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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 suggest "What drugs treat melanoma?"
biomcp skill
biomcp skill render
biomcp skill list
biomcp skill article-follow-up
biomcp skill install ~/.claude

Read the overview

biomcp suggest "<question>" is the quickest way to choose the matching worked-example playbook when you only know the biomedical question. It returns the playbook slug, two starter commands, and the biomcp skill <slug> command 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

Current builds ship 15 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, and negative-evidence. 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

Force replacement of an existing install:

biomcp skill install ~/.claude --force

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
  • use-cases/
  • jq-examples.md
  • examples/
  • schemas/

The install payload also includes schemas/workflow-ladder.schema.json and seven use-cases/<slug>.ladder.json sidecars for workflow ladders: treatment-lookup, article-follow-up, variant-pathogenicity, trial-recruitment, mechanism-pathway, pharmacogene-cumulative, and mutation-catalog. These JSON sidecars are not listed by biomcp skill list; they are runtime metadata assets paired with the numbered markdown playbooks.

When a first-call JSON response matches a ladder trigger, BioMCP can emit _meta.workflow plus _meta.ladder[]. The ladder commands are static copies of the matching playbook's fenced bash block; they are not templated with user input. _meta.next_commands remains the dynamic one-hop follow-up list for the current result.