Five-Year GO Impact Report

Source notebook: ../../notebooks/03_go_diff_with_duckdb.ipynb

This tutorial treats GO temporal change analysis as a configured convenience report. The report command runs the two enrichments, performs the threshold-crossing comparison, writes Parquet plus YAML/JSON metadata, and records the timing and parameters used. The notebook then inspects those report artifacts with DuckDB instead of rebuilding the workflow step by step.

uv run --project python/genesets-workflows genesets-workflows go-impact evals/go_impact_5y_expression500.yaml

Output:

Wrote notebooks/generated/go_impact_5y_expression500/summary.yaml
Diff rows: gained_significant=23378, lost_significant=954, shared_significant=2760
Timings: old=3.925s, new=5.114s, compare=0.174s, total=9.744s

Output:

Output:

Output:

Output:

Output:

For each high-impact expression signature, the term columns identify the GO term with the largest signed change in -log10(Bonferroni adjusted p) after applying the configured ranked-term scope. In this report, candidates are current GO terms in goslim_generic or descendants of a goslim_generic term, with at most 1,000 annotated genes in the relevant snapshot. Positive values mean stronger enrichment in 2026; negative values mean weaker enrichment. For gained/lost calls, the non-significant side is anchored at the report cutoff (0.05) because this report stores significant-only result tables.

This is an inclusion slim plus a size guard. The complementary antislim is the same idea with the go_term_filter join inverted, which is useful when the goal is to explicitly remove a known broad region of the ontology from a report.

Output:

The next table asks which GO terms changed status across the largest number of expression signatures. It reuses the configured goslim_generic descendant scope and adds a stricter display guard of at most 500 genes so the table stays biologically interpretable.

Output:

Output: