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Skills

BioMCP ships one embedded guide plus supporting reference files and worked examples for agent workflows. The current workflow is:

biomcp skill list
biomcp skill
biomcp skill render
biomcp skill article-follow-up
biomcp skill exact-variant-literature
biomcp skill install ~/.claude

Read the overview

biomcp skill list is the quickest way to choose the matching worked-example playbook when you only know the biomedical question. It lists playbook slugs you can open with biomcp skill <slug> for the full workflow.

biomcp skill prints the embedded skills/SKILL.md overview. Start there if you want the current BioMCP workflow guidance without installing anything into an agent directory.

biomcp skill render prints the same canonical agent-facing prompt for scripts and eval runners. Redirected output from biomcp skill render is the same content installed as SKILL.md.

Learn the workflows

Use biomcp skill list to browse the embedded worked examples and biomcp skill <slug|number> to open one in the CLI:

biomcp skill list
biomcp skill article-follow-up
biomcp skill variant-pathogenicity
biomcp skill exact-variant-literature

Current builds ship 17 worked examples. The catalog keeps the original treatment lookup, symptom lookup, gene-disease orientation, and article follow-up examples, plus expanded playbooks such as variant-pathogenicity, drug-regulatory, trial-recruitment, mutation-catalog, negative-evidence, normalize-to-codes, and exact-variant-literature. The installed skills/ tree also includes worked examples you can read directly in the repo or in an agent directory:

  • Guide Workflows - variant pathogenicity, drug safety, and broad gene-disease investigation

Install into an agent directory

Install the embedded skills/ tree into your agent directory:

biomcp skill install ~/.claude

Check whether an installed skill matches this BioMCP binary:

biomcp --json skill status ~/.claude

A fresh managed install reports current. Missing or invalid management metadata reports unmanaged; changed managed files report locally_modified; and an intact older payload reports stale. Only current omits the recovery command.

Plain install never overwrites an existing skill. Repair an installation explicitly:

biomcp skill install ~/.claude --force

Force replacement updates only BioMCP-managed files and preserves unrelated files. The dir argument can point at an agent root such as ~/.claude, an existing skills/ directory, or a skills/biomcp/ directory. When you omit dir, BioMCP attempts supported agent-directory detection in your home directory and the current working tree, then prompts before installing when stdin is a TTY.

Install payload

Current builds install the full embedded reference tree into <agent>/skills/biomcp/, including:

  • SKILL.md
  • .biomcp-skill.json (schema, BioMCP version, canonical render hash, install time, and managed-file hashes)
  • AUTHORING.md
  • use-cases/
  • use-cases/_TEMPLATE.md and use-cases/_TEMPLATE.ladder.json
  • jq-examples.md
  • examples/
  • schemas/

The install payload also includes schemas/workflow-ladder.schema.json, seven runtime use-cases/<slug>.ladder.json sidecars, and the normalize-to-codes.ladder.json worked-example sidecar. The runtime sidecars are treatment-lookup, article-follow-up, variant-pathogenicity, trial-recruitment, mechanism-pathway, pharmacogene-cumulative, and mutation-catalog; BioMCP can attach their name, rationale, and stable playbook reference when a command matches their triggers. The normalize-to-codes sidecar is installed authoring reference material paired with its numbered markdown playbook, not runtime metadata. JSON sidecars are not listed by biomcp skill list. The _TEMPLATE.* files are authoring references, not routed playbooks.

When a JSON response matches a workflow, BioMCP can emit _meta.workflow, _meta.workflow_rationale, and _meta.workflow_playbook. Executable examples remain in the installed playbook. _meta.next_commands remains the dynamic one-hop follow-up list for the current result.