wikidata.md

BioClients.wikidata

Wikidata

Wikidata is a collaboratively edited RDF/Sparql knowledge graph used by Wikipedia. The structured infobox data in Wikipedia is from Wikidata. Not to be confused with DBPedia which is built from Wikipedia.

• https://en.wikipedia.org/wiki/Wikidata

This module provides access to Wikidata Sparql endpoint. Focus on biomedical entities and particularly GeneWiki.

• https://www.wikidata.org
• https://www.wikidata.org/wiki/User:ProteinBoxBot/SPARQL_Examples

GeneWiki

• https://www.wikidata.org/wiki/Wikidata:WikiProject_Gene_Wiki
• https://github.com/SuLab/genewikiworld

Dependencies

• WikidataIntegrator

Usage

$ python3 -m BioClients.wikidata.Client -h
usage: Client.py [-h] [--o OFILE] [--rqfile RQFILE] [--rq RQ] [-v]
                 {query,list_drugTargetPairs,list_geneDiseasePairs}

Wikidata utilities

positional arguments:
  {list_drugTargetPairs,list_geneDiseasePairs,query,test}
                        OPERATION

options:
  -h, --help            show this help message and exit
  --o OFILE             output (TSV)
  --rqfile RQFILE       input Sparql file
  --rq RQ               input Sparql string
  -v, --verbose

$ python3 -m BioClients.wikidata.Client list_geneDiseasePairs