Reports And Evals
Reports and evals live above the Rust compute engine. They answer questions that require source-specific preparation, repeated runs, metadata, comparison logic, and human review.
The main implementation lives in python/genesets-workflows. It prepares
inputs, calls genesets-rs in coarse batches, writes Parquet and YAML/JSON
artifacts, and then summarizes those artifacts with DuckDB, notebooks, docs, or
the local web explorer.
What Belongs Here
- fetching public source data from GO, GOA, Reactome, MyGeneSet, or similar;
- applying evidence-code and relation policies;
- preparing normalized term, closure, annotation, query, and background files;
- running configured batches through the Rust CLI;
- comparing ontology releases or annotation variants;
- writing report bundles that can be inspected by SQL, notebooks, or the web UI;
- using curated interpretations as precision/recall fixtures.
Core Pages
- Workflow Layer: package boundary and commands.
- Evals: current eval datasets and report findings.
- Diffing: threshold-crossing comparisons.
- Post-Processing: term filtering and interpretation.
- Tutorials: runnable shell and notebook workflows.
- Notebook Workflows: notebook conventions.