Scientific Data / AI in Biomedicine
SEA CDM: Study-Experiment-Assay Common Data Model and Databases for Cross-Domain Data Integration and Analysis
This paper introduces the Study-Experiment-Assay (SEA) common data model (CDM) for standardizing and integrating heterogeneous biomedical experimental data. Comprising 10 core and 3 auxiliary classes, SEA CDM uses interoperable ontologies for data standardization and knowledge inference. Building on this, the Ontology-based SEA Network (OSEAN) relational database and knowledge graph were developed. The system was applied to represent 1,278 immune studies with over two million samples from VIGET, ImmPort, and CELLxGENE. Robust queries revealed scientific insights into sex-specific immune responses to influenza vaccination, laying a foundation for an integrative biodata ecosystem.
Executive Impact: Transforming Scientific Data / AI in Biomedicine with AI
The SEA CDM offers a novel, ontology-supported framework for unifying diverse biomedical data. Our OSEAN database and tools have successfully integrated over 2 million samples from key immune study repositories. This integration enabled the discovery of sex-specific immune response patterns to influenza vaccines, demonstrating the system's power for advanced data analysis and accelerating biomedical research. This approach reduces data fragmentation, enhances interoperability, and provides a scalable solution for complex biodata management.
1278+
Studies Integrated
2000000+
Samples Processed
3
Domains Covered
7+
Scientific Insights
Deep Analysis & Enterprise Applications
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CDM Model Overview
Ontology Support
Data Integration & Use Cases
Scientific Findings
CDM Model Overview
The Study-Experiment-Assay (SEA) Common Data Model (CDM) is designed for cross-domain data integration, featuring 10 core and 3 auxiliary classes based on object-oriented modeling. It leverages interoperable ontologies for robust data standardization and knowledge inference, enabling a unified approach to diverse biomedical experimental data.
Ontology Support
SEA CDM extensively uses interoperable ontologies, such as Vaccine Ontology (VO) and Ontology of Biomedical Investigation (OBI), for standardizing key concepts and attributes. This ontological foundation ensures data FAIRness, supports semantic queries, and allows for knowledge inference beyond simple term matching.
Data Integration & Use Cases
The Ontology-based SEA Network (OSEAN) relational database and knowledge graph, built on SEA CDM, facilitate the integration of heterogeneous data from resources like VIGET, ImmPort, and CELLxGENE. Use cases demonstrate the system's ability to consolidate over two million samples and 1,278 studies, enabling cross-platform analysis.
Scientific Findings
Applying the SEA CDM system to influenza vaccine studies revealed significant sex-specific immune responses. Insights include differential neutrophil degranulation and TNF binding patterns in males versus females following live attenuated and trivalent inactivated influenza vaccination, enhancing understanding of vaccine immunology.
Enterprise Process Flow
Study Design & Data Collection
→
Data ETL to SEA CDM
→
OSEAN Database / KG Population
→
Ontology-Driven Query & Analysis
→
Scientific Insight Generation
Integrated Studies
1278+ Biomedical studies seamlessly unified for comprehensive analysis.| Immune Metric | LAIV-Vaccinated | TIV-Vaccinated |
|---|---|---|
| Stimulated Genes (All Sexes) |
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| Neutrophil Degranulation |
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| TNF Binding |
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Samples Unified
2M+ Diverse biological samples harmonized for cross-domain research.Case Study: Sex-Specific Influenza Vaccine Responses
Our analysis using SEA CDM revealed that LAIV stimulates more genes than TIV in vaccinated humans. Specifically, LAIV-vaccinated females showed unique immune responses, including 'TNF binds physiological receptors'. In contrast, neutrophil degranulation, a key innate immune process, was observed in males and TIV-vaccinated females but not in LAIV-vaccinated females, aligning with recent findings of sex-biased degranulation activity. This highlights the critical need for sex-specific considerations in vaccine design.
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Estimated Annual Savings
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Your Path to Integrated Biodata: Implementation Roadmap
A structured approach to adopting the SEA CDM framework, ensuring a smooth transition and rapid value realization for your scientific endeavors.
Phase 1: Data Model Adoption
Adopt SEA CDM principles, establishing a standardized schema for your data across domains.
Phase 2: ETL Development
Develop Extract, Transform, Load (ETL) pipelines to ingest your raw data into the OSEAN-DB or OSEAN-KG.
Phase 3: Ontology Integration
Map your enterprise concepts to existing ontologies, enriching data with semantic meaning and inference capabilities.
Phase 4: Advanced Analytics Enablement
Utilize PELAGIC and custom query tools to perform sophisticated cross-domain analyses and generate new insights.
Phase 5: Ecosystem Expansion
Integrate new data sources and expand your biodata ecosystem, continuously leveraging the SEA CDM for scalability.
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