Getting Started
Welcome to the Molecular AOP Builder documentation. This application helps researchers map Key Events from AOP-Wiki to WikiPathways, creating valuable connections between adverse outcome pathways and biological pathways.
What is Molecular AOP Builder?
The Molecular AOP Builder enables you to:
- Map Key Events (KEs) from AOP-Wiki to WikiPathways
- Map Key Events to Gene Ontology Biological Process (GO BP) terms
- Map Key Events to Reactome pathways (in active refinement)
- Assess mapping confidence using a structured 4-question workflow
- Explore existing mappings created by the community, with coverage-gap analysis per AOP
- Download mapping data as GMT, RDF/TTL, CSV or JSON
- Propose changes to existing mappings
Suggestions across all three resources are ranked by BioBERT semantic similarity to the Key Event description. Approved mappings are exposed via a public REST API and feed the Molecular AOP Analyser, which uses them for KE-level enrichment of gene-expression data.
Quick Start
- Login (optional) — sign in with GitHub to submit mappings or propose changes. Workshop participants can use a guest access code instead.
- Navigate to Mapping — go to the main mapping interface
- Select a Key Event — a details panel shows the KE description, biological level, and AOP-Wiki link; an inline AOP-context graph fans out from the KE; a context panel lists AOP membership and any existing WP/GO/Reactome mappings
- Select a target — pick a pathway or GO term from the KE-WP Mapping, KE-GO Mapping, or KE-Reactome Mapping tab (each offers Suggested / Search / Browse sub-tabs)
- Complete Confidence Assessment — answer 4 questions to determine mapping quality
- Submit Mapping — your submission enters the proposal queue and is published once an admin approves it
Note: This application is part of the VHP4Safety project, integrating data from AOP-Wiki and WikiPathways to support toxicology research.
System Requirements
- Modern web browser (Chrome, Firefox, Safari, Edge)
- A GitHub account (only required for submitting / proposing mappings; workshops can use a guest access code instead)
- Internet connection (for live SPARQL queries to AOP-Wiki and WikiPathways)
Live tool & related resources
- Live instance: molaop-builder.vhp4safety.nl
- AOP network graph: /aop-network — interactive view of AOPs and KE coverage
- Statistics: /stats — mapping counts and coverage by confidence level
- Downloads: /downloads — GMT, RDF/TTL, CSV and JSON exports
- Public REST API: /api/docs (Swagger UI), with /docs for Python & R consumer examples
- Sister tool: Molecular AOP Analyser consumes these mappings for KE-level enrichment of gene-expression data