The Allen Institute for Brain Science has developed cell type naming conventions and standards for organizing and presenting cell type taxonomies in an effort to ensure these references are accessible to the scientific community. The resources below enable exploration of these standards and empower researchers to apply them to their own datasets.
For taxonomies to be broadly useful, the information they contain should be formatted and shared in a consistent manner. One major challenge in creating a cell type taxonomy schema is in defining its various components, such as annotations, metadata, and the underlying transcriptomic data. It is becoming increasingly important to separate out the data from the other components, and compartmentalize all components to avoid the need to download, open, or upload huge and unwieldy files. AIT addresses this challenge by extending and modifying the popular CELLxGENE schema.
Intuitive and informative cell type naming conventions are significant challenge in developing cell type taxonomies. To address this, we developed the Common Cell Type Nomenclature (CCN), which provides a framework for designating names for cell types. Since its initial development, some aspects of CCN have been wrapped into the Allen Institute Taxonomy Format and/or updated and implemented in the ABC Atlas Access schemas
