{"doi":"10.1093/nar/gkaf1057","title":"PRIME: a database for 16S rRNA microbiome data with phenotypic reference and comprehensive metadata","abstract":"PRIME (Phenotypic Reference for Integrated Microbiome Enrichment) is a curated and standardized database of human microbiome 16S rRNA amplicon sequencing data, designed to facilitate cross-study analysis, reproducibility, and phenotype-driven discovery. PRIME aggregates 53 449 samples from 111 public studies, covering 93 body sites and 101 phenotypic categories, with detailed harmonization of sample-level metadata such as disease status, demographics, body sites, sequencing protocols, and experimental design. Each sample includes taxonomic abundance profiles generated via a consistent pipeline using both SILVA (138.2) and Greengenes2 (2024.09) reference databases, with results reported at multiple taxonomic levels as observed abundances (read counts) and relative abundances (proportions). A major strength of PRIME is its extensive manual curation, which standardizes phenotypic and contextual metadata across studies, enabling precise querying and robust phenotype-based comparisons. Users can interactively explore the database through a modern web interface, filter and visualize data by metadata fields, and download customized subsets. Programmatic access is supported via RESTful APIs and R package. PRIME aims to advance microbiome data integration and is continuously updated to incorporate new studies and features. The database is freely available at https://primedb.sjtu.edu.cn.","journal":"Nucleic Acids Research","year":2025,"id":279,"datarank":0.10397207708399181,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.0,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.0,"corpus_percentile":22.178386323199504,"corpus_rank":9377,"citation_count":1,"citer_count":1,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9507,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-10-31","fair_score":87.5,"fair_percentile":99.41913787832468,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":2737,"name":"Luca Pinello","orcid":"0000-0003-1195-9607","position":1,"is_corresponding":false},{"id":2738,"name":"Tao Wang","orcid":"0000-0002-1218-4017","position":2,"is_corresponding":false},{"id":2736,"name":"Zhizhuo Zhang","orcid":"0000-0003-1202-4037","position":0,"is_corresponding":true}],"reference_count":36,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"41171140","pmcid":"PMC12807763","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":83.3333,"fair_a":87.5,"fair_i":20.0,"fair_r":75.0,"fair_zscore":2.0998,"fair_rationale":{"fair_score":87.5,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":83.33,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"https://doi.org/10.5281/zenodo.15711237","grounded":true,"rationale":"The paper gives a DOI for the dataset, a persistent identifier scheme.","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"permanently archived at https://doi.org/10.5281/zenodo.15711237","grounded":true,"rationale":"Zenodo is a named data repository listed in re3data/FAIRsharing. 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