def on_explore_event(self, phrase, document):
results = []
client = kend.client.Client()
annotations = client.lookup(term='"%s"'%phrase, database='ChEMBL', limit='30')
xhtml = ''
# Query to see if a page is returned
# Extent information needs to be included FIXME
if annotations is not None and len(annotations) >= 1:
for group in annotations:
for result in group.annotations:
annotation=kend.converter.Annotation.kend2spineapi(result)
entry = self.visualiser.visualisable(annotation) and self.visualiser.visualise(annotation) or ''
if len(entry) > 0:
name = annotation['property:name']
if 'property:moleculeType' in annotation:
name += ' ({0})'.format(annotation['property:moleculeType'])
xhtml += u'<div class="expandable" title="{0}">{1}</div>'.format(name, entry)
if len(xhtml) > 0:
xhtml = '<style>.formula {font-weight:bold; font-size: 1.2em;}</style>' + xhtml
annotation = spineapi.Annotation()
annotation['concept'] = 'Collated'
annotation['property:html'] = xhtml
annotation['property:name'] = 'ChEMBL'
annotation['property:description'] = 'Related bioactive small molecules'
annotation['property:sourceDatabase'] = 'chembl'
annotation['property:sourceDescription'] = '<p><a href="https://www.ebi.ac.uk/chembl/">ChEMBL</a> is a database of bioactive drug-like small molecules.</p>'
annotation['displayRelevance']='1000'
annotation['displayRank']="%d" % -len(annotation['property:name'])
results.append(annotation)
return results
def on_explore_event(self, phrase, document):
results = []
client = kend.client.Client()
annotations = client.lookup(term='"%s"'%phrase, database='UniProt', limit='30')
xhtml = ''
if annotations is not None and len(annotations) >= 1:
for group in annotations[:10]:
for result in group.annotations[:10]:
annotation=kend.converter.Annotation.kend2spineapi(result)
annotation['property:sourceDatabase'] = 'uniprot'
entry = self.visualiser.visualisable(annotation) and self.visualiser.visualise(annotation) or ''
if len(entry) > 0:
xhtml += u'<div class="expandable" title="{0}">{1}</div>'.format('UniProt entry %s' % annotation.get('property:mnemonic', '???'), entry)
if len(xhtml) > 0:
annotation = spineapi.Annotation()
annotation['concept'] = 'Collated'
annotation['property:html'] = xhtml
annotation['property:name'] = 'UniProt sequences'
annotation['property:description'] = 'Protein sequence information'
annotation['property:sourceDatabase'] = 'uniprot'
annotation['property:sourceDescription'] = '<p>The Universal Protein Resource (<a href="http://www.uniprot.org/">UniProt</a>) is a comprehensive resource for protein sequence and annotation data.</p>'
annotation['displayRelevance']='700'
annotation['displayRank']="%d" % -len(annotation['property:name'])
results.append(annotation)
return results
def on_explore_event(self, phrase, document):
results = []
client = kend.client.Client()
annotations = client.lookup(term='"%s"'%phrase, database='PDB', limit='30')
xhtml = ''
if annotations is not None and len(annotations) >= 1:
for group in annotations:
for result in group.annotations:
annotation=kend.converter.Annotation.kend2spineapi(result)
annotation['property:sourceDatabase'] = 'pdb'
entry = self.visualiser.visualisable(annotation) and self.visualiser.visualise(annotation) or ''
if len(entry) > 0:
xhtml += u'<div class="expandable" title="{0}">{1}</div>'.format(annotation['property:name'], entry)
if len(xhtml) > 0:
annotation = spineapi.Annotation()
annotation['concept'] = 'Collated'
annotation['property:html'] = xhtml
annotation['property:name'] = 'Protein Data Bank structures'
annotation['property:description'] = 'Biological macromolecular structures'
annotation['property:sourceDatabase'] = 'pdb'
annotation['property:sourceDescription'] = '<p>The <a href="http://www.rcsb.org/">Protein Data Bank</a> of the Research Collaboratory for Structural Bioinformatics (<a href="http://home.rcsb.org/">RCSB</a>).</p>'
annotation['displayRelevance']='800'
annotation['displayRank']="%d" % -len(annotation['property:name'])
results.append(annotation)
return results
def on_explore_event(self, phrase, document):
results = []
client = kend.client.Client()
annotations = client.lookup(term='"%s"'%phrase, database='Glick', limit='30')
xhtml = ''
# Query to see if a page is returned
# Extent information needs to be included FIXME
if annotations is not None and len(annotations) >= 1:
for group in annotations:
for result in group.annotations:
annotation=kend.converter.Annotation.kend2spineapi(result)
annotation['property:sourceDatabase'] = 'glick'
entry = self.visualiser.visualisable(annotation) and self.visualiser.visualise(annotation) or ''
if len(entry) > 0:
xhtml += u'<div class="expandable" title="{0}">{1}</div>'.format(annotation['property:name'], entry)
if len(xhtml) > 0:
xhtml += '<p><em>(Glick Glossary/Portland Press Ltd.)</em></p>'
annotation = spineapi.Annotation()
annotation['concept'] = 'Collated'
annotation['property:html'] = xhtml
annotation['property:name'] = 'Glick glossary entries'
annotation['property:description'] = 'Biomedical definitions'
annotation['property:sourceDatabase'] = 'glick'
annotation['property:sourceDescription'] = '<p>David M. Glick\'s <a href="http://www.portlandpress.com/pp/books/online/glick/search.htm">Glossary of Biochemistry and Molecular Biology</a>.</p><p>Made available by <a href="http://www.portlandpress.com/">Portland Press Limited</a>.</p>'
annotation['displayRelevance']='1000'
annotation['displayRank']="%d" % -len(annotation['property:name'])
results.append(annotation)
return results
def on_explore_event(self, phrase, document):
results = []
client = kend.client.Client()
annotations = client.lookup(term='"%s"'%phrase, database='drugbank', limit='30')
xhtml = ''
# Query to see if a page is returned
# Extent information needs to be included FIXME
if annotations is not None and len(annotations) >= 1:
for group in annotations:
for result in group.annotations:
annotation=kend.converter.Annotation.kend2spineapi(result)
entry = self.visualiser.visualisable(annotation) and self.visualiser.visualise(annotation) or ''
if len(entry) > 0:
name = annotation['property:name']
if 'property:entryType' in annotation:
name += ' ({0})'.format(annotation['property:entryType'])
xhtml += u'<div class="expandable" title="{0}">{1}</div>'.format(name, entry)
if len(xhtml) > 0:
xhtml = '<style>.formula {font-weight:bold; font-size: 1.2em;} .formula sub{font-size:xx-small; position:relative; bottom:-0.3em;}</style>' + xhtml
annotation = spineapi.Annotation()
annotation['concept'] = 'Collated'
annotation['property:html'] = xhtml
annotation['property:name'] = 'DrugBank'
annotation['property:description'] = 'Related drugs and their targets'
annotation['property:sourceDatabase'] = 'drugbank'
annotation['property:sourceDescription'] = '<p><a href="http://www.drugbank.ca">DrugBank</a> is a database that combines detailed drug data with comprehensive drug target information.</p>'
annotation['displayRelevance']='1000'
annotation['displayRank']="%d" % -len(annotation['property:name'])
results.append(annotation)
return results
def on_explore_event(self, phrase, document):
results = []
client = kend.client.Client()
annotations = client.lookup(term='"%s"' % phrase.strip(),
database='genecards',
limit='30')
xhtml = u''
if annotations is not None and len(annotations) >= 1:
for group in annotations[:10]:
for result in group.annotations[:10]:
annotation = kend.converter.Annotation.kend2spineapi(
result)
annotation['property:sourceDatabase'] = 'genecards'
entry = self.visualiser.visualisable(
annotation) and self.visualiser.visualise(
annotation) or ''
if len(entry) > 0:
symbol = annotation.get('property:geneSymbol', u'')
name = annotation.get('property:geneName', u'')
if name:
name = u'(%s)' % name
#print symbol
#print type(symbol)
#print name
#print type(name)
xhtml += u'<div class="expandable" title="Gene {0} {1}">{2}</div>'.format(
symbol, name, entry)
if len(xhtml) > 0:
annotation = spineapi.Annotation()
annotation['concept'] = 'Collated'
annotation['property:html'] = xhtml
annotation['property:name'] = 'GeneCards'
annotation['property:description'] = 'Human genomic information'
annotation['property:sourceIcon'] = utopia.get_plugin_data_as_url(
'images/genecards.png', 'image/png')
annotation[
'property:sourceDescription'] = '<p><a href="http://www.genecards.org">GeneCards</a> is a database of concise genomic related information on all known and predicted human genes.</p>'
annotation['displayRelevance'] = '700'
annotation['displayRank'] = "%d" % -len(
annotation['property:name'])
results.append(annotation)
return results
def on_explore_event(self, phrase, document):
results = []
client = kend.client.Client()
annotations = client.lookup(term='"%s"' % phrase,
database='drugbank',
limit='30')
xhtml = ''
# Query to see if a page is returned
# Extent information needs to be included FIXME
if annotations is not None and len(annotations) >= 1:
for group in annotations:
for result in group.annotations:
annotation = kend.converter.Annotation.kend2spineapi(
result)
entry = self.visualiser.visualisable(
annotation) and self.visualiser.visualise(
annotation) or ''
if len(entry) > 0:
name = annotation['property:name']
if 'property:entryType' in annotation:
name += ' ({0})'.format(
annotation['property:entryType'])
xhtml += u'<div class="expandable" title="{0}">{1}</div>'.format(
name, entry)
if len(xhtml) > 0:
xhtml = '<style>.formula {font-weight:bold; font-size: 1.2em;} .formula sub{font-size:xx-small; position:relative; bottom:-0.3em;}</style>' + xhtml
annotation = spineapi.Annotation()
annotation['concept'] = 'Collated'
annotation['property:html'] = xhtml
annotation['property:name'] = 'DrugBank'
annotation[
'property:description'] = 'Related drugs and their targets'
annotation['property:sourceDatabase'] = 'drugbank'
annotation[
'property:sourceDescription'] = '<p><a href="http://www.drugbank.ca">DrugBank</a> is a database that combines detailed drug data with comprehensive drug target information.</p>'
annotation['displayRelevance'] = '1000'
annotation['displayRank'] = "%d" % -len(
annotation['property:name'])
results.append(annotation)
return results
def on_explore_event(self, phrase, document):
results = []
client = kend.client.Client()
annotations = client.lookup(term='"%s"' % phrase,
database='ChEMBL',
limit='30')
xhtml = ''
# Query to see if a page is returned
# Extent information needs to be included FIXME
if annotations is not None and len(annotations) >= 1:
for group in annotations:
for result in group.annotations:
annotation = kend.converter.Annotation.kend2spineapi(
result)
entry = self.visualiser.visualisable(
annotation) and self.visualiser.visualise(
annotation) or ''
if len(entry) > 0:
name = annotation['property:name']
if 'property:moleculeType' in annotation:
name += ' ({0})'.format(
annotation['property:moleculeType'])
xhtml += u'<div class="expandable" title="{0}">{1}</div>'.format(
name, entry)
if len(xhtml) > 0:
xhtml = '<style>.formula {font-weight:bold; font-size: 1.2em;}</style>' + xhtml
annotation = spineapi.Annotation()
annotation['concept'] = 'Collated'
annotation['property:html'] = xhtml
annotation['property:name'] = 'ChEMBL'
annotation[
'property:description'] = 'Related bioactive small molecules'
annotation['property:sourceDatabase'] = 'chembl'
annotation[
'property:sourceDescription'] = '<p><a href="https://www.ebi.ac.uk/chembl/">ChEMBL</a> is a database of bioactive drug-like small molecules.</p>'
annotation['displayRelevance'] = '1000'
annotation['displayRank'] = "%d" % -len(
annotation['property:name'])
results.append(annotation)
return results
def on_explore_event(self, phrase, document):
results = []
client = kend.client.Client()
annotations = client.lookup(term='"%s"' % phrase.strip(), database='genecards', limit='30')
xhtml = u''
if annotations is not None and len(annotations) >= 1:
for group in annotations[:10]:
for result in group.annotations[:10]:
annotation=kend.converter.Annotation.kend2spineapi(result)
annotation['property:sourceDatabase'] = 'genecards'
entry = self.visualiser.visualisable(annotation) and self.visualiser.visualise(annotation) or ''
if len(entry) > 0:
symbol=annotation.get('property:geneSymbol', u'')
name=annotation.get('property:geneName', u'')
if name:
name=u'(%s)' % name
#print symbol
#print type(symbol)
#print name
#print type(name)
xhtml += u'<div class="expandable" title="Gene {0} {1}">{2}</div>'.format(symbol, name, entry)
if len(xhtml) > 0:
annotation = spineapi.Annotation()
annotation['concept'] = 'Collated'
annotation['property:html'] = xhtml
annotation['property:name'] = 'GeneCards'
annotation['property:description'] = 'Human genomic information'
annotation['property:sourceIcon'] = utopia.get_plugin_data_as_url('images/genecards.png', 'image/png')
annotation['property:sourceDescription'] = '<p><a href="http://www.genecards.org">GeneCards</a> is a database of concise genomic related information on all known and predicted human genes.</p>'
annotation['displayRelevance']='700'
annotation['displayRank']="%d" % -len(annotation['property:name'])
results.append(annotation)
return results
def on_explore_event(self, phrase, document):
results = []
client = kend.client.Client()
annotations = client.lookup(term='"%s"' % phrase,
database='Glick',
limit='30')
xhtml = ''
# Query to see if a page is returned
# Extent information needs to be included FIXME
if annotations is not None and len(annotations) >= 1:
for group in annotations:
for result in group.annotations:
annotation = kend.converter.Annotation.kend2spineapi(
result)
annotation['property:sourceDatabase'] = 'glick'
entry = self.visualiser.visualisable(
annotation) and self.visualiser.visualise(
annotation) or ''
if len(entry) > 0:
xhtml += u'<div class="expandable" title="{0}">{1}</div>'.format(
annotation['property:name'], entry)
if len(xhtml) > 0:
xhtml += '<p><em>(Glick Glossary/Portland Press Ltd.)</em></p>'
annotation = spineapi.Annotation()
annotation['concept'] = 'Collated'
annotation['property:html'] = xhtml
annotation['property:name'] = 'Glick glossary entries'
annotation['property:description'] = 'Biomedical definitions'
annotation['property:sourceDatabase'] = 'glick'
annotation[
'property:sourceDescription'] = '<p>David M. Glick\'s <a href="http://www.portlandpress.com/pp/books/online/glick/search.htm">Glossary of Biochemistry and Molecular Biology</a>.</p><p>Made available by <a href="http://www.portlandpress.com/">Portland Press Limited</a>.</p>'
annotation['displayRelevance'] = '1000'
annotation['displayRank'] = "%d" % -len(
annotation['property:name'])
results.append(annotation)
return results
def on_explore_event(self, phrase, document):
results = []
client = kend.client.Client()
annotations = client.lookup(term='"%s"' % phrase,
database='UniProt',
limit='30')
xhtml = ''
if annotations is not None and len(annotations) >= 1:
for group in annotations[:10]:
for result in group.annotations[:10]:
annotation = kend.converter.Annotation.kend2spineapi(
result)
annotation['property:sourceDatabase'] = 'uniprot'
entry = self.visualiser.visualisable(
annotation) and self.visualiser.visualise(
annotation) or ''
if len(entry) > 0:
xhtml += u'<div class="expandable" title="{0}">{1}</div>'.format(
'UniProt entry %s' %
annotation.get('property:mnemonic', '???'), entry)
if len(xhtml) > 0:
annotation = spineapi.Annotation()
annotation['concept'] = 'Collated'
annotation['property:html'] = xhtml
annotation['property:name'] = 'UniProt sequences'
annotation['property:description'] = 'Protein sequence information'
annotation['property:sourceDatabase'] = 'uniprot'
annotation[
'property:sourceDescription'] = '<p>The Universal Protein Resource (<a href="http://www.uniprot.org/">UniProt</a>) is a comprehensive resource for protein sequence and annotation data.</p>'
annotation['displayRelevance'] = '700'
annotation['displayRank'] = "%d" % -len(
annotation['property:name'])
results.append(annotation)
return results
def on_explore_event(self, phrase, document):
results = []
client = kend.client.Client()
annotations = client.lookup(term='"%s"' % phrase,
database='PDB',
limit='30')
xhtml = ''
if annotations is not None and len(annotations) >= 1:
for group in annotations:
for result in group.annotations:
annotation = kend.converter.Annotation.kend2spineapi(
result)
annotation['property:sourceDatabase'] = 'pdb'
entry = self.visualiser.visualisable(
annotation) and self.visualiser.visualise(
annotation) or ''
if len(entry) > 0:
xhtml += entry
if len(xhtml) > 0:
annotation = spineapi.Annotation()
annotation['concept'] = 'Collated'
annotation['property:html'] = xhtml
annotation['property:name'] = 'Protein Data Bank structures'
annotation[
'property:description'] = 'Biological macromolecular structures'
annotation['property:sourceDatabase'] = 'pdb'
annotation[
'property:sourceDescription'] = '<p>The <a href="http://www.rcsb.org/">Protein Data Bank</a> of the Research Collaboratory for Structural Bioinformatics (<a href="http://home.rcsb.org/">RCSB</a>).</p>'
annotation['displayRelevance'] = '800'
annotation['displayRank'] = "%d" % -len(
annotation['property:name'])
results.append(annotation)
return results
