cxg-census-mcp
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| CXG_CENSUS_MCP_CACHE_DIR | No | Disk cache root | platformdirs default |
| CXG_CENSUS_MCP_LOG_LEVEL | No | stdlib log level | WARNING |
| CXG_CENSUS_MCP_MOCK_MODE | No | If 1, never opens a real Census handle | 0 |
| CXG_CENSUS_MCP_CENSUS_VERSION | No | Census release to pin | stable |
Capabilities
Features and capabilities supported by this server
| Capability | Details |
|---|---|
| tools | {
"listChanged": false
} |
| prompts | {
"listChanged": false
} |
| resources | {
"subscribe": false,
"listChanged": false
} |
| experimental | {} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| census_summaryC | Pinned Census summary: cells, schema, build date. |
| get_census_versionsA | List available Census versions visible to this server. |
| list_available_valuesC | Distinct values for an obs column (discovery before resolve_term). |
| resolve_termC | Resolve text or CURIE to one term; typed refusal if ambiguous. |
| expand_termC | Expand a CURIE to descendants/ancestors filtered to Census presence. |
| term_definitionA | Return label, definition, synonyms, IRI for a CURIE. |
| count_cellsC | Count cells (filters + optional group_by); tier 0. |
| list_datasetsC | List datasets matching a structured filter, sorted by cell count. |
| gene_coverageC | Report whether a list of Ensembl gene IDs is present in Census var. |
| preview_obsC | Small obs slice + column cardinality (before a big scan). |
| aggregate_expressionC | Per-gene expression stats by group; caps → export_snippet if over. |
| export_snippetC | Runnable Python for a stored plan; pass call_id from a prior response. |
| get_server_limitsB | Report cap configuration so clients can size their requests. |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
| census_workflow | Default workflow guidance for Census exploration. |
| disambiguation | How to handle TERM_AMBIGUOUS responses. |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
| Census schema overview | Census schema overview |
| Ontology resolution rules | Ontology resolution rules |
| Server limitations and non-goals | Server limitations and non-goals |
| Recommended agent workflow | Recommended agent workflow |
| Structured error model | Structured error model |
| Progress and cancellation | Progress and cancellation |
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