def create_reference(self):
"""
Create wikidata references for interpro
Items:
Q3047275: InterPro
Properties:
stated in (P248)
imported from (P143)
software version (P348)
publication date (P577)
"""
# This same reference will be used for everything. Except for a ref to the interpro item itself
ref_stated_in = PBB_Core.WDItemID("Q3047275",
'P248',
is_reference=True)
ref_imported = PBB_Core.WDItemID("Q3047275", 'P143', is_reference=True)
ref_version = PBB_Core.WDString(self.version,
'P348',
is_reference=True)
ref_date = PBB_Core.WDTime(self.date.strftime("+%Y-%m-%dT00:00:00Z"),
'P577',
is_reference=True)
ref_ipr = PBB_Core.WDString(self.id, "P2926", is_reference=True)
self.reference = [
ref_stated_in, ref_imported, ref_version, ref_date, ref_ipr
]
for ref in self.reference:
ref.overwrite_references = True
def create_reference(self):
ref_stated_in = PBB_Core.WDItemID(self.MONDO_WDID, 'P248', is_reference=True)
ref_retrieved = PBB_Core.WDTime(self.retrieved.strftime('+%Y-%m-%dT00:00:00Z'), 'P813',
is_reference=True) # interpro ID
#ref_archive_url = PBB_Core.WDUrl(self.ref_url, 'P1065', is_reference=True)
#reference = [ref_stated_in, ref_retrieved, ref_archive_url]
reference = [ref_stated_in, ref_retrieved]
self.reference = reference
def make_ref_source(source_doc, id_prop, identifier, login=None):
"""
Reference is made up of:
stated_in: if the source has a release #:
release edition
else, stated in the source
link to id: link to identifier in source
retrieved: only if source has no release #
login: must be passed if you want to be able to create new release items
:param source_doc:
:param id_prop:
:param identifier:
:return:
"""
# source_doc = {'_id': 'uniprot', 'timestamp': '20161006'}
# source_doc = {'_id': 'ensembl', 'release': 86, 'timestamp': '20161005'}
source = source_doc['_id']
if source not in source_items:
raise ValueError(
"Unknown source for reference creation: {}".format(source))
if id_prop not in prop_ids:
raise ValueError(
"Unknown id_prop for reference creation: {}".format(id_prop))
link_to_id = PBB_Core.WDString(value=str(identifier),
prop_nr=prop_ids[id_prop],
is_reference=True)
if "release" in source_doc:
source_doc['release'] = str(source_doc['release'])
title = "{} Release {}".format(source_doc['_id'],
source_doc['release'])
description = "Release {} of {}".format(source_doc['release'],
source_doc['_id'])
edition_of_wdid = source_items[source_doc['_id']]
release = PBB_Helpers.Release(
title,
description,
source_doc['release'],
edition_of_wdid=edition_of_wdid).get_or_create(login)
stated_in = PBB_Core.WDItemID(value=release,
prop_nr='P248',
is_reference=True)
reference = [stated_in, link_to_id]
else:
date_string = source_doc['timestamp']
retrieved = datetime.strptime(date_string, "%Y%m%d")
stated_in = PBB_Core.WDItemID(value=source_items[source],
prop_nr='P248',
is_reference=True)
retrieved = PBB_Core.WDTime(retrieved.strftime('+%Y-%m-%dT00:00:00Z'),
prop_nr='P813',
is_reference=True)
reference = [stated_in, retrieved, link_to_id]
return reference
def make_ref(retrieved, genome_id):
refs = [
PBB_Core.WDItemID(value='Q20641742', prop_nr='P248',
is_reference=True), # stated in ncbi gene
PBB_Core.WDString(value=genome_id, prop_nr='P2249',
is_reference=True), # Link to Refseq Genome ID
PBB_Core.WDTime(retrieved.strftime('+%Y-%m-%dT00:00:00Z'),
prop_nr='P813',
is_reference=True)
]
return refs
def make_reference(source, id_prop, identifier, retrieved):
reference = [
PBB_Core.WDItemID(value=source_items[source],
prop_nr='P248',
is_reference=True), # stated in
PBB_Core.WDString(value=str(identifier),
prop_nr=prop_ids[id_prop],
is_reference=True), # Link to ID
PBB_Core.WDTime(retrieved.strftime('+%Y-%m-%dT00:00:00Z'),
prop_nr='P813',
is_reference=True)
]
return reference
def create_protein_ipr(uniprot_id, uniprot_wdid, families, has_part,
release_info, login):
"""
Create interpro relationships to one protein
:param uniprot_id: uniprot ID of the protein to modify
:type uniprot_id: str
:param uniprot_wdid: wikidata ID of the protein
:param families: list of ipr wd ids the protein is a (P279) subclass of
:param has_part: list of ipr wd ids the protein has (P527) has part
:return:
"""
date = release_info['date']
version = release_info['version']
# create ref
ref_stated_in = PBB_Core.WDItemID("Q3047275", 'P248', is_reference=True)
ref_imported = PBB_Core.WDItemID("Q3047275", 'P143', is_reference=True)
ref_version = PBB_Core.WDString(version, 'P348', is_reference=True)
ref_date = PBB_Core.WDTime(date.strftime("+%Y-%m-%dT00:00:00Z"),
'P577',
is_reference=True)
ref_ipr = PBB_Core.WDString(
"http://www.ebi.ac.uk/interpro/protein/{}".format(uniprot_id),
"P854",
is_reference=True)
reference = [ref_stated_in, ref_imported, ref_version, ref_date, ref_ipr]
for ref in reference:
ref.overwrite_references = True
statements = []
if families:
for f in families:
statements.append(
PBB_Core.WDItemID(value=f,
prop_nr='P279',
references=[reference]))
if has_part:
for hp in has_part:
statements.append(
PBB_Core.WDItemID(value=hp,
prop_nr='P527',
references=[reference]))
item = PBB_Core.WDItemEngine(wd_item_id=uniprot_wdid,
data=statements,
server=SERVER,
append_value=["P279", "P527", "P361"])
# print(item.get_wd_json_representation())
try:
item.write(login)
except WDApiError as e:
print(e)
PBB_Core.WDItemEngine.log(
'ERROR',
'{main_data_id}, "{exception_type}", "{message}", {wd_id}, {duration}'
.format(main_data_id=uniprot_id,
exception_type=type(e),
message=e.__str__(),
wd_id=uniprot_wdid,
duration=datetime.now()))
return
PBB_Core.WDItemEngine.log(
'INFO',
'{main_data_id}, "{exception_type}", "{message}", {wd_id}, {duration}'.
format(main_data_id=uniprot_id,
exception_type='',
message='created protein interpro relationships: {}'.format([
(x.prop_nr, x.value) for x in statements
]),
wd_id=uniprot_wdid,
duration=datetime.now()))
def __init__(self, object):
"""
:type self: object
"""
self.start = object["start"]
self.entrezgene = object["entrezgene"]
self.uniprotwikidataids = object["uniprotwikidataids"]
gene_annotations = self.annotate_gene()
self.genomeInfo = object["speciesInfo"][str(gene_annotations['taxid'])]
self.content = object
self.name = gene_annotations["name"]
self.logincreds = object["logincreds"]
if "_timestamp" in gene_annotations.keys():
self.annotationstimestamp = gene_annotations["_timestamp"]
self.wdid = object["wdid"]
# symbol:
self.symbol = gene_annotations["symbol"]
print(self.symbol)
# HGNC
if "HGNC" in gene_annotations:
if isinstance(gene_annotations["HGNC"], list):
self.hgnc = gene_annotations["HGNC"]
else:
self.hgnc = [gene_annotations["HGNC"]]
else:
self.hgnc = None
# Ensembl Gene & transcript
if "ensembl" in gene_annotations:
if "gene" in gene_annotations["ensembl"]:
if isinstance(gene_annotations["ensembl"]["gene"], list):
self.ensembl_gene = gene_annotations["ensembl"]["gene"]
else:
self.ensembl_gene = [gene_annotations["ensembl"]["gene"]]
else:
self.ensembl_gene = None
if "transcript" in gene_annotations["ensembl"]:
if isinstance(gene_annotations["ensembl"]["transcript"], list):
self.ensembl_transcript = gene_annotations["ensembl"]["transcript"]
else:
self.ensembl_transcript = [gene_annotations["ensembl"]["transcript"]]
else:
self.ensembl_transcript = None
# Homologene
if "homologene" in gene_annotations:
if isinstance(gene_annotations["homologene"]["id"], list):
self.homologene = [str(i) for i in gene_annotations["homologene"]["id"]]
else:
self.homologene = [str(gene_annotations["homologene"]["id"])]
else:
self.homologene = None
# Refseq
if "refseq" in gene_annotations:
if "rna" in gene_annotations["refseq"]:
if isinstance(gene_annotations["refseq"]["rna"], list):
self.refseq_rna = gene_annotations["refseq"]["rna"]
else:
self.refseq_rna = [gene_annotations["refseq"]["rna"]]
else:
self.refseq_rna = None
else:
self.refseq_rna = None
# MGI
if "MGI" in gene_annotations:
if isinstance(gene_annotations["MGI"], list):
self.MGI = gene_annotations["MGI"]
else:
self.MGI = [gene_annotations["MGI"]]
else:
self.MGI = None
self.chromosome = None
self.startpost = None
self.endpos = None
if "genomic_pos" in gene_annotations:
if isinstance(gene_annotations["genomic_pos"], list):
self.chromosome = []
self.startpos = []
self.endpos = []
for i in range(len(gene_annotations["genomic_pos"])):
if gene_annotations["genomic_pos"][i]["chr"] in ProteinBoxBotKnowledge.chromosomes[
self.genomeInfo["name"]].keys():
self.chromosome.append(ProteinBoxBotKnowledge.chromosomes[self.genomeInfo["name"]][
gene_annotations["genomic_pos"][i]["chr"]])
self.startpos.append(gene_annotations["genomic_pos"][i]["start"])
self.endpos.append(gene_annotations["genomic_pos"][i]["end"])
else:
self.chromosome = []
self.startpos = []
self.endpos = []
if gene_annotations["genomic_pos"]["chr"] in ProteinBoxBotKnowledge.chromosomes[
self.genomeInfo["name"]].keys():
self.chromosome.append(ProteinBoxBotKnowledge.chromosomes[self.genomeInfo["name"]][
gene_annotations["genomic_pos"]["chr"]])
self.startpos.append(gene_annotations["genomic_pos"]["start"])
self.endpos.append(gene_annotations["genomic_pos"]["end"])
self.encodes = None
if "uniprot" in gene_annotations.keys():
if "Swiss-Prot" in gene_annotations["uniprot"].keys():
if isinstance(gene_annotations["uniprot"]["Swiss-Prot"], list):
self.encodes = []
for uniprot in gene_annotations["uniprot"]["Swiss-Prot"]:
self.encodes.append(uniprot)
else:
self.encodes = [gene_annotations["uniprot"]["Swiss-Prot"]]
self.chromosomeHg19 = None
self.startposHg19 = None
self.endposHg19 = None
if "genomic_pos_hg19" in gene_annotations:
if isinstance(gene_annotations["genomic_pos_hg19"], list):
self.chromosomeHg19 = []
self.startposHg19 = []
self.endposHg19 = []
for i in range(len(gene_annotations["genomic_pos_hg19"])):
if gene_annotations["genomic_pos_hg19"][i]["chr"] in ProteinBoxBotKnowledge.chromosomes[
self.genomeInfo["name"]].keys():
self.chromosomeHg19.append(ProteinBoxBotKnowledge.chromosomes[self.genomeInfo["name"]][
gene_annotations["genomic_pos_hg19"][i]["chr"]])
self.startposHg19.append(gene_annotations["genomic_pos_hg19"][i]["start"])
self.endposHg19.append(gene_annotations["genomic_pos_hg19"][i]["end"])
else:
self.chromosomeHg19 = []
self.startposHg19 = []
self.endposHg19 = []
if gene_annotations["genomic_pos_hg19"]["chr"] in ProteinBoxBotKnowledge.chromosomes[
self.genomeInfo["name"]].keys():
self.chromosomeHg19.append(ProteinBoxBotKnowledge.chromosomes[self.genomeInfo["name"]][
gene_annotations["genomic_pos_hg19"]["chr"]])
self.startposHg19.append(gene_annotations["genomic_pos_hg19"]["start"])
self.endposHg19.append(gene_annotations["genomic_pos_hg19"]["end"])
# type of Gene
if "type_of_gene" in gene_annotations:
self.type_of_gene = []
if gene_annotations["type_of_gene"] == "ncRNA":
self.type_of_gene.append("Q427087")
if gene_annotations["type_of_gene"] == "snRNA":
self.type_of_gene.append("Q284578")
if gene_annotations["type_of_gene"] == "snoRNA":
self.type_of_gene.append("Q284416")
if gene_annotations["type_of_gene"] == "rRNA":
self.type_of_gene.append("Q215980")
if gene_annotations["type_of_gene"] == "tRNA":
self.type_of_gene.append("Q201448")
if gene_annotations["type_of_gene"] == "pseudo":
self.type_of_gene.append("Q277338")
if gene_annotations["type_of_gene"] == "protein-coding":
self.type_of_gene.append("Q20747295")
else:
self.type_of_gene = None
# Reference section
# Prepare references
refStatedIn = PBB_Core.WDItemID(value=self.genomeInfo["release"], prop_nr='P248', is_reference=True)
refStatedIn.overwrite_references = True
refImported = PBB_Core.WDItemID(value='Q20641742', prop_nr='P143', is_reference=True)
refImported.overwrite_references = True
timeStringNow = strftime("+%Y-%m-%dT00:00:00Z", gmtime())
refRetrieved = PBB_Core.WDTime(timeStringNow, prop_nr='P813', is_reference=True)
refRetrieved.overwrite_references = True
gene_reference = [refStatedIn, refImported, refRetrieved]
refStatedInEnsembl = PBB_Core.WDItemID(value= 'Q21996330', prop_nr='P248', is_reference=True)
refStatedInEnsembl.overwrite_references = True
refImportedEnsembl = PBB_Core.WDItemID(value='Q1344256', prop_nr='P143', is_reference=True)
refImportedEnsembl.overwrite_references = True
ensembl_reference = [refStatedInEnsembl, refImportedEnsembl, refRetrieved]
genomeBuildQualifier = PBB_Core.WDItemID(value=self.genomeInfo["genome_assembly"], prop_nr='P659',
is_qualifier=True)
genomeBuildPreviousQualifier = PBB_Core.WDItemID(value=self.genomeInfo["genome_assembly_previous"],
prop_nr='P659', is_qualifier=True)
prep = dict()
prep['P703'] = [PBB_Core.WDItemID(value=self.genomeInfo['wdid'], prop_nr='P703',
references=[copy.deepcopy(gene_reference)])]
if self.genomeInfo["name"] == "human":
prep['P353'] = [
PBB_Core.WDString(value=self.symbol, prop_nr='P353', references=[copy.deepcopy(gene_reference)])]
prep['P351'] = [
PBB_Core.WDString(value=str(self.entrezgene), prop_nr='P351', references=[copy.deepcopy(gene_reference)])]
prep['P279'] = [PBB_Core.WDItemID(value='Q7187', prop_nr='P279', references=[copy.deepcopy(gene_reference)])]
if "type_of_gene" in vars(self):
if self.type_of_gene != None:
for i in range(len(self.type_of_gene)):
prep['P279'].append(PBB_Core.WDItemID(value=self.type_of_gene[i], prop_nr='P279',
references=[copy.deepcopy(gene_reference)]))
if "ensembl_gene" in vars(self):
if self.ensembl_gene != None:
prep['P594'] = []
for ensemblg in self.ensembl_gene:
prep['P594'].append(
PBB_Core.WDString(value=ensemblg, prop_nr='P594', references=[copy.deepcopy(gene_reference)]))
if "ensembl_transcript" in vars(self):
if self.ensembl_transcript != None:
prep['P704'] = []
for ensemblt in self.ensembl_transcript:
prep['P704'].append(
PBB_Core.WDString(value=ensemblt, prop_nr='P704', references=[copy.deepcopy(gene_reference)]))
if "encodes" in vars(self):
if self.encodes != None:
prep['P688'] = []
for uniprot in self.encodes:
if uniprot in self.uniprotwikidataids.keys():
prep['P688'].append(PBB_Core.WDItemID(value=self.uniprotwikidataids[uniprot], prop_nr='P688', references=[copy.deepcopy(gene_reference)]))
if "hgnc" in vars(self):
if self.hgnc != None:
prep['P354'] = []
for hugo in self.hgnc:
prep['P354'].append(
PBB_Core.WDString(value=hugo, prop_nr='P354', references=[copy.deepcopy(gene_reference)]))
if "homologene" in vars(self):
if self.homologene != None:
prep['P593'] = []
for ortholog in self.homologene:
prep['P593'].append(
PBB_Core.WDString(value=ortholog, prop_nr='P593', references=[copy.deepcopy(gene_reference)]))
if "refseq_rna" in vars(self):
if self.refseq_rna != None:
prep['P639'] = []
for refseq in self.refseq_rna:
prep['P639'].append(
PBB_Core.WDString(value=refseq, prop_nr='P639', references=[copy.deepcopy(gene_reference)]))
if "chromosome" in vars(self):
prep['P1057'] = []
if self.chromosome != None:
for chrom in list(set(self.chromosome)):
prep['P1057'].append(
PBB_Core.WDItemID(value=chrom, prop_nr='P1057', references=[copy.deepcopy(gene_reference)]))
if "startpos" in vars(self):
if not 'P644' in prep.keys():
prep['P644'] = []
if self.startpos != None:
for pos in self.startpos:
prep['P644'].append(
PBB_Core.WDString(value=str(pos), prop_nr='P644', references=[copy.deepcopy(ensembl_reference)],
qualifiers=[copy.deepcopy(genomeBuildQualifier)]))
if "endpos" in vars(self):
if not 'P645' in prep.keys():
prep['P645'] = []
if self.endpos != None:
for pos in self.endpos:
prep['P645'].append(
PBB_Core.WDString(value=str(pos), prop_nr='P645', references=[copy.deepcopy(ensembl_reference)],
qualifiers=[copy.deepcopy(genomeBuildQualifier)]))
if "startposHg19" in vars(self):
if not 'P644' in prep.keys():
prep['P644'] = []
if self.startposHg19 != None:
for pos in self.startposHg19:
prep['P644'].append(
PBB_Core.WDString(value=str(pos), prop_nr='P644', references=[copy.deepcopy(ensembl_reference)],
qualifiers=[copy.deepcopy(genomeBuildPreviousQualifier)]))
if "endposHg19" in vars(self):
if not 'P644' in prep.keys():
prep['P645'] = []
if self.endposHg19 != None:
for pos in self.endposHg19:
prep['P645'].append(
PBB_Core.WDString(value=str(pos), prop_nr='P645', references=[copy.deepcopy(ensembl_reference)],
qualifiers=[copy.deepcopy(genomeBuildPreviousQualifier)]))
if "MGI" in vars(self):
prep['P671'] = []
if self.MGI != None:
for mgi in self.MGI:
prep['P671'].append(PBB_Core.WDString(value=mgi, prop_nr='P671',
references=[copy.deepcopy(gene_reference)]))
if "alias" in gene_annotations.keys():
if isinstance(gene_annotations["alias"], list):
self.synonyms = []
for alias in gene_annotations["alias"]:
self.synonyms.append(alias)
else:
self.synonyms = [gene_annotations["alias"]]
self.synonyms.append(self.symbol)
print(self.synonyms)
else:
self.synonyms = None
data2add = []
for key in prep.keys():
for statement in prep[key]:
data2add.append(statement)
print(statement.prop_nr, statement.value)
if self.wdid != None:
# if self.encodes != None:
wdPage = PBB_Core.WDItemEngine(self.wdid, item_name=self.name, data=data2add, server="www.wikidata.org",
domain="genes")
if wdPage.get_description() == "":
wdPage.set_description(description=self.genomeInfo['name'] + ' gene', lang='en')
if wdPage.get_description(lang='fr') == "" or wdPage.get_description(lang='fr') == "gène":
wdPage.set_description(description="Un gène " + self.genomeInfo['fr-name'], lang='fr')
if wdPage.get_description(lang='nl') == "" or wdPage.get_description(lang='nl') == "gen":
wdPage.set_description(description="Een "+ self.genomeInfo['nl-name']+ " gen", lang='nl')
if self.synonyms != None:
wdPage.set_aliases(aliases=self.synonyms, lang='en', append=True)
print(self.wdid)
self.wd_json_representation = wdPage.get_wd_json_representation()
PBB_Debug.prettyPrint(self.wd_json_representation)
PBB_Debug.prettyPrint(data2add)
# print(self.wd_json_representation)
wdPage.write(self.logincreds)
print("aa")
else:
#if self.encodes != None:
wdPage = PBB_Core.WDItemEngine(item_name=self.name, data=data2add, server="www.wikidata.org",
domain="genes")
if wdPage.get_description() != "":
wdPage.set_description(description=self.genomeInfo['name'] + ' gene', lang='en')
if wdPage.get_description(lang='fr') == "" or wdPage.get_description(lang='fr') == "gène":
wdPage.setdescription(description="Un gène " + self.genomeInfo['fr-name'], lang='fr')
if wdPage.get_description(lang='nl') == "" or wdPage.get_description(lang='nl') == "gen":
wdPage.setdescription(description="Een "+ self.genomeInfo['nl-name']+ " gen", lang='nl')
if self.synonyms != None:
wdPage.set_aliases(aliases=self.synonyms, lang='en', append=True)
self.wd_json_representation = wdPage.get_wd_json_representation()
PBB_Debug.prettyPrint(self.wd_json_representation)
PBB_Debug.prettyPrint(data2add)
# print(self.wd_json_representation)
self.wdid = wdPage.write(self.logincreds)
PBB_Core.WDItemEngine.log('INFO', '{main_data_id}, "{exception_type}", "{message}", {wd_id}, {duration}'.format(
main_data_id=str(self.entrezgene),
exception_type='',
message=f.name,
wd_id=self.wdid,
duration=time.time()-self.start
))