def searchAlias(key, propertyID, value):
'''
To search wikidata through "Also known as"(alias) field.
Here keys maybe "entrez:1234" or "uniprot:P1234" or "go:1234"
'''
ID = ""
res = wikidata.search_Item(key)
if res:
ID = wikidata.search_claim(res, propertyID, value)
return ID
def run_MouseProtein(self, MouseProtein):
''' Run the bot for Mouse Protein item
Arguments:
MouseProtein : MouseProtein item constructed from mygeneinfo.api
Search for already created Human Gene item by wikidata label. If fails, as backup search from "Also known as"(alias) field
which has values as "uniprot:1234".
'''
key = MouseProtein.fieldsdict['Uniprot ID']
title = MouseProtein.fieldsdict['Name']
res = wikidata.search_Item(title)
uniprot = 'P352'
if res:
ID = wikidata.search_claim(res, uniprot, key)
if not ID:
res = wikidata.search_Item('uniprot:' + str(key))
ID = wikidata.search_claim(res, uniprot, key)
if not ID:
message = 'Failed to retreive MouseProtein item with uniprot:{UP} from search result:{RES}'.format(
RES=res, UP=key)
raise wikidata.WikidataSearchError(message)
Item = self.genewikidata.get_item(ID)
else:
message = 'Failed to search already created MouseProtein Wikidata item with UniprotID={val}'.format(
val=key)
raise wikidata.WikidataSearchError(message)
try:
CurMProtein = wikidata.construct_from_item(Item,
WItem.MouseProtein())
updatedMProtein, summary, updatedClaims = CurMProtein.updateWith(
MouseProtein)
#print updatedClaims
except Exception as err:
if isinstance(err, wikidata.WikidataConstructItem):
message = 'WikidataParseFailure. ErrorCause:{e} '.format(e=err)
raise wikidata.WikidataConstructItem(message)
else:
raise err
#ipdb.set_trace()
message = self.write(Item, updatedMProtein, updatedClaims)
self.logger(0, Item.getID(), msg=message)
def run_HumanGene(self, HumanGene):
''' Run the bot for the Human Gene item
Arguments:
HumanGene : HumanGene object constructed from mygeneinfo.api
Search for already created Human Gene item by wikidata label. If fails, as backup search from "Also known as"(alias) field
which has values as "entrez:1234".
'''
key = HumanGene.fieldsdict['Entrez Gene ID']
title = HumanGene.fieldsdict['Name']
res = wikidata.search_Item(title)
entrez = 'P351'
if res:
ID = wikidata.search_claim(res, entrez, key)
if not ID:
res = wikidata.search_Item('entrez:' + str(key))
ID = wikidata.search_claim(res, entrez, key)
if not ID:
message = 'Failed to retreive HumanGene item with entrez:{EZ} from search result:{RES}'.format(
RES=res, EZ=key)
raise wikidata.WikidataSearchError(message)
Item = self.genewikidata.get_item(ID)
else:
message = 'Failed to search by label already created HumanGene Wikidata item with EntrezID={val}'.format(
val=key)
raise wikidata.WikidataSearchError(message)
try:
CurHGene = wikidata.construct_from_item(Item, WItem.HumanGene())
updatedHGene, summary, updatedClaims = CurHGene.updateWith(
HumanGene)
#print updatedClaims
except Exception as err:
if isinstance(err, wikidata.WikidataConstructItem):
message = 'WikidataParseFailure. ErrorCause:{e} '.format(e=err)
raise wikidata.WikidataConstructItem(message)
else:
raise err
#ipdb.set_trace()
message = self.write(Item, updatedHGene, updatedClaims)
self.logger(0, Item.getID(), msg=message)
def parse_HumanProtein_json(gene_json, label):
'''Construct the Human Gene from gene_json. The entire fields are specified in WItem
Arguments:
gene_json - mygeneinfo json document for given gene
homoog_json - mygeneinfo json_documnet for corresponding mouse gene
'''
#ipdb.set_trace()
root = gene_json
HPItem = HumanProtein()
entrez = get(root, 'entrezgene')
uniprot = findReviewedUniprotEntry(get(root, 'uniprot'), entrez)
if not uniprot:
raise UniProtError('Could not find uniprot ID')
HPItem.setField("Uniprot ID", uniprot)
HPItem.setField("aliases", 'uniprot:' + str(uniprot))
#First setup Human protein Item with label = HGNC name and uniprot ID
name = get(root, 'name')
wikidata.setHumanProtein(name, label, uniprot)
#found in taxon wikidata item human=Q5 , protein=Q8054
#for proteins label= HGNC fullname
HPItem.setField("Name", name)
HPItem.setField("description", "human protein")
HPItem.setField("found in taxon", "Q5")
HPItem.setField("subclass of", "Q8054")
name = get(root, 'name')
HPItem.setField("Name", name)
# HPItem.setField("EC number", get(root, 'ec'))
#adding refseq id's based on valid accession prefixes
initial = get(get(root, 'refseq'), 'protein')
HPItem.setField("RefSeq Protein ID",
parse_accession(initial, "RefSeq Protein ID"))
HPItem.setField("Ensembl Protein ID", get(get(root, 'ensembl'), 'protein'))
#Wikidata items for GO terms
GO_ID = 'P686'
if get(root, 'go'):
GO_DICT = get(root, 'go')
for key in GO_DICT:
res_list = GO_DICT[key]
ID = []
#single term
if 'term' in res_list:
GID = []
title = res_list['term']
res = wikidata.search_Item(title)
if res:
for val in res:
if val['label'] == title:
GID = val['id']
wikidata.setLabel(GID, res_list['id'])
wikidata.set_GO_Terms(str(GID), res_list['id'][3:])
break
if not GID:
GID = searchAlias(res_list['id'], GO_ID,
res_list['id'][3:])
#Create GO Item if it does not exist
if not GID:
GID = wikidata.create_Item(title)
print "created GO item ", GO_ID, GID
wikidata.setLabel(GID, res_list['id'])
#add created id's for the go terms
wikidata.addClaim(GID, GO_ID, res_list['id'][3:],
'Gene Ontology ID')
CreatedItemlogger(Item=GID,
Type='GO TERM',
field='Gene Ontology ID',
value=res_list['id'],
name=str(key))
if not GID.title() in ID:
ID.append(GID.title())
else:
#mutiple terms in go field
for val in res_list:
#search for the item
title = val['term']
# title has multiple words seperated by /
# found
if title.find('/') != -1:
match = re.search(r'([\w ]*)\/.*', title)
title = match.group(1)
res = wikidata.search_Item(title)
GID = []
#search for the corresponding go term
if res:
for each_val in res:
if each_val['label'] == title:
GID = each_val['id']
wikidata.setLabel(GID, val['id'])
wikidata.set_GO_Terms(str(GID), val['id'][3:])
break
if not GID:
GID = searchAlias(val['id'], GO_ID, val['id'][3:])
#Create GO Item if it does not exist
if not GID:
GID = wikidata.create_Item(title)
print "created GO item ", GO_ID, GID
wikidata.setLabel(GID, val['id'])
wikidata.addClaim(GID, GO_ID, val['id'][3:],
'Gene Ontology ID')
CreatedItemlogger(Item=GID,
Type='GO TERM',
field='Gene Ontology ID',
value=val['id'][3:],
name=str(title))
if not GID.title() in ID:
ID.append(GID.title())
if key == 'CC':
HPItem.setField("cell component", ID)
elif key == 'MF':
HPItem.setField("molecular function", ID)
elif key == 'BP':
HPItem.setField("biological process", ID)
#PDB
pdbs = rcsb.pdbs_for_uniprot(uniprot)
if not pdbs:
pdbs = get(root, 'pdb')
HPItem.setField("PDB", pdbs)
#For "encoded by" property search for corresponding gene item. If not present ,create it and obtain wikidata identifier
#search_title = HGNC symbol
key = get(root, 'symbol')
ID = []
res = wikidata.search_Item(key)
#search for human gene, property = entrez
entrezID = 'P351'
if res:
ID = wikidata.search_claim(res, entrezID, entrez)
if not ID:
ID = searchAlias("entrez:" + str(entrez), entrezID, entrez)
#search result is null or corresponding human gene doesnot exist
if not ID:
#create human gene item
ID = wikidata.create_Item(key)
print "created human gene", entrez
elabel = "entrez:" + str(entrez)
wikidata.setLabel(ID, elabel)
#add entrez claim to human gene item
wikidata.addClaim(ID, 'P351', str(entrez), 'Entrez Gene ID')
CreatedItemlogger(Item=ID,
Type='Human Gene',
field='Entrez Gene ID',
value=entrez,
name=str(key))
HPItem.setField("encoded by", ID.title())
#ipdb.set_trace()
return HPItem
def parse_MouseProtein_json(Homolog_json):
'''Construct the Mouse Protein from gene_json. The entire fields are specified in WItem
Arguments:
gene_json - mygeneinfo json document for given gene
homolog_json - mygeneinfo json_documnet for corresponding mouse gene
'''
#ipdb.set_trace()
root = Homolog_json
MPItem = MouseProtein()
#found in taxon wikidata item mouse=Q83310 , protein=Q8054
MPItem.setField("Name", get(root, 'name'))
MPItem.setField("description", "mouse protein")
MPItem.setField("found in taxon", "Q83310")
MPItem.setField("subclass of", "Q8054")
name = get(root, 'name')
MPItem.setField("Name", name)
entrez = get(root, 'entrezgene')
uniprot = findReviewedUniprotEntry(get(root, 'uniprot'), entrez)
if not uniprot:
raise UniProtError('Could not find uniprot ID')
MPItem.setField("Uniprot ID", uniprot)
MPItem.setField("aliases", 'uniprot:' + str(uniprot))
#MPItem.setField("EC number", get(root, 'ec'))
initial = get(get(root, 'refseq'), 'protein')
MPItem.setField("RefSeq Protein ID",
parse_accession(initial, "RefSeq Protein ID"))
MPItem.setField("Ensembl Protein ID", get(get(root, 'ensembl'), 'protein'))
#GO TERMS
#Wikidata items for GO terms
GO_ID = 'P686'
if get(root, 'go'):
GO_DICT = get(root, 'go')
for key in GO_DICT:
res_list = GO_DICT[key]
ID = []
#single term
if 'term' in res_list:
GID = []
title = res_list['term']
res = wikidata.search_Item(title)
if res:
for val in res:
if val['label'] == title:
GID = val['id']
wikidata.setLabel(GID, res_list['id'])
wikidata.set_GO_Terms(str(GID), res_list['id'][3:])
break
if not GID:
GID = searchAlias(res_list['id'], GO_ID,
res_list['id'][3:])
#Create GO Item if it does not exist
if not GID:
GID = wikidata.create_Item(title)
print "created GO item ", GO_ID, GID
#add created id's for the go terms
wikidata.setLabel(GID, str(res_list['id']))
wikidata.addClaim(GID, GO_ID, res_list['id'][3:],
'Gene Ontology ID')
CreatedItemlogger(Item=GID,
Type='GO TERM',
field='Gene Ontology ID',
value=res_list['id'],
name=str(key))
if not GID.title() in ID:
ID.append(GID.title())
else:
#mutiple terms in go field
for val in res_list:
#search for the item
title = val['term']
# title has multiple words seperated by /
# found
if title.find('/') != -1:
match = re.search(r'([\w ]*)\/.*', title)
title = match.group(1)
res = wikidata.search_Item(title)
GID = []
#search for the corresponding go term
if res:
for each_val in res:
if each_val['label'] == title:
GID = each_val['id']
wikidata.setLabel(GID, str(val['id']))
wikidata.set_GO_Terms(str(GID), val['id'][3:])
break
#Create GO Item if it does not exist
if not GID:
GID = searchAlias(val['id'], GO_ID, val['id'][3:])
if not GID:
GID = wikidata.create_Item(title)
print "created GO item ", GO_ID, GID
#add created id's for the go terms
wikidata.setLabel(GID, str(val['id']))
wikidata.addClaim(GID, GO_ID, val['id'][3:],
'Gene Ontology ID')
CreatedItemlogger(Item=GID,
Type='GO TERM',
field='Gene Ontology ID',
value=val['id'][3:],
name=str(title))
if not GID.title() in ID:
ID.append(GID.title())
if key == 'CC':
MPItem.setField("cell component", ID)
elif key == 'MF':
MPItem.setField("molecular function", ID)
elif key == 'BP':
MPItem.setField("biological process", ID)
#PDB - CHECK what if Human proteins donot have pdb Id?
pdbs = rcsb.pdbs_for_uniprot(uniprot)
if not pdbs:
pdbs = get(root, 'pdb')
MPItem.setField("PDB", pdbs)
#For "encoded by" property search for corresponding gene item. If not present ,create it and obtain wikidata identifier
#search_title = HGNC symbol
key = get(root, 'symbol')
ID = []
res = wikidata.search_Item(key)
entrezID = 'P351'
#search for mouse gene, property = entrez
if res:
ID = wikidata.search_claim(res, entrezID, entrez)
if not ID:
ID = searchAlias("entrez:" + str(entrez), entrezID, entrez)
#search result is null or corresponding mouse gene doesnot exist
if not ID:
message = "Failed to retreive Mouse Gene wikidata item with entrez:{ez}".format(
ez=entrez)
raise wikidata.WikidataSearchError(message)
MPItem.setField("encoded by", ID.title())
#ipdb.set_trace()
return MPItem
def parse_MouseGene_json(homolog_json, gene_json):
'''Construct the Mouse Gene from gene_json. The entire fields are specified in WItem
Arguments:
gene_json - mygeneinfo json document for given gene
homolog_json - mygeneinfo json_documnet for corresponding mouse gene
'''
#ipdb.set_trace()
MGItem = MouseGene()
root = homolog_json
MGItem.setField("found in taxon", "Q83310")
MGItem.setField("subclass of", "Q7187")
MGItem.setField("description", "mouse gene")
#for mouse gene label = MGI symbol
MGItem.setField("Name", get(root, 'symbol'))
entrez = get(root, 'entrezgene')
MGItem.setField("Entrez Gene ID", entrez)
MGItem.setField("aliases", 'entrez:' + str(entrez))
MGItem.setField("Homologene ID", get(get(root, 'homologene'), 'id'))
MGItem.setField("gene symbol", get(root, 'symbol'))
MGItem.setField("Ensembl Gene ID", get(get(root, 'ensembl'), 'gene'))
MGItem.setField("Ensembl Transcript ID",
get(get(root, 'ensembl'), 'transcript'))
MGItem.setField("GenLoc_chr", get(get(root, 'genomic_pos'), 'chr'))
MGItem.setField("GenLoc_start", get(get(root, 'genomic_pos'), 'start'))
MGItem.setField("GenLoc_end", get(get(root, 'genomic_pos'), 'end'))
#MGItem.setField("AltSymbols", get(root, 'alias'))
#adding id's based on valid refseq prefixes
initial = get(get(root, 'refseq'), 'rna')
MGItem.setField("RefSeq", parse_accession(initial, "RefSeq"))
initial = get(get(root, 'accession'), 'rna')
MGItem.setField("RefSeq RNA ID", parse_accession(initial, "RefSeq RNA ID"))
#encodes -- search for mouse protein
key = get(root, 'name')
ID = []
res = wikidata.search_Item(key)
#search for mouse protein, property = uniprot ID
#most surely mouse protein is present, but still....
uniprot = findReviewedUniprotEntry(get(root, 'uniprot'), entrez)
uniprotID = 'P352'
if res:
ID = wikidata.search_claim(res, uniprotID, uniprot)
if not ID:
ID = searchAlias("uniprot:" + str(uniprot), uniprotID, uniprot)
#search result is null or corresponding human gene doesnot exist
if not ID:
#create mouse protein item
print "creating mouse protein with uniprot ID", uniprot
ID = wikidata.create_Item(key)
ulabel = "uniprot:" + str(uniprot)
wikidata.setLabel(ID, ulabel)
#add uniprot claim to mouse protein item
wikidata.addClaim(ID, 'P352', uniprot, 'Uniprot ID')
CreatedItemlogger(Item=ID,
Type='Mouse Protein',
field='Uniprot',
value='uniprot',
name=str(key))
MGItem.setField("encodes", ID.title())
#ortholog
key = get(gene_json, 'symbol')
ID = []
res = wikidata.search_Item(key)
#search for human gene, property = entrez ID
entrezID = 'P351'
if res:
ID = wikidata.search_claim(res, entrezID, get(gene_json, 'entrezgene'))
if not ID:
ID = searchAlias("entrez:" + str(get(gene_json, 'entrezgene')),
entrezID, get(gene_json, 'entrezgene'))
#search result is null or corresponding human gene doesnot exist
if not ID:
message = "Failed to retreive Human Gene wikidata item with entrez:{ez}".format(
ez=get(gene_json, 'entrezgene'))
raise wikidata.WikidataSearchError(message)
MGItem.setField("ortholog", ID.title())
#ipdb.set_trace()
return MGItem
def parse_HumanGene_json(gene_json, homolog_json):
'''Construct the Human Gene from gene_json. The entire fields are specified in WItem
Arguments:
gene_json - mygeneinfo json document for given gene
homolog_json - mygeneinfo json_documnet for corresponding mouse gene
'''
#ipdb.set_trace()
HGItem = HumanGene()
root = gene_json
HGItem.setField("found in taxon", "Q5")
HGItem.setField("description", "human gene")
HGItem.setField("subclass of", "Q7187")
#for genes label = HGNC symbol
HGItem.setField("Name", get(root, 'symbol'))
entrez = get(root, 'entrezgene')
HGItem.setField("Entrez Gene ID", entrez)
HGItem.setField("aliases", 'entrez:' + str(entrez))
HGItem.setField("Homologene ID", get(get(root, 'homologene'), 'id'))
HGItem.setField("gene symbol", get(root, 'symbol'))
HGItem.setField("Ensembl Gene ID", get(get(root, 'ensembl'), 'gene'))
HGItem.setField("Ensembl Transcript ID",
get(get(root, 'ensembl'), 'transcript'))
HGItem.setField("GenLoc_chr", get(get(root, 'genomic_pos'), 'chr'))
HGItem.setField("GenLoc_start", get(get(root, 'genomic_pos'), 'start'))
HGItem.setField("GenLoc_end", get(get(root, 'genomic_pos'), 'end'))
#HGItem.setField("AltSymbols", get(root, 'alias'))
#adding id's based on valid refseq prefixes
initial = get(get(root, 'refseq'), 'rna')
HGItem.setField("RefSeq", parse_accession(initial, "RefSeq"))
initial = get(get(root, 'accession'), 'rna')
HGItem.setField("RefSeq RNA ID", parse_accession(initial, "RefSeq RNA ID"))
HGItem.setField("HGNC ID", get(root, 'HGNC'))
HGItem.setField("OMIM ID", get(root, 'MIM'))
#encodes -- search for human protein
key = get(root, 'name')
ID = []
res = wikidata.search_Item(key)
#search for human protein, property = uniprot ID
#ipdb.set_trace()
uniprot = findReviewedUniprotEntry(get(root, 'uniprot'), entrez)
uniprotID = 'P352'
if res:
ID = wikidata.search_claim(res, uniprotID, uniprot)
if not ID:
ID = searchAlias("uniprot:" + str(uniprot), uniprotID, uniprot)
#search result is null or corresponding human protein doesnot exist
if not ID:
message = "Failed to retreive HumanProteinItem with Uniprot:{up}".format(
up=uniprot)
raise wikidata.WikidataSearchError(message)
#following convention of having capitalised wikidata identifiers
HGItem.setField("encodes", ID.title())
if not homolog_json:
return HGItem
#ortholog
key = get(homolog_json, 'symbol')
ID = []
res = wikidata.search_Item(key)
#search for mouse gene, property = entrez ID
entrezID = 'P351'
mouse_entrez = get(homolog_json, 'entrezgene')
if res:
ID = wikidata.search_claim(res, entrezID, mouse_entrez)
#backup search
if not ID:
ID = searchAlias("entrez:" + str(mouse_entrez), entrezID, mouse_entrez)
#search result is null or corresponding mouse gene doesnot exist
if not ID:
#create mouse gene item
ID = wikidata.create_Item(key)
#add entrez claim to mouse gene item
mouse_entrez = get(homolog_json, 'entrezgene')
elabel = "entrez:" + str(mouse_entrez)
wikidata.setLabel(ID, elabel)
wikidata.addClaim(ID, 'P351', str(mouse_entrez), 'Entrez Gene ID')
CreatedItemlogger(Item=ID,
Type='Mouse Gene',
field='Entrez',
value=mouse_entrez,
name=str(key))
print "created mouse gene item -- with entrez", mouse_entrez
#following convention of having capitalised wikidata identifiers
HGItem.setField("ortholog", ID.title())
#ipdb.set_trace()
return HGItem