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Pathology coder

Skill patolojiAI/pathology-skills-collection/pathology-skills/pathology-coder

Comprehensive clinical pathology toolkit for Claude - skills for CAP/ICCR compliance, TNM staging, synoptic templates, SNOMED coding, tumor board summaries, scientific similarity checking, and reference verification.

Install
npx -y skills add patolojiAI/pathology-skills-collection --skill pathology-coder

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Suggests SNOMED CT and ICD-O-3 morphology/topography codes for pathology diagnoses, procedures, and biomarkers, with hierarchical parent/child relationships and synonyms. Use when the user asks "SNOMED code for [diagnosis]", "ICD-O-3 code for [tumor type]", "what's the code for invasive ductal carcinoma", "code this diagnosis", "morphology code for", or any pathology-coding lookup. Supports common cancer diagnoses (breast, colorectal, pancreas, gastric, prostate, lung, lymphoma, GIST) and standard pathology procedures.

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SKILL.md

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Pathology Coder

SNOMED CT and ICD-O-3 coding suggestions for pathology reports with clinical context.

When to Use This Skill

Use this skill for:

  • LIS integration and coding
  • Tumor registry reporting
  • Billing support
  • Standardizing terminology
  • Teaching pathology coding

Supported Code Systems

  • SNOMED CT: Morphology, topography, procedures, qualifiers
  • ICD-O-3: Morphology codes with behavior, topography codes

Key Features

  1. Diagnosis Coding: Tumor type, grade, behavior codes
  2. Procedure Coding: Specimen types, special stains, IHC
  3. Biomarker Coding: ER/PR/HER2/MSI/MMR codes
  4. Hierarchical Relationships: Parent concepts, synonyms
  5. Multi-code Support: Combined diagnoses and qualifiers

Reference Files

Reference on-demand (DO NOT load at startup):

  • Code tables: ../../shared-references/coding/snomed_ct_codes.md

Usage Examples

# Code diagnosis
claude "SNOMED code for invasive ductal carcinoma grade 2 using pathology-coder"

# Code procedure
claude "What is the code for HER2 immunohistochemistry using pathology-coder"

# Multiple codes
claude "Code breast lumpectomy with IDC and DCIS using pathology-coder"

Processing Instructions

  1. Parse diagnosis/procedure from user input
  2. Load code table from shared-references
  3. Look up SNOMED CT code and ICD-O-3 if applicable
  4. Provide hierarchical context: Parent concepts, synonyms
  5. Output: Code(s) with descriptions and relationships

Common Tumor Type Codes

Loaded on-demand from reference file when needed:

  • Breast carcinoma codes
  • Colorectal carcinoma codes
  • Pancreas carcinoma codes
  • Gastric carcinoma codes

Output Format

For each code suggestion:

  • SNOMED CT: [Code] | [Preferred term] | [Hierarchy]
  • ICD-O-3: [Morphology/Behavior] | [Topography] | [Description]

Note: Minimal skill definition. Code tables loaded on-demand during processing only.

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