Web Explorer

The explorer is a local browser for workflow report bundles. It is not deployed yet, and it does not run enrichment itself. It reads summary.yaml, query metadata, GMT query genes, and Parquet result/diff files from one or more existing report directories.

Install or run with the optional explorer dependencies:

just browser

This opens the default set of report bundles, currently:

• the 5,000-set current GOA all-vs-IBA comparison;
• the 5,000-set 2021-vs-2026 GO/GOA comparison;
• the 4,313-set current GOA all-vs-no-contributes_to comparison, excluding GO-derived query sets.

To open one directly:

just browser-iba
just browser-go5y
just browser-contributes

The equivalent explicit command for the IBA bundle is:

uv run --project python/genesets-workflows --extra explorer \
  genesets-workflows explore notebooks/generated/go_iba_impact_expression5000_diverse

To open the default browser automatically:

uv run --project python/genesets-workflows --extra explorer \
  genesets-workflows explore notebooks/generated/go_iba_impact_expression5000_diverse --open

The server defaults to http://127.0.0.1:8765.

Bundle Inputs

A bundle is any directory with a summary.yaml written by genesets-workflows go-impact. The summary points to:

• queries.gmt;
• queries.metadata.json;
• A-target and B-target result Parquet files;
• threshold-crossing diff Parquet;
• optional term-coverage Parquet files.

If no bundle path is supplied, the explorer looks for notebooks/generated/*/summary.yaml.

For the artifact contract, see Report Bundles.

Current Views

The first screen ranks gene sets. The table can be searched and filtered by source family or stratum, then sorted by criteria such as:

• specific IBA losses;
• all IBA losses;
• specific IBA gains;
• largest p-value delta;
• result rows in either run;
• gene count.

Selecting a gene set opens detail panels:

• Diffs: lost, gained, and shared enrichment calls for the configured comparison;
• A targets: retained enriched targets from the left run;
• B targets: retained enriched targets from the right run;
• Genes: the query genes from the selected gene set.

The current gene panel shows query genes. To show per-target overlap gene lists, the workflow layer should add a target-membership artifact such as target_gene_membership.parquet and let the explorer join query genes to target genes on demand.

Design Boundary

The web explorer belongs to the workflow layer. It is a reader over report artifacts and DuckDB queries; it should not add web-specific behavior to the Rust enrichment kernel.

Relationship To Curated Gene Set Browsing

The current explorer browses eval report bundles. A curated gene set browser is a related but separate surface: it should read validated interpretation YAML or generated JSON from curation/, then render one page per curated gene set plus indexes by context, collection, category, and recovery status.

Both browsers can share workflow-layer tooling and static assets, but they should keep different input contracts:

• eval explorer: summary.yaml plus Parquet report artifacts;
• curated browser: LinkML-validated YAML plus generated corpus indexes.

See Static Browser Plan.