HolobiomicsLab mibig-metadata-extraction
License: restricted — no clear open-source license detected for the underlying tool; verify licensing before commercial use or redistribution.
Summary
Extract and aggregate entry-level metadata from MIBiG JSON files, particularly the cluster.status field, to construct a comprehensive index of curation status across the repository. This skill enables systematic tracking and validation of annotation completeness in the MIBiG secondary metabolite database.
When to use
When you need to audit, inventory, or report on the curation state of MIBiG entries; when cluster.status values must be validated or aggregated for quality control; when building a status index to support data governance or release workflows.
When NOT to use
- When only sequence data or GenBank files are needed — use the genbanks directory instead
- When a pre-built, curated status index is already available from MIBiG's public API or web interface
- When cluster.status field semantics or controlled vocabulary are not documented — context required first
Inputs
- MIBiG JSON file collection (from mibig-json/data directory)
- Entry identifier mappings (filename or internal ID field)
Outputs
- Structured entry-status index (CSV or JSON format)
- Validation report (parsing completeness, missing status fields)
How to apply
Clone or download the mibig-json repository from github.com/mibig-secmet/mibig-json and locate the data directory. Iterate over all JSON files in the directory, parsing each file to extract the entry identifier (from filename or internal ID field) and the cluster.status field value. Aggregate the extracted tuples into a structured index using CSV or JSON format with columns for entry ID and cluster status. Validate that all JSON files have been parsed, that every entry has a status value present, and that status values conform to the expected controlled vocabulary. Manual expert review is recommended to spot-check a sample of entries against the original JSON structure.
Related tools
- mibig-json repository (Source repository containing JSON-formatted MIBiG curation data with cluster.status fields) — https://github.com/mibig-secmet/mibig-json
- MIBiG web interface (Reference for validating extracted status values and understanding entry metadata schema) — https://mibig.secondarymetabolites.org/
Evaluation signals
- All JSON files in the data directory have been successfully parsed with no read errors
- Entry count in output index matches the total number of JSON files in data directory
- Every entry in the index has a non-null cluster.status value
- Status values conform to the expected controlled vocabulary (manually verified against sample entries)
- Index is sortable, searchable, and can be linked back to original JSON files by entry ID
Limitations
- No changelog is available in the repository to document version history or changes to the cluster.status field semantics
- Manual expert review is required to validate status field values — automated validation alone cannot ensure semantic correctness
- The index will only be as current as the last repository clone/download; updates require re-running the extraction workflow
Evidence
- [intro] MIBiG curation data is maintained in JSON format with entry status tracked through the
cluster.statusfield: "MIBiG curation data in JSON format... entry status is now tracked via thecluster.statusfield" - [readme] The data directory contains the current MIBiG datasets: "The current datasets for [MIBiG] live in the
datadirectory, entry status is now tracked via thecluster.statusfield" - [other] Extraction workflow steps including cloning, JSON parsing, field extraction, and aggregation: "Clone or download the mibig-json repository from github.com/mibig-secmet/mibig-json. 2. Locate and read all JSON files in the
datadirectory. 3. For each JSON file, extract the entry identifier" - [other] Validation of extraction completeness and status value presence: "Validate that all entries have been parsed and status values are present"