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| Author | SHA1 | Date | |
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fc058e6fc2 |
@@ -1,8 +1,8 @@
|
||||
---
|
||||
lineage_type: import
|
||||
upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/089eb8e6/skills/setup-tooluniverse/SKILL.md
|
||||
upstream_sha: 089eb8e6
|
||||
imported_at: 2026-07-25
|
||||
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
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||||
@@ -68,7 +68,7 @@ Make sure Step 2 is done, then try:
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uvx --from tooluniverse tu status # How many tools?
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uvx --from tooluniverse tu find 'drug safety' # Search by topic
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uvx --from tooluniverse tu info FAERS_count_death_related_by_drug # See params
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uvx --from tooluniverse tu run FAERS_count_death_related_by_drug '{"medicinalproduct": "metformin"}'
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uvx --from tooluniverse tu run FAERS_count_death_related_by_drug '{"drug_name": "metformin"}'
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```
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First run takes ~30s (downloads package), then instant. **Shortcut**: `uv tool install tooluniverse` → then just use `tu` directly.
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@@ -93,30 +93,12 @@ Continue to **Step 3** (API Keys).
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|
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## SDK Setup
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|
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> **Install `uv` first (Step 2). Do not use system `pip`.** On a current Mac
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> (Homebrew Python 3.13/3.14) `pip install tooluniverse` stops with
|
||||
> `error: externally-managed-environment` (PEP 668), and `python3 -m venv` can
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> fail at `ensurepip`. `uv` avoids both because it downloads and manages its own
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> Python.
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Make sure Step 2 is done. For detailed patterns, invoke the `tooluniverse-sdk` skill.
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|
||||
```bash
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uv venv --python 3.12 # own Python + virtualenv, ignores system pip
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source .venv/bin/activate # Windows: .venv\Scripts\activate
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uv pip install tooluniverse
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```
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|
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`uv pip install` needs an active virtualenv — run `uv venv` first, or use
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`uv tool install tooluniverse` if you only want the `tu` command.
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|
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For detailed patterns, invoke the `tooluniverse-sdk` skill.
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|
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**Optional extras**: the base install covers API/database tools. Local ML,
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cheminformatics, and plotting tools need extras — `uv pip install
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'tooluniverse[ml]'`, `[visualization]`, `[bioinformatics]`, or `[all]`.
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Run `tooluniverse-doctor` to see which groups you are missing.
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Note `[all]` does **not** include `singlecell`, `smolagents`, `client`, or
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`build`; install those separately.
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|
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### Coding API — 3 calling patterns
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|
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**Pattern 1: Direct import** (typed, with autocomplete):
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@@ -148,34 +130,10 @@ Continue to **Step 3** (API Keys).
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|
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## MCP Setup (Chat Mode)
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|
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**Offer the two low-effort paths first.** Editing JSON by hand is the fallback,
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not the recommendation — a mistyped comma is the single most common setup
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failure. Only walk through the manual path if neither option below fits.
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**Path A — let an AI agent do it.** If the user already has any agent (Claude,
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Cursor, Copilot, Gemini, Codex...), they can paste this into it:
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```
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Read https://aiscientist.tools/setup.md and set up ToolUniverse for me.
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```
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|
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The agent handles config, keys, skills, and validation. No terminal, no JSON.
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|
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**Path B — Claude Code users: one-liner, no config file at all.**
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|
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```bash
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claude plugin marketplace add mims-harvard/ToolUniverse
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claude plugin install tooluniverse@tooluniverse
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```
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|
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Installs MCP server + 115 skills + slash commands in one step. Then see the
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`tooluniverse-claude-code-plugin` skill's "Recommended: turn on auto-update"
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step so future releases apply without manual `claude plugin update`.
|
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|
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### Manual config (fallback)
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Make sure Step 2 is done (`uv --version` works).
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|
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### Add ToolUniverse to your app's config
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|
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**Config file help** (if user seems unfamiliar): Config files are plain text that store settings — like a preference list for the app. You don't need to understand the format; just paste exactly what's shown below. Most apps have a Settings button that opens the file for you (see table). If the file is empty, paste the entire block. If it already has content, the agent should help merge it.
|
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|
||||
**Default config** (same for most clients):
|
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@@ -191,24 +149,15 @@ Make sure Step 2 is done (`uv --version` works).
|
||||
}
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||||
```
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||||
|
||||
> **Paste safely.** Copy the block whole — do not retype it. If the file already
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||||
> has an `mcpServers` block, add only the `"tooluniverse": { ... }` entry inside
|
||||
> it and put a comma after the previous entry. If the file was empty, paste the
|
||||
> whole block. Then validate before restarting the app:
|
||||
> ```bash
|
||||
> python3 -m json.tool < "<path-to-config>" > /dev/null && echo "JSON OK"
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||||
> ```
|
||||
> A trailing comma after the last entry, or a missing one between entries, is
|
||||
> the usual cause of "MCP server won't start".
|
||||
|
||||
**`args` — `["tooluniverse"]` vs `["--refresh", "tooluniverse"]`**: plain is the
|
||||
default and starts fast from `uv`'s cache, but can stay on a cached older
|
||||
release until you run `uv cache clean tooluniverse`. Adding `--refresh` checks
|
||||
PyPI for the newest version on every launch — always current, a few seconds
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||||
slower to start. Use plain unless the user specifically wants auto-updates.
|
||||
|
||||
**Config file locations:**
|
||||
|
||||
> **Claude Code users**: skip manual MCP config — use the plugin instead. Invoke the `tooluniverse-claude-code-plugin` skill or run:
|
||||
> ```bash
|
||||
> claude plugin marketplace add mims-harvard/ToolUniverse
|
||||
> claude plugin install tooluniverse@tooluniverse
|
||||
> ```
|
||||
> 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 |
|
||||
|--------|------|---------------|
|
||||
| Cursor | `~/.cursor/mcp.json` | Settings → MCP → Add new global MCP server |
|
||||
@@ -353,7 +302,7 @@ Skills activate automatically based on user's question. Try: "Research the drug
|
||||
> tu info PubMed_search_articles # Check parameters
|
||||
> tu run PubMed_search_articles '{"query": "CRISPR cancer", "max_results": 3}'
|
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> tu run UniProt_get_entry_by_accession '{"accession": "P12345"}'
|
||||
> tu run FAERS_count_death_related_by_drug '{"medicinalproduct": "metformin"}'
|
||||
> tu run FAERS_count_death_related_by_drug '{"drug_name": "metformin"}'
|
||||
> ```
|
||||
|
||||
## Write Agent Memory
|
||||
@@ -403,26 +352,14 @@ NVIDIA_API_KEY=your_shared_key
|
||||
|
||||
| Issue | Fix |
|
||||
|-------|-----|
|
||||
| `error: externally-managed-environment` (PEP 668) | System `pip` refuses to install. Use `uv` — `uv venv --python 3.12 && source .venv/bin/activate && uv pip install tooluniverse`. Never `sudo pip` or `--break-system-packages`. |
|
||||
| `python3 -m venv` fails at `ensurepip` | Homebrew Python (3.13/3.14) is missing a working `ensurepip`. Use `uv venv --python 3.12` — `uv` supplies its own Python. |
|
||||
| `uv pip install` → "No virtual environment found" | Run `uv venv` first, or use `uv tool install tooluniverse` for just the `tu` command. |
|
||||
| `requires-python >= 3.10` | `uv python install 3.12` |
|
||||
| `uvx: command not found` | Run install script from Step 2, restart terminal |
|
||||
| Context window overflow | Verify using `uvx tooluniverse` (compact mode is default) |
|
||||
| `ModuleNotFoundError` at tool runtime | An optional extra is missing. Run `tooluniverse-doctor` to see which group, then `uv pip install 'tooluniverse[ml]'` (or `[visualization]`, `[bioinformatics]`, `[all]`). |
|
||||
| Tools listed but fail when run | Normal for extras-backed tools — `tu status` counts loaded configs, not installed dependencies. `tooluniverse-doctor` reports which groups are missing. |
|
||||
| MCP server won't start | Test: `uvx tooluniverse` in terminal. Validate config with `python3 -m json.tool < <config>`. |
|
||||
| `ModuleNotFoundError` | `uv pip install tooluniverse[all]` |
|
||||
| MCP server won't start | Test: `uvx tooluniverse` in terminal. Check JSON syntax. |
|
||||
| API key 401/403 | Check key in `env` block, restart app, verify key name |
|
||||
| Upgrade needed | `uv cache clean tooluniverse` then restart app |
|
||||
|
||||
**Health check**: `tooluniverse-doctor` reports tools that failed to load *and*
|
||||
which optional dependency groups are not installed. Use it first whenever a tool
|
||||
errors unexpectedly.
|
||||
|
||||
**`[all]` is not everything**: it covers `dev, docs, graph, visualization,
|
||||
space, embedding, ml, bioinformatics`. `singlecell`, `smolagents`, `client`,
|
||||
and `build` must be installed by name.
|
||||
|
||||
Still stuck? [GitHub issues](https://github.com/mims-harvard/ToolUniverse/issues) or email [Shanghua Gao](mailto:[email protected]).
|
||||
|
||||
## Quick Reference
|
||||
|
||||
+3
-23
@@ -1,8 +1,8 @@
|
||||
---
|
||||
lineage_type: import
|
||||
upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/089eb8e6/skills/tooluniverse-admet-prediction/SKILL.md
|
||||
upstream_sha: 089eb8e6
|
||||
imported_at: 2026-07-25
|
||||
upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/tooluniverse-admet-prediction/SKILL.md
|
||||
upstream_sha: e2520a96
|
||||
imported_at: 2026-06-26
|
||||
prompt_class: unknown
|
||||
upstream_changes: accepted
|
||||
name: tooluniverse-admet-prediction
|
||||
@@ -33,26 +33,6 @@ Comprehensive pharmacokinetic and toxicity profiling integrating AI-based ADMET
|
||||
|
||||
**Input**: Drug name (e.g., "ibuprofen") OR SMILES string (e.g., "CC(C)Cc1ccc(cc1)C(C)C(=O)O")
|
||||
|
||||
## Before You Run
|
||||
|
||||
ADMETAI tools run a local model, so they need the `ml` extra:
|
||||
|
||||
```bash
|
||||
uv pip install 'tooluniverse[ml]'
|
||||
```
|
||||
|
||||
Without it the tools still appear in `tu list` (the config loads) but fail at
|
||||
call time with `ADMETModel requires 'admet-ai' package`. Run
|
||||
`tooluniverse-doctor` to confirm which optional groups are installed.
|
||||
|
||||
**Expected console noise — not errors.** The first ADMETAI call loads PyTorch
|
||||
and prints warnings such as missing-GPU / `Trainer` messages from
|
||||
PyTorch Lightning, and `TypedStorage is deprecated` from PyTorch. These are
|
||||
emitted by the underlying libraries during normal CPU inference. Predictions
|
||||
are unaffected — do not report them to the user as failures and do not retry
|
||||
the call because of them. Only treat output as a failure if the tool returns an
|
||||
`error` field or no predictions.
|
||||
|
||||
---
|
||||
|
||||
## COMPUTE, DON'T DESCRIBE
|
||||
|
||||
+34
-4
@@ -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:
|
||||
|
||||
+4
-4
@@ -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
|
||||
|
||||
+6
-9
@@ -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)
|
||||
|
||||
---
|
||||
|
||||
|
||||
+4
-4
@@ -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
|
||||
|
||||
|
||||
+4
-4
@@ -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 |
|
||||
|
||||
+4
-4
@@ -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
|
||||
|
||||
|
||||
+5
-5
@@ -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 |
|
||||
|
||||
@@ -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")` |
|
||||
|
||||
---
|
||||
|
||||
|
||||
Reference in New Issue
Block a user