# BioBricks ICE Knowledge Graph Exploration
š¤ **User**
@biobricks-ice
---
š§ **Assistant**
I'll help you explore this knowledge graph! Let me start by getting some information about it.
**BioBricks ICE (Integrated Chemical Environment)** is an open knowledge graph containing chemical safety and bioassay data from the EPA's NICEATM ICE database. It contains **27.4 million triples** describing:
- **206,543 chemical entities**
- **Over 3 million bioassay measurements**
- **2,063 standardized assays**
## Key Features
**Core Entity Types:**
- **Chemical Entities** - Molecules and compounds (identified via EPA DSSTox IDs)
- **Bioassays** - Laboratory tests measuring substance effects on living systems
- **Bioassay Results** - Measured outcomes from experiments
- **Biological Targets** - Molecules that substances interact with (linked to genes and UMLS terms)
- **Chemical Identifiers & Descriptors** - Unique codes and structural information
**Key Relationships:**
- Links chemicals to their bioassay test results
- Connects assays to biological targets and genes
- Provides mechanistic information about how chemicals produce effects
- Includes metadata like assay format, tissue type, and species tested
**Vocabularies Used:**
- BioAssay Ontology (BAO)
- Chemical Information Ontology (CHEMINF)
- Semanticscience Integrated Ontology (SIO)
- Relation Ontology (RO)
**Licensing:** Public domain (CC0-1.0) - freely available with no restrictions
## What can I help you explore?
I can help you query this knowledge graph to find information about:
- Specific chemicals and their safety data
- Bioassay results and experimental outcomes
- Biological targets and mechanisms of action
- Gene-chemical interactions
- Toxicity endpoints and health effects
---
š¤ **User**
Visualize the schema
---
š§ **Assistant**
Here's the schema visualization for the BioBricks ICE knowledge graph:
```mermaid
classDiagram
class ChemicalEntity {
+label
+identifier
}
class ChemicalIdentifier {
+value
+type
}
class ChemicalStructureDescriptor {
+structure_info
}
class Bioassay {
+label
+assay_source
+assay_species
+assay_tissue
+invitro_assay_format
}
class BioassayResult {
+value
+unit
}
class BiologicalTarget {
+label
+entrez_gene_id
}
class GeneIdentifier {
+gene_id
+label
}
class AssayDesign {
+format
+method
}
class DatabaseEntry {
+source
+identifier
}
ChemicalEntity --|> ChemicalIdentifier : has_identifier
ChemicalEntity --|> ChemicalStructureDescriptor : has_descriptor
ChemicalEntity --> DatabaseEntry : source
Bioassay --> BioassayResult : has_specified_output
Bioassay --> BiologicalTarget : through_mechanistic_target
Bioassay --> AssayDesign : has_assay_component
Bioassay --> ChemicalEntity : has_participant
BioassayResult --> ChemicalEntity : is_about
BioassayResult --> Bioassay : participates_in
BiologicalTarget --> GeneIdentifier : has_identifier
BiologicalTarget --> Bioassay : participates_in
ChemicalEntity --> BioassayResult : may_inform_on
```
## Key Schema Insights
The diagram shows the main structure of the BioBricks ICE knowledge graph:
**Central Hub:** The **Bioassay** class connects most entities together, linking chemicals to their test results and biological targets.
**Chemical Information:** Chemical entities are identified through various identifiers and descriptors, with links to external databases.
**Experimental Data Flow:**
- Chemicals participate in bioassays
- Bioassays produce results
- Results measure effects on biological targets
- Targets are linked to specific genes
This structure enables queries about chemical safety, toxicity mechanisms, and gene-chemical interactions across the EPA's CompTox database.
---
š¤ **User**
Create transcript
---
*Created by [mcp-proto-okn](https://github.com/sbl-sdsc/mcp-proto-okn) 0.4.0 using claude-sonnet-4-20250514 on 2025-12-22*
