Tabular data validation

tabular-data-validation

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Summary

Cross-reference curated structure-organism pairs against reference dictionaries (organism, structure, reference) and validate metadata completeness to filter a curated collection down to high-confidence, platinum-tier pairs. This skill ensures that only pairs with verified dictionary entries, complete metadata, and no conflicting assertions advance to downstream analysis.

When to use

Apply this skill after curating and integrating structure-organism pairs from multiple sources when you need to produce a high-confidence subset suitable for publication or computational validation. Specifically, use it when your input is a merged table of structure-organism pairs with associated literature references and you have authority dictionary files (organism, structure, reference) that define the canonical valid entries for your domain.

When NOT to use

• Input table is already validated or pre-filtered to high-confidence pairs — re-validation wastes computational resources and risks false rejection.
• Reference dictionaries are incomplete, out-of-date, or not authoritative for your domain — validation results will be unreliable.
• You need to include all curated pairs regardless of metadata completeness or conflicts — use the full curated table instead.

Inputs

• curated structure-organism pairs table (TSV/GZ format, e.g., interim/tables/3_curated/table.tsv.gz)
• organism reference dictionary (TSV/GZ format, e.g., interim/dictionary/organism/dictionary.tsv.gz)
• structure reference dictionary (TSV/GZ format, e.g., interim/dictionary/structure/dictionary.tsv.gz)
• reference metadata tables (TSV/GZ format, e.g., dictionaryOrganism.tsv.gz, metadata.tsv.gz)

Outputs

• platinum.tsv.gz — high-confidence structure-organism pairs with validation flags and complete metadata

How to apply

Load the curated table (e.g., interim/tables/3_curated/table.tsv.gz) alongside reference dictionaries (organism/dictionary.tsv.gz, structure/dictionary.tsv.gz, and reference metadata files). For each structure-organism pair in the curated table, perform three sequential validations: (1) verify that the organism identifier exists in the organism dictionary and that the structure identifier exists in the structure dictionary; (2) check that all associated reference identifiers and their metadata (e.g., literature citations from dictionaryOrganism.tsv.gz and metadata.tsv.gz) are present and non-null; (3) apply quality filters to flag and exclude pairs with conflicting or incomplete assertions. Retain only pairs meeting platinum-tier standards and write them to a new table (platinum.tsv.gz) with all validation flags and metadata columns preserved for traceability.

Related tools

• R (Primary execution environment for loading, cross-referencing, and filtering tabular data using vectorized operations and file I/O (2_validating.R)) — https://github.com/lotusnprod/lotus-processor
• Make (Orchestrates the 3_analyzing stage pipeline, including validation workflow invocation) — https://github.com/lotusnprod/lotus-processor

Examples

Rscript 2_validating.R --input interim/tables/3_curated/table.tsv.gz --organism interim/dictionary/organism/dictionary.tsv.gz --structure interim/dictionary/structure/dictionary.tsv.gz --reference interim/dictionary/reference/ --output platinum.tsv.gz

Evaluation signals

• Platinum table row count is strictly ≤ curated table row count (no rows added, only filtered).
• Every structure identifier in platinum.tsv.gz has a matching entry in structure/dictionary.tsv.gz with no null values.
• Every organism identifier in platinum.tsv.gz has a matching entry in organism/dictionary.tsv.gz with no null values.
• All reference metadata columns (e.g., literature citations, dictionaryOrganism entries) are non-null for every platinum row.
• Validation flags and conflict indicators are logged and preserved as columns in platinum.tsv.gz for audit traceability.

Limitations

• Validation accuracy depends entirely on the completeness and currency of reference dictionaries — stale or sparse dictionaries will over-filter or miss real conflicts.
• The skill does not resolve conflicts or ambiguities; it only flags and excludes pairs with inconsistencies — manual curation may still be needed for borderline cases.
• Performance scales with the size of the curated table and reference dictionaries; very large datasets may require indexed lookups or database queries for efficiency.

Evidence

• [other] Cross-reference each structure-organism pair against organism and structure dictionaries: "Cross-reference each structure-organism pair against organism dictionary (interim/dictionary/organism/dictionary.tsv.gz) and structure dictionary (interim/dictionary/structure/dictionary.tsv.gz) to"
• [other] Validate reference metadata for literature citations: "Validate reference metadata (interim/dictionary/reference/dictionaryOrganism.tsv.gz and metadata.tsv.gz) for each pair's associated literature citations."
• [other] Apply quality filters to retain platinum-tier pairs: "Apply quality filters to retain only pairs meeting platinum-tier standards (e.g., high-confidence mappings, complete metadata, no conflicting assertions)."
• [other] Write passing pairs with validation flags preserved: "Write passing pairs to platinum.tsv.gz with all validation flags and metadata columns preserved."
• [methods] 3_analyzing stage produces platinum collection: "3_analyzing: 1_sampling.R, 2_validating.R producing platinum.tsv.gz"