{"doi":"10.1101/2025.08.26.671804","title":"SEA CDM: Study-Experiment-Assay Common Data Model and Databases for Cross-Domain Data Integration and Analysis","abstract":"With the increasing volume of biomedical experimental data, standardizing, sharing, and integrating heterogeneous experimental data across domains has become a major challenge. To address this challenge, we have developed an ontology-supported Study-Experiment-Assay (SEA) common data model (CDM), which includes 10 core and 3 auxiliary classes based on object-oriented modeling. SEA CDM uses interoperable ontologies for data standardization and knowledge inference. Building on the SEA CDM, we developed the Ontology-based SEA Network (OSEAN) relational database and knowledge graph, along with a set of ETL (Extract, Transform, Load) and query tools, and further applied them to represent 1,278 immune studies with over two million samples from three resources: VIGET, ImmPort, and CELLxGENE. Using simple, robust queries and analyses, our research identified multiple scientific insights into sex-specific immune responses, such as neutrophil degranulation and TNF binding to physiological receptors, following live attenuated and trivalent inactivated influenza vaccination. The novel SEA CDM system lays a foundation for establishing an integrative biodata ecosystem across biological and biomedical domains.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":573698,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":0.0,"corpus_rank":10062,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.5256,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1480851,"name":"Feng-Yu Yeh","orcid":"0000-0003-2294-3571","position":1,"is_corresponding":false},{"id":350442,"name":"Junguk Hur","orcid":"0000-0002-0736-2149","position":2,"is_corresponding":false},{"id":770685,"name":"Jie Zheng","orcid":"0000-0001-6774-9786","position":3,"is_corresponding":false},{"id":755060,"name":"Anna Maria Masci","orcid":"0000-0003-1940-6740","position":4,"is_corresponding":false},{"id":614243,"name":"Guanming Wu","orcid":"0000-0001-8196-1177","position":5,"is_corresponding":false},{"id":23317,"name":"Cui Tao","orcid":"0000-0002-4267-1924","position":6,"is_corresponding":false},{"id":551211,"name":"Brian Athey","orcid":null,"position":7,"is_corresponding":false},{"id":90652,"name":"Yongqun He","orcid":"0000-0001-9189-9661","position":8,"is_corresponding":false},{"id":227981,"name":"Anthony Huffman","orcid":"0000-0002-0576-550X","position":0,"is_corresponding":true}],"reference_count":45,"raw_metadata":null,"created_at":"2026-07-19T02:57:36.753600Z","pmid":"40909744","pmcid":"PMC12407955","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}