def createAnnotation(self, domain, document, html, mentions):
annotation = Annotation()
annotation['concept'] = 'Bio3DMInformation'
annotation['property:name'] = '%s: "%s"' % (
mentions[0]['mentionType'].title(),
mentions[0]['formalRepresentation'])
annotation['property:description'] = '3DM %s record' % mentions[0][
'mentionType'].title()
annotation['property:sourceDatabase'] = domain
annotation['property:html'] = mentions[0]['html']
annotation['property:css'] = mentions[0]['css']
annotation['property:js'] = mentions[0]['js']
annotation['property:sourceDatabase'] = 'bioprodict'
annotation[
'property:sourceDescription'] = '<p><a href="http://www.bio-prodict.nl">Bio-Prodict\'s</a> 3DM information systems provide protein family-specific annotations for this article</p>'
annotation['session:overlay'] = 'hyperlink'
annotation['session:color'] = '#336611'
for mention in mentions:
for textRange in mention['textRangeList']:
start = int(textRange['start'])
end = int(textRange['end'])
match = document.substr(start, end - start)
annotation.addExtent(match)
return annotation
def createAnnotation(self, document, html, mentions):
annotation = spineapi.Annotation()
annotation['concept'] = 'NucleaRDBInformation'
annotation['property:name'] = '%s: "%s"' % (mentions[0].mentionType.title(), mentions[0].formalRepresentation)
annotation['property:description'] = 'NucleaRDB %s record' % mentions[0].mentionType.title()
annotation['property:sourceDatabase'] = 'nucleardb'
annotation['property:sourceDescription'] = '<p>The <a href="http://www.receptors.org/nucleardb/">NucleaRDB</a> is a molecular-class information system that collects, combines, validates and stores large amounts of heterogenous data on nuclear hormone receptors.</p>'
annotation['property:html'] = html
for mention in mentions:
#print mention
start = int(mention.textStart)
end = int(mention.textEnd)
match = document.substr(start, end-start)
annotation.addExtent(match)
return annotation
def createAnnotation(self, document, html, mentions):
annotation = spineapi.Annotation()
annotation['concept'] = 'NucleaRDBInformation'
annotation['property:name'] = '%s: "%s"' % (mentions[0].mentionType.title(), mentions[0].formalRepresentation)
annotation['property:description'] = 'NucleaRDB %s record' % mentions[0].mentionType.title()
annotation['property:sourceDatabase'] = 'nucleardb'
annotation['property:sourceDescription'] = '<p>The <a href="http://www.receptors.org/nucleardb/">NucleaRDB</a> is a molecular-class information system that collects, combines, validates and stores large amounts of heterogenous data on nuclear hormone receptors.</p>'
annotation['property:html'] = html
for mention in mentions:
#print mention
start = int(mention.textStart)
end = int(mention.textEnd)
match = document.substr(start, end-start)
annotation.addExtent(match)
return annotation
def createAnnotation(self, domain, document, html, mentions):
annotation = Annotation()
annotation["concept"] = "Bio3DMInformation"
annotation["property:name"] = '%s: "%s"' % (mentions[0].mentionType.title(), mentions[0].formalRepresentation)
annotation["property:description"] = "3DM %s record" % mentions[0].mentionType.title()
annotation["property:sourceDatabase"] = domain
annotation["property:html"] = mentions[0].html
annotation["property:css"] = mentions[0].css
annotation["property:js"] = mentions[0].js
annotation["property:sourceDatabase"] = "bioprodict"
annotation[
"property:sourceDescription"
] = '<p><a href="http://www.bio-prodict.nl">Bio-Prodict\'s</a> 3DM information systems provide protein family-specific annotations for this article</p>'
for mention in mentions:
for textRange in mention.textRangeList:
start = int(textRange.start)
end = int(textRange.end)
match = document.substr(start, end - start)
annotation.addExtent(match)
return annotation
