From fc058e6fc29eb9fe3f03b80f8c2d2a68525e4ba6 Mon Sep 17 00:00:00 2001 From: promptadmin Date: Tue, 21 Jul 2026 09:44:14 +0000 Subject: [PATCH 1/9] [upstream-sync] skills/setup-tooluniverse/SKILL.md from mims-harvard/ToolUniverse@be422b18 [catalogue] --- .../catalogue/skills/setup-tooluniverse/SKILL.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/upstream/mims-harvard-ToolUniverse/catalogue/skills/setup-tooluniverse/SKILL.md b/upstream/mims-harvard-ToolUniverse/catalogue/skills/setup-tooluniverse/SKILL.md index 24c8a69c..c6adb8d1 100644 --- a/upstream/mims-harvard-ToolUniverse/catalogue/skills/setup-tooluniverse/SKILL.md +++ b/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 | |--------|------|---------------| -- 2.54.0 From 171c0f0ecd15783f4307e80514e594d9b2c06f66 Mon Sep 17 00:00:00 2001 From: promptadmin Date: Tue, 21 Jul 2026 09:44:31 +0000 Subject: [PATCH 2/9] [upstream-sync] skills/tooluniverse-claude-code-plugin/SKILL.md from mims-harvard/ToolUniverse@be422b18 [catalogue] --- .../tooluniverse-claude-code-plugin/SKILL.md | 38 +++++++++++++++++-- 1 file changed, 34 insertions(+), 4 deletions(-) diff --git a/upstream/mims-harvard-ToolUniverse/catalogue/skills/tooluniverse-claude-code-plugin/SKILL.md b/upstream/mims-harvard-ToolUniverse/catalogue/skills/tooluniverse-claude-code-plugin/SKILL.md index 22be67d1..541865c9 100644 --- a/upstream/mims-harvard-ToolUniverse/catalogue/skills/tooluniverse-claude-code-plugin/SKILL.md +++ b/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: -- 2.54.0 From 6d606440b2b6b0ca1caa79892e933bb4aaff3856 Mon Sep 17 00:00:00 2001 From: promptadmin Date: Tue, 21 Jul 2026 09:44:57 +0000 Subject: [PATCH 3/9] [upstream-sync] skills/tooluniverse-precision-oncology/API_USAGE_PATTERNS.md from mims-harvard/ToolUniverse@be422b18 [prompt] --- .../tooluniverse-precision-oncology/API_USAGE_PATTERNS.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-precision-oncology/API_USAGE_PATTERNS.md b/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-precision-oncology/API_USAGE_PATTERNS.md index 30bbfed2..7e8060e0 100644 --- a/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-precision-oncology/API_USAGE_PATTERNS.md +++ b/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 -- 2.54.0 From 596accceb51bbbd65a8e372dde6cdc86206fc042 Mon Sep 17 00:00:00 2001 From: promptadmin Date: Tue, 21 Jul 2026 09:45:20 +0000 Subject: [PATCH 4/9] [upstream-sync] skills/tooluniverse-precision-oncology/TOOLS_REFERENCE.md from mims-harvard/ToolUniverse@be422b18 [unknown] --- .../tooluniverse-precision-oncology/TOOLS_REFERENCE.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/upstream/mims-harvard-ToolUniverse/catalogue/skills/tooluniverse-precision-oncology/TOOLS_REFERENCE.md b/upstream/mims-harvard-ToolUniverse/catalogue/skills/tooluniverse-precision-oncology/TOOLS_REFERENCE.md index a4610f19..620c2fe3 100644 --- a/upstream/mims-harvard-ToolUniverse/catalogue/skills/tooluniverse-precision-oncology/TOOLS_REFERENCE.md +++ b/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 -- 2.54.0 From 3ab34992365bfe47159d14c48715e468eb4b9ed8 Mon Sep 17 00:00:00 2001 From: promptadmin Date: Tue, 21 Jul 2026 09:45:42 +0000 Subject: [PATCH 5/9] [upstream-sync] skills/tooluniverse-protein-interactions/DOMAIN_ANALYSIS.md from mims-harvard/ToolUniverse@be422b18 [unknown] --- .../DOMAIN_ANALYSIS.md | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/upstream/mims-harvard-ToolUniverse/catalogue/skills/tooluniverse-protein-interactions/DOMAIN_ANALYSIS.md b/upstream/mims-harvard-ToolUniverse/catalogue/skills/tooluniverse-protein-interactions/DOMAIN_ANALYSIS.md index 10b71c53..757d64fc 100644 --- a/upstream/mims-harvard-ToolUniverse/catalogue/skills/tooluniverse-protein-interactions/DOMAIN_ANALYSIS.md +++ b/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) --- -- 2.54.0 From cc11704adff7cf67a4d7078f2b3e6823ffeb332b Mon Sep 17 00:00:00 2001 From: promptadmin Date: Tue, 21 Jul 2026 09:46:07 +0000 Subject: [PATCH 6/9] [upstream-sync] skills/tooluniverse-rare-disease-diagnosis/TOOLS_REFERENCE.md from mims-harvard/ToolUniverse@be422b18 [prompt] --- .../TOOLS_REFERENCE.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-rare-disease-diagnosis/TOOLS_REFERENCE.md b/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-rare-disease-diagnosis/TOOLS_REFERENCE.md index 6933c51f..0faf6e90 100644 --- a/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-rare-disease-diagnosis/TOOLS_REFERENCE.md +++ b/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 | -- 2.54.0 From 1ee997aae574f72068d269d822854db2fd71b409 Mon Sep 17 00:00:00 2001 From: promptadmin Date: Tue, 21 Jul 2026 09:46:33 +0000 Subject: [PATCH 7/9] [upstream-sync] skills/tooluniverse-statistical-modeling/TOOLS_REFERENCE.md from mims-harvard/ToolUniverse@be422b18 [prompt] --- .../tooluniverse-statistical-modeling/TOOLS_REFERENCE.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-statistical-modeling/TOOLS_REFERENCE.md b/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-statistical-modeling/TOOLS_REFERENCE.md index 6d8f3e99..a5053c14 100644 --- a/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-statistical-modeling/TOOLS_REFERENCE.md +++ b/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 -- 2.54.0 From 000d085571542b5d9881e35a8d764c16772f4fac Mon Sep 17 00:00:00 2001 From: promptadmin Date: Tue, 21 Jul 2026 09:46:55 +0000 Subject: [PATCH 8/9] [upstream-sync] skills/tooluniverse-variant-interpretation/TOOLS_REFERENCE.md from mims-harvard/ToolUniverse@be422b18 [prompt] --- .../TOOLS_REFERENCE.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-variant-interpretation/TOOLS_REFERENCE.md b/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-variant-interpretation/TOOLS_REFERENCE.md index b6341e77..8033aef6 100644 --- a/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-variant-interpretation/TOOLS_REFERENCE.md +++ b/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 | -- 2.54.0 From a0199807d7201f53866bd36c5d09c7746ef58262 Mon Sep 17 00:00:00 2001 From: promptadmin Date: Tue, 21 Jul 2026 09:47:19 +0000 Subject: [PATCH 9/9] [upstream-sync] skills/tooluniverse/SKILL.md from mims-harvard/ToolUniverse@be422b18 [skill] --- .../skills/tooluniverse/SKILL.md | 19 ++++++++++++++++--- 1 file changed, 16 insertions(+), 3 deletions(-) diff --git a/upstream/mims-harvard-ToolUniverse/skills/tooluniverse/SKILL.md b/upstream/mims-harvard-ToolUniverse/skills/tooluniverse/SKILL.md index b9c22e04..6d1dbc22 100644 --- a/upstream/mims-harvard-ToolUniverse/skills/tooluniverse/SKILL.md +++ b/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")` | --- -- 2.54.0