1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
|
###############################################################################
#
# This file is part of the Utopia Documents application.
# Copyright (c) 2008-2014 Lost Island Labs
# <info@utopiadocs.com>
#
# Utopia Documents is free software: you can redistribute it and/or modify
# it under the terms of the GNU GENERAL PUBLIC LICENSE VERSION 3 as
# published by the Free Software Foundation.
#
# Utopia Documents is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
# Public License for more details.
#
# In addition, as a special exception, the copyright holders give
# permission to link the code of portions of this program with the OpenSSL
# library under certain conditions as described in each individual source
# file, and distribute linked combinations including the two.
#
# You must obey the GNU General Public License in all respects for all of
# the code used other than OpenSSL. If you modify file(s) with this
# exception, you may extend this exception to your version of the file(s),
# but you are not obligated to do so. If you do not wish to do so, delete
# this exception statement from your version.
#
# You should have received a copy of the GNU General Public License
# along with Utopia Documents. If not, see <http://www.gnu.org/licenses/>
#
###############################################################################
#? name: GEO
#? www: http://www.ncbi.nlm.nih.gov/geo/
#? urls: http://www.ncbi.nlm.nih.gov/geo/ https://insilico.ulb.ac.be/
import spineapi
import utopia.document
import common.utils
import urllib2
class GeneExpressionOmnibusAnnotator(utopia.document.Annotator, utopia.document.Visualiser):
"""Find GEO Data Sets"""
def _fetchGEO(self, gse):
url='http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={0}&form=text&view=full'.format(gse)
response = urllib2.urlopen(url, timeout=8)
data= response.read()
entry={}
keys=('title', 'summary', 'pubmed_id', 'submission_date', 'last_update_date',
'geo_accession', 'overall_design', 'type', 'contributor', 'supplementary_file')
for line in data.split('\n'):
if len(line)==0 or line[0]!='!':
continue
key,value= line.replace('!Series_','').strip().split(' = ')
if key in keys:
try:
entry[key].append(value)
except KeyError:
entry[key]=[value]
contributors=[]
for c in entry['contributor']:
contrib=[x.strip() for x in c.split(',')]
last_name=contrib.pop()
initials=''.join([c[0].upper() if len(c)>0 else '' for c in contrib])
contributors.append("%s %s" % (last_name, initials))
# flatten lists of duplicate values for keys
for k,v in entry.iteritems():
entry[k]=' '.join(v)
entry['contributors']=', '.join(contributors)
entry['InSilicoDB_url'] = 'https://insilico.ulb.ac.be/app/browse?q=%s' % entry['geo_accession']
entry['GEO_url'] = 'http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=%s' % entry['geo_accession']
return entry
@utopia.document.buffer
def on_ready_event(self, document):
# Find distinguishing ID
pmid = common.utils.metadata(document, 'pmid')
# Compile distinct GEO IDs in the text
matches = {}
for match in document.search(r'GSE\d+', spineapi.IgnoreCase + spineapi.WholeWordsOnly + spineapi.RegExp):
matches.setdefault(match.text(), [])
matches[match.text()].append(match)
# Create annotations for each GEO ID
for gse, extents in matches.iteritems():
entry = self._fetchGEO(gse)
dates = u'Submitted {0}'.format(entry['submission_date'])
if 'last_update_date' in entry:
dates += u'; last updated {0}'.format(entry['last_update_date'])
dates += '.'
dataCitation=u'''<p>{0}. <strong>{1}</strong>.</p><p>{2}<br>({3})</p><p>{4}</p>'''.format(
entry['contributors'].decode('utf8'), entry['title'].decode('utf8'), entry['overall_design'].decode('utf8'), entry['type'].decode('utf8'), dates)
xhtml = u'<div class="box">{0}{{0}}<p>GEO Accession: <a href="{1}">{2}</a></p></div>'.format(
dataCitation, entry['GEO_url'].decode('utf8'), gse)
xhtml += u'<p><a href="{0}">Explore in InSilico DB...</a></p>'.format(entry['InSilicoDB_url'])
srcdesc='''<p>The <a href="http://www.ncbi.nlm.nih.gov/geo">Gene
Expression Omnibus (GEO)</a> is a public repository
that archives and freely distributes microarray,
next-generation sequencing, and other forms of
high-throughput functional genomic data submitted
by the scientific community.</p>'''
if entry.get('pubmed_id') == pmid:
# add a global annotation
annotation = spineapi.Annotation()
annotation['concept'] = 'GEO'
annotation['property:name'] = 'Gene Expression Omnibus'
annotation['property:sourceDatabase'] = 'geo'
annotation['property:description'] = '{0} (Data associated with this article)'.format(gse)
annotation['property:sourceDescription'] = srcdesc
annotation['property:xhtml'] = xhtml.format('') # Keep summary blank
document.addAnnotation(annotation)
# Generate summary
summary = entry.get('summary', '')
if len(summary) > 0:
summary_words = summary.split(' ')
summary = u'<p><em>Summary:</em> '
summary += u'{0}'.format(' '.join(summary_words[:32]))
if len(summary_words) > 32:
summary += u' <span class="readmore">{0}</span>'.format(' '.join(summary_words[32:]))
summary += u'</p>'
# local annotation
annotation = spineapi.Annotation()
annotation['concept'] = 'GEO'
annotation['property:name'] = 'Gene Expression Omnibus'
annotation['property:sourceDatabase'] = 'geo'
annotation['property:description'] = gse
annotation['property:sourceDescription'] = srcdesc
annotation['property:xhtml'] = xhtml.format(summary)
for extent in extents:
annotation.addExtent(extent)
document.addAnnotation(annotation)
def visualisable(self, a):
return a.get('concept') == 'GEO'
def visualise(self, a):
return a.get('property:xhtml')
|
