dismech: Skill for Claude Code

.claude/skills/dismech-terms/SKILL.md

dismech-terms is a skill for Claude Code from monarch-initiative/dismech. It costs 92 tokens per session (2,132 once invoked), scanned A, original, BSD-3-Clause.

A workflow for managing links between dismech data fields and ontology terms. Ontologies are structured lists of agreed concepts, such as diseases, cell types, body parts, or biological processes.

In plain words
What is it for?
Use it when adding or repairing ontology annotations, changing term IDs or labels, choosing an ontology lookup adapter, or validating mappings for phenotypes, diseases, anatomy, exposures, treatments, and related fields.
Why use it?
It helps ensure that selected term IDs and labels are valid for the schema and can be checked using the configured ontology source. It also helps keep derived term caches consistent after annotations change.

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 →

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/dismech-terms/SKILL.md
Clone the repo
git clone --depth 1 https://github.com/monarch-initiative/dismech

Made for: Claude Code.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for dismech-terms

README.md
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Your own site
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Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for dismech-terms

Your own site · 80×15
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Per session 92 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 2,132 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 $0.00092 $0.02132
Opus 5 $0.00046 $0.01066
Sonnet 5 $0.00018 $0.00426
Haiku 4.5 $0.00009 $0.00213

Measured 9d ago against content hash 637d604b7720, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-08, from the pricing page.

Security

Grade A, and why

dismech-terms 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 9d ago.

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/dismech-terms/SKILL.md · 234 lines

How it starts

The opening of the file, as written. The whole thing — 234 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Curate Ontology Terms

Follow the session-wide ontology and cache contract in CLAUDE.md. Use this workflow for each concrete term decision.

Core workflow

1. Inspect the field and its range

Read the relevant slot or class in src/dismech/schema/dismech.yaml. Determine:

  • which descriptor or term field owns the binding;
  • which ontology prefixes the schema permits;
  • whether the field is constrained by a dynamic enum and reachable_from;
  • whether a dedicated qualifier or category slot already captures part of the intended meaning.

Do not infer validity from similar-looking entries alone. Nearby entries are useful examples, but the schema and ontology remain authoritative.

2. Choose the validator's ontology source

Check conf/oak_config.yaml before looking up a term. Automated validation uses the adapter configured there and is cache-first.

For prefixes configured with OLS, use OLS for a lightweight search or a local SQLite build when definitions, relationships, or -O obo output are needed:

uv run runoak -i ols:hp search "cognitive impairment"
uv run runoak -i ols:hp info HP:0002014
uv run runoak -i sqlite:obo:hp info HP:0002014 -O obo

-O obo is not implemented by OLS adapters. A local inspection adapter may differ from the configured validation adapter, so never mechanically replace one with the other.

ECTO and XCO are pinned local exceptions. Read Exposure-term decisions before selecting or changing those bindings.

3. Search, inspect, and choose

Search broadly enough to find synonyms, then inspect candidate definitions and ancestry:

uv run runoak -i ols:cl search "regulatory T cell"
uv run runoak -i sqlite:obo:cl info CL:0000815 -O obo
uv run runoak -i sqlite:obo:cl ancestors CL:0000815 -p i

Choose the most specific term that accurately represents the curated claim. Do not choose a narrow term merely because it is available. If only a broad ontology term fits, bind that term and use preferred_term for justified human-readable specificity.

Read the full file on GitHub · 234 lines

Files

What ships with it

2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

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. 9d ago First seen · 234 lines · 92 tokens per session scan A 637d604b7720

Subscribe to this mod's changes

dismech-terms is a skill published in the GitHub repository monarch-initiative/dismech (59 stars, last pushed today), licensed BSD-3-Clause. It adds 92 tokens to every session and 2,132 once invoked, about $0.0005 per session on Opus 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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