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SEA CDM: Study-Experiment-Assay Common Data Model and Databases for Cross-Domain Data Integration and Analysis.

Anthony Huffman1, Feng-Yu Yeh2, Junguk Hur3

  • 1Department of Computational Medicine and Biology, University of Michigan Medicine, Ann Arbor, MI 48109, USA.

Biorxiv : the Preprint Server for Biology
|September 5, 2025
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.

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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.