NicheAgent Artifacts: Prompts, Schemas, Alias Maps, and Ontology Rules for Training-Free Spatial Transcriptomics Annotation

Description This record contains the full set of artifacts used by NicheAgent, a training-free framework for spatial transcriptomics annotation that combines prototype-based inference with ontology-constrained LLM verification. The archive includes: LLM prompt templates used across all stages of the pipeline, including: system prompts, cell-level label selection prompts, strict JSON-output prompts, and role-specific prefixes for Analyst, Consensus, and Reviewer agents. JSON schemas defining the exact input–output contracts expected from LLMs, ensuring deterministic parsing and reproducibility. Alias maps specifying the mapping between canonical region labels and LLM-facing aliases, including documentation of how aliases are constructed and applied during inference. Ontology rule files encoding biological constraints (required and forbidden marker genes) used to validate or reject LLM-proposed labels. These artifacts correspond exactly to the logic implemented in the NicheAgent codebase and are intended to support transparent reuse, replication, and extension of training-free, LLM-assisted spatial transcriptomics annotation pipelines. The files are provided in plain-text and JSON formats for long-term accessibility. For full reproducibility, users are encouraged to pair these artifacts with the corresponding dataset-specific alias maps and runtime configuration used in each experiment.