SEA CDM: Study-Experiment-Assay Common Data Model and Databases for Cross-Domain Data Integration and Analysis
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View abstract on PubMed
Summary
This summary is machine-generated.We developed a Study-Experiment-Assay (SEA) common data model (CDM) to standardize and integrate diverse biomedical data. This enables new insights into immune responses, like sex-specific differences after influenza vaccination.
Area Of Science
- Biomedical Informatics
- Immunology
- Data Science
Background
- Increasing volumes of heterogeneous biomedical experimental data pose challenges for standardization and integration.
- Existing data formats lack interoperability, hindering cross-domain analysis and knowledge discovery.
Purpose Of The Study
- To develop an ontology-supported common data model (CDM) for standardizing and integrating diverse biomedical experimental data.
- To establish a robust system for data representation, querying, and analysis to uncover scientific insights.
Main Methods
- Developed the Study-Experiment-Assay (SEA) common data model (CDM) using object-oriented principles and interoperable ontologies.
- Built the Ontology-based SEA Network (OSEAN) relational database and knowledge graph with ETL and query tools.
- Applied the SEA CDM to represent 1,278 immune studies from VIGET, ImmPort, and CELLxGENE.
Main Results
- Successfully represented over two million samples from multiple immune study resources using the SEA CDM.
- Identified scientific insights into sex-specific immune responses, including neutrophil degranulation and TNF binding, post-influenza vaccination.
- Demonstrated the utility of the SEA CDM for robust data querying and analysis.
Conclusions
- The ontology-supported SEA CDM provides a standardized framework for heterogeneous biomedical data.
- The OSEAN system facilitates data integration and knowledge discovery across biological and biomedical domains.
- This approach lays the foundation for an integrative biodata ecosystem.
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