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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 Medical School, Ann Arbor, MI, 48109, USA.

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Summary
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A new Study-Experiment-Assay (SEA) common data model (CDM) standardizes biomedical data. This enables new insights into sex-specific immune responses after influenza vaccination, paving the way for an integrated biodata ecosystem.

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Area of Science:

  • Biomedical Informatics
  • Immunology
  • Data Science

Background:

  • Increasing biomedical data volume presents challenges in standardization and integration.
  • Heterogeneous experimental data across domains requires robust solutions for sharing and analysis.
  • Existing data models may not adequately support cross-domain integration and knowledge inference.

Purpose of the Study:

  • To develop an ontology-supported common data model (CDM) for standardizing and integrating biomedical experimental data.
  • To build a relational database and knowledge graph (OSEAN) based on the SEA CDM for enhanced data analysis.
  • To apply the developed system to large-scale immune study datasets for scientific discovery.

Main Methods:

  • Developed the Study-Experiment-Assay (SEA) common data model (CDM) using object-oriented modeling with 10 core and 3 auxiliary classes.
  • Utilized interoperable ontologies within the SEA CDM for data standardization and knowledge inference.
  • Constructed the Ontology-based SEA Network (OSEAN) relational database and knowledge graph, incorporating ETL and query tools.

Main Results:

  • Successfully represented 1,278 immune studies with over two million samples from VIGET, ImmPort, and CELLxGENE using the OSEAN system.
  • Identified scientific insights into sex-specific immune responses, including neutrophil degranulation and TNF binding, following influenza vaccination.
  • Demonstrated the utility of simple, robust queries and analyses on the integrated data.

Conclusions:

  • The novel SEA CDM system provides a foundational framework for an integrative biodata ecosystem.
  • The OSEAN system facilitates data standardization, sharing, and knowledge discovery across diverse biomedical domains.
  • This approach enables robust analysis of complex immunological data, revealing important sex-specific vaccination responses.