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OMIM Configuration Setup

This document explains how to configure access to OMIM (Online Mendelian Inheritance in Man) data for the HPO/OMIM neoplasm gene identification feature.

Overview

The HPO/OMIM data source identifies cancer-related genes by: 1. Fetching all descendant terms of HP:0002664 (Neoplasm) from the HPO API 2. Downloading the phenotype.hpoa file (automatically cached) 3. Filtering phenotype annotations for neoplasm-related HPO terms 4. Cross-referencing with OMIM genemap2 data to find associated genes

OMIM Access Requirements

OMIM requires registration and personal access tokens for downloading their genemap2.txt file, which contains gene-to-disease mappings.

Step 1: Register with OMIM

  1. Go to https://omim.org/downloads
  2. Register for an account (free for academic/research use)
  3. Accept the terms and conditions
  4. You will receive a personal access token/URL

Step 2: Configure Your Access Token

You have two options:

  1. Copy the template configuration: 

    cp config.local.yml.template config.local.yml

  2. Edit config.local.yml and replace YOUR_TOKEN with your actual token: 

    data_sources:
  hpo_neoplasm:
    omim_genemap2_url: "https://data.omim.org/downloads/YOUR_ACTUAL_TOKEN/genemap2.txt"

Example with a real token: 

data_sources:
  hpo_neoplasm:
    omim_genemap2_url: "https://data.omim.org/downloads/9GJLEFvqSmWaImCijeRdVA/genemap2.txt"

Option B: Environment Variable

Set the URL as an environment variable: 

export OMIM_GENEMAP2_URL="https://data.omim.org/downloads/YOUR_TOKEN/genemap2.txt"

Then in your config.local.yml: 

data_sources:
  hpo_neoplasm:
    omim_genemap2_url: "${OMIM_GENEMAP2_URL}"

Option C: Manual Download

If you prefer to download the file manually:

  1. Download genemap2.txt from your OMIM downloads page
  2. Place it in data/omim/genemap2.txt
  3. The system will use the local file automatically

Configuration Options

All HPO/OMIM configuration options:

data_sources:
  hpo_neoplasm:
    enabled: true

    # Option 1: Direct URL with access token (recommended)
    omim_genemap2_url: "https://data.omim.org/downloads/YOUR_TOKEN/genemap2.txt"

    # Option 2: Local file path (fallback)
    omim_genemap2_path: "data/omim/genemap2.txt"

    # Cache settings
    cache_dir: ".cache/hpo"
    cache_expiry_days: 30

    # Scoring parameters
    base_evidence_score: 0.7

Security Notes

  • Never commit your access token to version control
  • The config.local.yml file is automatically ignored by git
  • Keep your access token private and secure
  • OMIM tokens may expire and need renewal

Usage

Once configured, use the HPO data source:

# Fetch HPO/OMIM neoplasm genes
custom-panel fetch hpo --output-dir results/hpo

# Use in full pipeline
custom-panel run --output-dir results/final

Troubleshooting

"No OMIM genemap2 URL or file path configured"

  • Ensure you have created config.local.yml with your access token
  • Check that the token URL is correct

"Failed to download OMIM genemap2"

  • Verify your access token is still valid
  • Check your internet connection
  • Try downloading manually from the OMIM website

"OMIM genemap2 file not found"

  • If using local file option, ensure the file exists at the specified path
  • Check file permissions

Empty results

  • Verify the genemap2.txt file downloaded correctly (should be ~3MB)
  • Check that the HPO API is accessible

Expected Results

When working correctly, the HPO/OMIM data source should identify: - ~15-50 cancer-related genes (depending on genemap2.txt version) - Well-known cancer genes like TP53, BRCA1/2, MLH1, MSH2, APC, VHL, etc. - Evidence scores based on number of associated HPO terms and diseases

File Locations

  • Configuration: config.local.yml (create from template)
  • Template: config.local.yml.template
  • Cache: .cache/hpo/ directory
  • Local files: data/omim/ directory