# Gene Expression Atlas Knowledge Graph Exploration
👤 **User**
@gene-expression-atlas-okn
---
🧠 **Assistant**
I'll help you explore the gene expression atlas knowledge graph. Let me first get some information about what's available in this resource.
Great! I can help you explore the **Gene Expression Atlas** knowledge graph, which contains selected studies from the EMBL-EBI Gene Expression Atlas. This resource includes:
- **243 studies** with 797 assays
- Expression data for **152,879 genes**
- Differential expression measurements with statistical metrics
- Links to anatomical entities, cell types, diseases, developmental stages, and biological sex categories
Let me get the schema to show you what kinds of data and relationships are available:
Perfect! Here's what you can explore in this knowledge graph:
## Main Entity Types:
- **Study** - 243 gene expression studies from the Atlas
- **Assay** - 797 individual assays/experiments
- **Gene** - 152,879 genes with expression data
- **AnatomicalEntity** - Tissue/organ locations
- **Cell** - Cell types
- **Disease** - Disease conditions
- **BiologicalSex** - Sex-specific data
- **LifeStage** - Developmental stages
- **BiologicalProcess**, **Pathway**, **ProteinDomain** - Functional annotations
## Key Relationships:
- Studies contain assays (has_output)
- Assays measure gene expression with statistical metrics
- Studies can be linked to diseases, populations, and organisms
## Important Properties:
- **Statistical metrics**: p_value, effect_size, genes_significant
- **Study metadata**: project_title, pubmed_id, experimental_factors
- **Assay details**: technology, array_design, test/reference groups
- **Gene identifiers**: ncbi_gene_id, ensembl_id, symbol
## What would you like to explore?
I can help you:
1. Search for genes and their expression patterns
2. Find studies related to specific diseases or tissues
3. Analyze differential expression data
4. Explore experimental factors and contrasts
5. Visualize the knowledge graph structure
What interests you?
---
👤 **User**
Visualize schema
---
🧠 **Assistant**
I'll create a visual schema diagram for you. Let me generate the Mermaid class diagram showing all the entity types and their relationships.
```mermaid
classDiagram
direction TB
class Study {
string id
string project_title
string project_type
string pubmed_id
string experimental_factors
string secondary_accessions
string source
string submitter_name
string submitter_email
string submitter_affiliation
}
class Assay {
string id
string description
string study_id
string technology
string array_design
string measurement
string factors_1
string factors_2
string test_group_id
string test_group_label
string reference_group_id
string reference_group_label
}
class Gene {
string id
string symbol
string category
string ncbi_gene_id
string ensembl_id
string id_source
}
class AnatomicalEntity {
string id
string name
string uri
}
class Cell {
string id
string name
}
class Disease {
string id
string name
}
class BiologicalSex {
string id
string name
}
class LifeStage {
string id
string name
}
class BiologicalProcess {
string id
string name
}
class Pathway {
string id
string name
}
class ProteinDomain {
string id
string name
}
class PopulationOfIndividualOrganisms {
string id
string name
}
class Association {
string contrast_id
string experiment_accession
string term_id
float p_value
float effect_size
int genes_significant
int genes_total
string enrichment_type
}
class GeneExpressionMixin {
string id
}
Study --> Assay : has_output
Study --> Disease : studies
Study --> PopulationOfIndividualOrganisms : has_attribute
Assay --> Disease : has_input
GeneExpressionMixin --> Assay : subject
GeneExpressionMixin --> Gene : object
Association --> ProteinDomain : participates_in
```
Here's the schema visualization for the Gene Expression Atlas knowledge graph! The diagram shows:
**Core Structure:**
- **Study** entities contain multiple **Assay** experiments
- **GeneExpressionMixin** connects assays to genes, representing the actual expression measurements
- **Association** entities capture enrichment and statistical relationships
**Biological Context:**
- Studies can be linked to **Disease** conditions and **PopulationOfIndividualOrganisms**
- The schema includes entities for anatomical locations, cell types, life stages, biological sex, pathways, and protein domains
**Key Properties:**
- Studies have metadata like titles, PubMed IDs, and experimental factors
- Assays track technology platforms, test/reference groups, and measurement types
- Genes have multiple identifiers (NCBI, Ensembl) and symbols
- Associations include statistical measures (p-values, effect sizes)
The downloadable .mermaid file is ready for you to use in documentation or presentations!
---
*Created by [mcp-proto-okn](https://github.com/sbl-sdsc/mcp-proto-okn) 0.5.0 on 2026-01-15*
*Model: Claude Sonnet 4.5 (claude-sonnet-4-5-20250929)*
