/go-check

Run quality checks on GO-CAM annotations that go beyond schema validation.

Usage

/go-check [file-path]

If no file is specified, checks the most recent .json file in output/.

Examples

/go-check output/gocam-20250101-120000.json

/go-check

What It Checks

GO Term Existence

• Verifies each GO term exists in the Gene Ontology
• Checks that terms are not obsolete
• Reports the term label for human verification

Evidence Code Appropriateness

• Validates ECO (Evidence and Conclusion Ontology) terms
• Flags experimental evidence codes (IDA, IMP, IGI) used without a PMID
• Flags IEA (electronic annotation) for manual curation contexts

Taxon Consistency

• Verifies the taxon ID exists
• Checks that the gene product (UniProtKB ID) matches the declared organism
• Cross-references with UniProt

Structural Completeness

• Every activity has a gene product (enabled_by)
• Every activity has a molecular function
• Every assertion has evidence
• Every evidence item has a reference

Overly Generic Terms

Flags commonly overused terms and suggests more specific alternatives:

Term	Suggestion
GO:0005515 (protein binding)	Use a more specific binding term
GO:0003824 (catalytic activity)	Specify the type of catalytic activity
GO:0005575 (cellular_component)	Specify a more precise location
GO:0008150 (biological_process)	Name the specific biological process
GO:0003674 (molecular_function)	Name the specific molecular function

Report Format

Results are presented as a checklist:

Quality Checks for output/gocam-20250101-120000.json
─────────────────────────────────────────────────────

GO Terms
  [PASS] GO:0019901 (protein kinase binding) — exists, not obsolete

Evidence
  [PASS] ECO:0000314 (direct assay) with PMID:20154695

Taxon
  [PASS] NCBITaxon:9606 (Homo sapiens)

Structure
  [PASS] All activities have gene products

Specificity
  [PASS] Terms are appropriately specific

Summary: 5/5 checks passed

Next Steps

• /go-pr — Submit your quality-checked annotation for review
• /go-try — Create another annotation