Get Python code for Wikidata query to get source code repos of software used by a paper identified by uppercase-normalized DOI

[Daniel-Mietchen]

What we would like is to provide a DOI (which has to be uppercase-normalized, by Wikidata convention) and then find the source code repos for any software that Wikidata knows as having been used (via P4510) in the paper identified by the provided DOI.

[Daniel-Mietchen]

Here is a Wikidata query for that:

#title: Source code repos of software used by a paper identified by uppercase-normalized DOI
SELECT ?paper ?repo WHERE {
  VALUES ?doi { "10.1371/JOURNAL.PONE.0134894"}
  ?paper wdt:P356 ?doi ;
         wdt:P4510 ?software .
  ?software wdt:P1324 ?repo .
}

It can be run directly on the Wikidata SPARQL endpoint or via the following Python snippet:

# pip install sparqlwrapper
# https://rdflib.github.io/sparqlwrapper/

import sys
from SPARQLWrapper import SPARQLWrapper, JSON

endpoint_url = "https://query.wikidata.org/sparql"

query = """#title: Source code repos of software used by a paper identified by uppercase-normalized DOI
SELECT ?paper ?repo WHERE {
  VALUES ?doi { "10.1371/JOURNAL.PONE.0134894"}
  ?paper wdt:P356 ?doi ;
         wdt:P4510 ?software .
  ?software wdt:P1324 ?repo .
}"""


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)

for result in results["results"]["bindings"]:
    print(result)

[Daniel-Mietchen]

Here is a query that gives the list of source code repos for which Wikidata has information about papers using the corresponding software.

[Daniel-Mietchen]

Here is a list of upper-case normalized DOIs for which Wikidata knows at least some software that (1) has been used in the corresponding paper and (2) has its source code repo indicated in Wikidata

[Daniel-Mietchen]

Here is a list of upper-case normalized DOIs for which Wikidata knows at least some software that (1) has been used in the corresponding paper and (2) has its CRAN repo indicated in Wikidata.

[Daniel-Mietchen]

Here is a list of CRAN packages sorted by number of papers for which Wikidata knows at least one paper having used the package.

[Daniel-Mietchen]

Here is a list of Bioconductor packages sorted by number of papers for which Wikidata knows at least one paper having used the package.