biocypher_mcp

Provides guidance on BioCypher schema configuration. For comprehensive details, refer to the dedicated BioCypher LLM documentation. Returns: Dict containing schema configuration overview and references to detailed documentation

Returns the expected BioCypher project structure and instructions for project creation. This function provides the expected structure that should be created by the cookiecutter template. You should check the files and directories yourself to determine if a project already exists. IMPORTANT: If you determine that the project does NOT exist, you MUST use cookiecutter to create it. Do NOT manually create the project structure. Always use the cookiecutter template. Args: project_path: Path to check for an existing project (default: current directory) Returns: Dict containing: - project_path: The path that was checked - expected_structure: The expected directory structure from cookiecutter template - instruction_if_not_exists: Clear instruction on what to do if the project doesn't exist - cookiecutter_template_url: URL of the cookiecutter template

Provides detailed information about the adapter creation workflow. For implementation details, code examples, and patterns, refer to the dedicated BioCypher LLM documentation. Returns: Dict containing the workflow structure and phases

Provides guidance on BioCypher resource management and download/cache functionality. For comprehensive details, refer to the dedicated BioCypher LLM documentation. Returns: Dict containing resource management overview and references to detailed documentation

Provides guidance on which implementation approach to use based on data characteristics. Args: data_characteristics: Dictionary describing the data source characteristics Returns: Dict containing decision guidance and recommendations

Provides detailed guidance for a specific phase of the adapter creation workflow. For implementation code examples and patterns, refer to the BioCypher LLM documentation: - https://biocypher.org/BioCypher/llms-adapters.txt (adapter guide) - https://biocypher.org/BioCypher/llms-example-adapter.txt (working example) Args: phase_number: The phase number (1-5) to get guidance for Returns: Dict containing detailed guidance for the specified phase

Main entry point tool that provides information about available BioCypher workflows. Returns: Dict containing available workflows and their descriptions

Provides implementation patterns for different data scenarios. For comprehensive adapter patterns and working examples, refer to: - https://biocypher.org/BioCypher/llms.txt > Common Patterns > Adapter Patterns - https://biocypher.org/BioCypher/llms-adapters.txt (complete adapter guide) - https://biocypher.org/BioCypher/llms-example-adapter.txt (working GEO adapter example) Args: pattern_type: Optional specific pattern type to retrieve Returns: Dict containing implementation patterns

Provides instructions on how to create a BioCypher project using cookiecutter. This function informs users how to install cookiecutter (if not present) and how to run it to create a new BioCypher project. It does not make assumptions about directory structure or project name - the LLM should check with the user for these details. Returns: Dict containing installation and usage instructions for cookiecutter