Variantbot

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Welcome to WikiProject Gene Wiki This page documents the Variant bot, that it is maintained within the Wikiproject Gene Wiki. It is a WikiProject dedicated to make and maintiain Wikidata as a central hub of linked knowledge on Genes, Proteins, Diseases, Drugs, and related concepts.

Purpose

The Variantbot aims at synchronising Wikidata with knowledge on genetic variants. The bot account is a spin of of the ProteinBoxBot, where currently genetic variants with an association with cancer from the CIViC database are being synchronised with Wikidata Integrator. It is our intention to continue this effort under this bot account. At the same time gradually extending the coverage of other variant resources on Wikidata. The Variantbot will be a sisterbot of the ProteinBoxBot and as such will use the same platform

The team

• Andra Waagmeester (genewiki)
• Greg stupp (genewiki)
• Emitraka (genewiki)
• Annika Jacobsen (LUMC/FAIR)

Data models

• CIViC
• Clinvar
• Cancer Biomarkers database

Sources

• CIViC
• clinvar
• Cancer Biomarkers Database

Query examples

Source specific queries

Source-specific queries are those queries that are written with one specific primary source in mind.

1. The different variant types covered in CIViCdb
2. Get the CIViC citation corpus

Combinatorial queries

Combinatorial queries are those queries that are written with the intention to combine Wikidata items from multiple primary sources

1. Get known variants reported in CIViC database for genes reported in a Wikipathways pathway : Bladder Cancer

Federated queries

Federated queries are SPARQL queries that allow querying across SPARQL endpoints. The Wikidata Query Service supports Federated queries against a set of vetted external endpoints. The SPARQL endpoint of Wikidata can be any remote SPARQL endpoint as long that endpoint supports federation.