# Chat Transcript: Exploring BioBricks AOP-Wiki Knowledge Graph
## Chat Transcript
š¤ **User**
@biobricks-aopwiki
---
š§ **Assistant**
I'll help you explore the biobricks-aopwiki knowledge graph. Let me start by getting some information about this endpoint.
Great! I can see this is the **BioBricks AOP-Wiki** knowledge graph, which contains data about Adverse Outcome Pathways (AOPs) from the AOP-Wiki project.
This knowledge graph is particularly useful for toxicology and environmental health research. It contains:
- **493 AOPs** (Adverse Outcome Pathways)
- **1,469 key events**
- **2,060 key event relationships**
- **184,303 total triples**
The data links molecular initiating events to adverse health outcomes, with extensive cross-references to chemical databases like ChEBI, ChEMBL, PubChem, KEGG, and Wikidata.
Would you like me to:
1. Show you the schema of available classes and relationships?
2. Run a specific query to explore AOPs, key events, or chemical relationships?
3. Visualize the knowledge graph structure?
4. Answer a specific question about toxicology pathways?
Let me know what you'd like to explore!
---
š¤ **User**
Visualize the schema
---
š§ **Assistant**
Let me get the schema and create a visualization for you.
Here's the schema visualization for the BioBricks AOP-Wiki knowledge graph!
```mermaid
classDiagram
direction TB
class AdverseOutcomePathway["Adverse Outcome Pathway (AOP)"] {
+title : string
+description : string
+creator : string
+identifier : string
+created : date
+modified : date
}
class KeyEvent["Key Event (KE)"] {
+label : string
+title : string
+description : string
+identifier : string
}
class KeyEventRelationship["Key Event Relationship (KER)"] {
+label : string
+description : string
+identifier : string
}
class BiologicalProcess["Biological Process"] {
+label : string
+description : string
}
class OrganContext["Organ Context"] {
+label : string
}
class CellTypeContext["Cell Type Context"] {
+label : string
}
class ChemicalIdentifier["Chemical Identifier"] {
+label : string
}
class ChemicalInformation["Chemical Information"]
class CASRegistryNumber["CAS Registry Number"] {
+identifier : string
}
class InChI {
+identifier : string
}
class InChIKey {
+identifier : string
}
class PubChemCompoundID["PubChem Compound ID"] {
+identifier : string
}
class ChEBIIdentifier["ChEBI Identifier"] {
+identifier : string
}
class SMILES {
+identifier : string
}
class TaxonomicClassification["Taxonomic Classification"] {
+label : string
}
class GeneIdentifier["Gene Identifier"] {
+identifier : string
}
class ProteinIdentifier["Protein Identifier"] {
+identifier : string
}
class PathwayIdentifier["Pathway Identifier"] {
+identifier : string
}
class DiseaseOrDisorder["Disease or Disorder"] {
+label : string
+description : string
}
AdverseOutcomePathway --> KeyEvent : has_molecular_initiating_event
AdverseOutcomePathway --> KeyEvent : has_key_event
AdverseOutcomePathway --> KeyEvent : has_adverse_outcome
AdverseOutcomePathway --> KeyEventRelationship : has_key_event_relationship
AdverseOutcomePathway --> ChemicalIdentifier : has_chemical_entity
KeyEventRelationship --> KeyEvent : has_upstream_key_event
KeyEventRelationship --> KeyEvent : has_downstream_key_event
KeyEvent --> BiologicalProcess : associated_with
KeyEvent --> OrganContext : occurs_in
KeyEvent --> CellTypeContext : occurs_in
KeyEvent --> ChemicalIdentifier : has_chemical_entity
ChemicalInformation --> CASRegistryNumber : has_identifier
ChemicalInformation --> InChI : has_identifier
ChemicalInformation --> InChIKey : has_identifier
ChemicalInformation --> PubChemCompoundID : has_identifier
ChemicalInformation --> ChEBIIdentifier : has_identifier
ChemicalInformation --> SMILES : has_representation
KeyEvent --> TaxonomicClassification : applies_to_organism
KeyEvent --> GeneIdentifier : involves_gene
KeyEvent --> ProteinIdentifier : involves_protein
KeyEvent --> PathwayIdentifier : part_of_pathway
KeyEvent --> DiseaseOrDisorder : associated_with_disease
```
The diagram shows the main structure:
**Core Components:**
- **Adverse Outcome Pathway (AOP)** - The central entity linking molecular events to adverse health outcomes
- **Key Events (KE)** - Measurable biological changes in the pathway
- **Key Event Relationships (KER)** - Causal linkages between key events
**Supporting Entities:**
- **Chemical identifiers** (CAS, InChI, SMILES, PubChem, ChEBI)
- **Biological contexts** (organ, cell type, biological processes)
- **Cross-references** (genes, proteins, pathways, diseases, taxonomic classifications)
The relationships show how AOPs connect to their molecular initiating events, intermediate key events, and final adverse outcomes, with all the supporting chemical and biological context information.
---
*Created by [mcp-proto-okn](https://github.com/sbl-sdsc/mcp-proto-okn) 0.4.0 for biobricks-aopwiki on 2025-12-24*
claude-sonnet-4-20250514
