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analyse-issue

Analyze MONDO GitHub disease issues for validity and generate structured reports with duplication checks and identifier validation.

317|66|Updated Sep 20, 2017
Search Tags:#ontology#github#validation#report generation#issue analysis#disease classification#MONDO
One-click install
npx skills add https://github.com/monarch-initiative/mondo --skill analyse-issue
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: analyse-issue
Source: https://github.com/monarch-initiative/mondo/tree/main/.claude/skills/analyse-issue
Command: npx skills add https://github.com/monarch-initiative/mondo --skill analyse-issue

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Manually analyzing complex GitHub issues for the MONDO Disease Ontology is a time-consuming, expert-intensive, and error-prone process. This Skill automates the rigorous validation, pattern identification, and structured reporting of these issues, freeing up valuable human curator time and ensuring consistent, high-quality ontological development.

Core Features & Use Cases

  • Automated Issue Validation: Automatically assess the medical and terminological validity of MONDO GitHub issues, cross-referencing against existing design patterns and suggesting improvements.
  • Structured Report Generation: Produce comprehensive, AI-generated reports that include Mermaid diagrams for proposed changes, medical/clinical justifications, and terminological correctness, formatted for direct use.
  • Duplication & Identifier Checks: Perform checks for existing terms and validate identifiers using obo-grepl.obo, preventing redundancy and ensuring data integrity.
  • Use Case: A MONDO curator receives a new GitHub issue requesting a novel disease term. Instead of spending hours on manual research and report drafting, they activate this Skill. The AI analyzes the request, identifies relevant design patterns, proposes a classification, and generates a detailed, ready-to-post report, allowing the curator to focus on high-level review.

Quick Start

Analyze GitHub issue number 12345 for the MONDO ontology, generating a detailed report and saving it to 'src/ontology/tmp/issue_12345_analysis.md'.

Frequently Asked Questions about analyse-issue

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I automate validation and reporting for GitHub disease ontology issues?▼

Automated validation and reporting for ontology issues analyzes GitHub submissions against design patterns and identifier databases, generating structured reports with duplication checks and medical validity assessments. This Skill processes MONDO disease issues, cross-references them against existing patterns in src/patterns/dosdp-patterns/, and produces comprehensive analysis files ready for curator review.

Can I use AI to check for duplicate disease terms and validate identifiers in my ontology?▼

Yes. This Skill performs duplication detection and identifier validation using obo-grepl.obo to ensure new disease terms don't conflict with existing entries. It validates terminology correctness and provides structured output highlighting conflicts or pattern misalignments before terms are added to your ontology.

What's the best way to generate structured reports from complex disease classification issues?▼

Structured report generation for disease classification issues produces comprehensive analysis files with Mermaid diagrams, medical justifications, and terminological assessments. This Skill generates timestamp-stamped reports at src/ontology/tmp/issue_x_analysis.md, ready for direct posting or curator refinement, eliminating manual drafting time.

How do I validate MONDO GitHub issues against existing design patterns?▼

Pattern validation for disease ontology issues compares incoming submissions against curated design-pattern YAMLs stored in your repository. This Skill identifies relevant patterns, assesses alignment, and suggests improvements to proposed terms, ensuring consistency with established ontological structure and preventing redundant classifications.

Do I need medical expertise to analyze and report on disease ontology issues?▼

No. This Skill automates medical and terminological validity assessment, eliminating the need for manual expert analysis on every issue. It surfaces medical justifications, validates clinical terminology, and generates expert-quality reports, letting curators focus on high-level decisions rather than time-consuming research and drafting.

What happens when duplicate disease terms or identifier conflicts are detected?▼

Duplication and conflict detection identifies existing terms matching the submitted issue and flags identifier mismatches against your ontology database. The generated analysis report documents these findings with specific references, allowing curators to make informed decisions about whether to merge, reject, or modify the proposed term.

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