CellOntologyMapper: Consensus mapping of cell type annotation.

CellOntologyMapper automates the standardization of cell type annotations in single-cell RNA-seq by mapping user-defined names to the Cell Ontology (CL) and Cell Taxonomy (CT). The framework constructs a comprehensive embedding database of 19,381 curated cell types using sentence transformers, large language models, and synonym expansion. User inputs, such as abbreviations (e.g., "dNK"), are processed through embedding similarity ranking and LLM amplification to resolve ambiguous or context-dependent labels. The system outputs standardized ontology terms with high accuracy (0.835 for CL, 0.911 for CT). Implemented as a Python package within the OmicVerse ecosystem and available via a web interface, CellOntologyMapper enables reproducible, large-scale single-cell meta-analysis by unifying diverse nomenclatures across studies, tissues, species, and disease states.