Wikidata as a semantic framework for the Gene Wiki initiative

Area of Science:

• Bioinformatics
• Computational Biology
• Molecular Biology

Background:

• Biological data is fragmented across numerous resources, hindering integration and rapid dissemination.
• Wikidata offers a collaborative, open platform for data consolidation and integration with Wikipedia.

Purpose of the Study:

• To enhance the accessibility and management of biological data by importing human and mouse genes and proteins into Wikidata.
• To establish a foundational dataset within Wikidata for improved data dissemination and integration by the scientific community and citizen scientists.

Main Methods:

• Imported 59,721 human genes and 73,355 mouse genes from NCBI into Wikidata.
• Imported 27,306 human proteins and 16,728 mouse proteins from UniProt's Swissprot subset into Wikidata.
• Utilized Wikidata's open and collaborative framework for data integration.

Main Results:

• Successfully created a comprehensive open dataset of human and mouse genes and proteins in Wikidata.
• Enabled direct population of Wikipedia Gene Wiki infoboxes using Wikidata, allowing for real-time data updates.
• Facilitated multilingual accessibility of biological data across 280 language Wikipedias.

Conclusions:

• Established a robust, open, and extensible data resource for human and mouse molecular biology and biochemistry.
• Enriched Wikipedia with structured biological information, serving as a central linking hub for the biological semantic web.
• Provided a SPARQL endpoint and data export functionality for scientific use and further integration.