Appendix

Reference routes

For a term definition, function lookup, citation, or version record, use the glossary and API index. This appendix remains a concise route map rather than a duplicate function catalog.

• Data and identifiers: The data contract — identifier namespace, ranking, universe, custom annotations, and result classes.
• Analysis decisions: Choose a route — ORA, GSEA, comparison, network-aware, and custom-enrichment routes.
• Knowledge resources: GSON, GO, KEGG, Reactome, DO, and MeSH.
• Evidence integration: Result objects, semantic similarity, and Bayesian term selection.
• Presentation and interpretation: Visualization and evidence-guided interpretation.

Reproducibility record

For a published or shared analysis, retain the input file or accession, identifier type, universe definition, genome/annotation/database release, package versions, function parameters, result objects, exported figures, and citations. The capability map provides the package-to-layer index; it does not replace this provenance record.