# SPOKE-OKN Schema Visualization
## Chat Transcript
š¤ **User**
@spoke-okn
---
š§ **Assistant**
I'll help you explore the SPOKE-OKN knowledge graph! Let me first get some information about this resource.
Great! I can help you work with the **SPOKE-OKN (SPOKE Open Knowledge Network)** knowledge graph. This is a comprehensive biomedical and environmental health knowledge graph that integrates diverse data across genomics, environmental science, and public health.
**Key features of SPOKE-OKN:**
- Integrates data on organisms, genes, diseases, chemical compounds, social determinants of health, and environmental contexts
- Includes detailed geographic information (countries down to ZIP codes)
- Supports spatial analyses of health outcomes, environmental exposures, and socioeconomic factors
- Maintained by the Baranzini Lab at UCSF
**What would you like to explore?** I can help you:
- Understand what types of data are available (genes, diseases, locations, environmental factors, etc.)
- Search for specific information (e.g., genes related to diseases, environmental exposures in certain areas)
- Analyze relationships between different entities
- Visualize the knowledge graph structure
Would you like me to show you the schema to see what kinds of data and relationships are available, or do you have a specific question you'd like to explore?
---
š¤ **User**
Visualize the schema
---
š§ **Assistant**
I'll visualize the schema for you. Let me first get the schema information and then create a visual diagram.
```mermaid
classDiagram
direction TB
class SDoH {
data_source
domain
mesh_ids
topic
}
class AdministrativeArea {
abbr
city_fips
code
county_fips
iso3
latitude
longitude
state
state_fips
state_name
zipcode_type
}
class ChemicalEntity {
max_phase
smiles
standardized_smiles
synonyms
}
class Disease {
mesh_list
omim_list
}
class EnvironmentalFeature {
synonyms
}
class Gene {
ensembl
}
class OrganismTaxon {
antimicrobial_resistance
biovar
collection_date
disease
genbank_accessions
genome_size
gram_stain
has_amr_phenotype
host_age
host_gender
host_health
host_is_human
host_name
is_resistant
isolation_country
isolation_source
level
motility
oxygen_requirement
pathovar
salinity
serovar
sporulation
strain
temperature_range
usa_isolation_country
}
class CONTRAINDICATES_CcD {
Activity Sources
}
class TREATS_CtD {
Activity Sources
Phase
}
class ASSOCIATES_SaD {
Co-occurrence
Enrichment
Fisher's Test
Odds Ratio
}
class RESEMBLES_DrD {
Co-occurrence
Enrichment
Fisher's Test
Odds Ratio
}
class PREVALENCE_DpL {
Data Value
Data Value Type
Data Value Unit
Location Name
Lower Bound
Metric Name
Short Question Text
State Abbreviation
State Description
Total Population
Upper Bound
Value
Year
}
class FOUNDIN_CfL {
Date
Date Type
Media
Metrics
Unit
Value
Year
}
class INTERACTS_CiC {
Drug-Drug Interaction Risk
}
class MORTALITY_DmL {
Global Health Estimate Code
Mortality Per 100k
Population
Usability
Value
}
class RESPONDS_TO_OrC {
Laboratory Typing Method
Laboratory Typing Platform
Measurement Sign
Measurement Unit
Measurement Value
Resistant Phenotype
Testing Standard Year
Vendor
}
class PREVALENCEIN_SpL {
Method
Value
Variable
Year
}
class FOUNDIN_EfL {
Metrics
Unit
Value
Year
}
class PARTOF_LpL {
Percent of Place Area in ZIP
Percent of ZIP Area in Place
}
SDoH --> SDoH : ISA_SiS
Disease --> Disease : ISA_DiD
ChemicalEntity --> ChemicalEntity : ISA_CiC
EnvironmentalFeature --> EnvironmentalFeature : ISA_EiE
AdministrativeArea --> AdministrativeArea : PARTOF_LpL_simple
ChemicalEntity --> ChemicalEntity : PARTOF_CpC
ChemicalEntity --> FOUNDIN_CfL
FOUNDIN_CfL --> AdministrativeArea
EnvironmentalFeature --> FOUNDIN_EfL
FOUNDIN_EfL --> AdministrativeArea
OrganismTaxon --> AdministrativeArea : ISOLATEDIN_OiL
Disease --> PREVALENCE_DpL
PREVALENCE_DpL --> AdministrativeArea
SDoH --> PREVALENCEIN_SpL
PREVALENCEIN_SpL --> AdministrativeArea
Disease --> MORTALITY_DmL
MORTALITY_DmL --> AdministrativeArea
Disease --> Gene : ASSOCIATES_DaG
SDoH --> ASSOCIATES_SaD
ASSOCIATES_SaD --> Disease
ChemicalEntity --> TREATS_CtD
TREATS_CtD --> Disease
ChemicalEntity --> CONTRAINDICATES_CcD
CONTRAINDICATES_CcD --> Disease
ChemicalEntity --> INTERACTS_CiC
INTERACTS_CiC --> ChemicalEntity
ChemicalEntity --> Gene : UPREGULATES_CuG
ChemicalEntity --> Gene : DOWNREGULATES_CdG
Gene --> Disease : EXPRESSEDIN_GeiD
OrganismTaxon --> RESPONDS_TO_OrC
RESPONDS_TO_OrC --> ChemicalEntity
Gene --> ChemicalEntity : RESISTANT_TO_mGrC
Gene --> ChemicalEntity : RESPONSE_TO_mGrC
Gene --> ChemicalEntity : ADVRESPONSE_TO_mGarC
Gene --> Disease : MARKER_POS_GmpD
Gene --> Disease : MARKER_NEG_GmnD
Disease --> RESEMBLES_DrD
RESEMBLES_DrD --> Disease
ChemicalEntity --> ChemicalEntity : HASROLE_ChC
AdministrativeArea --> PARTOF_LpL
PARTOF_LpL --> AdministrativeArea
```
Here's a visual representation of the SPOKE-OKN knowledge graph schema!
**Key Components:**
**7 Main Entity Types:**
- **SDoH** (Social Determinants of Health) - social and economic factors affecting health
- **AdministrativeArea** - geographic locations (countries, states, counties, ZIP codes)
- **ChemicalEntity** - drugs and chemical compounds
- **Disease** - disorders and illnesses
- **EnvironmentalFeature** - environmental quality entities
- **Gene** - units of heredity
- **OrganismTaxon** - bacterial strains and organisms
**Relationship Types:**
- **Simple arrows** show direct relationships (e.g., Gene ā Disease, Chemical ā Gene)
- **Box-shaped relationships** contain edge properties - these store quantitative data on the relationships themselves (like disease prevalence values, drug interaction risk levels, mortality rates, etc.)
The diagram shows how SPOKE-OKN integrates biomedical, environmental, and geographic data to support research on health outcomes, environmental exposures, and social determinants of health.
---
*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
