6 changed files with 36 additions and 26 deletions
@@ -2,9 +2,9 @@
 title: "Drug Research Tools Reference"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/tooluniverse-drug-research/TOOLS_REFERENCE.md
-upstream_sha: e2520a96
-imported_at: 2026-06-26
+upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/cf5566c3/skills/tooluniverse-drug-research/TOOLS_REFERENCE.md
+upstream_sha: cf5566c3
+imported_at: 2026-08-11
 prompt_class: catalogue
 upstream_changes: accepted
 author: upstream
@@ -280,7 +280,7 @@ result = tu.tools.FAERS_analyze_temporal_trends(
 ### MedDRA Hierarchy
 | Tool | Purpose | Key Output |
 |------|---------|------------|
-| `FAERS_rollup_meddra_hierarchy` | Aggregate by Preferred Term level | Top 50 PTs with counts |
+| `FAERS_rollup_meddra_hierarchy` | Aggregate by Preferred Term level | Most-reported PTs with counts (up to 999). `unique_PTs_returned` is a row count, NOT a total — openFDA reports no total; check `truncated` |

 **Example**:
 ```python
@@ -2,9 +2,9 @@
 title: "Tool Parameters Reference"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/tooluniverse-gene-enrichment/references/tool_parameters.md
-upstream_sha: e2520a96
-imported_at: 2026-06-26
+upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/cf5566c3/skills/tooluniverse-gene-enrichment/references/tool_parameters.md
+upstream_sha: cf5566c3
+imported_at: 2026-08-11
 prompt_class: catalogue
 upstream_changes: accepted
 author: upstream
@@ -237,11 +237,12 @@ kegg = [d for d in data if d.get('category') == 'KEGG']
 - `is_lowest_level`: Boolean (leaf pathway or parent)
 - `entities_found`: Count in your gene list
 - `entities_total`: Total entities in pathway
- `entities_ratio`: Found/Total ratio
- `p_value`: Raw p-value
+- `entities_coverage`: `entities_found / entities_total` — the coverage figure
+- `p_value`: Raw p-value (rank pathways by this or `fdr`)
 - `fdr`: FDR-corrected p-value
 - `reactions_found`: Reactions with your genes
 - `reactions_total`: Total reactions
+- `pathway_size_fraction_of_reactome`: pathway size divided by Reactome's entity universe for the species. Depends only on the pathway, not on the identifiers you submitted, so never rank by it. Deprecated alias `entities_ratio` carries the same value — despite its name it is not found/total

 **Example**:
 ```python
@@ -2,9 +2,9 @@
 title: "Response Format Examples"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/tooluniverse-multiomic-disease-characterization/response-formats.md
-upstream_sha: e2520a96
-imported_at: 2026-06-26
+upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/cf5566c3/skills/tooluniverse-multiomic-disease-characterization/response-formats.md
+upstream_sha: cf5566c3
+imported_at: 2026-08-11
 prompt_class: unknown
 upstream_changes: accepted
 author: upstream
@@ -86,17 +86,21 @@ Verified JSON response structures for key tools used in multi-omics disease char
        "is_lowest_level": true,
        "entities_found": 3,
        "entities_total": 47,
-        "entities_ratio": 0.00291,
+        "entities_coverage": 0.0638,
        "p_value": 4.0e-06,
        "fdr": 0.00068,
        "reactions_found": 3,
-        "reactions_total": 34
+        "reactions_total": 34,
+        "pathway_size_fraction_of_reactome": 0.00289,
+        "entities_ratio": 0.00289
      }
    ]
  }
 }
 ```

+`entities_coverage` is found/total (3/47). `pathway_size_fraction_of_reactome` is the pathway's share of Reactome's entity universe (47/16251) and is the same for any gene list; its deprecated alias `entities_ratio` holds that same value. Rank by `fdr`/`p_value`.
+
 ## HPA RNA Expression
 ```json
 {
@@ -2,9 +2,9 @@
 title: "Over-Representation Analysis (ORA) Workflow"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/tooluniverse-gene-enrichment/references/ora_workflow.md
-upstream_sha: e2520a96
-imported_at: 2026-06-26
+upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/cf5566c3/skills/tooluniverse-gene-enrichment/references/ora_workflow.md
+upstream_sha: cf5566c3
+imported_at: 2026-08-11
 prompt_class: prompt
 upstream_changes: accepted
 author: upstream
@@ -285,8 +285,12 @@ reactome_result = tu.tools.ReactomeAnalysis_pathway_enrichment(
 )
 # Returns: {data: {token, analysis_type, identifiers_not_found, 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}
+#    entities_coverage, p_value, fdr, reactions_found, reactions_total,
+#    pathway_size_fraction_of_reactome}
 # ]}}
+# entities_coverage = entities_found/entities_total; rank pathways by fdr or p_value.
+# pathway_size_fraction_of_reactome (deprecated alias entities_ratio) is pathway size over
+# Reactome's entity universe - independent of the submitted genes, so never rank by it.

 reactome_pathways = reactome_result.get('data', {}).get('pathways', [])
 # Filter significant
@@ -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)
@@ -2,9 +2,9 @@
 title: "Target Intelligence Tool Reference"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/tooluniverse-target-research/REFERENCE.md
-upstream_sha: e2520a96
-imported_at: 2026-06-26
+upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/cf5566c3/skills/tooluniverse-target-research/REFERENCE.md
+upstream_sha: cf5566c3
+imported_at: 2026-08-11
 prompt_class: prompt
 upstream_changes: accepted
 author: upstream
@@ -489,7 +489,7 @@ actives = tu.tools.PubChem_get_assay_active_compounds(aid=504526)
 | `Reactome_get_reaction` | `stId` | Reaction details |
 | `Reactome_get_complex` | `stId` | Complex details |
 | `Reactome_list_species` | - | All species |
-| `Reactome_query_by_ids` | `ids`, `species` | ID query |
+| `Reactome_query_by_ids` | `ids` | ID query (no species/type filtering — filter results on `speciesName`/`schemaClass`) |
 | `Reactome_get_events_hierarchy` | `species` | Full hierarchy |
 | `Reactome_get_diseases` | - | Disease pathways |