ChatSpatial/CITATION.cff at main · cafferychen777/ChatSpatial · GitHub

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cff-version: 1.2.0
message: "If you use this software, please cite it as below."
type: software
title: "ChatSpatial: Schema-Enforced Orchestration for Auditable Cross-Ecosystem Spatial Transcriptomics Workflows"
version: "1.2.10"
date-released: "2026-05-21"
doi: "10.5281/zenodo.20647930"
url: "https://github.com/cafferychen777/ChatSpatial"
repository-code: "https://github.com/cafferychen777/ChatSpatial"
license: MIT
authors:
  - family-names: "Yang"
    given-names: "Caffery(Chen)"
    orcid: "https://orcid.org/0009-0009-9151-2901"
    affiliation: "Texas A&M University"
    email: "cafferychen777@tamu.edu"
abstract: >-
  ChatSpatial is a schema-enforced orchestration framework for spatial transcriptomics
  in which the LLM selects versioned tools and parameters rather than generating
  executable code. Built on the Model Context Protocol (MCP), it exposes 65 methods
  across 15 analytical categories from fragmented Python and R ecosystems through 20
  high-level tools with parameter constraints encoded in auditable schemas, enabling
  researchers to execute complex multi-tool workflows through natural language.
  ChatSpatial prioritizes human-steered discovery through schema-enforced tool-calling
  that ensures reproducibility and analytical fidelity, while leaving biological
  interpretation and method choice under expert control.
keywords:
  - spatial transcriptomics
  - artificial intelligence
  - bioinformatics integration
  - natural language processing
  - computational biology
  - software platform
  - cancer research
  - model context protocol
  - agentic workflow
preferred-citation:
  type: software
  title: "ChatSpatial: Schema-Enforced Orchestration for Auditable Cross-Ecosystem Spatial Transcriptomics Workflows"
  authors:
    - family-names: "Yang"
      given-names: "Caffery(Chen)"
      orcid: "https://orcid.org/0009-0009-9151-2901"
      affiliation: "Texas A&M University"
      email: "cafferychen777@tamu.edu"
  version: "1.2.10"
  date-released: "2026-05-21"
  doi: "10.5281/zenodo.20647930"
  url: "https://github.com/cafferychen777/ChatSpatial"
  repository-code: "https://github.com/cafferychen777/ChatSpatial"
  license: MIT