Wikidata as a knowledge graph for the life sciences

Area of Science:

• Biomedical Informatics
• Knowledge Representation
• Data Science

Background:

• Wikidata is a collaborative knowledge base integrating data from genomics, proteomics, pathways, chemical compounds, and diseases.
• It adheres to FAIR principles (Findability, Accessibility, Interoperability, Reusability).

Purpose of the Study:

• To describe the scope of biomedical knowledge within Wikidata.
• To present open-source tools for data integration and synchronization.
• To demonstrate Wikidata's utility in biomedical research.

Main Methods:

• Utilized Wikidata's existing data structures for biomedical information.
• Developed open-source tools for data ingestion and synchronization with source databases.
• Showcased use cases through practical applications.

Main Results:

• Wikidata encompasses a broad and deep collection of biomedical data.
• Developed tools effectively add and synchronize information, enhancing data quality and accessibility.
• Demonstrated successful applications in ontology curation, disease diagnosis, and drug repurposing.

Conclusions:

• Wikidata serves as a valuable, community-driven resource for biomedical knowledge.
• The developed tools streamline data integration, supporting diverse research applications.
• Wikidata has significant potential to advance biomedical research and applications.