PRIME Database Archive Data

Description

This deposit contains the full metadata and abundance tables from the PRIME database (Phenotypic Reference for Integrated Microbiome Enrichment), along with the accompanying R package primeDB.

Included files:

Sample-level and project-level metadata

samples_metadata.csv: curated metadata for 53,449 microbiome samples.

projects_metadata.csv: metadata summarizing the 111 individual studies.

Taxonomic abundance tables (n = 24)

Format: [ref]_[level]_[type].csv

ref: reference database used for taxonomic assignment (silva for SILVA 138.2 or gg for Greengenes2 2024.09)

level: taxonomic rank (phylum, class, order, family, genus, species)

type: abundance type (absolute(for observed abundance) or relative(for relative abundance)

Each file provides an abundance matrix (samples × taxa) at the specified level.

R package

primeDB_0.1.0.tar.gz: an R package providing programmatic access to the PRIME API and data.

Classifier

silva-138-99-nb-classifier.qza: official classifier from QIIME2 of SILVA 138.2

gg_2024_09_backbone_full_length.nb.qza: official classifier from QIIME2 of Greengenes2 2024.09

ASV sequences and taxonomy mapping

asv_map.zip: all ASV sequences and its taxonomy assigned

These resources are provided as part of the PRIME project for reproducible research, data reuse, and transparent microbiome meta-analysis. All files are freely available for academic use.