[upstream-sync] skills/tooluniverse/SKILL.md from mims-harvard/ToolUniverse@be422b18 [skill]

upstream/mims-harvard-ToolUniverse/catalogue/skills/setup-tooluniverse/SKILL.md

@@ -1,8 +1,8 @@
 ---
 lineage_type: import
-upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/setup-tooluniverse/SKILL.md
-upstream_sha: e2520a96
-imported_at: 2026-06-26
+upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/be422b18/skills/setup-tooluniverse/SKILL.md
+upstream_sha: be422b18
+imported_at: 2026-07-21
 prompt_class: catalogue
 upstream_changes: accepted
 name: setup-tooluniverse
@@ -84,7 +84,7 @@ First run takes ~30s (downloads package), then instant. **Shortcut**: `uv tool i
 | `tu info` | Show tool parameters and schema | `tu info PubMed_search_articles` |
 | `tu run` | Execute a tool | `tu run PubMed_search_articles '{"query": "CRISPR"}'` |
 | `tu test` | Test a tool with its example inputs | `tu test UniProt_get_entry_by_accession` |
-| `tu build` | Generate typed Python wrappers for Coding API | `tu build --output ./my_tools` |
+| `tu build` | Generate typed Python wrappers for Coding API (also regenerates the internal lazy-load registry in place — unaffected by `--output`) | `tu build --output ./my_tools` |
 | `tu serve` | Start MCP stdio server (same as `uvx tooluniverse`) | `tu serve` |
 
 **Output flags** (most commands except `build`/`serve`): `--json` (pretty) or `--raw` (compact, pipe-friendly).
@@ -156,7 +156,7 @@ Make sure Step 2 is done (`uv --version` works).
 > claude plugin marketplace add mims-harvard/ToolUniverse
 > claude plugin install tooluniverse@tooluniverse
 > ```
-> This installs MCP server + 115 skills + slash commands in one step.
+> This installs MCP server + 115 skills + slash commands in one step. Then see the `tooluniverse-claude-code-plugin` skill's "Recommended: turn on auto-update" step so future releases apply without manual `claude plugin update`.
 
 | Client | File | How to Access |
 |--------|------|---------------|

upstream/mims-harvard-ToolUniverse/catalogue/skills/tooluniverse-claude-code-plugin/SKILL.md

@@ -1,8 +1,8 @@
 ---
 lineage_type: import
-upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/tooluniverse-claude-code-plugin/SKILL.md
-upstream_sha: e2520a96
-imported_at: 2026-06-26
+upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/be422b18/skills/tooluniverse-claude-code-plugin/SKILL.md
+upstream_sha: be422b18
+imported_at: 2026-07-21
 prompt_class: catalogue
 upstream_changes: accepted
 name: tooluniverse-claude-code-plugin
@@ -21,7 +21,7 @@ uv --version      # must exist; if not:  curl -LsSf https://astral.sh/uv/install
 claude --version  # Claude Code CLI; if not: https://claude.com/claude-code
 ```
 
-## Install (two commands)
+## Install
 
 ```bash
 # 1. Register the ToolUniverse marketplace from GitHub
@@ -33,6 +33,29 @@ claude plugin install tooluniverse@tooluniverse
 
 That's it. Restart Claude Code. The MCP server auto-starts via `uvx tooluniverse` on first use (~30 s cold start, instant after).
 
+### Recommended: turn on auto-update
+
+Third-party marketplaces default to **no auto-update** — without this, new tools/skills only reach you when you remember to run `claude plugin update tooluniverse` (see Update below). Turn it on once:
+
+```bash
+python3 -c "
+import json, pathlib, sys
+p = pathlib.Path.home() / '.claude/plugins/known_marketplaces.json'
+d = json.loads(p.read_text())
+if 'tooluniverse' not in d:
+    sys.exit('Run the marketplace add command above first')
+d['tooluniverse']['autoUpdate'] = True
+p.write_text(json.dumps(d, indent=2))
+print('autoUpdate enabled for tooluniverse')
+"
+```
+
+Equivalent interactive path: `/plugin` → Marketplaces → `tooluniverse` → Enable auto-update.
+
+With this on, Claude Code checks for marketplace + plugin updates in the background after each session start (up to a ~10 min random delay) and updates the installed plugin on disk automatically. You'll get a `/reload-plugins` prompt when an update lands, or it applies on your next launch — no more manual `claude plugin update`.
+
+This is local, per-machine state — it can't be shipped as a default from the plugin's own manifest. `marketplace.json` has no `autoUpdate` field; Claude Code intentionally keeps this a per-installation trust boundary so a publisher can't force silent auto-updates onto a user's machine.
+
 ### Important: Remove global skills if previously installed
 
 If you previously installed ToolUniverse skills globally (via `tooluniverse-install-skills` or manual copy), **remove them**. The plugin includes all skills — global copies interfere with the plugin's skill routing.
@@ -82,6 +105,9 @@ The router skill auto-dispatches to the right specialized skill — no command p
 | **`/tooluniverse:cross-validate`** | Verify a claim across 3+ independent databases | Slash command |
 | **`/tooluniverse:compare`** | N-way side-by-side comparison with domain-appropriate columns | Slash command |
 | **`/tooluniverse:literature-sweep`** | Graded mini-review across PubMed + EuropePMC + Semantic Scholar | Slash command |
+| **`/tooluniverse:verify-references`** | Check that cited references are real and accurately described, including retraction status | Slash command |
+| **`/tooluniverse:self-review`** | Generate weighted success criteria for a task and check work against them (what's missing / done well) | Slash command |
+| **`/tooluniverse:setup-keys`** | Configure ToolUniverse API keys | Slash command |
 | **`/tooluniverse:researcher`** | Same investigation as `research`, delegated to a forked subagent | Slash command |
 | **120+ skills** | Structured workflows (drug research, variant interpretation, pharmacovigilance, CRISPR screens, statistical modeling, etc.) | Auto-activate on matching questions |
 
@@ -121,6 +147,10 @@ Full API-key list: `setup-tooluniverse` skill → `API_KEYS_REFERENCE.md`.
 
 ## Update
 
+If you enabled auto-update above, this happens automatically in the background — no action needed.
+
+Otherwise, update manually:
+
 ```bash
 claude plugin update tooluniverse
 # Also refresh the MCP server's tool cache:

upstream/mims-harvard-ToolUniverse/catalogue/skills/tooluniverse-precision-oncology/TOOLS_REFERENCE.md

@@ -2,9 +2,9 @@
 title: "Precision Oncology - Tool Reference"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/tooluniverse-precision-oncology/TOOLS_REFERENCE.md
-upstream_sha: e2520a96
-imported_at: 2026-06-26
+upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/be422b18/skills/tooluniverse-precision-oncology/TOOLS_REFERENCE.md
+upstream_sha: be422b18
+imported_at: 2026-07-21
 prompt_class: unknown
 upstream_changes: accepted
 author: upstream
@@ -328,7 +328,7 @@ cells = tu.tools.DepMap_get_cell_lines(
 | Tool | Purpose | Key Parameters |
 |------|---------|----------------|
 | `ChEMBL_search_drugs` | Search drugs | `query`, `max_phase` |
-| `ChEMBL_get_drug_mechanisms_of_action_by_chemblId` | Drug MOA | `chemblId` |
+| `ChEMBL_get_drug_mechanisms` | Drug MOA | `drug_chembl_id` |
 | `ChEMBL_get_target_activities` | Bioactivity data | `target_chembl_id` |
 
 ### DailyMed

upstream/mims-harvard-ToolUniverse/catalogue/skills/tooluniverse-protein-interactions/DOMAIN_ANALYSIS.md

@@ -2,9 +2,9 @@
 title: "Protein Interaction Network Analysis - Domain Analysis"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/tooluniverse-protein-interactions/DOMAIN_ANALYSIS.md
-upstream_sha: e2520a96
-imported_at: 2026-06-26
+upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/be422b18/skills/tooluniverse-protein-interactions/DOMAIN_ANALYSIS.md
+upstream_sha: be422b18
+imported_at: 2026-07-21
 prompt_class: unknown
 upstream_changes: accepted
 author: upstream
@@ -188,12 +188,9 @@ validated: false
 - **Use Case**: Protein structure and complex formation
 - **API**: Public REST API
 
-**Tools (5)** - Use for structural analysis:
-1. `SASBDB_search_entries` - Find structural data
-2. `SASBDB_get_entry` - Get entry metadata
-3. `SASBDB_get_entry` - Get structural models
-4. `SASBDB_get_entry` - Get scattering data
-5. `SASBDB_download_data` - Download raw data
+**Tools (2)** - Use for structural analysis:
+1. `SASBDB_search_entries` - Find structural data (by molecular type, or list all entries)
+2. `SASBDB_get_entry` - Get entry metadata, experimental conditions, publication info, and data file URLs (one call covers structure/scattering data access — there is no separate download tool)
 
 ---
 

upstream/mims-harvard-ToolUniverse/skills/tooluniverse-precision-oncology/API_USAGE_PATTERNS.md

@@ -2,9 +2,9 @@
 title: "API Usage Patterns for Precision Oncology"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/tooluniverse-precision-oncology/API_USAGE_PATTERNS.md
-upstream_sha: e2520a96
-imported_at: 2026-06-26
+upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/be422b18/skills/tooluniverse-precision-oncology/API_USAGE_PATTERNS.md
+upstream_sha: be422b18
+imported_at: 2026-07-21
 prompt_class: prompt
 upstream_changes: accepted
 author: upstream
@@ -355,7 +355,7 @@ def get_tumor_expression_context(tu, gene_symbol, cancer_type):
 ### Query Order
 1. `OpenTargets_get_associated_drugs_by_target_ensemblID` -> Approved drugs
 2. `DailyMed_search_spls` -> FDA label details
-3. `ChEMBL_get_drug_mechanisms_of_action_by_chemblId` -> Mechanism
+3. `ChEMBL_get_drug_mechanisms` -> Mechanism
 
 ### Treatment Output Example
 

upstream/mims-harvard-ToolUniverse/skills/tooluniverse-rare-disease-diagnosis/TOOLS_REFERENCE.md

@@ -2,9 +2,9 @@
 title: "Rare Disease Diagnosis - Tool Reference"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/tooluniverse-rare-disease-diagnosis/TOOLS_REFERENCE.md
-upstream_sha: e2520a96
-imported_at: 2026-06-26
+upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/be422b18/skills/tooluniverse-rare-disease-diagnosis/TOOLS_REFERENCE.md
+upstream_sha: be422b18
+imported_at: 2026-07-21
 prompt_class: prompt
 upstream_changes: accepted
 author: upstream
@@ -761,7 +761,7 @@ def analyze_vus_structure(tu, uniprot_id, variant_position):
 | Primary | Fallback 1 | Fallback 2 |
 |---------|------------|------------|
 | `kegg_get_gene_info` | `ReactomeContent_search` | `KEGG_get_gene_pathways` |
-| `intact_search_interactions` | `STRING_interactions` | Literature search |
+| `intact_search_interactions` | `STRING_get_interaction_partners` | Literature search |
 
 ### Variant Annotation
 | Primary | Fallback 1 | Fallback 2 |

upstream/mims-harvard-ToolUniverse/skills/tooluniverse-statistical-modeling/TOOLS_REFERENCE.md

@@ -2,9 +2,9 @@
 title: "Tools Reference: Statistical Modeling Skill"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/tooluniverse-statistical-modeling/TOOLS_REFERENCE.md
-upstream_sha: e2520a96
-imported_at: 2026-06-26
+upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/be422b18/skills/tooluniverse-statistical-modeling/TOOLS_REFERENCE.md
+upstream_sha: be422b18
+imported_at: 2026-07-21
 prompt_class: prompt
 upstream_changes: accepted
 author: upstream
@@ -90,7 +90,7 @@ These ToolUniverse tools can be used to retrieve data before modeling:
 |------|-----------|---------|
 | `FAERS_calculate_disproportionality` | `drug_name`, `adverse_event` | `{metrics: {PRR, ROR, IC}, signal_detection}` |
 | `FAERS_stratify_by_demographics` | `drug_name`, `adverse_event`, `stratify_by` | Stratified counts |
-| `FAERS_count_patient_reaction` | `medicinalproduct` | `[{term, count}]` |
+| `FAERS_count_reactions_by_drug_event` | `medicinalproduct` | `[{term, count}]` (grouped by MedDRA Preferred Term) |
 
 ### Gene-Disease Evidence
 

upstream/mims-harvard-ToolUniverse/skills/tooluniverse-variant-interpretation/TOOLS_REFERENCE.md

@@ -2,9 +2,9 @@
 title: "Clinical Variant Interpreter - Tool Reference"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/3038dcbe/skills/tooluniverse-variant-interpretation/TOOLS_REFERENCE.md
-upstream_sha: 3038dcbe
-imported_at: 2026-06-30
+upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/be422b18/skills/tooluniverse-variant-interpretation/TOOLS_REFERENCE.md
+upstream_sha: be422b18
+imported_at: 2026-07-21
 prompt_class: prompt
 upstream_changes: accepted
 author: upstream
@@ -774,8 +774,8 @@ result = tu.tools.OMIM_search(query="BRCA1")
 
 | Tool | Purpose | Key Parameters |
 |------|---------|----------------|
-| `ClinGen_gene_validity` | Get curation status | `gene` |
-| `ClinGen_dosage` | Dosage sensitivity | `gene` |
+| `ClinGen_get_gene_validity` | Get curation status | `gene` |
+| `ClinGen_dosage_by_gene` | Dosage sensitivity | `gene` |
 
 **Gene Validity Levels**:
 | Level | Meaning |

upstream/mims-harvard-ToolUniverse/skills/tooluniverse/SKILL.md

@@ -1,8 +1,8 @@
 ---
 lineage_type: import
-upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/tooluniverse/SKILL.md
-upstream_sha: e2520a96
-imported_at: 2026-06-26
+upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/be422b18/skills/tooluniverse/SKILL.md
+upstream_sha: be422b18
+imported_at: 2026-07-21
 prompt_class: skill
 upstream_changes: accepted
 name: tooluniverse
@@ -130,6 +130,8 @@ These reminders are for fast pattern recognition during routing. Detailed `❌ W
 | "**TCGA**", "cancer genomics cohort", "GDC analysis", "TCGA mutations", "pan-cancer" | `Skill(skill="tooluniverse-cancer-genomics-tcga")` |
 | "**immunotherapy response**", "checkpoint inhibitor response", "TMB", "MSI", "PD-L1", "ICI response" | `Skill(skill="tooluniverse-immunotherapy-response-prediction")` |
 | "**rare disease diagnosis**", "differential diagnosis", "phenotype matching", "HPO", "patient with [symptoms]" | `Skill(skill="tooluniverse-rare-disease-diagnosis")` |
+| "**clinical risk score**", "CHA2DS2-VASc", "HAS-BLED", "CURB-65", "qSOFA", "Child-Pugh", "MELD-Na", "Wells score", "ASCVD risk", "eGFR CKD-EPI", "bedside risk calculator" | `Skill(skill="tooluniverse-clinical-risk-scoring")` |
+| "**device adverse events**", "device recall", "MAUDE", "food/supplement adverse event", "CAERS", "veterinary adverse event", "drug shortage" | `Skill(skill="tooluniverse-product-safety-surveillance")` |
 | "**variant interpretation**", "VUS", "pathogenicity", "clinical significance", "is [variant] pathogenic" | `Skill(skill="tooluniverse-variant-interpretation")` |
 | "**clinical guidelines**", "practice guidelines", "treatment guidelines", "dosing recommendations", "standard of care" | `Skill(skill="tooluniverse-clinical-guidelines")` |
 | "**patient stratification**", "precision medicine", "biomarker stratification", "treatment selection" | `Skill(skill="tooluniverse-precision-medicine-stratification")` |
@@ -149,6 +151,7 @@ These reminders are for fast pattern recognition during routing. Detailed `❌ W
 | "**small molecule discovery**", "chemical biology", "compound sourcing", "hit finding", "chemical probe" | `Skill(skill="tooluniverse-small-molecule-discovery")` |
 | "**chemical sourcing**", "buy compound", "vendor search", "Enamine", "MolPort", "compound availability" | `Skill(skill="tooluniverse-chemical-sourcing")` |
 | "**GPCR**", "G-protein coupled receptor", "GPCRdb", "receptor ligand", "biased agonist" | `Skill(skill="tooluniverse-gpcr-structural-pharmacology")` |
+| "**dereplicate**", "natural product identification", "NPAtlas", "ChemOnt classification", "ClassyFire", "producing organism" | `Skill(skill="tooluniverse-natural-product-dereplication")` |
 
 ### 5. Genomics & Variant Analysis
 
@@ -165,6 +168,13 @@ These reminders are for fast pattern recognition during routing. Detailed `❌ W
 | "**regulatory variant**", "non-coding variant", "eQTL variant", "regulatory region variant" | `Skill(skill="tooluniverse-regulatory-variant-analysis")` |
 | "**rare disease genomics**", "Orphanet gene", "rare disease gene", "causative gene", "exome diagnosis" | `Skill(skill="tooluniverse-rare-disease-genomics")` |
 | "**1000 Genomes**", "IGSR", "population frequency", "superpopulation", "AFR/EUR/EAS/SAS/AMR" | `Skill(skill="tooluniverse-population-genetics-1000genomes")` |
+| "**PheWAS**", "phenome-wide association", "cross-ancestry replication", "cross-biobank", "FinnGen", "BioBank Japan", "pleiotropy of a variant" | `Skill(skill="tooluniverse-phewas")` |
+| "**Mendelian randomization**", "MR causal inference", "instrumental variable", "does X cause Y", "genetic causal evidence" | `Skill(skill="tooluniverse-mendelian-randomization")` |
+| "**loss-of-function mechanism**", "LoF mechanism", "why is this variant LoF", "structural stability vs functional disruption" | `Skill(skill="tooluniverse-protein-lof-mechanism")` |
+| "**SAE feature**", "sparse autoencoder variant", "ESMC SAE", "mechanistic variant interpretation" | `Skill(skill="tooluniverse-protein-sae-variant-interpretation")` |
+| "**per-residue annotation**", "binding interface residues", "ligand pocket residues", "buried vs surface residues", "PDB structural annotation" | `Skill(skill="tooluniverse-protein-structural-annotation-pdb")` |
+| "**why are these residues critical**", "residue functional mechanism", "DMS hotspot interpretation", "catalytic vs structural residue" | `Skill(skill="tooluniverse-residue-functional-mechanism-interpretation")` |
+| "**validate variant predictor**", "DMS validation", "deep mutational scanning benchmark", "predictor vs experimental effect" | `Skill(skill="tooluniverse-variant-predictor-dms-validation")` |
 
 ### 6. Systems & Network Analysis
 
@@ -214,6 +224,7 @@ These reminders are for fast pattern recognition during routing. Detailed `❌ W
 | "**protein modification**", "PTM analysis", "phosphorylation site", "ubiquitination", "glycosylation" | `Skill(skill="tooluniverse-protein-modification-analysis")` |
 | "**structural proteomics**", "cross-linking mass spec", "XL-MS", "HDX-MS", "structural biology" | `Skill(skill="tooluniverse-structural-proteomics")` |
 | "**protein structure prediction**", "AlphaFold prediction", "structure modeling", "homology modeling" | `Skill(skill="tooluniverse-protein-structure-prediction")` |
+| "**FASTQ QC**", "FastQC", "MultiQC", "adapter trimming", "fastp", "Cutadapt", "read quality", "sequence duplication" | `Skill(skill="tooluniverse-fastq-qc")` |
 
 ### 8. Clinical Trials & Study Design
 
@@ -237,6 +248,7 @@ These reminders are for fast pattern recognition during routing. Detailed `❌ W
 | "**ecology**", "biodiversity", "invasive species", "pollinator", "food web", "conservation", "community ecology", "trophic" | `Skill(skill="tooluniverse-ecology-biodiversity")` |
 | "**microbiome**", "gut microbiota", "dysbiosis", "microbiome composition", "16S rRNA" | `Skill(skill="tooluniverse-microbiome-research")` |
 | "**adverse outcome pathway**", "AOP", "key event", "molecular initiating event", "KER" | `Skill(skill="tooluniverse-adverse-outcome-pathway")` |
+| "**genome assembly**", "assembly N50", "RefSeq assembly QC", "plasmid count", "NCBI Datasets genome" | `Skill(skill="tooluniverse-microbial-genome-characterization")` |
 
 ### 10. Specialized Biology
 
@@ -278,6 +290,7 @@ These reminders are for fast pattern recognition during routing. Detailed `❌ W
 | "**custom tool**", "add my own tool", "local tool", "create tool", "extend ToolUniverse" | `Skill(skill="tooluniverse-custom-tool")` |
 | "**SDK**", "Python SDK", "build AI scientist", "programmatic access", "**import tooluniverse**", "**coding API**", "**tu build**", "**typed wrappers**" | `Skill(skill="tooluniverse-sdk")` |
 | "**install skills**", "missing skills", "skill not found", "add skills" | `Skill(skill="tooluniverse-install-skills")` |
+| "**self-review**", "check my work", "definition of done", "evaluation rubric", "success criteria", "grading criteria", "LLM-as-judge" | `Skill(skill="tooluniverse-self-review")` |
 
 ---