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, 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