,7 +1092,7 @@ def tableview0(): for line in file_edges.readlines(): if ':' not in line: nodata_temp = 1 - else: + else: nodata_temp = 0 with open(gene_url_tmp+"/edges.json") as edgesjsonfile: jedges = json.load(edgesjsonfile) @@ -1129,9 +1139,9 @@ def userarchive(): session_id=session['id'] def sorted_alphanumeric(data): convert = lambda text: int(text) if text.isdigit() else text.lower() - alphanum_key = lambda key: [ convert(c) for c in re.split('([0-9]+)', key) ] + alphanum_key = lambda key: [ convert(c) for c in re.split('([0-9]+)', key) ] return sorted(data, key=alphanum_key) - dirlist = sorted_alphanumeric(os.listdir(session['user_folder'])) + dirlist = sorted_alphanumeric(os.listdir(session['user_folder'])) folder_list = [] directory_list = [] gene_list=[] @@ -1243,7 +1253,7 @@ def cytoscape(): genes_session_tmp=tf_path + "/" + genes_url rnd_url_tmp=tf_path +"/" + rnd_url message2="<ul><li><font color=\"#E74C3C\">Click on a line to read the sentences </font> <li>Click on a keyword to see the terms included in the search<li>Hover a pointer over a node to hide other links <li>Move the nodes around to adjust visibility <li> Reload the page to restore the default layout<li>View the results in <a href='\\tableview/?rnd={}&genequery={}'\ ><b>a table. </b></a></ul>".format(rnd_url,genes_url) - + if ('email' in session): filename = rnd_url.split("_0_")[0] rnd_url_tmp = datadir+"/user/"+str(session['hashed_email'])+"/"+rnd_url+"/"+filename @@ -1293,7 +1303,7 @@ def sentences(): line = ' '.join(tokens) line = [line] tokenized_sent = tokenizer.texts_to_sequences(line) - tokenized_sent = pad_sequences(tokenized_sent, maxlen=max_length, padding='post') + tokenized_sent = pad_sequences(tokenized_sent, maxlen=max_length, padding='post') predict_sent = model.predict(tokenized_sent, verbose=0) percent_sent = predict_sent[0,0] if round(percent_sent) == 0: @@ -1329,10 +1339,10 @@ def sentences(): if(cat0=='stress'): out4 = predict_sent(text) if(out4 == 'pos'): - out_pred_pos = "<li> "+ text + " <a href=\"https://www.ncbi.nlm.nih.gov/pubmed/?term=" + pmid +"\" target=_new>PMID:"+pmid+"<br></a>" + out_pred_pos = "<li> "+ text + " <a href=\"https://www.ncbi.nlm.nih.gov/pubmed/?term=" + pmid +"\" target=_new>PMID:"+pmid+"<br></a>" out_pos += out_pred_pos else: - out_pred_neg = "<li>"+ text + " <a href=\"https://www.ncbi.nlm.nih.gov/pubmed/?term=" + pmid +"\" target=_new>PMID:"+pmid+"<br></a>" + out_pred_neg = "<li>"+ text + " <a href=\"https://www.ncbi.nlm.nih.gov/pubmed/?term=" + pmid +"\" target=_new>PMID:"+pmid+"<br></a>" out_neg += out_pred_neg out1="<h3>"+gene0 + " and " + cat0 + "</h3>\n" if len(pmid_list)>1: @@ -1383,18 +1393,18 @@ def synonyms(): node=node.upper() allnodes={**genes} try: - synonym_list = list(allnodes[node].split("|")) + synonym_list = list(allnodes[node].split("|")) session['synonym_list'] = synonym_list session['main_gene'] = node.upper() out="<hr><li>"+ allnodes[node].replace("|", "<li>") - synonym_list_str = ';'.join([str(syn) for syn in synonym_list]) + synonym_list_str = ';'.join([str(syn) for syn in synonym_list]) synonym_list_str +=';' + node case = 1 return render_template('genenames.html', case = case, gene = node.upper(), synonym_list = synonym_list, synonym_list_str=synonym_list_str) except: try: synonym_list = session['synonym_list'] - synonym_list_str = ';'.join([str(syn) for syn in synonym_list]) + synonym_list_str = ';'.join([str(syn) for syn in synonym_list]) synonym_list_str +=';' + node case = 1 return render_template('genenames.html', case=case, gene = session['main_gene'] , synonym_list = synonym_list, synonym_list_str=synonym_list_str) @@ -1443,7 +1453,7 @@ def gene_gene(): pmid = tiab.pop(0) tiab= " ".join(tiab) sentences = sent_tokenize(tiab) - ## keep the sentence only if it contains the gene + ## keep the sentence only if it contains the gene for sent in sentences: if findWholeWord(query)(sent): sent=re.sub(r'\b(%s)\b' % query, r'<strong>\1</strong>', sent, flags=re.I) @@ -1472,7 +1482,7 @@ def gene_gene(): sentword="sentences" topGeneHits[ "<li> <a href=/sentences?edgeID=" + url+ " target=_new>" + "Show " + str(hitGenes[key]) + " " + sentword +" </a> about "+query+" and <a href=/showTopGene?topGene="+key+" target=_gene><span style=\"background-color:#FcF3cf\">"+key+"</span></a>" ]=hitGenes[key] topSorted = [(k, topGeneHits[k]) for k in sorted(topGeneHits, key=topGeneHits.get, reverse=True)] - + for k,v in topSorted: results+=k saveResult=open(result_file, "w+") @@ -1480,7 +1490,7 @@ def gene_gene(): saveResult.close() progress=100 yield "data:"+str(progress)+"\n\n" - + # Start the run query=session['forTopGene'] return Response(generate(query), mimetype='text/event-stream') 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/layout.html b/templates/layout.html index 20dbcbe..814e5b6 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> @@ -20,7 +20,7 @@ <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> @@ -95,10 +95,17 @@ {% block content %}{% endblock %} </div> +</ hr> +<div id="footer" align="right"> + <a href="https://git.genenetwork.org/genecup/">Source code</a> + | + Cite <a href="https://academic.oup.com/g3journal/article/12/5/jkac059/6548160">GeneCup: mining PubMed and GWAS catalog for gene-keyword relationships. doi:10.1093/g3journal/jkac059. PMID: 35285473; PMCID: PMC9073678.</a> + | + Powered by Tensorflow on <a href="https://genenetwork.org/">GeneNetwork.org</a> +</div> + <script src="https://code.jquery.com/jquery-3.2.1.slim.min.js" integrity="sha384-KJ3o2DKtIkvYIK3UENzmM7KCkRr/rE9/Qpg6aAZGJwFDMVNA/GpGFF93hXpG5KkN" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js" integrity="sha384-ApNbgh9B+Y1QKtv3Rn7W3mgPxhU9K/ScQsAP7hUibX39j7fakFPskvXusvfa0b4Q" crossorigin="anonymous"></script> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js" integrity="sha384-JZR6Spejh4U02d8jOt6vLEHfe/JQGiRRSQQxSfFWpi1MquVdAyjUar5+76PVCmYl" crossorigin="anonymous"></script> </body> - - |