Getting Started

Welcome to the Molecular AOP Builder documentation. This application helps researchers connect the Key Events of an Adverse Outcome Pathway to the molecular pathways and processes that underlie them — building the molecular layer of an AOP.

What is Molecular AOP Builder?

A Key Event can be mapped to three target resources, which answer different questions and are curated independently. WikiPathways and Reactome supply curated pathway models, so a mapping to either says this Key Event is realised by this pathway. Gene Ontology supplies biological processes and molecular functions rather than pathways, so a GO mapping names the process the Key Event is — often the better fit for a Key Event that describes a single event rather than a mechanism with a diagram.

The Molecular AOP Builder enables you to:

  • Map Key Events (KEs) from AOP-Wiki to WikiPathways pathways
  • Map Key Events to Gene Ontology Biological Process (GO BP) terms
  • Map Key Events to Reactome pathways
  • Assess mapping confidence using a structured 4-question workflow
  • Explore existing mappings created by the community, with coverage-gap analysis per AOP
  • View a whole AOP as a graph, with per-resource coverage shown on each Key Event
  • Download mapping data as GMT, RDF/TTL, CSV or JSON, or cite a frozen Zenodo release
  • Propose changes to existing mappings, including corrections to already-approved ones

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

  1. Login (optional) — sign in with GitHub to submit mappings or propose changes. Workshop participants can use a guest access code instead.
  2. Navigate to Mapping — go to the main mapping interface
  3. 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
  4. Select a target — pick a pathway or a GO term from the KE-WikiPathways, KE-GO, or KE-Reactome tab (each offers Suggested / Search / Browse sub-tabs). The three are peers: start with whichever resource best describes the Key Event, and map it to more than one where more than one fits.
  5. Complete Confidence Assessment — answer 4 questions to determine mapping quality
  6. 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, WikiPathways, Gene Ontology and Reactome 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 Explorer: /aop-explorer — interactive AOP graph with per-resource coverage on each Key Event, gap filters and OECD status filtering
  • 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