# SPOKE GeneLab Schema Visualization
š¤ **User**
@spoke-genelab
---
š§ **Assistant**
I'll help you explore the spoke-genelab knowledge graph. Let me first get some information about this resource.
Great! I'm now working with the **SPOKE GeneLab** knowledge graph. This is a specialized resource that integrates omics data from NASA's Open Science Data Repository (GeneLab), focusing on spaceflight experiments.
This knowledge graph includes:
- **Transcriptional profiling** data (RNA-Seq, DNA microarray)
- **Epigenomic profiling** data (DNA methylation)
- **Model organisms** flown in space or maintained as ground controls
- Pre-computed **differential expression and methylation signatures**
- **Cross-species mapping** to human orthologs
- Integration with **SPOKE's human biology network** (pathways, phenotypes, therapeutic targets)
- **Cell and tissue type mappings** to standard ontologies (CL and UBERON)
What would you like to explore? I can help you:
- Understand the structure of the data (view the schema)
- Search for specific genes, studies, or experimental conditions
- Analyze differential expression or methylation patterns
- Explore relationships between spaceflight conditions and biological responses
- Compare data across different organisms or tissue types
What are you interested in learning about?
---
š¤ **User**
Visualize the schema
---
š§ **Assistant**
Let me visualize the SPOKE GeneLab schema for you. I'll start by retrieving the schema information.
Perfect! Now let me create the Mermaid class diagram:
Here's the SPOKE GeneLab schema visualization! The diagram shows:
**Core Entities:**
- **Mission** ā **Study** ā **Assay**: The organizational hierarchy of spaceflight experiments
- **Gene**: Genetic elements from model organisms, with ortholog mappings to human genes
- **Anatomy** & **CellType**: Biological contexts investigated in assays
- **MethylationRegion**: Genomic regions showing differential methylation
**Key Relationships with Quantitative Data** (shown as intermediary classes):
- **MEASURED_DIFFERENTIAL_EXPRESSION**: Links assays to genes with log2 fold change and adjusted p-values
- **MEASURED_DIFFERENTIAL_METHYLATION**: Links assays to methylation regions with methylation differences and q-values
- **METHYLATED_IN**: Connects genes to methylation regions with detailed genomic location data (chromosome, position, overlap with exons/introns/promoters)
This structure enables powerful queries to explore how spaceflight affects gene expression and DNA methylation across different organisms and tissue types!
```mermaid
classDiagram
direction TB
class Mission {
date end_date
string flight_program
string space_program
date start_date
}
class Study {
string project_title
string project_type
}
class Assay {
string factor_space_1
string factor_space_2
string[] factors_1
string[] factors_2
string material_1
string material_2
string material_id_1
string material_id_2
string material_name_1
string material_name_2
string measurement
string technology
}
class Anatomy
class CellType
class Gene {
string organism
string symbol
string taxonomy
}
class MethylationRegion
class MEASURED_DIFFERENTIAL_EXPRESSION_ASmMG {
float adj_p_value
float log2fc
}
class METHYLATED_IN_MGmMR {
string chromosome
int dist_to_feature
int end
boolean in_exon
boolean in_intron
boolean in_promoter
int start
}
class MEASURED_DIFFERENTIAL_METHYLATION_ASmMR {
float methylation_diff
float q_value
}
Mission --> Study : CONDUCTED_MIcS
Study --> Assay : PERFORMED_SpAS
Assay --> Anatomy : INVESTIGATED_ASiA
Assay --> CellType : INVESTIGATED_ASiCT
Gene --> Gene : IS_ORTHOLOG_MGiG
Assay --> MEASURED_DIFFERENTIAL_EXPRESSION_ASmMG
MEASURED_DIFFERENTIAL_EXPRESSION_ASmMG --> Gene
Gene --> METHYLATED_IN_MGmMR
METHYLATED_IN_MGmMR --> MethylationRegion
Assay --> MEASURED_DIFFERENTIAL_METHYLATION_ASmMR
MEASURED_DIFFERENTIAL_METHYLATION_ASmMR --> MethylationRegion
```
---
*Created by [mcp-proto-okn](https://github.com/sbl-sdsc/mcp-proto-okn) 0.4.0 on 2025-12-31*
Model: claude-sonnet-4-20250514
