1 changed files with 5 additions and 4 deletions
@@ -2,9 +2,9 @@
 title: "Tool Reference: Multi-Omics Disease Characterization"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/tooluniverse-multiomic-disease-characterization/tool-reference.md
-upstream_sha: e2520a96
-imported_at: 2026-06-26
+upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/cf5566c3/skills/tooluniverse-multiomic-disease-characterization/tool-reference.md
+upstream_sha: cf5566c3
+imported_at: 2026-08-11
 prompt_class: prompt
 upstream_changes: accepted
 author: upstream
@@ -230,7 +230,8 @@ genomics_genes = {

 **ReactomeAnalysis_pathway_enrichment**:
 - **Input**: `identifiers` (string - space-separated gene list), optional `page_size` (int, default 20), `include_disease` (bool), `projection` (bool)
- **Output**: `{data: {token, analysis_type, pathways_found, pathways: [{pathway_id, name, species, is_disease, is_lowest_level, entities_found, entities_total, entities_ratio, p_value, fdr, reactions_found, reactions_total}]}}`
+- **Output**: `{data: {token, analysis_type, pathways_found, pathways: [{pathway_id, name, species, is_disease, is_lowest_level, entities_found, entities_total, entities_coverage, p_value, fdr, reactions_found, reactions_total, pathway_size_fraction_of_reactome}]}}`
+- **NOTE**: rank by `fdr`/`p_value`. `entities_coverage` = found/total. `pathway_size_fraction_of_reactome` (deprecated alias `entities_ratio`) is pathway size over Reactome's entity universe and is independent of the submitted genes — never rank by it

 **Reactome_map_uniprot_to_pathways**:
 - **Input**: `id` (string - UniProt accession)