Wikidata

Wikidata aggregates and exposes biomedical knowledge—including genomics, proteomics, genetic variants, pathways, chemical compounds, and diseases—to support data integration, curation, and computational queries in biomedical research.

Key Features:

• FAIR principles: Implements Findability, Accessibility, Interoperability, and Reusability for biomedical data.
• Domain coverage: Hosts structured statements covering genomics, proteomics, genetic variants, pathways, chemical compounds, and diseases.
• Data integration and synchronization: Supports addition and synchronization of data from primary source databases using open-source integration tools.
• Programmatic access: Provides programmatic access via the MediaWiki API and the Wikidata SPARQL endpoint for querying and manipulating data.
• Crowdsourced curation: Enables community-driven curation and collaborative editing of biomedical ontologies and knowledge.
• Phenotype-based resources: Provides datasets usable for phenotype-based diagnosis and mining of disease markers and correlations.
• Drug repurposing data: Contains chemical compound data and pathway interaction information applicable to drug repurposing investigations.

Scientific Applications:

• Biomedical ontology curation: Supports collaborative refinement and expansion of biomedical ontologies through community curation.
• Phenotype-based diagnosis research: Facilitates mining of phenotypic and disease-associated data to identify diagnostic markers and correlations.
• Drug repurposing investigations: Enables exploration of chemical compounds and pathway relationships for repurposing existing drugs.
• Integrative and translational research: Aggregates and synchronizes data from multiple repositories to support integrative and translational biomedical analyses.

Methodology:

Addition and synchronization of data from source databases using open-source tools, with programmatic querying and manipulation via the MediaWiki API and the Wikidata SPARQL endpoint.