def _get_name_by_id(self, entity_id):
entity_term = self.tree.find("TERM/[@id='%s']" % entity_id)
if entity_term is None:
logger.debug('Term %s for entity not found' % entity_id)
return None
name = entity_term.find("name")
if name is None:
logger.debug('Entity without a name')
return None
try:
dbid = entity_term.attrib["dbid"]
except:
#logger.debug('No grounding information for %s' % name.text)
return self._get_valid_name(name.text)
dbids = dbid.split('|')
hgnc_ids = [i for i in dbids if i.startswith('HGNC')]
up_ids = [i for i in dbids if i.startswith('UP')]
#TODO: handle protein families like 14-3-3 with IDs like
# XFAM:PF00244.15, FA:00007
if hgnc_ids:
if len(hgnc_ids) > 1:
lisp_str = entity_term.attrib.get('lisp')
if lisp_str is None:
hgnc_id = re.match(r'HGNC\:([0-9]*)',
hgnc_ids[0]).groups()[0]
else:
parts = lisp_str.split('(TERM :ID ')
scores = {}
for p in parts:
res = re.findall('HGNC::\|(.*)\|', p)
if res:
hgnc_id = res[0]
score = re.findall(':SCORE ([^ ]+)', p)[0]
scores[hgnc_id] = float(score)
if scores:
sorted_ids = sorted(scores.items(), key=operator.itemgetter(1))
hgnc_id = sorted_ids[-1][0]
else:
hgnc_id = re.match(r'HGNC\:([0-9]*)', hgnc_ids[0]).groups()[0]
hgnc_name = self._get_hgnc_name(hgnc_id)
return self._get_valid_name(hgnc_name)
elif up_ids:
if len(hgnc_ids) > 1:
logger.debug('%d UniProt IDs reported.' % len(up_ids))
up_id = re.match(r'UP\:([A-Z0-9]*)', up_ids[0]).groups()[0]
# First try to get HGNC name
hgnc_name = up_client.get_hgnc_name(up_id)
if hgnc_name is not None:
return self._get_valid_name(hgnc_name)
# Next, try to get the gene name
gene_name = up_client.get_gene_name(up_id)
if gene_name is not None:
return self._get_valid_name(gene_name)
# By default, return the text of the name tag
name_txt = name.text.strip('|')
return self._get_valid_name(name_txt)
def _get_name_by_id(self, entity_id):
entity_term = self.tree.find("TERM/[@id='%s']" % entity_id)
name = entity_term.find("name")
if name is None:
warnings.warn('Entity without a name')
return ''
try:
dbid = entity_term.attrib["dbid"]
except:
warnings.warn('No grounding information for %s' % name.text)
return self._get_valid_component_name(name.text)
dbids = dbid.split('|')
hgnc_ids = [i for i in dbids if i.startswith('HGNC')]
up_ids = [i for i in dbids if i.startswith('UP')]
#TODO: handle protein families like 14-3-3 with IDs like
# XFAM:PF00244.15, FA:00007
if hgnc_ids:
if len(hgnc_ids) > 1:
warnings.warn('%d HGNC IDs reported.' % len(hgnc_ids))
hgnc_id = re.match(r'HGNC\:([0-9]*)', hgnc_ids[0]).groups()[0]
hgnc_name = self._get_hgnc_name(hgnc_id)
return self._get_valid_component_name(hgnc_name)
elif up_ids:
if len(hgnc_ids) > 1:
warnings.warn('%d UniProt IDs reported.' % len(up_ids))
up_id = re.match(r'UP\:([A-Z0-9]*)', up_ids[0]).groups()[0]
up_rdf = up_client.query_protein(up_id)
# First try to get HGNC name
hgnc_name = up_client.get_hgnc_name(up_rdf)
if hgnc_name is not None:
return self._get_valid_component_name(hgnc_name)
# Next, try to get the gene name
gene_name = up_client.get_gene_name(up_rdf)
if gene_name is not None:
return self._get_valid_component_name(gene_name)
# By default, return the text of the name tag
name_txt = name.text.strip('|')
return self._get_valid_component_name(name_txt)
def _get_name_by_id(self, entity_id):
entity_term = self.tree.find("TERM/[@id='%s']" % entity_id)
name = entity_term.find("name")
if name is None:
warnings.warn('Entity without a name')
return ''
try:
dbid = entity_term.attrib["dbid"]
except:
warnings.warn('No grounding information for %s' % name.text)
return self._get_valid_component_name(name.text)
dbids = dbid.split('|')
hgnc_ids = [i for i in dbids if i.startswith('HGNC')]
up_ids = [i for i in dbids if i.startswith('UP')]
#TODO: handle protein families like 14-3-3 with IDs like
# XFAM:PF00244.15, FA:00007
if hgnc_ids:
if len(hgnc_ids) > 1:
warnings.warn('%d HGNC IDs reported.' % len(hgnc_ids))
hgnc_id = re.match(r'HGNC\:([0-9]*)', hgnc_ids[0]).groups()[0]
hgnc_name = self._get_hgnc_name(hgnc_id)
return self._get_valid_component_name(hgnc_name)
elif up_ids:
if len(hgnc_ids) > 1:
warnings.warn('%d UniProt IDs reported.' % len(up_ids))
up_id = re.match(r'UP\:([A-Z0-9]*)', up_ids[0]).groups()[0]
up_rdf = up_client.query_protein(up_id)
# First try to get HGNC name
hgnc_name = up_client.get_hgnc_name(up_rdf)
if hgnc_name is not None:
return self._get_valid_component_name(hgnc_name)
# Next, try to get the gene name
gene_name = up_client.get_gene_name(up_rdf)
if gene_name is not None:
return self._get_valid_component_name(gene_name)
# By default, return the text of the name tag
name_txt = name.text.strip('|')
return self._get_valid_component_name(name_txt)
def _get_agent_from_entity(self, entity_id):
qstr = "$.entities.frames[(@.frame_id is \'%s\')]" % entity_id
res = self.tree.execute(qstr)
if res is None:
return None
try:
entity_term = res.next()
except StopIteration:
logger.debug(' %s is not an entity' % entity_id)
return None
# This is the default name, which can be overwritten
# below for specific database entries
agent_name = self._get_valid_name(entity_term['text'])
db_refs = {}
for xr in entity_term['xrefs']:
ns = xr['namespace']
if ns == 'uniprot':
up_id = xr['id']
db_refs['UP'] = up_id
# Look up official names in UniProt
hgnc_name = up_client.get_hgnc_name(up_id)
if hgnc_name is not None:
agent_name = self._get_valid_name(hgnc_name)
else:
gene_name = up_client.get_gene_name(up_id)
if gene_name is not None:
agent_name = self._get_valid_name(gene_name)
elif ns == 'interpro':
db_refs['IP'] = xr['id']
elif ns == 'chebi':
db_refs['CHEBI'] = xr['id'][6:]
elif ns == 'go':
db_refs['GO'] = xr['id'][3:]
elif ns == 'hmdb':
db_refs['HMDB'] = xr['id'][4:]
db_refs['TEXT'] = entity_term['text']
mod_terms = entity_term.get('modifications')
mods = []
muts = []
if mod_terms is not None:
for m in mod_terms:
if m['type'].lower() == 'mutation':
# Evidence is usualy something like "V600E"
# We could parse this to get the amino acid
# change that happened.
mutation_str = m.get('evidence')
# TODO: sometimes mutation_str is "mutant", "Mutant",
# "mutants" - this indicates that there is a mutation
# but not the specific type. We should encode this
# somehow as a "blank" mutation condition
mut = self._parse_mutation(mutation_str)
if mut is not None:
muts.append(mut)
elif m['type'].lower() == 'phosphorylation' or\
m['type'].lower() == 'phosphorylated':
site = m.get('site')
if site is not None:
mod_res, mod_pos = self._parse_site_text(site)
mod = ModCondition('phosphorylation', mod_res, mod_pos)
mods.append(mod)
else:
mods.append(ModCondition('phosphorylation'))
elif m['type'].lower() == 'ubiquitination':
mods.append(ModCondition('ubiquitination'))
else:
logger.warning('Unhandled entity modification type: %s' %
m['type'])
agent = Agent(agent_name, db_refs=db_refs, mods=mods, mutations=muts)
return agent
def test_get_hgnc_name_nonhuman():
hgnc_name = uniprot_client.get_hgnc_name('P31938')
assert(hgnc_name is None)
def test_get_hgnc_name_human():
hgnc_name = uniprot_client.get_hgnc_name('P00533')
assert(hgnc_name == 'EGFR')
def test_query_protein_deprecated():
g = uniprot_client.query_protein('Q8NHX1')
assert(g is not None)
assert(uniprot_client.get_hgnc_name('Q8NHX1') == 'MAPK3')
