scrape_icd_9.py

# pip install sparqlwrapper
# https://rdflib.github.io/sparqlwrapper/
import wikipediaapi
import urllib.parse
import sys
from SPARQLWrapper import SPARQLWrapper, JSON
import json
from tqdm import tqdm
endpoint_url = "https://query.wikidata.org/sparql"

query = """SELECT DISTINCT ?item ?itemLabel ?article ?icd9code WHERE {
  SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE]". }
  {
    SELECT DISTINCT ?item ?article ?icd9code WHERE {
        ?item p:P1692 ?statement0.
        ?statement0 (ps:P1692) _:anyValueP1692.
        FILTER(EXISTS { ?statement0 prov:wasDerivedFrom ?reference. })
        OPTIONAL {
          ?article schema:about ?item .
          ?article schema:inLanguage "en" .
          FILTER (SUBSTR(str(?article), 1, 25) = "https://en.wikipedia.org/")
        }
        ?item wdt:P1692 ?icd9code.
      }
    }
}
"""


def get_results(endpoint_url, query):
    user_agent = "WDQS-example Python/%s.%s" % (sys.version_info[0], sys.version_info[1])
    # TODO adjust user agent; see https://w.wiki/CX6
    sparql = SPARQLWrapper(endpoint_url, agent=user_agent)
    sparql.setQuery(query)
    sparql.setReturnFormat(JSON)
    return sparql.query().convert()


results = get_results(endpoint_url, query)

parsed_urls = set()

wiki_wiki = wikipediaapi.Wikipedia('MyProjectName ([email protected])', 'en')

parsed_wikipedia = {}
article_to_icd_mapping = {}
sections_to_ignore = ["See also", "Explanatory notes","External links", "References", "Citations", "Cited texts", "Further reading"]

for result in tqdm(results["results"]["bindings"]):
    if "article" not in result:
        continue
    wikipedia_url = result["article"]["value"]
    icd_code = result["icd9code"]["value"]
    qid = result["itemLabel"]
    entity_name = wikipedia_url.split("/")[-1]
    entity_name = urllib.parse.unquote(entity_name)

    if wikipedia_url not in parsed_urls:
        page = wiki_wiki.page(entity_name)
        if not page.exists():
            continue
        if wikipedia_url == page.fullurl:
            parsed_urls.add(wikipedia_url)
            sections = list(filter(lambda s: s.title not in sections_to_ignore, page.sections))
            sections = [{"title": s.title, "text": s.full_text()} for s in sections]
            article = {"title": entity_name, "icd_code": [icd_code], "sections": sections, "summary": page.summary}
            parsed_wikipedia[entity_name] = article
    else:
        article = parsed_wikipedia[entity_name]
        if icd_code not in article["icd_code"]:
            article["icd_code"].append(icd_code)
            parsed_wikipedia[entity_name] = article

with open("wiki_icd_9.json", "w+") as f:
    json.dump(parsed_wikipedia, f)
print("DONE")