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###############################################################################
#
# 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: Utopia Documents standard biological lookups
#? www: http://utopiadocs.com/
#? urls: https://utopia.cs.manchester.ac.uk/
import kend.client
import kend.converter.Annotation
import re
import spineapi
import utopia.document
class CollatedVisualiser(utopia.document.Visualiser):
'''Visualise new (temporary) style collated definition annotations.'''
def visualisable(self, a):
return a.get('concept') == 'Collated' and 'property:html' in a
def visualise(self, a):
return a['property:html']
class ChEMBLVisualiser(utopia.document.Visualiser):
def visualisable(self, annotation):
return annotation.get('concept') == 'Definition' and 'property:name' in annotation and annotation.get('property:sourceDatabase') == 'ChEMBL'
def visualise(self, annotation):
entry = ''
moleculeFormula = annotation.get('property:moleculeFormula')
webpageUrl = annotation.get('property:webpageUrl')
imageUrl = annotation.get('property:imageUrl')
smiles = annotation.get('property:moleculeCanonicalSmiles')
inchi = annotation.get('property:moleculeStandardInchi')
synonyms = list(annotation.getAllProperties('property:synonym'))
description = annotation.get('property:description')
if moleculeFormula is not None:
moleculeFormula = moleculeFormula.replace(' ', '')
moleculeFormula = re.sub(r'([A-Z][a-z]?)', r'<span class="element">\1</span>', moleculeFormula)
moleculeFormula = re.sub(r'(\d+)', r'<sub>\1</sub>', moleculeFormula)
entry += u'<p><span class="formula">{0}</span></p>'.format(moleculeFormula)
if description is not None:
description = description.split(' ')
entry += u'<p>'
entry += u'{0}'.format(' '.join(description[:32]))
if len(description) > 32:
entry += u' <span class="readmore">{0}</span>'.format(' '.join(description[32:]))
entry += u'</p>'
if len(synonyms) > 0:
entry += u'<p>'
entry += u'Synonyms: {0}'.format(', '.join(synonyms[:10]))
if len(synonyms) > 10:
entry += u', <span class="readmore">{0}</span>'.format(', '.join(synonyms[10:]))
entry += u'</p>'
if webpageUrl is not None:
entry += u'<p><a href="{0}">See in ChEMBL...</a></p>'.format(webpageUrl)
if imageUrl is not None:
entry += u'<center><img src="{0}" /></center>'.format(imageUrl)
return entry
class BioLookupChEMBLAnnotator(utopia.document.Annotator):
"""ChEMBL lookup"""
visualiser = ChEMBLVisualiser()
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
class DrugBankVisualiser(utopia.document.Visualiser):
def visualisable(self, annotation):
return annotation.get('concept') == 'Definition' and 'property:name' in annotation and annotation.get('property:sourceDatabase') == 'Drugbank'
def visualise(self, annotation):
entry = ''
moleculeFormula = annotation.get('property:moleculeFormula')
webpageUrl = annotation.get('property:webpageUrl')
imageUrl = annotation.get('property:imageUrl')
smiles = annotation.get('property:smiles')
description = annotation.get('property:description')
inchi = annotation.get('property:inchi')
synonyms = list(annotation.getAllProperties('property:synonym'))
if moleculeFormula is not None:
moleculeFormula = moleculeFormula.replace(' ', '')
moleculeFormula = re.sub(r'([A-Z][a-z]?)', r'<span class="element">\1</span>', moleculeFormula)
moleculeFormula = re.sub(r'(\d+)', r'<sub>\1</sub>', moleculeFormula)
entry += u'<p><span class="formula">{0}</span></p>'.format(moleculeFormula)
if description is not None:
description = description.split(' ')
entry += u'<p>'
entry += u'{0}'.format(' '.join(description[:32]))
if len(description) > 32:
entry += u' <span class="readmore">{0}</span>'.format(' '.join(description[32:]))
entry += u'</p>'
if len(synonyms) > 0:
entry += u'<p>'
entry += u'Synonyms: {0}'.format(', '.join(synonyms[:10]))
if len(synonyms) > 10:
entry += u', <span class="readmore">{0}</span>'.format(', '.join(synonyms[10:]))
entry += u'</p>'
if webpageUrl is not None:
entry += u'<p><a href="{0}">See in DrugBank...</a></p>'.format(webpageUrl)
if imageUrl is not None:
entry += u'<center><img src="{0}" /></center>'.format(imageUrl)
return entry
class BioLookupDrugBankAnnotator(utopia.document.Annotator):
"""DrugBank lookup"""
visualiser = DrugBankVisualiser()
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
class GlickVisualiser(utopia.document.Visualiser):
def visualisable(self, annotation):
return annotation.get('concept') == 'Definition' and 'property:description' in annotation and annotation.get('property:sourceDatabase') == 'glick'
def visualise(self, annotation):
if 'property:description' in annotation:
return u'<p>{0}</p>'.format(annotation['property:description'])
class BioLookupGlickAnnotator(utopia.document.Annotator):
"""Glick lookup"""
visualiser = GlickVisualiser()
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
class PDBVisualiser(utopia.document.Visualiser):
def visualisable(self, annotation):
return annotation.get('concept') == 'Definition' and 'property:name' in annotation and annotation.get('property:sourceDatabase') == 'pdb'
def visualise(self, annotation):
entry = ''
desc = annotation['property:name'][0:200]
if len(desc) > 200:
desc += '...'
if 'property:identifier' in annotation:
entry += u'<p>%s</p>' % ('PDB entry %s' % annotation['property:identifier'].upper()[-4:]).strip()
if 'property:molecularDescription' in annotation:
entry += u'<p>{0}</p>'.format(annotation['property:molecularDescription'])
if 'property:imageUrl' in annotation:
entry += u'<center><img src="%s" width="200" heighth="200" /></center>' % annotation['property:imageUrl']
if 'property:webpageUrl' in annotation:
entry += u'<p><a href="%s">View RCSB web page...</a></p>' % annotation['property:webpageUrl']
return entry
class BioLookupPDBAnnotator(utopia.document.Annotator):
"""BioLookup PDB queries"""
visualiser = PDBVisualiser()
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
class UniProtVisualiser(utopia.document.Visualiser):
def visualisable(self, annotation):
return annotation.get('concept') == 'Definition' and 'property:webpageUrl' in annotation and annotation.get('property:sourceDatabase') == 'uniprot'
def visualise(self, annotation):
entry = ''
if 'property:description' in annotation:
entry += u'<p>{0}<p>'.format(annotation['property:description'])
if 'property:webpageUrl' in annotation:
entry += u'<p><a href="%s">View UniProt web page...</a></p>' % annotation['property:webpageUrl']
return entry
class BioLookupUniProtAnnotator(utopia.document.Annotator):
"""BioLookup UniProt queries"""
visualiser = UniProtVisualiser()
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
class DBpediaVisualiser(utopia.document.Visualiser):
def visualisable(self, annotation):
return annotation.get('concept') == 'Definition' and 'property:summary' in annotation and annotation.get('property:identifier', '').startswith('http://dbpedia.org/resource/')
def visualise(self, annotation):
entry = u'<p>{0}<p>'.format(annotation['property:summary'])
if 'property:imageUrl' in annotation:
entry += u'<center><img src="%s" width="200" heighth="200" /></center>' % annotation['property:imageUrl']
if 'property:webpageUrl' in annotation:
webpageUrl = annotation['property:webpageUrl']
if '?' in webpageUrl:
webpageUrl += '&'
else:
webpageUrl += '?'
webpageUrl += 'useformat=mobile'
entry += u'<p><a href="%s" target="sidebar">View Wikipedia web page...</a></p>' % webpageUrl
return entry
class BioLookupDBpediaAnnotator(utopia.document.Annotator):
"""BioLookup DBpedia queries"""
visualiser = DBpediaVisualiser()
def on_explore_event(self, phrase, document):
results = []
client = kend.client.Client()
annotations = client.lookupDBpedia(term='"%s"'%phrase, category=['Molecular_biology', 'Biochemistry', 'UtopiaBiology'], 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)
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'] = 'Wikipedia entries'
annotation['property:description'] = 'Community curated encyclopedia entries'
annotation['property:sourceDatabase'] = 'wikipedia'
annotation['property:sourceDescription'] = '<p>Structured <a href="http://www.wikipedia.org/">Wikipedia</a> information provided by the <a href="http://DBpedia.org/">DBpedia</a> project.</p>'
annotation['displayRelevance']='900'
annotation['displayRank']="%d" % -len(annotation['property:name'])
results.append(annotation)
return results
# class BioLookupGlickAnnotator(utopia.document.Annotator):
# """Glick lookup"""
#
# def on_explore_event(self, phrase, document):
# results = []
# client = kend.client.Client()
#
# annotations = client.lookup(term='"%s"'%phrase.encode('utf-8'), database='Glick', limit='30')
#
# # 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[:10]:
# for result in group.annotations[:10]:
# annotation=kend.converter.Annotation.kend2spineapi(result)
# annotation['property:html'] = annotation['property:description']
# annotation['property:description'] = 'Glick glossary entry'
# annotation['property:sourceDatabase'] = 'glick'
# annotation['displayRelevance']='1000'
# annotation['displayRank']="%d" % -len(annotation['property:name'])
# results.append(annotation)
#
# return results
#
# class BioLookupPDBAnnotator(utopia.document.Annotator):
# """BioLookup PDB queries"""
#
# def on_explore_event(self, phrase, document):
# results = []
#
# client = kend.client.Client()
#
# annotations = client.lookup(term='"%s"'%phrase.encode('utf-8'), database='PDB', limit='30')
#
# 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:description']=('PDB entry %s' % annotation.get('property:identifier', '').upper()[-4:]).strip()
# annotation['property:sourceDatabase'] = 'pdb'
# annotation['displayRelevance']='800'
# annotation['displayRank']="%d" % -len(annotation['property:name'])
# results.append(annotation)
#
# return results
#
# class BioLookupUniProtAnnotator(utopia.document.Annotator):
# """BioLookup UniProt queries"""
#
# def on_explore_event(self, phrase, document):
# results = []
#
# client = kend.client.Client()
# annotations = client.lookup(term='"%s"'%phrase.encode('utf-8'), database='UniProt', limit='30')
# 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:description'] = ('UniProt entry %s' % annotation.get('property:mnemonic', '')).strip()
# annotation['property:sourceDatabase'] = 'uniprot'
# annotation['displayRelevance']='700'
# annotation['displayRank']="%d" % -len(annotation['property:name'])
# results.append(annotation)
#
# return results
#
# class BioLookupDBpediaAnnotator(utopia.document.Annotator):
# """BioLookup DBpedia queries"""
#
# def on_explore_event(self, phrase, document):
# results = []
#
# client = kend.client.Client()
#
# annotations = client.lookupDBpedia(term='"%s"'%phrase.encode('utf-8'), category=['Molecular_biology', 'Biochemistry', 'UtopiaBiology'], limit='30')
#
# 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'] = 'wikipedia'
# annotation['displayRelevance']='900'
# annotation['displayRank']="%d" % -len(annotation['property:name'])
# results.append(annotation)
#
# return results
|
