MAG2ENA: Environment-aware curation and metadata lifecycle management of metagenome-assembled genomes in the European Nucleotide Archive

Résumé fourni par la source

MAG2ENA is an open-source web and command-line platform for the curation, validation, submission, and post-submission maintenance of metagenome-assembled genome (MAG) metadata in the European Nucleotide Archive (ENA). The platform implements the MIMAG-based ENA MAG checklist (ERC000047) and provides a guided workflow for preparing standards-compliant MAG submissions while reducing repetitive manual metadata processing. MAG2ENA can retrieve contextual metadata from linked parent INSDC records, import quality estimates from CheckM and CheckM2, integrate taxonomic assignments from GTDB-Tk, and resolve missing NCBI taxonomy identifiers through ENA. Environmental metadata are supported by a field-aware, curator-in-the-loop resolver that distinguishes broad-scale environmental context, local environmental context, and environmental medium, searches ENVO through OLS4 using field-specific constraints, ranks candidate ontology terms, and abstains when evidence is insufficient. An interactive map enables visual inspection of parent-sample locations and associated MAGs. The web interface provides asynchronous processing, checklist-derived validation, downloadable provenance records, and encrypted job artifacts. MAG2ENA also supports retrieval and metadata-only modification of existing ENA samples, including comparison of metadata changes, local and ENA validation, explicit curator confirmation, concurrent-change checking, provenance tracking, and rollback information. A complementary CLI supports larger batch submissions and the same core metadata-assistance functions. MAG2ENA was validated using 100 marine and human-gut MAGs successfully deposited in ENA, and metadata-only updates were subsequently verified in production for the associated records. The software is designed to support transparent, reproducible, and curator-controlled management of MAG metadata throughout the deposition lifecycle.

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