tcm-cli 0.1.0

An autonomous agent for Traditional Chinese Medicine research and discovery

tcm-cli

An autonomous agent for Traditional Chinese Medicine research and discovery.

Ask questions in natural language. tcm-cli plans the analysis, selects the right tools, executes them, validates results, and returns data-backed conclusions.

Why tcm?

• 30+ TCM research tools — Herb lookup, formula analysis, syndrome differentiation, network pharmacology, safety checks, literature search, and more.
• Multi-model reasoning — Powered by leading LLMs (OpenAI GPT-4o, o3, and more). Automatically plans multi-step research workflows, calls tools, and synthesizes findings.
• Bilingual — Supports both Chinese (中文) and English terminology throughout.
• 10+ database APIs — PubMed, TCMSP, UniProt, STRING, KEGG, ClinicalTrials.gov, Open Targets — no setup required.
• Research UX — Interactive terminal with slash commands, session export, and clipboard support.
• Open source — MIT licensed.

Requirements

• Python 3.10+
• An LLM API key (OpenAI or compatible)

Installation

Quick install (script)

curl -fsSL https://raw.githubusercontent.com/tigerneil/tcm-cli/main/install.sh | bash

The script detects pipx, uv, or falls back to pip --user, then runs tcm setup.

With pipx (recommended)

pipx install tcm-cli

With pip

# Core install
pip install tcm-cli

# With chemistry support (RDKit)
pip install "tcm-cli[chemistry]"

# With ML support (PyTorch + Transformers)
pip install "tcm-cli[ml]"

# With analysis stack (scikit-learn, seaborn, scipy)
pip install "tcm-cli[analysis]"

# Everything
pip install "tcm-cli[all]"

Authentication

# Interactive setup wizard (recommended)
tcm setup

# Or export directly
export OPENAI_API_KEY="sk-..."

# Non-interactive (CI/scripting)
tcm setup --api-key YOUR_API_KEY

API keys are stored at ~/.tcm/config.json. Check key status with:

tcm keys

Getting Started

Basic usage

# Start interactive session
tcm

# Single query
tcm "What herbs are used for Spleen Qi deficiency?"

# Use a specific model
tcm --model gpt-4o "Analyze 四君子汤"

# Validate setup
tcm doctor

Interactive commands

Inside tcm interactive mode:

• /help — command reference + examples
• /tools — list all tools with status
• /model — switch LLM model/provider
• /usage — token and cost tracking
• /copy — copy last answer to clipboard
• /export — export session transcript
• /clear — clear screen
• /exit — exit

Quick examples

Herb lookup

$ tcm "Tell me about 黄芪 (Astragalus) — properties, compounds, and clinical evidence"

Formula analysis

$ tcm "Analyze the composition of 四君子汤 using the 君臣佐使 framework"

Syndrome differentiation

$ tcm "Patient has fatigue, loose stools, poor appetite, pale tongue. What TCM syndrome?"

Network pharmacology

$ tcm "Build a network pharmacology analysis for 补中益气汤 against diabetes targets"

Safety check

$ tcm "Check interactions between 人参, 藜芦, and Warfarin"

Key Features

30+ Domain Tools

Category	Examples
Herbs	Lookup, property classification, meridian search, compound listing
Formulas	Classical formula search, 君臣佐使 analysis, modifications
Syndromes	Pattern differentiation, symptom-to-syndrome mapping, treatment plans
Compounds	Active compound search, ADMET prediction, target identification
Pharmacology	Network pharmacology, pathway enrichment, herb-target networks
Interactions	十八反/十九畏 checks, herb-drug interactions, formula safety
Literature	PubMed search, systematic review finder, CNKI integration
Meridians	Channel lookup, Five Element associations, meridian-herb mapping
Safety	Toxicity profiling, pregnancy safety, dosage validation
Modern	Clinical trial search, ICD-10 mapping, evidence summaries
Data APIs	TCMSP, UniProt, STRING, KEGG, ClinicalTrials.gov, Open Targets
Code	Python sandbox for custom analysis (experimental)

List all tools and their status:

tcm tool list

Supported Models

Provider	Model	Context	Notes
OpenAI	gpt-4o	128k	Default — best balance
OpenAI	gpt-4o-mini	128k	Fast and affordable
OpenAI	o3-mini	200k	Reasoning model
OpenAI	gpt-4.1	1M	Latest flagship with 1M context
OpenAI	gpt-4.1-mini	1M	Balanced speed and intelligence
OpenAI	gpt-4.1-nano	1M	Fastest, most cost-effective

Switch models:

tcm model list              # Show all models with pricing
tcm model set gpt-4o        # Switch to GPT-4o
tcm model show              # Show current model

Local Datasets

Without local data, tcm works via database APIs and built-in knowledge. To boost accuracy and offline support, install local datasets:

tcm data pull herbs      # Install bundled herb monograph data (instant)
tcm data pull formulas   # Install bundled classical formula data (instant)
tcm data pull tcmsp      # TCMSP — herbs, compounds, targets (~50 MB)
tcm data pull tcmid      # TCMID — herb-compound-disease (~30 MB)
tcm data pull batman     # BATMAN-TCM bioinformatics data (~100 MB)
tcm data pull symmap     # SymMap symptom-mapping database (~20 MB)
tcm data status          # Show all dataset statuses

Install modes:

• herbs and formulas install instantly from bundled package data.
• Datasets with a direct download URL are fetched automatically with a progress bar and extracted.
• Datasets that require registration (tcmsp, tcmid, batman, symmap) print step-by-step instructions. After downloading manually, register the file:

tcm data import tcmsp ~/Downloads/tcmsp.zip
tcm data import tcmsp ~/Downloads/tcmsp-extracted/   # or a directory

Use --force to re-download or reinstall any dataset:

tcm data pull herbs --force

Configuration

tcm config show             # Show all settings
tcm config set key value    # Set a value
tcm config get key          # Get a single value
tcm config validate         # Check for issues

Config is stored at ~/.tcm/config.json.

Common config keys

tcm config set llm.provider openai          # openai or compatible
tcm config set llm.model gpt-4o
tcm config set ui.language zh               # en (default) or zh

Agent profiles

tcm config set agent.profile research    # Default — balanced, allows hypotheses
tcm config set agent.profile clinical    # Strict evidence only, no hypotheses
tcm config set agent.profile education   # Relaxed, creative responses

Troubleshooting

Symptom	Fix
tcm fails at startup	tcm doctor
Authentication error	tcm setup or tcm keys
Missing API key	export OPENAI_API_KEY=... or tcm config set llm.openai_api_key ...
Missing dependency	pip install "tcm-cli[all]"
Tool module failed	tcm tool list — check for load errors

Contributing

git clone https://github.com/tigerneil/tcm-cli.git
cd tcm-cli
pip install -e ".[dev]"
tcm setup
pytest tests/

License

MIT