From c99c290c136ec124895475e5b2a082a89e46d0e7 Mon Sep 17 00:00:00 2001 From: promptadmin Date: Tue, 11 Aug 2026 22:02:48 +0000 Subject: [PATCH 1/6] [upstream-sync] skills/tooluniverse-drug-research/TOOLS_REFERENCE.md from mims-harvard/ToolUniverse@cf5566c3 [catalogue] --- .../skills/tooluniverse-drug-research/TOOLS_REFERENCE.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/upstream/mims-harvard-ToolUniverse/catalogue/skills/tooluniverse-drug-research/TOOLS_REFERENCE.md b/upstream/mims-harvard-ToolUniverse/catalogue/skills/tooluniverse-drug-research/TOOLS_REFERENCE.md index 42519dc1..13ef4ae5 100644 --- a/upstream/mims-harvard-ToolUniverse/catalogue/skills/tooluniverse-drug-research/TOOLS_REFERENCE.md +++ b/upstream/mims-harvard-ToolUniverse/catalogue/skills/tooluniverse-drug-research/TOOLS_REFERENCE.md @@ -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 -- 2.54.0 From 4961ded38bc08b1d77eda2ed1d53f38277cb2d5c Mon Sep 17 00:00:00 2001 From: promptadmin Date: Tue, 11 Aug 2026 22:02:49 +0000 Subject: [PATCH 2/6] [upstream-sync] skills/tooluniverse-gene-enrichment/references/ora_workflow.md from mims-harvard/ToolUniverse@cf5566c3 [prompt] --- .../references/ora_workflow.md | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-gene-enrichment/references/ora_workflow.md b/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-gene-enrichment/references/ora_workflow.md index abaeb74a..a2b13799 100644 --- a/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-gene-enrichment/references/ora_workflow.md +++ b/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-gene-enrichment/references/ora_workflow.md @@ -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 -- 2.54.0 From 188ad5d00022693fa449b353871918ec1e9628bd Mon Sep 17 00:00:00 2001 From: promptadmin Date: Tue, 11 Aug 2026 22:02:52 +0000 Subject: [PATCH 3/6] [upstream-sync] skills/tooluniverse-gene-enrichment/references/tool_parameters.md from mims-harvard/ToolUniverse@cf5566c3 [catalogue] --- .../references/tool_parameters.md | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/upstream/mims-harvard-ToolUniverse/catalogue/skills/tooluniverse-gene-enrichment/references/tool_parameters.md b/upstream/mims-harvard-ToolUniverse/catalogue/skills/tooluniverse-gene-enrichment/references/tool_parameters.md index a46a7204..81217133 100644 --- a/upstream/mims-harvard-ToolUniverse/catalogue/skills/tooluniverse-gene-enrichment/references/tool_parameters.md +++ b/upstream/mims-harvard-ToolUniverse/catalogue/skills/tooluniverse-gene-enrichment/references/tool_parameters.md @@ -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 -- 2.54.0 From bf439c505a5d669a76b036e252a4c9417473126e Mon Sep 17 00:00:00 2001 From: promptadmin Date: Tue, 11 Aug 2026 22:02:54 +0000 Subject: [PATCH 4/6] [upstream-sync] skills/tooluniverse-multiomic-disease-characterization/response-formats.md from mims-harvard/ToolUniverse@cf5566c3 [unknown] --- .../response-formats.md | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/upstream/mims-harvard-ToolUniverse/catalogue/skills/tooluniverse-multiomic-disease-characterization/response-formats.md b/upstream/mims-harvard-ToolUniverse/catalogue/skills/tooluniverse-multiomic-disease-characterization/response-formats.md index 5a4f3866..26a3f4de 100644 --- a/upstream/mims-harvard-ToolUniverse/catalogue/skills/tooluniverse-multiomic-disease-characterization/response-formats.md +++ b/upstream/mims-harvard-ToolUniverse/catalogue/skills/tooluniverse-multiomic-disease-characterization/response-formats.md @@ -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 { -- 2.54.0 From 2ed97b345ef4f1ecc871b6416b6064b08f217e4b Mon Sep 17 00:00:00 2001 From: promptadmin Date: Tue, 11 Aug 2026 22:02:56 +0000 Subject: [PATCH 5/6] [upstream-sync] skills/tooluniverse-multiomic-disease-characterization/tool-reference.md from mims-harvard/ToolUniverse@cf5566c3 [prompt] --- .../tool-reference.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-multiomic-disease-characterization/tool-reference.md b/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-multiomic-disease-characterization/tool-reference.md index 208de4a1..ca7db4dd 100644 --- a/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-multiomic-disease-characterization/tool-reference.md +++ b/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-multiomic-disease-characterization/tool-reference.md @@ -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) -- 2.54.0 From 9c9d9c6dd860eef7fefc78aa4a1165accd066f2c Mon Sep 17 00:00:00 2001 From: promptadmin Date: Tue, 11 Aug 2026 22:02:58 +0000 Subject: [PATCH 6/6] [upstream-sync] skills/tooluniverse-target-research/REFERENCE.md from mims-harvard/ToolUniverse@cf5566c3 [prompt] --- .../skills/tooluniverse-target-research/REFERENCE.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-target-research/REFERENCE.md b/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-target-research/REFERENCE.md index 637e18dc..c91c722b 100644 --- a/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-target-research/REFERENCE.md +++ b/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-target-research/REFERENCE.md @@ -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 | -- 2.54.0