Entry Status Classification

entry-status-classification

License: restricted — no clear open-source license detected for the underlying tool; verify licensing before commercial use or redistribution.

Summary

Extract and aggregate entry status values from MIBiG JSON curation records to build a searchable index of data quality and curation state across the repository. This skill is essential for understanding the completeness and validation stage of secondary metabolite biosynthetic gene cluster annotations.

When to use

Apply this skill when you need to assess the overall curation coverage and quality of a MIBiG repository snapshot, identify which entries require further review, or track how entry validation status changes over time. Specifically use it when the data directory contains JSON files with cluster.status fields that must be indexed and reported.

When NOT to use

• Input data is not from the MIBiG data directory or lacks cluster.status fields
• The goal is to retrieve sequence data rather than assess curation metadata — use the genbanks directory instead
• Entry status has already been indexed or is available from a pre-built status table

Inputs

• MIBiG JSON files from the data directory
• Entry identifier fields (filename or internal ID)
• cluster.status field values from parsed JSON objects

Outputs

• Structured index (CSV or JSON format) with entry ID and cluster status columns
• Aggregated entry-status mapping suitable for filtering or reporting

How to apply

Clone or download the mibig-json repository, then systematically traverse all JSON files in the data directory. For each file, parse the JSON structure and extract two key fields: the entry identifier (from the filename or an internal ID field) and the cluster.status value, which indicates the curation or validation state of that entry. Aggregate these pairs into a structured format (CSV or JSON with columns for entry ID and cluster status). Validate completeness by confirming that all files in the data directory have been parsed and that no entries lack a status value. The rationale is that cluster.status is the authoritative field tracking entry state in MIBiG's curation workflow.

Related tools

• mibig-json repository (Source repository containing JSON-formatted curation data with cluster.status fields) — https://github.com/mibig-secmet/mibig-json
• MIBiG web interface (Reference for understanding entry status terminology and curation guidelines) — https://mibig.secondarymetabolites.org/

Examples

cd mibig-json && find data -name '*.json' -exec jq -r '[.cluster_number // .filename, .cluster.status] | @csv' {} + > entry_status_index.csv

Evaluation signals

• All JSON files in the data directory are successfully parsed without errors
• Every entry in the index has a non-null, non-empty cluster.status value
• The count of indexed entries matches the total number of JSON files in data
• The generated index can be loaded and queried to filter entries by status
• Manual spot-check of 5–10 entries confirms that status values and IDs are correctly extracted

Limitations

• No changelog is available in the repository, so version history and documentation of status value changes cannot be tracked
• The skill assumes cluster.status field is present in all JSON files; files with missing or malformed status fields may cause parsing failures or incomplete indexing
• Status terminology and valid values are not formally documented in the provided README, so interpretation of status strings requires external knowledge of MIBiG curation workflow

Evidence

• [intro] MIBiG annotations are maintained in JSON format with entry status tracked via cluster.status field: "MIBiG curation data in JSON format. The current datasets for [MIBiG] live in the data directory, entry status is now tracked via the cluster.status field."
• [other] Workflow includes extraction of entry identifier and status field, aggregation into structured format, and validation of completeness: "For each JSON file, extract the entry identifier (filename or internal ID field) and the cluster.status field value. Aggregate results into a structured index (CSV or JSON format) with columns for"
• [discussion] No changelog available limits ability to track status changes over time: "No changelog found — version history and documentation of changes not available"