Roadmap

Short Term

• Add Benjamini-Hochberg FDR.
• Add top-k and p-value-threshold output modes.
• Add serialized prepared indexes.
• Reframe docs around compute, workflows/evals, local explorer, and curated interpretation corpus.
• Add eval adapters for GOATOOLS and clusterProfiler.
• Add file digests and ontology metadata joins to compare metadata.
• Keep eval runners on Parquet by default.
• Move remaining ad hoc eval/source scripts into genesets-workflows.
• Add workflow config schema validation and genesets-rs version checks.
• Add a genesets-workflows curate build-pages command or equivalent static corpus page generator.

Medium Term

• Add OAK-based ontology prep examples.
• Add native Horned-OWL graph-walk prep as an optional crate or feature.
• Add ranked-list input schema.
• Add ranked-list enrichment statistics.
• Add richer benchmark reports for GitHub Pages.
• Add DuckDB notebooks over Parquet result and diff tables.
• Add hierarchy-aware Reactome prep and compare it with the flat baseline.
• Generate LinkML schema docs and curated gene set instance pages for the docs site.
• Add a curated gene set browser over generated corpus JSON.

Longer Term

• Add topology-aware model families.
• Explore gene-set-informed factor models (f-scLVM / slalom and expiMap-style) as downstream consumers of curated libraries, and reuse the curated recovery_status / membership_gap judgments as a benchmark for data-driven annotation refinement. See the Competitive Landscape.
• Add richer version-diff reports for ontology release comparisons.
• Add wrapper layers for species, release metadata, and identifier mapping.
• Add visualization notebooks that consume normalized result TSVs.
• Deploy the eval explorer and curated corpus browser from stable generated artifacts.