agentmods.dev

medical-graphrag-assistant: Instructions file for Codex

AGENTS.md

medical-graphrag-assistant AGENTS.md is an instructions file for Codex, OpenCode from intersystems-community/medical-graphrag-assistant. It costs 3,008 tokens per session, scanned A, original, MIT.

An AGENTS.md guide for working on a medical GraphRAG Assistant repository. It describes the project's folders, development workflow, dependencies, and commands.

In plain words
What is it for?
Use it when developing the repository's MCP server, Streamlit interface, search and graph-based retrieval code, databases, embeddings, memory, or tests.
Why use it?
It gives coding agents project-specific context before they change the code. This reduces mistakes caused by misunderstanding where components and tests belong.

Instructions file for CodexOpenCode

Written for Codex and OpenCode: the file is AGENTS.md. Also seen: mentions AGENTS.md.

This is intersystems-community/medical-graphrag-assistant's own configuration. It tells Codex and OpenCode how to work on medical-graphrag-assistant itself, so it is not a mod to install elsewhere. Copy it as a starting point and replace the rules that are about this project. Everything medical-graphrag-assistant configures →

not rated 0repo 7mo ago A scan 3,008 tokens original MIT
View source ↗ intersystems-community/medical-graphrag-assistant
Reuse

Borrowing it

Nothing to install: this file belongs to intersystems-community/medical-graphrag-assistant. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file
curl -O https://raw.githubusercontent.com/intersystems-community/medical-graphrag-assistant/main/AGENTS.md
Clone the repo
git clone --depth 1 https://github.com/intersystems-community/medical-graphrag-assistant

Made for: Codex, OpenCode.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for medical-graphrag-assistant AGENTS.md

README.md
[![agentmods](https://agentmods.dev/badge/instructions/intersystems-community/medical-graphrag-assistant/agents-md.svg)](https://agentmods.dev/instructions/intersystems-community/medical-graphrag-assistant/agents-md)
Your own site
<a href="https://agentmods.dev/instructions/intersystems-community/medical-graphrag-assistant/agents-md"><img src="https://agentmods.dev/badge/instructions/intersystems-community/medical-graphrag-assistant/agents-md.svg" alt="Measured on agentmods" height="20"></a>
Per session 3,008 This file is loaded in full into every session.
When invoked 3,008 The same file — it is already loaded in full.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.03008 $0.03008
Opus 5 $0.01504 $0.01504
Sonnet 5 $0.00602 $0.00602
Haiku 4.5 $0.00301 $0.00301

Measured 7d ago against content hash f4a339297038, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-07, from the pricing page.

Security

Grade A, and why

medical-graphrag-assistant AGENTS.md scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 7d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

AGENTS.md · 198 lines

How it starts

The opening of the file, as written. The whole thing — 198 lines — stays where its author put it; the contents beside it link to each section on GitHub.

AGENTS.md - Agentic Development Guide

This guide provides essential information for AI agents (like Claude, GPT-4, or specialized coding assistants) working on the Medical GraphRAG Assistant repository.

📂 Project Structure

medical-graphrag-assistant/
├── mcp-server/          # MCP server and Streamlit app
│   ├── fhir_graphrag_mcp_server.py  # MCP server logic
│   └── streamlit_app.py             # Streamlit Chat UI
├── src/                 # Core logic and source code
│   ├── db/              # Database connection and clients
│   ├── embeddings/      # Embedding generation (NIM/NV-CLIP)
│   ├── memory/          # Agent memory system
│   ├── query/           # Search query processing
│   └── search/          # RAG and GraphRAG implementations
├── tests/               # Test suite
│   ├── unit/            # Unit tests
│   ├── integration/     # Integration tests
│   ├── e2e/             # End-to-end tests
│   └── ux/              # Playwright UI tests
├── config/              # YAML configuration files
├── scripts/             # Deployment and utility scripts
└── docs/                # Project documentation

🚀 Commands & Workflow

📦 Setup & Dependencies

  • Install: pip install -r requirements.txt
  • AWS Profile: Use PowerUserPlusAccess-AWS_ACCOUNT_ID for all AWS operations.
  • AWS Login: aws sso login --profile PowerUserPlusAccess-AWS_ACCOUNT_ID
  • Environment Variables: Required keys: AWS_PROFILE, IRIS_HOST, IRIS_PORT, IRIS_NAMESPACE, IRIS_USERNAME, IRIS_PASSWORD, NVCLIP_BASE_URL, NVIDIA_API_KEY.
  • Python Driver: ALWAYS use intersystems-irispython (NOT iris or intersystems-iris).

🖥️ EC2 Environment

  • Instance Name: fhir-graphrag-spot
  • Instance ID: i-0fee5f32e867e65c1 (us-east-1)
  • Public IP: 44.200.206.67 (Verified 2026-01-17)
  • Streamlit URL: http://44.200.206.67:8501
  • IRIS Port: 1972 (SQL), 52773 (Portal)
  • Namespace: DEMO (Used for FHIR and Vector data)
  • Status: ✅ Up, Tables Created, Hosted NIM Active.

Read the full file on GitHub · 198 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 7d ago First seen · 198 lines · 3,008 tokens per session scan A f4a339297038

Subscribe to this mod's changes

medical-graphrag-assistant AGENTS.md is an instructions file published in the GitHub repository intersystems-community/medical-graphrag-assistant (0 stars, last pushed 7mo ago), licensed MIT. It adds 3,008 tokens to every session, about $0.0150 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

fhirgraphragintersystems-irismcpmedical-ainvidia-nim
Related

Other instructions, from other repositories

codex AGENTS.md

AGENTS.md instructions for openai/codex, covering rust/codex-rs, the codex-core crate, code review rules, crate api surface and model visible context.

openai/codex · 5,153 tokens

vscode buildNext.instructions.md

Working notes and architecture documentation for the new esbuild-based build system in build/next. Use when making changes to the new build pipeline (transpile/bundle commands, NLS plugin, source-map handling, resource copying, or self-hosting watch tasks).

microsoft/vscode · 6,785 tokens

next.js AGENTS.md

AGENTS.md instructions for vercel/next.js, covering next.js development guide, codebase structure, monorepo overview, core package: packages/next and other important packages.

vercel/next.js · 7,296 tokens

langchain AGENTS.md

AGENTS.md instructions for langchain-ai/langchain, covering global development guidelines for the langchain monorepo, corridor security analysis, project architecture and context, monorepo structure and development tools & commands.

langchain-ai/langchain · 4,469 tokens

vscode oss-third-party-notices.instructions.md

Instructions for microsoft/vscode, covering vs code oss third-party-notices pipeline, architecture, pipeline flow in ci, applying the notice (cutover) and fallback chain (never fail the build).

microsoft/vscode · 5,001 tokens

spec-kit AGENTS.md

AGENTS.md instructions for github/spec-kit, covering agents.md, about spec kit and specify, quickstart — add a new integration in 5 steps, integration architecture and integrationmanifest — file tracking.

github/spec-kit · 7,104 tokens