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Agent skill

Analyse Issue

by monarch-initiative in monarch-initiative/mondo

Analyze MONDO GitHub issues for validity, suggest improvements, and generate structured reports with duplication checks and identifier validation

CC-BY-4.0Auto-check passedDevelopment

Install Analyse Issue

skills CLI
$ npx skills add monarch-initiative/mondo --skill analyse-issue -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install monarch-initiative/mondo analyse-issue --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/monarch-initiative/mondo.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.claude/skills/analyse-issue .claude/skills/analyse-issue && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
analyse-issue
GitHub stars
326
Token cost
~1.1k tokens
SKILL.md length
531 words
Files
1
Skills in repo
4
Repo updated
First seen
Licence
CC-BY-4.0

At a glance

Analyze MONDO GitHub issues for validity, suggest improvements, and generate structured reports with duplication checks and identifier validation

  • Works in 5 steps: View the issue: Use gh issue view… → Analyze validity: Assess if the request… → Search for improvements: Look, for… → …
  • Development work in your project
  • Calls gh

What it does

Analyse Issue is an agent skill from monarch-initiative/mondo. Analyze MONDO GitHub issues for validity, suggest improvements, and generate structured reports with duplication checks and identifier validation

Its SKILL.md is about 1.1k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Development. It works with GitHub. The repository describes itself as: Mondo Disease Ontology. The licence is CC-BY-4.0.

When your agent uses it

  • Development work in your project

Example prompts

  • “/analyse-issue”

Workflow steps

5 steps, taken from the first numbered list in SKILL.md.

  1. View the issue: Use gh issue view [number] to read the issue
  2. Analyze validity: Assess if the request is medically and terminologically valid (this is NOT always the case, so please be careful)
  3. Search for improvements: Look, for example, for more specific parents/terms that might be better
  4. Present findings in the following format (see below). Write them to a file @src/ontology/tmp/issue_x_analysis.md, where "x" should be the…
  5. Post comment. ALWAYS ASK FOR PERMISSION TO DO THIS. Offer to post the the file created as a comment to the issue being analysed (using…

What it can do on your machine

Read from SKILL.md and the folder at commit 9bfccbe. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Shell commands in SKILL.md call:

    • gh

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md. Its commands use gh, which can reach the network depending on how they are called.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Analyse Issue loads about 1.1k tokens when it runs. Until then it costs about 40 tokens; SKILL.md has 531 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~40
When it runs · the whole SKILL.md, loaded when a task matches
~1.1k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from monarch-initiative/mondo at commit 9bfccbe, republished under its CC-BY-4.0 licence (© monarch-initiative). 531 words, ~1,053 tokens.

Download SKILL.mdSave it as .claude/skills/analyse-issue/SKILL.md (or your agent's skills folder).
name
analyse-issue
description
Analyze MONDO GitHub issues for validity, suggest improvements, and generate structured reports with duplication checks and identifier validation

Analyze a GitHub issue for validity

Instructions

When handling GitHub issues:

  1. View the issue: Use gh issue view [number] to read the issue
  2. Analyze validity: Assess if the request is medically and terminologically valid (this is NOT always the case, so please be careful)
  • Try to understand the specific design pattern a disease belongs to. Do that by looking at similar classes, and by carefully considering the yaml files in src/patterns/dosdp-patterns/, which define design patterns.
  • If a suitable pattern exists, but you think its underspecified, you may suggest improvements to the pattern (as part of your final report, read on)
  • If no suitable pattern exists, you should propose one, at least in a rough outline, as part of the final report (read on)
  1. Search for improvements: Look, for example, for more specific parents/terms that might be better
    • As usual, use obo-grepl.obo for the search
    • If any of the diseases analysed as part of this issue belongs to a design pattern (as determined above) but lacks a logical definition and human readable definition, you may propose one as part of the issue
  2. Present findings in the following format (see below). Write them to a file @src/ontology/tmp/issue_x_analysis.md, where "x" should be the issue number.
  3. Post comment. ALWAYS ASK FOR PERMISSION TO DO THIS. Offer to post the the file created as a comment to the issue being analysed (using gh). ALWAYS ASK FOR PERMISSION TO DO THIS.
Model information

Include at the top of your report:

⚠️ **WARNING: This report is AI-generated**
**Model:** [Retrieve programmatically - check environment context or system information]
**Generated:** [Use date command to get current timestamp in UTC]

IMPORTANT:

  • NEVER write the model name from memory or training data
  • Look for the model information in the system environment or context provided at the start of the conversation
  • If the exact model ID is provided in your system context (e.g., "claude-sonnet-4-5-20250929"), use that
  • If unavailable, state "Model information unavailable"
  • Always generate the timestamp programmatically using date -u +"%Y-%m-%d %H:%M:%S UTC" or similar
  • Always check if an example you give is valid by using obo-grepl.obo. Be very very careful not to hallucinate subclass (is_a) relations.
Show full SKILL.md (197 more words)Show less
✅ Why the user request is valid:

  • Mermaid diagram that describes SPECIFICALLY THE USER REQUESTED change.

    • Use bottom UP (BT) for arrow direction

    • Use -.->|PROPOSED<br/>NEW PARENT| for proposed new parents and -.->|PROPOSED<br/>REMOVED PARENT| for proposed removed parents

    • Example:

      mermaid
      graph BT
    B[MONDO:0005341 skin basal cell carcinoma] -->  A[MONDO:0004993 carcinoma]
    C[MONDO:0019317 follicular atrophoderma-basal cell carcinoma] -.->|PROPOSED<br/>NEW PARENT| B
    C --> D[MONDO:0010535 Bazex-Dupre-Christol syndrome]
    
    style C fill:#ccffcc
    style A fill:#ccffcc
    style B fill:#ccffcc

  • Medical/clinical justification, ideally with pubmed evidence

  • Terminological correctness

  • Ontological gaps being addressed

💡 Suggested improvements:
  • Section to describe changes / refinements over what the user is suggesting
  • Mermaid diagram that describes the change (ONLY include this if there are actual changes being suggested!)
  • More specific parent/classification if applicable, ideally with pubmed evidence
  • Additional relationships that should be considered
  • Supporting literature/references

Example: For classification requests, always check if there's a more specific parent term (e.g., "benign vascular tumor" instead of general "cancer or benign tumor").

High level action items
  • Example: Add X as subclass to Y.
General formatting instructions on the report
  • The title in the issue report should just be "Issue analysis"
  • Do not include an "implementation plan" in the report
  • If there are no suggested improvements over the user request

© monarch-initiative, CC-BY-4.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in .claude/skills/analyse-issue of monarch-initiative/mondo.

Open the folder on GitHubat commit 9bfccbe

Compare with similar skills

Analyse Issue next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Analyse Issue compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Analyse Issue this skillmonarch-initiative/mondo326—~1.1kAutomated safety check: PassCC-BY-4.0
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Greplooponyx-dot-app/onyx32k4 repos~3.3kAutomated safety check: PassMIT
Check PRonyx-dot-app/onyx32k2 repos~2.3kAutomated safety check: PassMIT
Setup Matt Pocock Skillsbestofjs/bestofjs3.1k20 repos~1.7kAutomated safety check: PassMIT
Contributor-First PR MergeHKUDS/OpenHarness16k1 repos~847Automated safety check: PassMIT

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Works with

Categories

Questions about Analyse Issue

What does Analyse Issue do?

Analyze MONDO GitHub issues for validity, suggest improvements, and generate structured reports with duplication checks and identifier validation. Analyse Issue is an agent skill from monarch-initiative/mondo.

When should I use Analyse Issue?

Analyse Issue fits situations like: development work in your project.

How do I install Analyse Issue in Claude Code?

Run `npx skills add monarch-initiative/mondo --skill analyse-issue -a claude-code`. Or copy the skill folder (.claude/skills/analyse-issue in monarch-initiative/mondo) into .claude/skills/analyse-issue in your project. Claude Code loads it when a task matches its description.

How do I install Analyse Issue in Codex?

Run `npx skills add monarch-initiative/mondo --skill analyse-issue -a codex`. Or copy the skill folder (.claude/skills/analyse-issue in monarch-initiative/mondo) into .agents/skills/analyse-issue in your project. Codex loads it when a task matches its description.

Can I use Analyse Issue in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add monarch-initiative/mondo --skill analyse-issue -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/analyse-issue, .gemini/skills/analyse-issue, .github/skills/analyse-issue and .opencode/skills/analyse-issue in your project.

What does Analyse Issue need to run?

Going by SKILL.md and its folder, Analyse Issue needs the command-line tools its instructions call (gh).

Does Analyse Issue access the network?

SKILL.md contains no URLs. Its commands use gh, which can reach the network depending on how they are called. This is read from the text; nothing was executed.

Is Analyse Issue safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Analyse Issue use?

Analyse Issue is published under the CC-BY-4.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Analyse Issue use?

About 1.1k tokens (SKILL.md is roughly 4.2k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Analyse Issue?

Skills that share tags, products or a category with Analyse Issue: PR Babysitter (openinterpreter/openinterpreter, 69k stars), Greploop (onyx-dot-app/onyx, 32k stars), Check PR (onyx-dot-app/onyx, 32k stars) and Setup Matt Pocock Skills (bestofjs/bestofjs, 3.1k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Analyse Issue?

monarch-initiative (a GitHub organization) maintains it in monarch-initiative/mondo, which has 326 GitHub stars. The repository holds 4 skills in this directory. The repository was last updated on October 9, 2026.

Source: monarch-initiative/mondo on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.