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basic.py
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# ----------------- Infectious ----------------- #
import logging
import rdflib
from rdflib.graph import Graph, URIRef
from SPARQLWrapper import SPARQLWrapper, RDF
from rdflib.plugins.memory import IOMemory
logging.basicConfig()
sparql = SPARQLWrapper("https://query.wikidata.org/sparql")
construct_query="""
PREFIX dis: <http://www.semanticweb.org/dorsa/ontologies/diseases.owl#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX wd: <http://www.wikidata.org/entity/>
PREFIX wikibase: <http://wikiba.se/ontology#>
PREFIX bd: <http://www.bigdata.com/rdf#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
CONSTRUCT {
?d rdf:type dis:disease .
?d dis:caused_by ?cause .
?cause rdf:type dis:infectious .
?d dis:named_after ?doctor .
?doctor rdf:type dis:doctor .
?doctor dis:name ?name .
?doctor dis:date_of_birth ?birth .
?doctor dis:date_of_death ?death .
?d dis:affects ?entity .
?entity rdf:type dis:biological_entity .
?d dis:associated_with ?specialty .
?specialty rdf:type dis:medical_specialty .
?d dis:has_symptom ?symptom .
?symptom rdf:type dis:symptom .
?d dis:outbreak_in ?country .
?country rdf:type dis:country .
?d dis:treated_with ?drug .
?drug rdf:type dis:drug .
?d dis:incidence ?number_of_cases .
?d dis:death_toll ?number_of_deaths .
?d dis:has_risk_factor ?risk_factor .
?risk_factor rdf:type dis:risk_factor .
?d dis:has_genetic_association ?gene .
?gene rdf:type dis:gene .
?d dis:confirmed_by ?test .
?test rdf:type dis:medical_examination .
?gene dis:determined_by ?determination_method .
?determination_method rdf:type dis:determination_method .
?article rdf:type dis:scientific_article .
?article dis:written_on ?d .
?article dis:written_by ?author .
?d dis:name ?dLabel .
?cause dis:name ?causeLabel .
?specialty dis:name ?specialtyLabel .
?symptom dis:name ?symptomLabel .
?drug dis:name ?drugLabel .
?gene dis:name ?geneLabel .
?determination_method dis:name ?determination_methodLabel .
?doctor dis:name ?doctorLabel .
?risk_factor dis:name ?risk_factorLabel .
?test dis:name ?testLabel .
?determination_method dis:name ?determination_methodLabel .
?country dis:name ?countryLabel .
}
WHERE{
?d wdt:P31 wd:Q18123741 .
OPTIONAL {?d wdt:P828 ?cause}
OPTIONAL {?d wdt:P1478 ?cause}
OPTIONAL {?d wdt:P1995 ?specialty}
OPTIONAL {?d wdt:P780 ?symptom}
OPTIONAL {?d wdt:P2176 ?drug}
OPTIONAL {?d wdt:P2293 ?gene}
OPTIONAL {?d wdt:P138 ?doctor}
OPTIONAL {?d wdt:P1120 ?number_of_deaths}
OPTIONAL {?d wdt:P1603 ?number_of_cases}
OPTIONAL {?d wdt:P1479 ?risk_factor}
OPTIONAL {?d wdt:P923 ?test}
OPTIONAL {?d wdt:P459 ?determination_method}
SERVICE wikibase:label { bd:serviceParam wikibase:language "en". }
}"""
sparql.setQuery(construct_query)
sparql.setReturnFormat(RDF)
memory_store=IOMemory()
graph_id=URIRef('http://www.semanticweb.org/store/diseases')
g = Graph(store=memory_store, identifier=graph_id)
rdflib.plugin.register('sparql', rdflib.query.Processor, 'rdfextras.sparql.processor', 'Processor')
rdflib.plugin.register('sparql', rdflib.query.Result, 'rdfextras.sparql.query', 'SPARQLQueryResult')
g = sparql.query().convert()
g.parse("diseases_rdf.owl", format="xml")
g.serialize("diseases_populated_1.owl", "xml")