Tiago Lubiana -  Wikidata as a tool for biocuration of cell types
Channel: Biocuration Conference 2023
Date: 22/06/2023

*Session:* April 26 - Community 2

*Abstract:* The Human Cell Atlas and the boom of single-cell omics have put cell types at the center of modern biology. Various databases have become central to bioinformaticians, providing information about cell features (especially markers), which are core for labeling new datasets. Despite the centrality of cell types, the organization of information about these biological entities is still in its infancy. Unlike species and genes, there is no standard nomenclatural scheme for cell types nor clear boundaries for cell type assignment. Though most datasets use only ambiguous natural language, the Cell Ontology has provided unique identifiers for cell types for the past two decades. It is re-used in large efforts such as the Human Cell Atlas and HuBMAP. The Cell Ontology, however, is relatively cumbersome to contribute, requiring advanced skills in GitHub and ontology development. It currently provides identifiers for less than 2700 cell types. Wikidata - the all-purpose, open knowledge graph of the Wikimedia Foundation, gathering more than 100 million entities - is increasingly being used to integrate biomedical knowledge. It enables navigation and editing both from a visual interface and well-documented APIs. After efforts integrating data from Gene Ontology, Cellosaurus, Complex Portal, and beyond, its web-based SPARQL Query Service is mighty for biomedical discovery. In this work, we describe a 3-year effort to explore Wikidata as a platform to represent information about cell types. Wikidata currently hosts identifiers for over 4600 cell types, with over 1000 cross-references to CL, 8400 markers genes, 500 links to Wikipedia pages, and 150 links to openly-licensed images, all queryable via SPARQL. Its simple, anyone-can-contribute infrastructure enables fast biocuration, improving coverage and providing a field laboratory for large-scale organization of information about cell types. Wikidata is at a mature stage for cell type information and ready to be harnessed by Cell Ontology and bioinformatics workflows.