dismech: Skill for Claude Code

.claude/skills/create-module/SKILL.md

create-module is a skill for Claude Code from monarch-initiative/dismech. It costs 102 tokens per session (2,121 once invoked), scanned A, original, BSD-3-Clause.

A guide for creating a mechanism module in the DisMech database—a reusable description of a disease process that occurs in multiple disorders.

In plain words
What is it for?
Adding modules for recurring pathological processes, including the formation of cysts, clots, scars, deposits, or tumors, and checking related disorder records for consistency.
Why use it?
It helps decide when several disorders truly share one mechanism and ensures the new module follows the project’s data format and consistency rules.

Skill for Claude Code

Written for Claude Code: installed under .claude/. Also seen: mentions CLAUDE.md.

This is monarch-initiative/dismech's own configuration. It tells Claude Code how to work on dismech itself, so it is not a mod to install elsewhere. Copy it as a starting point and replace the rules that are about this project. Everything dismech configures →

Needs its repository: it runs a file that does not travel with it, so clone the repository first. The line is bash scripts/run_reference_validator.sh validate data kb/modules/<name>.yaml \.

Reuse

Borrowing it

Nothing to install: this file belongs to monarch-initiative/dismech. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file
curl -O https://raw.githubusercontent.com/monarch-initiative/dismech/main/.claude/skills/create-module/SKILL.md
Clone the repo
git clone --depth 1 https://github.com/monarch-initiative/dismech

Made for: Claude Code.

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README.md
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Per session 102 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 2,121 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits
  • NVIDIA SkillSpector pass 7 Sept 2026
How audits are shown
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00102 $0.02121
Opus 5.5 $0.00041 $0.00848
Sonnet 5.5 $0.00020 $0.00424
Haiku 4.5 $0.00010 $0.00212

Measured today against content hash aa9966d861f7, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

create-module scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured today.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.claude/skills/create-module/SKILL.md · 162 lines

How it starts

The opening of the file, as written. The whole thing — 162 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Create a Mechanism Module

When to use

  • The user asks to create a new kb/modules/*.yaml module.
  • A conserved mechanism (a final-common pathway, a recurrent downstream convergence point, a shared drug-target pattern) recurs across ≥2 disorders and is worth checking for consistency via conforms_to.
  • The user asks for an Xogenesis module — the formation of a pathological material anatomical entity (cyst, calculus, granuloma, thrombus, amyloid deposit, atheroma, neoplasm, fibrous scar).

Read docs/primers/modules-and-conformance.md first for the conformance mental model (conformance is a consistency check, not DRY inheritance).

Does it clear the module bar?

Only create a module when there is one conserved mechanism reducible to a short linear causal chain with one rate-limiting "key conformance target" node that every conformer funnels through. If the candidate is mechanistically heterogeneous (many unrelated pathways to the same label), it is not a module — consider a Grouping (SHARED_PHENOTYPE) instead.

Module shape

  • Validates against the Disease class with category: Module.
  • Top-level: name, description, category: Module, creation_date, notes, pathophysiology. Optional: module_categories, treatments, mechanistic_hypotheses, discussions.
  • module_categories tags the areas of study the module is relevant to (ModuleCategoryEnum — TOXICOLOGY, PHARMACOLOGY, ONCOLOGY, INFECTIOUS_DISEASE, IMMUNOLOGY, NEUROSCIENCE, DEVELOPMENTAL_BIOLOGY, METABOLISM, AGING) and renders as coloured pills on the module pages. It is a browsing aid, so tag every area that genuinely applies and leave it off when none fits — a wrong pill is worse than no pill. See the Module categories section of CLAUDE.md.
  • Nodes bind GO and CL terms only (plus UBERON locations, GO cellular_components). No CHEBI/MONDO term bindings in nodes — describe chemistry/disease in prose. (Exception: a treatments block's therapeutic_agent carries a CHEBI/NCIT id per the treatment schema.)
  • Chain of ~5 nodes, each with a role: trigger → amplifier → central_effector → effector → consequence. The central_effector is normally the key conformance target — the disorder-agnostic, rate-limiting step. Every node carries evidence and downstream edges; the notes spell out the disorder-specific substitutions conforming entries make.
  • Treatment drug-target pattern (optional but preferred when a drug acts on a specific node): a treatments[] entry uses target_mechanisms with a treatment_effect (INHIBITS/ACTIVATES) pointing at the node name it acts on. Model after cellular_senescence (senolytic) or renal_cystogenesis (tolvaptan).

Read the full file on GitHub · 162 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. today Changed · +2 lines aa9966d861f7
  2. 1mo ago Changed · +10 lines 1684bd7ba218
  3. 1mo ago First seen · 150 lines · 102 tokens per session scan A ca739947c513

Subscribe to this mod's changes

create-module is a skill published in the GitHub repository monarch-initiative/dismech (69 stars, last pushed today), licensed BSD-3-Clause. It adds 102 tokens to every session and 2,121 once invoked, about $0.0004 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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