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Merge pull request #2 from wikipathways/ontologies-and-authors
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merging ontologies and authors back into master
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@AlexanderPico
AlexanderPico authored Oct 18, 2019
2 parents 59c341a + b619e02 commit 7e43a9b
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Showing 2 changed files with 143 additions and 7 deletions.
2 changes: 1 addition & 1 deletion scheduled_bots/geneprotein/OrthologBot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -163,7 +163,7 @@ def do_item(entrezgene, orthologs, reference, entrez_homo, entrez_taxon, taxon_w

# get metadata about sources
mgd = MyGeneDownloader()
metadata = mgd.get_metadata()['src_version']
metadata = mgd.get_metadata()['src']['src_version']

log_name = '{}-{}.log'.format(__metadata__['name'], run_id)
if wdi_core.WDItemEngine.logger is not None:
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148 changes: 142 additions & 6 deletions scheduled_bots/wikipathways/bot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,12 @@
'found in taxon': 'P703',
'PubMed ID': 'P698',
'curator': 'P1640',
'retrieved': 'P813'
'retrieved': 'P813',
'medical condition': 'P1050',
'author': 'P50',
'author name string': 'P2093',
'main subject': 'P921',
'anatomical location': 'P927'
}

core_props = get_default_core_props()
Expand Down Expand Up @@ -91,8 +96,16 @@ def main(retrieved, fast_run, write):
if filename not in files:
if filename != "./":
files.append(url + filename)
wpids = []
for file in set(files):
if "rdf-authors" in file: # get the most accurate file
print(file)
u = requests.get(file)
with closing(u), zipfile.ZipFile(io.BytesIO(u.content)) as archive:
for member in archive.infolist():
nt_content = archive.read(member)
temp.parse(data=nt_content.decode(), format="turtle")
print("size: "+str(len(temp)))

if "rdf-wp" in file: # get the most accurate file
print(file)
u = requests.get(file)
Expand All @@ -102,6 +115,18 @@ def main(retrieved, fast_run, write):
temp.parse(data=nt_content.decode(), format="turtle")
print("size: "+str(len(temp)))

# Disease Ontology
doid_qid_query = wdi_core.WDItemEngine.execute_sparql_query("SELECT * WHERE {?qid wdt:P699 ?doid . }")
doid_qid = dict()
for result in doid_qid_query["results"]["bindings"]:
doid_qid[result["doid"]["value"]] = result["qid"]["value"].replace("http://www.wikidata.org/entity/", "")

# Pathway Ontology
poid_qid_query = wdi_core.WDItemEngine.execute_sparql_query("SELECT * WHERE {?qid wdt:P7333 ?poid . }")
poid_qid = dict()
for result in poid_qid_query["results"]["bindings"]:
poid_qid[result["poid"]["value"]] = result["qid"]["value"].replace("http://www.wikidata.org/entity/", "")

wp_query = """prefix dcterm: <http://purl.org/dc/terms/>
prefix wp: <http://vocabularies.wikipathways.org/wp#>
SELECT DISTINCT ?wpid WHERE {
Expand All @@ -111,6 +136,7 @@ def main(retrieved, fast_run, write):
wp:organism <http://purl.obolibrary.org/obo/NCBITaxon_9606> .
}"""

wpids = []
qres = temp.query(wp_query)
for row in qres:
wpids.append(str(row[0]))
Expand Down Expand Up @@ -153,17 +179,22 @@ def run_one(pathway_id, retrieved, fast_run, write, login, temp):
qres3 = temp.query(query)

for row in qres3:
#pathway_iri = str(row[0])
pw_id = str(row[1])
pw_label = str(row[2])
description = str(row[3])

# P31 = instance of
prep["P31"] = [
wdi_core.WDItemID(value="Q4915012", prop_nr="P31", references=[copy.deepcopy(pathway_reference)])]

prep["P1476"] = [wdi_core.WDMonolingualText(value=str(row[2]), prop_nr="P1476", references=[copy.deepcopy(pathway_reference)])]
prep["P1476"] = [wdi_core.WDMonolingualText(value=pw_label, prop_nr="P1476", references=[copy.deepcopy(pathway_reference)])]

# P2410 = WikiPathways ID
prep["P2410"] = [wdi_core.WDString(pathway_id, prop_nr='P2410', references=[copy.deepcopy(pathway_reference)])]

# P2888 = exact match
prep["P2888"] = [wdi_core.WDUrl("http://identifiers.org/wikipathways/" + str(row[1]), prop_nr='P2888',
prep["P2888"] = [wdi_core.WDUrl("http://identifiers.org/wikipathways/" + pw_id, prop_nr='P2888',
references=[copy.deepcopy(pathway_reference)])]

query = """
Expand Down Expand Up @@ -199,6 +230,111 @@ def run_one(pathway_id, retrieved, fast_run, write, login, temp):
prep["P2860"] = []
prep['P2860'].append(wdi_core.WDItemID(value=str(pmid_qid), prop_nr='P2860', references=[copy.deepcopy(pathway_reference)]))

author_query = """
PREFIX wp: <http://vocabularies.wikipathways.org/wp#>
SELECT ?author ?authorName ?authorHomepage ?authorQIRI
WHERE {
<http://identifiers.org/wikipathways/""" + pathway_id + """> dc:creator ?author .
?author a foaf:Person ;
foaf:name ?authorName ;
foaf:homepage ?authorHomepage .
OPTIONAL { ?author owl:sameAs ?authorQIRI . }
"""
author_query_res = temp.query(author_query)
prep["P2093"] = []

authors = {pathway_id: {"author_strings": [], "authors_qid": []}}
for row in author_query_res:
author_name = str(row[1])
print("author_name")
print(author_name)
author_homepage = str(row[2])
print("author_homepage")
print(author_homepage)

# P2093 = author name string
author_url_qualifier = wdi_core.WDString(value=author_homepage, prop_nr="P2699", is_qualifier=True)
prep["P2093"].append(wdi_core.WDString(author_name, prop_nr='P2093', qualifiers=[copy.deepcopy(author_url_qualifier)], references=[copy.deepcopy(pathway_reference)]))

prep["P50"] = []
if row[3] != 'None': # TODO: only if row[3] exists (authorQIRI)
for row in author_query_res:
author_iri = str(row[0])
author_name = str(row[1])
print("author_name")
print(author_name)
author_qiri = str(row[3])
author_qid = author_qiri.replace("https://www.wikidata.org/wiki/", "")
print("author_qid")
print(author_qid)

# P50 = author
prep["P50"].append(wdi_core.WDString(author_qid, prop_nr='P50', references=[copy.deepcopy(pathway_reference)]))

disease_ontology_query = """
PREFIX wp: <http://vocabularies.wikipathways.org/wp#>
PREFIX dcterms: <http://purl.org/dc/terms/>
SELECT ?diseaseOntologyTerm
WHERE {
?pathwayRDF wp:diseaseOntologyTag ?diseaseOntologyTerm ;
foaf:page ?pathway ;
dcterms:identifier \"""" + pathway_id + """\"^^xsd:string .
}
"""
disease_ontology_query_res = temp.query(disease_ontology_query)
prep["P1050"] = []
for row in disease_ontology_query_res:
disease_ontology_iri = str(row[0])
doid = disease_ontology_iri.replace("http://purl.obolibrary.org/obo/DOID_", "DOID:")
print("doid")
print(doid)

# P1050 = medical condition
prep["P1050"].append(wdi_core.WDItem(doid_qid[doid], prop_nr='P1050', references=[copy.deepcopy(pathway_reference)]))

pw_ontology_query = """
PREFIX wp: <http://vocabularies.wikipathways.org/wp#>
PREFIX dcterms: <http://purl.org/dc/terms/>
SELECT ?pwOntologyTerm
WHERE {
?pathwayRDF wp:pathwayOntologyTag ?pwOntologyTerm ;
foaf:page ?pathway ;
dcterms:identifier \"""" + pathway_id + """\"^^xsd:string .
}
"""
pw_ontology_query_res = temp.query(pw_ontology_query)
prep["P921"] = []
for row in pw_ontology_query_res:
pw_ontology_iri = str(row[0])
poid = pw_ontology_iri.replace("http://purl.obolibrary.org/obo/PW_", "PW:")
print("poid")
print(poid)

# P921 = main subject
prep["P921"].append(wdi_core.WDItem(poid_qid[poid], prop_nr='P921', references=[copy.deepcopy(pathway_reference)]))

#TODO: Propose Cell Type Ontology ID as new property, add release item, associate terms with WD items.
#cell_type_ontology_query = """
# PREFIX wp: <http://vocabularies.wikipathways.org/wp#>
# PREFIX dcterms: <http://purl.org/dc/terms/>
# SELECT ?cellTypeOntologyTerm
# WHERE {
# ?pathwayRDF wp:cellTypeOntologyTag ?cellTypeOntologyTerm ;
# foaf:page ?pathway ;
# dcterms:identifier \"""" + pathway_id + """\"^^xsd:string .
# }
# """
#cell_type_ontology_query_res = temp.query(cell_type_ontology_query)
#prep["P927"] = []
#for row in cell_type_ontology_query_res:
# cell_type_ontology_iri = str(row[0])
# ctoid = cell_type_ontology_iri.replace("http://purl.obolibrary.org/obo/CL_", "CL:")
# print("ctoid")
# print(ctoid)

# P927 = anatomical location
# prep["P927"].append(wdi_core.WDItem(qid[ctoid], prop_nr='P927', references=[copy.deepcopy(pathway_reference)]))

data2add = []
for key in prep.keys():
for statement in prep[key]:
Expand All @@ -212,8 +348,8 @@ def run_one(pathway_id, retrieved, fast_run, write, login, temp):
ref_handler=update_retrieved_if_new_multiple_refs,
core_props=core_props)

wdPage.set_label(str(row[2]), lang="en")
wdPage.set_description(str(row[3]), lang="en")
wdPage.set_label(pw_label, lang="en")
wdPage.set_description(description, lang="en")

try_write(wdPage, record_id=pathway_id, record_prop=PROPS['Wikipathways ID'],
edit_summary="Updated a Wikipathways pathway", login=login, write=write)
Expand Down

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