linkml-mcp
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
| LINKML_MCP_WORKSPACE_ROOT | No | The root directory for workspaces. Overrides the default .linkml-mcp/workspaces. | |
| LINKML_MCP_GENERATOR_OUTPUT_ROOT | No | The root directory for generated output. Overrides the default. |
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
Capabilities
Features and capabilities supported by this server
Protocol revision2025-11-25
| Capability | Details |
|---|---|
| tools | {
"listChanged": false
} |
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| init_workspaceA | Create a new LinkML editing workspace backed by a bare git repository. Returns workspace_id and initial_commit. If files are omitted, creates a minimal schema.yaml. |
| read_schemaA | Read a LinkML YAML schema file from a specific workspace commit. Use path to read schema.yaml or another local imported YAML file. |
| list_filesA | List files present in a LinkML workspace at a specific commit. Use this before targeting imported local schema files. |
| get_entityA | Fetch one LinkML entity from a schema file at a specific commit. entity_type must be class, slot, enum, prefix, or import. |
| validate_schemaA | Validate a LinkML YAML schema at a specific workspace commit. This performs schema validation only and does not create a commit. |
| apply_changesetA | Apply an atomic ordered semantic changeset to a LinkML workspace. Requires base_commit; validates before and after edits; returns a new commit id. Supported operations include create/delete/rename class, slot, enum, prefix, import, file, plus set_field, unset_field, list_append, list_remove, list_replace, map_set, and map_remove. |
| list_generatorsA | List the LinkML generators supported by this MCP server. Milestone generators are shacl, owl, and doc. |
| describe_generatorA | Describe one supported LinkML generator and the option format accepted by run_generator. Generator options are passed as CLI-style option names without leading dashes. |
| run_generatorA | Run a supported LinkML generator against a schema file at a specific commit. Does not validate automatically and does not commit generated artifacts. Returns inline content for small outputs or a temporary path for large/multi-file outputs. |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
TDQS
Scored across 9 tools
Each tool targets a distinct concern: workspace setup, file listing, schema reading, entity retrieval, validation, semantic editing, and generator metadata/execution. Even related tools like validate_schema and apply_changeset are clearly separated by read-only vs. mutating behavior.
Tool names consistently follow a verb_noun pattern using lowercase snake_case: list_files, init_workspace, read_schema, get_entity, validate_schema, apply_changeset, list_generators, describe_generator, run_generator. There are no mixed conventions or vague verbs.
Nine tools is well-scoped for a LinkML workspace server. The count covers setup, inspection, validation, modification, and generation without redundant or bloated surface area.
The tool set covers the core workflow well: creating a workspace, reading files, fetching entities, validating, applying semantic changes, and running generators. Minor gaps exist, such as no direct list-entities operation or workspace metadata lookups, but these can be worked around with read_schema and get_entity.