Prototype Open Knowledge Network (Proto-OKN): SPOKE for Space Health

SPOKE for Space Health: Connecting Biomedical Information on Earth and in Space Via the SPOKE Knowledge Graph

Project Overview


Through this project, development of SPOKE is directed towards space biology and medicine to facilitate bi-directional translation of knowledge and identification of meaningful analogues to maximize ongoing efforts to make humans a multi-planetary species. 
 

information integrations from SPACE
Proposed information integration from Space and Earth sources to build realistic analogues that can improve experience and mitigate risks of spaceflight.

 

AIM 1: The first aim is to integrate SPOKE with primary data from NASA’s Open Data Science Repository (OSDR), starting with the GeneLab platform - a massive repository of more than 100,000 experiments of relevance to space flight.

AIM 2: The second aim is integration of environmental and social factors into SPOKE. Studying such factors on Earth can provide valuable insights and analogues for understanding and addressing health issues during spaceflight. This aim will involve use of de-identified electronic health records and integration of data from multiple population-based databases from the Centers for Disease Control and prevention, Environmental Protection Agency, and the World Health Organization.
 

OSDR-SPOKE Data Fabric

The SPOKE integration with a select number of OSDR studies is now available!

This early GeneLab-SPOKE Demo provides an overview and explanation of the possible analyses.

You may access the OSDR-SPOKE Data Fabric via graphical user interface available at NASA GeneLab visualization portal.

OSDR-SPOKE Data Fabric Visualization Example Video

The following video shows an example use case of navigating the OSDR-SPOKE Data Fabric:

Proto-OKN Masterclass: Building and Querying the SPOKE-GeneLab Knowledge Graph

The following video shows how you can query the SPOKE-GeneLab KG:

 

OSDR-SPOKE Data Fabric Integration Schema

NASA Genelab study schema

 

 

GeneLab Study Statistics

study

GeneLab Visualization

 

Spaceflight Health Analogues on Earth

The project team is utilizing data from electronic health records to model certain conditions that may present analagous health challenges for space flight. These conditions include social drivers of health such as isolation and lack of social connection, limited mobility, and nutritional challenges; as well as environmental factors such as exposure to radiation and chemical compounds.

 

 

 

 

Further Information & Engagement

 

NEWS & EVENTS

  • 🌐 Introducing the mcp-proto-okn Model Context Protocol Server Part of the NSF Prototype Open Knowledge Network (Proto-OKN) program, a $26.7M initiative to build a publicly accessible, interconnected set of knowledge graphs that enable data-driven, AI-powered solutions across domains, we developed mcp-proto-okn to bring natural-language querying to federated graph data. Our mcp-proto-okn MCP server empowers AI assistants to interpret plain-English questions, convert them into structured SPARQL queries, execute them against configured endpoints, and return meaningful results across distributed linked datasets. 

    ✅ Federated Knowledge Graph Access Ask AI assistants questions spanning multiple SPARQL endpoints including biomedical, environmental, justice, space, or other data sources without writing SPARQL. 

    ✅ Seamless AI Integration Use mcp-proto-okn with Claude Desktop or other MCP-aware hosts, letting users frame questions naturally and receive structured insights from linked data. 

    ✅ Open, Extensible, and Federatable The server’s design makes it easy to add endpoints, expand datasets, and extend analyses as the Proto-OKN continues to grow.

    💻 Explore the Code 📦 GitHub – mcp-proto-okn

    📺 See It in Action 👉 Proto-OKN & MCP demo

  • 🚀 Introducing the mcp-genelab Model Context Protocol Our mcp-genelab MCP server lets AI assistants turn natural language questions into Cypher graph queries against Neo4j Knowledge Graphs, empowering researchers to interact with complex biological data without writing code. 📌 Connects to the NASA GeneLab Knowledge Graph Built from multi-omics spaceflight experiments in GeneLab, part of the NASA Open Science Data Repository (OSDR), this graph captures gene expression, DNA methylation, and other space biology metadata across organisms. 🔗 Integrates Biomedical Knowledge from SPOKE Link spaceflight results to broader biological context, including genes, proteins, pathways, anatomical structures, and diseases, for richer AI-assisted insights. 

     ✅ Natural language querying Ask in plain English, no graph query syntax needed. 

    ✅ Spaceflight omics analytics Explore differential gene expression and epigenetic changes. 

    ✅ Multi-organism & tissue-specific analysis Filter by species, organs, or cell types. 

    ✅ Federated knowledge graph queries Combine GeneLab with external Neo4j KGs via MCP. 

    ✅ AI-ready access methods Use via AI assistants (e.g., Claude Desktop) or programmatically. 

    💻 Explore code & examples: MCP-GeneLab Github

    📺 Watch it in action: Querying SPOKE-GeneLab KG

  • To support the 2025 KnowHax Hackathon and build upon the SPOKE-OSDR KG integration, NASA OSDR worked with UCSF to design the SPOKE for Space Health Challenge. This challenge sought to expand the OSDR-SPOKE fabric to include physiological, phenotypic, and environmental data types associated with Spaceflight Associated Neuro-ocular Syndrome (SANS). Three teams worked on the SPOKE for Space Health Challenge under the guidance of NASA mentors, Dr. Amanda Saravia-Butler, Ryan Scott, and Ana Uriarte Acuna, and SPOKE mentors, Drs. Charlotte Nelson and Peter Rose. Each team tackled a unique aspect of the 3-part challenge and all teams pitched their final products at the 2025 Knowledge Graph Conference on May 6th. Two of the teams took home second and third place for the Hackathon. The advancements made by all 3 teams will be integrated into the OSDR-SPOKE data visualization portal and made publicly available. This will enable OSDR users to evaluate physiologic, phenotypic, and environmental data types, alongside ‘omics data, to address critical questions related to astronaut health.
  • The SPOKE for Space Health team presented a poster at UCSF Research AI Day in San Francisco, CA (Mar '25)
  • UCSF Innovation Showcase at JPM25 - MATE bioservices selected to be in the “HIGHLIGHT” Showcase which is comprised of tabletop exhibits in the main reception at JPM25
  • The SPOKE for Space Health team presented a poster at NASA Human Research Program Investigators’ Workshop in Austin, TX (Jan '25)

FUNDING

Spoke for Space Health project is proud to be funded through the NSF Proto-OKN Program