User Guide

This guide walks you through the complete mapping workflow, from selecting Key Events to submitting high-quality mappings.

Creating a New Mapping

Step 1: Select Key Event

Use the searchable dropdown to find a Key Event from AOP-Wiki. You can search by:

  • Key Event ID (e.g., "KE 55")
  • Key Event title or keywords

After selecting a KE, a details panel appears showing the KE description, biological level, and a link to measurement methods on AOP-Wiki. A context panel also loads showing AOP membership and any existing WP/GO mappings.

Step 2: Select WikiPathway — KE-WP Mapping

Choose a related WikiPathway using the KE-WP Mapping tab. The system provides three sub-tabs:

  • Suggested - Ranked pathway recommendations based on gene overlap, semantic similarity, and ontology tag matching
  • Search - Search for pathways by name or keywords
  • Browse All - Browse all available WikiPathways

If the selected KE-WP pair already exists in the database, a duplicate warning is shown before submission.

Step 2 (alternative): Select GO Term — KE-GO Mapping

To map a KE to a Gene Ontology Biological Process term, use the KE-GO Mapping tab. The system provides two sub-tabs:

  • Suggested - GO BP term suggestions ranked by gene overlap and semantic similarity, displayed as cards with GO term name, definition, matched genes, and similarity scores
  • Search - Search for GO terms by name or GO ID (e.g. GO:0006915)

Step 3: Confidence Assessment (4 Questions)

Answer four questions to evaluate mapping quality:

Question Options Purpose
1. Relationship Type Causative / Responsive / Bidirectional / Unclear Determines connection direction
2. Evidence Basis Known / Likely / Possible / Uncertain Your confidence level (0-3 points)
3. Pathway Specificity KE-specific / Includes KE / Loosely related Pathway scope evaluation (0-2 points)
4. KE Coverage Complete / Key steps / Minor aspects Pathway completeness (0-1.5 points)

Confidence Scoring

The system calculates confidence based on your answers:

  • High Confidence: ≥5.0 points (strong evidence + good coverage)
  • Medium Confidence: 2.5-4.9 points (moderate evidence or limitations)
  • Low Confidence: <2.5 points (weak evidence or poor coverage)
Biological Level Weighting: Molecular, cellular, and tissue-level KEs receive a +1 bonus point because they're closer to pathway mechanisms than organ/population-level KEs.
KE-GO Assessment: KE-GO mapping has its own confidence assessment with GO-specific connection types. The assessment evaluates the biological relevance of the KE-to-GO-term relationship.

Exploring Existing Mappings

Navigate to Explore to view all mappings in an interactive AJAX-powered DataTable with:

  • Filtering by AOP and confidence level
  • Coverage gaps tab showing unmapped KEs
  • Inline WikiPathways embed viewer (click the eye icon to preview a pathway diagram)
  • Export to CSV, Excel, PDF formats
  • Proposal system for suggesting changes

Proposing Changes

If you notice an issue with an existing mapping:

  1. Login with GitHub
  2. Click "Propose Change" on the mapping
  3. Describe your proposed change
  4. Submit for admin review