User:ProteinBoxBot/2020 sarscov2

Overall summary

This sprint is aimed at covering the gene (Q7187) and protein (Q8054) of the sars-cov2 and related corona viruses in Wikidata. This is achieved through drafting a set of entity schemas that describe the semantic landscape and drive the bot development. Deliverables are this linked-data landschape, two bots that regularly update genes, proteins and pathways on Wikidata.

Status

Sprint ended. Preparing a manuscript for peer review.

Participants

• Andra Waagmeester
• Jjkoehorst
• Egon Willighagen
• Jose Emilio Labra Gayo
• Martina Kutmon

Gameplan

• Create an EntitySchema for Virus Done
• Create a draft bot to populate Viral reference genomes for Corona Virusses Done
• Run the bot on a single strain Done
• Adapt the bot to handle other strains Done

Entity Schema

We have developed a schema for Virus Gene (EntitySchema)

Bot development

We developed a first bot specifically for SARS-CoV-2 (Q82069695). This bot used mygene.info to get gene annotation into Wikidata. The next step is to adapt the bot to work with other strains.

Example virus

Virus	Virus ID	wikidata item	mapping
SARS-CoV-2 (Q82069695)	2697049	Q82069695

Results

Bots

• Bot to align genes and proteins from mygene.info, NCBI Eutils and Uniprot on Wikidata
  • weekly updates
• Bot to align COVID19 pathways from WikiPathways on Wikidata
  • 2x weekly updates

EntitySchemas

• virus
• strain
• disease
• virus gene
• virus protein

Publications

• (biorxiv) A protocol for adding knowledge to Wikidata, a case report

Downstream use

• BridgeDb identifier mapping database
• WikiPathways.org website linking to Wikidata, Scholia, and other databases using ID mappings