def add_citations(self, property_list, result):
"""
Function to add the cites property
This looks up the pudmed id in wikidata so that it can create the appropriate link
This is copied from lines 170 - 188 of PathwayBot.py as of Mar 13
:param property_list: the list of property entries that will be made
:param result: the data from Reactome
:return:
"""
pubmed_citations = []
for citation in result['publication']['value']:
pubmed_citations.append(
"\"" + citation.replace("http://identifiers.org/pubmed/", "") +
"\"")
if not pubmed_citations:
return
term_to_add = acquire_wikidata_links.WDGetData('pmid', 'P2860',
self.wikidata_sparql)
term_to_add.add_multiple_terms(pubmed_citations, property_list,
self.reference)
for term in term_to_add.get_missing_terms():
if term not in global_variables.used_wd_ids['pmid']:
global_variables.used_wd_ids['pmid'].append(term)
def add_go_term(self, property_list, result):
"""
Function to add the instance of property for a GO term
This looks up the go identifier id in wikidata so that it can create the appropriate link
:param property_list: the list of property entries that will be made
:param result: the data from Reactome
:return:
"""
term_to_add = acquire_wikidata_links.WDGetData('goterm', 'P31',
self.wikidata_sparql)
term_to_add.add_term(result['goTerm']['value'], property_list,
self.reference)
for term in term_to_add.get_missing_terms():
if term not in global_variables.used_wd_ids['goterms']:
global_variables.used_wd_ids['goterms'].append(term)
def add_part_of(self, property_list, result):
""" Function to add the part of property
This looks up the reactome id in wikidata so that it can create the appropriate lin
:param property_list: the list of property entries that will be made
:param result: the data from Reactome
:return:
"""
part_of = []
for partof in result['isPartOf']['value']:
part_of.append("\"" + partof + "\"")
if not part_of:
return
term_to_add = acquire_wikidata_links.WDGetData('reactomeid', 'P361',
self.wikidata_sparql)
term_to_add.add_multiple_terms(part_of, property_list, self.reference)
for term in term_to_add.get_missing_terms():
if term not in global_variables.used_wd_ids['reactome']:
global_variables.used_wd_ids['reactome'].append(term)
def add_modprot(self, property_list, result):
"""
function to add modified protein item to wikidata
:param property_list: the list of property entries that will be made
:param result: the data from Reactome
:return:
"""
# P279 = subclass of
term_to_add = acquire_wikidata_links.WDGetData('uniprotid', 'P279',
self.wikidata_sparql)
term_to_add.add_term(result['protein']['value'], property_list,
self.reference)
for term in term_to_add.get_missing_terms():
if term not in global_variables.used_wd_ids['proteins']:
global_variables.used_wd_ids['proteins'].append(term)
# P703 = found in taxon
property_list["P703"] = [
wdi_core.WDItemID(value=self.species,
prop_nr='P703',
references=[copy.deepcopy(self.reference)])
]
# P2888 = exact match
pro = global_variables.get_pro_for_id(self.reactome_id)
if pro != '':
pro = pro.replace(':', '_')
url = 'http://purl.obolibrary.org/obo/{0}'.format(pro)
property_list["P2888"] = [
wdi_core.WDUrl(url,
prop_nr='P2888',
references=[copy.deepcopy(self.reference)])
]
# P3937 = Reactome ID
property_list["P3937"] = [
wdi_core.WDString(value=self.reactome_id, prop_nr='P3937')
]
AddModProt.add_modprot_parts(self, property_list, result)
def add_modprot_parts(self, property_list, result):
"""
Function to write the parts of a modified protein which might be
other reactome entities such as sets containing complexes
:param property_list: the list of property entries that will be made
:param result: the data from Reactome
:return:
"""
has_part = []
part_qty = []
for partof in result['hasPart']['value']:
vars = partof.split(' [')
if len(vars) != 2:
continue
else:
modref_parts = vars[1].split('] ')
if len(modref_parts) != 2:
continue
else:
name = vars[0]
modref = modref_parts[0]
loc = modref_parts[1]
chebi = global_variables.get_chebi_from_mod(modref)
if chebi != '':
has_part.append('\"' + chebi + '\"')
part_qty.append(loc)
term_to_add = acquire_wikidata_links.WDGetData('chebi', 'P527',
self.wikidata_sparql)
term_to_add.add_multiple_terms(has_part, property_list, self.reference,
None, '', part_qty)
for term in term_to_add.get_missing_terms():
if term not in global_variables.used_wd_ids['chebi']:
global_variables.used_wd_ids['chebi'].append(term)
def add_entity_parts(self, property_list, result, part_type=''):
"""
Function to write the parts of an entity which might be
other reactome entities such as sets containing complexes
:param property_list: the list of property entries that will be made
:param result: the data from Reactome
:return:
"""
has_part = []
part_qty = []
has_protein = []
protein_qty = []
has_simple = []
simple_qty = []
partname = 'hasPart'
if part_type != '':
partname = part_type
for partof in result[partname]['value']:
if partof == 'null':
break
datatype, ref, quantity, st_id = partof.split(' ')
if datatype == 'EWASMOD':
# ignore these for now
continue
elif datatype == 'EWAS':
protein = "\"" + ref + "\""
if protein not in has_protein:
has_protein.append(protein)
protein_qty.append(quantity)
elif datatype == "SE":
se = "\"" + ref + "\""
if se not in has_simple:
has_simple.append(se)
simple_qty.append(quantity)
elif self.is_reactome_datatype(datatype):
part = "\"" + st_id + "\""
if part not in has_part:
has_part.append(part)
part_qty.append(quantity)
term_to_add = acquire_wikidata_links.WDGetData('reactomeid', 'P527',
self.wikidata_sparql)
term_to_add.add_multiple_terms(has_part, property_list, self.reference,
part_qty, part_type)
for term in term_to_add.get_missing_terms():
if term not in global_variables.used_wd_ids['reactome']:
global_variables.used_wd_ids['reactome'].append(term)
term_to_add = acquire_wikidata_links.WDGetData('uniprotid', 'P527',
self.wikidata_sparql)
term_to_add.add_multiple_terms(has_protein, property_list,
self.reference, protein_qty, part_type)
for term in term_to_add.get_missing_terms():
if term not in global_variables.used_wd_ids['proteins']:
global_variables.used_wd_ids['proteins'].append(term)
term_to_add = acquire_wikidata_links.WDGetData('chebi', 'P527',
self.wikidata_sparql)
term_to_add.add_multiple_terms(has_simple, property_list,
self.reference, simple_qty, part_type)
for term in term_to_add.get_missing_terms():
if term not in global_variables.used_wd_ids['chebi']:
global_variables.used_wd_ids['chebi'].append(term)