bridgedb / Wikidata2Bridgedb

Creation of BridgeDb mapping databases from Wikidata

Wikidata2Bridgedb

Creation of human and SARS-related corona virus gene/protein mapping database.

How to get the data in the BridgeDb files?

The data comes from Wikidata, and can be retrieved by running the SPARQL queries in the queries folder with the Wikidata Query Service.

curl -H "Accept: text/tab-separated-values" --data-urlencode query@queries/publications.rq -G https://query.wikidata.org/bigdata/namespace/wdq/sparql -o publications.tsv

How to create a Derby file

mvn clean install assembly:single
java -cp target/Wikidata2BridgeDb-0.0.2-SNAPSHOT-jar-with-dependencies.jar org.bridgedb.wikidata.Publications

How to cite?

If you use material from this repository, please cite either or both of these:

• Kutmon, Martina, & Willighagen, Egon. (2020). BridgeDb: Human and SARS-related corona virus gene/protein mapping database derived from Wikidata (Version 2020-05-20) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.3835696
• Waagmeester A, Willighagen EL, Su AI, Kutmon M, Labra Gayo JE, Fernández-Álvarez D, et al. (2020). A protocol for adding knowledge to Wikidata, a case report. bioRxiv. http://biorxiv.org/lookup/doi/10.1101/2020.04.05.026336