{
 "cells": [
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": [
    "# Understanding Ontologies with Cognee\n",
    "\n",
    "This notebook demonstrates how to work with ontologies in scientific research using the Cognee framework. We'll explore how ontologies can enhance our understanding and querying of scientific papers.\n",
    "\n",
    "## What is an Ontology?\n",
    "\n",
    "An ontology is a formal representation of knowledge that defines:\n",
    "- Concepts within a domain\n",
    "- Relationships between concepts\n",
    "- Properties and attributes\n",
    "- Rules and constraints\n",
    "\n",
    "Key terms:\n",
    "- **Classes**: Categories or types (e.g., Disease, Symptom)\n",
    "- **Instances**: Specific examples of classes (e.g., Type 2 Diabetes)\n",
    "- **Properties**: Relationships between classes/instances (e.g., hasSymptom)\n",
    "- **Axioms**: Logical statements defining relationships"
   ],
   "id": "25cf0a40e669a70"
  },
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": [
    "## Setup\n",
    "\n",
    "First, let's install the required packages and set up our environment:"
   ],
   "id": "441248da37f2b901"
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-03-26T16:17:55.937140Z",
     "start_time": "2025-03-26T16:17:55.908542Z"
    }
   },
   "cell_type": "code",
   "source": [
    "# Install required package\n",
    "# !pip install cognee"
   ],
   "id": "8cf7ba29f9a150af",
   "outputs": [],
   "execution_count": 17
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-03-26T16:18:09.382400Z",
     "start_time": "2025-03-26T16:18:09.342349Z"
    }
   },
   "cell_type": "code",
   "source": [
    "# Import required libraries\n",
    "import cognee\n",
    "import asyncio\n",
    "from cognee.shared.logging_utils import get_logger\n",
    "import os\n",
    "import textwrap\n",
    "from cognee.api.v1.search import SearchType\n",
    "from cognee.api.v1.visualize.visualize import visualize_graph\n",
    "\n",
    "logger = get_logger()\n",
    "\n",
    "# Set up OpenAI API key (required for Cognee's LLM functionality)\n",
    "os.environ[\"LLM_API_KEY\"] = \"your-api-key-here\"  # Replace with your API key"
   ],
   "id": "d825d126b3a0ec26",
   "outputs": [],
   "execution_count": 18
  },
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": [
    "## Creating the Pipeline\n",
    "\n",
    "Let's create a pipeline that will:\n",
    "1. Clean existing data\n",
    "2. Process scientific papers\n",
    "3. Apply ontological knowledge"
   ],
   "id": "6af350837e86b7a1"
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-04-09T17:12:54.006718Z",
     "start_time": "2025-04-09T17:12:53.992906Z"
    }
   },
   "cell_type": "code",
   "source": [
    "async def run_pipeline(ontology_path=None):\n",
    "    # Clean existing data\n",
    "    await cognee.prune.prune_data()\n",
    "    await cognee.prune.prune_system(metadata=True)\n",
    "    \n",
    "    # Set up path to scientific papers\n",
    "    scientific_papers_dir = os.path.join(\n",
    "        os.path.dirname(os.path.dirname(os.path.abspath(\".\"))), \n",
    "        \"cognee\",\n",
    "        \"examples\",\n",
    "        \"data\", \n",
    "        \"scientific_papers/\"\n",
    "    )\n",
    "    \n",
    "    # Add papers to the system\n",
    "    await cognee.add(scientific_papers_dir)\n",
    "    \n",
    "    # Cognify with optional ontology\n",
    "    return await cognee.cognify(ontology_file_path=ontology_path)\n",
    "\n",
    "async def query_pipeline(questions):\n",
    "    answers = []\n",
    "    for question in questions:\n",
    "        search_results = await cognee.search(\n",
    "            query_type=SearchType.GRAPH_COMPLETION,\n",
    "            query_text=question,\n",
    "        )\n",
    "        answers.append(search_results)\n",
    "    return answers"
   ],
   "id": "4d0e4a58e4207a7d",
   "outputs": [],
   "execution_count": 26
  },
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": [
    "## Running the Demo\n",
    "\n",
    "Let's test our system with some medical questions, comparing results with and without ontological knowledge:"
   ],
   "id": "c87c21a75d6f4d79"
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-04-09T17:14:31.818452Z",
     "start_time": "2025-04-09T17:12:55.491598Z"
    }
   },
   "cell_type": "code",
   "source": [
    "# Test questions\n",
    "questions = [\n",
    "    \"What are common risk factors for Type 2 Diabetes?\",\n",
    "    \"What preventive measures reduce the risk of Hypertension?\",\n",
    "    \"What symptoms indicate possible Cardiovascular Disease?\",\n",
    "    \"What diseases are associated with Obesity?\"\n",
    "]\n",
    "\n",
    "# Path to medical ontology\n",
    "ontology_path = \"examples/python/ontology_input_example/enriched_medical_ontology_with_classes.owl\"  # Update with your ontology path\n",
    "\n",
    "# Run with ontology\n",
    "print(\"\\n--- Results WITH ontology ---\\n\")\n",
    "await run_pipeline(ontology_path=ontology_path)\n",
    "answers_with = await query_pipeline(questions)\n",
    "for q, a in zip(questions, answers_with):\n",
    "    print(f\"Q: {q}\\nA: {a}\\n\")"
   ],
   "id": "1363772d2b48f5c0",
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "--- Results WITH ontology ---\n",
      "\n",
      "\n",
      "\u001B[2m2025-04-09T17:12:55.499538Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mGraph deleted successfully.   \u001B[0m [\u001B[0m\u001B[1m\u001B[34mcognee.shared.logging_utils\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:12:55.588613Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mDatabase deleted successfully.\u001B[0m [\u001B[0m\u001B[1m\u001B[34mcognee.shared.logging_utils\u001B[0m]\u001B[0mUser 312efe9d-380c-4f8d-9848-f628fe3dc177 has registered.\n",
      "<cognee.modules.pipelines.models.PipelineRun.PipelineRun object at 0x371baf650>\n",
      "\n",
      "\u001B[2m2025-04-09T17:12:55.747683Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mPipeline run started: `4b84e400-23fc-5976-bbb4-f8ee303eed81`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:12:55.749122Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task started: `resolve_data_directories`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:12:55.750745Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task started: `ingest_data`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:12:56.069185Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task completed: `ingest_data`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:12:56.069591Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task completed: `resolve_data_directories`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:12:56.070114Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mPipeline run completed: `4b84e400-23fc-5976-bbb4-f8ee303eed81`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m<cognee.modules.pipelines.models.PipelineRun.PipelineRun object at 0x38691c350>\n",
      "\n",
      "\u001B[2m2025-04-09T17:12:56.081871Z\u001B[0m [\u001B[33m\u001B[1mwarning  \u001B[0m] \u001B[1mOntology file 'examples/python/ontology_input_example/enriched_medical_ontology_with_classes.owl' not found. Using fallback ontology at http://example.org/empty_ontology\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:12:56.083270Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mLookup built: 0 classes, 0 individuals\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:12:56.099230Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mPipeline run started: `af81ab41-8243-522f-a10a-b7b5febcc577`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:12:56.100778Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task started: `classify_documents`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:12:56.102874Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task started: `check_permissions_on_documents`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:12:56.105891Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mAsync generator task started: `extract_chunks_from_documents`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/vasilije/cognee/.venv/lib/python3.11/site-packages/dlt/destinations/impl/sqlalchemy/merge_job.py:194: SAWarning: Table 'file_metadata' already exists within the given MetaData - not copying.\n",
      "  staging_table_obj = table_obj.to_metadata(\n",
      "/Users/vasilije/cognee/.venv/lib/python3.11/site-packages/dlt/destinations/impl/sqlalchemy/merge_job.py:229: SAWarning: implicitly coercing SELECT object to scalar subquery; please use the .scalar_subquery() method to produce a scalar subquery.\n",
      "  order_by=order_dir_func(order_by_col),\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[2m2025-04-09T17:12:56.490952Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task started: `extract_graph_from_data`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m19:12:56 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
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      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
     ]
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      "\u001B[92m19:12:56 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
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      "\n",
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      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
     ]
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      "\u001B[92m19:12:56 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
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      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
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      "\u001B[92m19:12:56 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
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      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
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      "\u001B[92m19:12:56 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
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      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
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      "\u001B[92m19:12:56 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.028895Z\u001B[0m [\u001B[33m\u001B[1mwarning  \u001B[0m] \u001B[1mFile /Users/vasilije/cognee/cognee/.cognee_system/databases/cognee_graph.pkl not found. Initializing an empty graph.\u001B[0m [\u001B[0m\u001B[1m\u001B[34mcognee.shared.logging_utils\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.031340Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'study' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.031582Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'coffee consumption study' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.031815Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'nutrient' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.032000Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'caffeinated coffee' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.032523Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'decaffeinated coffee' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.032768Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'health outcome' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.033005Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'mortality' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.033326Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'population' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.033618Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'participant population' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.033907Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'dietary pattern' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.034121Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'mediterranean diet' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.034391Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'eureye spain and valencia nutrition study' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.034592Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'statistical measurement' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.034943Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'p-value' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.035127Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'risk of death' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.035397Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'all-cause mortality' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.035564Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'cardiovascular disease mortality' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.035764Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'cancer mortality' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.035957Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'behavior' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.036177Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'coffee consumption' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.036551Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'beverage type' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.036791Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'demographic characteristic' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.036971Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'sex distribution' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.037179Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'age distribution' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.037412Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'education level' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.037593Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'health indicator' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.037748Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'body mass index' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.037952Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'waist circumference' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.038237Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'smoking status' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.038622Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'health condition' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.038857Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'diabetes status' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.039193Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'cholesterol status' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.039524Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'hypertension status' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.039801Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'physical activity' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.040067Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'tv watching' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.040355Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'sleeping time' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.040619Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'dietary index' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.040847Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'relative mediterranean diet index' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.041182Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'concept' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.041404Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'group' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.041719Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'mediterranean population' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.041914Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'metric' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.042158Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'research' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.042377Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'study 2021' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.042579Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'country' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.043107Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'spain' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.043321Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'person' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.043627Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'torres-collado, l.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.043899Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'garcia-de-la-hera, m.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.044128Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'navarrete-muñoz, e.m.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.044345Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'notario-barandiaran, l.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.044588Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'gonzalez-palacios, s.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.044959Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'zurriaga, o.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.045232Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'melchor, i.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.045447Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'vioque, j.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.045630Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'navarro, a.m.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.045956Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'martinez-gonzalez, m. á.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.046206Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'gea, a.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.046422Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'grosso, g.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.046629Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'martin-moreno, j.m.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.046939Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'lopez-garcia, e.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.047166Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'martin-calvo, n.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.047426Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'toledo, e.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.047719Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'ruggiero, e.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.048060Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'di castelnuovo, a.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.048339Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'costanzo, s.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.048603Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'persichillo, m.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.048831Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'de curtis, a.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.049031Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'cerletti, c.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.049243Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'donati, m.b.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.049458Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'de gaetano, g.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.049693Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'iacoviello, l.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.049907Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'bonaccio, m.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.050227Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'moli-sani study' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.050482Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'quiles, j.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.050703Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'organization' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.050875Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'u.s. department of agriculture' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.051151Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'database' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.051437Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'usda national nutrient database' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.051639Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'palma, i.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.051816Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'cantós, d.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.052024Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'lean, m.e.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.052242Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'harlow, s.d.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.052466Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'malerba, s.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.052723Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'crippa, a.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.052949Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'je, y.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.053201Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'park, s.-y.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.053447Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'gunter, m.j.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.053667Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'sado, j.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.053863Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'dinu, m.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.054068Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'gökcen, b.b.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.054375Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'yu, x.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.054586Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'gonzalez de mejia, e.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.054764Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'yamagata, k.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.054991Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'machado-fragua, m.d.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.055251Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'date' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.055480Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for '2018' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.056014Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'michael f. mendoza' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.056232Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'ralf martz sulague' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.056451Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'therese posas-mendoza' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.056709Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'carl j. lavie' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.057211Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'publication' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.057503Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'ochsner journal' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.057723Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'cardiovascular health' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.057989Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'impact of coffee consumption on cardiovascular health' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.058182Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'condition' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.058357Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'hypertension' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.058542Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'coronary heart disease' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.058710Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'heart failure' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.058870Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'atrial fibrillation' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.059039Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for '2000-2021' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.059210Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'compound' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.059397Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'caffeine' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.059735Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'mendoza, mf' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.060066Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'coronary artery risk development in young adults study' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:45.060328Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'bodar et al. (2019)' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:52.506030Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task started: `summarize_text`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m19:13:52 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m19:13:52 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m19:13:52 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m19:13:52 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m19:13:52 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m19:13:52 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m\n",
      "\u001B[2m2025-04-09T17:13:58.267490Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task started: `add_data_points`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:14:07.439855Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task completed: `add_data_points`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:14:07.440337Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task completed: `summarize_text`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:14:07.440524Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task completed: `extract_graph_from_data`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:14:07.440690Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mAsync generator task completed: `extract_chunks_from_documents`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:14:07.440886Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task completed: `check_permissions_on_documents`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:14:07.441125Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task completed: `classify_documents`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T17:14:07.441383Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mPipeline run completed: `af81ab41-8243-522f-a10a-b7b5febcc577`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m19:14:09 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m19:14:23 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m19:14:27 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m19:14:30 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0mQ: What are common risk factors for Type 2 Diabetes?\n",
      "A: ['Common risk factors for Type 2 Diabetes include:\\n1. **Obesity** - particularly a high body mass index (BMI) (≥30 kg/m2).\\n2. **Waist circumference** - increased risk is associated with larger waist sizes.\\n3. **Sedentary lifestyle** - low levels of physical activity are linked to higher risk.\\n4. **Age** - the risk increases with age, especially for those over 45 years.\\n5. **Diet** - poor dietary choices, including low adherence to a Mediterranean diet, may contribute.\\n6. **Smoking** - current smoking status is a risk factor.\\n7. **Hypertension** - having high blood pressure increases risk.\\n8. **Cholesterol levels** - high cholesterol levels may also be a factor.']\n",
      "\n",
      "Q: What preventive measures reduce the risk of Hypertension?\n",
      "A: ['Preventive measures to reduce the risk of hypertension include moderate coffee consumption, which has been associated with a decreased risk of developing hypertension, particularly in non-smokers. Other potential mechanisms of benefit from coffee include inhibition of sodium and water reabsorption, as well as anti-inflammatory effects.']\n",
      "\n",
      "Q: What symptoms indicate possible Cardiovascular Disease?\n",
      "A: ['Possible symptoms indicating cardiovascular disease include: hypertension, heart failure, atrial fibrillation, elevated cholesterol levels, and increased risk of myocardial infarction. Regular coffee consumption is associated with decreased risks of some of these conditions, whereas heavy coffee consumption may have inconsistent effects.']\n",
      "\n",
      "Q: What diseases are associated with Obesity?\n",
      "A: ['Obesity is associated with the following health conditions:\\n1. Cardiovascular disease mortality (as a health outcome).\\n2. Diabetes status (as a health condition).\\n3. Cholesterol status (as a health condition).']\n",
      "\n"
     ]
    }
   ],
   "execution_count": 27
  },
  {
   "metadata": {},
   "cell_type": "code",
   "outputs": [],
   "execution_count": null,
   "source": "",
   "id": "89e2e53dcecb78eb"
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-04-09T14:32:24.891560Z",
     "start_time": "2025-04-09T14:30:47.863808Z"
    }
   },
   "cell_type": "code",
   "source": [
    "# Run without ontology\n",
    "print(\"\\n--- Results WITHOUT ontology ---\\n\")\n",
    "await run_pipeline()\n",
    "answers_without = await query_pipeline(questions)\n",
    "for q, a in zip(questions, answers_without):\n",
    "    print(f\"Q: {q}\\nA: {a}\\n\")"
   ],
   "id": "3aa18f4cdd5ceff6",
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "--- Results WITHOUT ontology ---\n",
      "\n",
      "\n",
      "\u001B[2m2025-04-09T14:30:47.865578Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mGraph deleted successfully.   \u001B[0m [\u001B[0m\u001B[1m\u001B[34mcognee.shared.logging_utils\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:30:47.879242Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mDatabase deleted successfully.\u001B[0m [\u001B[0m\u001B[1m\u001B[34mcognee.shared.logging_utils\u001B[0m]\u001B[0mUser 5fcea8fd-95ce-4a3b-861e-d8f8a5d01fe5 has registered.\n",
      "<cognee.modules.pipelines.models.PipelineRun.PipelineRun object at 0x38b7e78d0>\n",
      "\n",
      "\u001B[2m2025-04-09T14:30:47.952091Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mPipeline run started: `4b84e400-23fc-5976-bbb4-f8ee303eed81`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:30:47.952386Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task started: `resolve_data_directories`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:30:47.952810Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task started: `ingest_data`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:30:48.127543Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task completed: `ingest_data`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:30:48.127926Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task completed: `resolve_data_directories`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:30:48.128135Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mPipeline run completed: `4b84e400-23fc-5976-bbb4-f8ee303eed81`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m<cognee.modules.pipelines.models.PipelineRun.PipelineRun object at 0x382fc3d50>\n",
      "\n",
      "\u001B[2m2025-04-09T14:30:48.135862Z\u001B[0m [\u001B[33m\u001B[1mwarning  \u001B[0m] \u001B[1mOntology file 'None' not found. Using fallback ontology at http://example.org/empty_ontology\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:30:48.136338Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mLookup built: 0 classes, 0 individuals\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:30:48.145025Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mPipeline run started: `af81ab41-8243-522f-a10a-b7b5febcc577`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:30:48.145316Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task started: `classify_documents`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:30:48.145568Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task started: `check_permissions_on_documents`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:30:48.148188Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mAsync generator task started: `extract_chunks_from_documents`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/vasilije/cognee/.venv/lib/python3.11/site-packages/dlt/destinations/impl/sqlalchemy/merge_job.py:194: SAWarning: Table 'file_metadata' already exists within the given MetaData - not copying.\n",
      "  staging_table_obj = table_obj.to_metadata(\n",
      "/Users/vasilije/cognee/.venv/lib/python3.11/site-packages/dlt/destinations/impl/sqlalchemy/merge_job.py:229: SAWarning: implicitly coercing SELECT object to scalar subquery; please use the .scalar_subquery() method to produce a scalar subquery.\n",
      "  order_by=order_dir_func(order_by_col),\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[2m2025-04-09T14:30:48.491623Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task started: `extract_graph_from_data`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m16:30:48 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m16:30:48 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m16:30:48 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m16:30:48 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m16:30:48 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m16:30:48 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.725114Z\u001B[0m [\u001B[33m\u001B[1mwarning  \u001B[0m] \u001B[1mFile /Users/vasilije/cognee/cognee/.cognee_system/databases/cognee_graph.pkl not found. Initializing an empty graph.\u001B[0m [\u001B[0m\u001B[1m\u001B[34mcognee.shared.logging_utils\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.728424Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'person' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.728765Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'michael f. mendoza' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.729061Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'ralf martz sulague' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.729298Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'therese posas-mendoza' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.729489Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'carl j. lavie' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.729721Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'organization' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.729906Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'ochsner clinic foundation' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.730134Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'georgetown university' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.730308Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'publication' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.730488Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'ochsner journal' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.730684Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'concept' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.730862Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'coffee consumption' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.731104Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'cardiovascular health' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.731289Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'cardiovascular disease' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.731461Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'hypertension' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.731690Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'cholesterol' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.731955Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'heart failure' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.732126Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'atrial fibrillation' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.732315Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'coronary heart disease' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.732488Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'phenolic acid' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.732691Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'diterpenes' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.732873Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'gene' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.733046Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'cyp1a2' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.733274Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'coffee preparation methods' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.733593Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'mendoza, mf' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.733935Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'diabetes mellitus' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.734489Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'infarction' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.734817Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'left ventricular function' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.735100Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'mortality' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.735288Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'oxidative stress' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.735482Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'research methodology' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.735649Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'meta-analysis' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.735816Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'antioxidants' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.736048Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'laura torres-collado' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.736250Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'laura maría compañ-gabucio' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.736442Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'sandra gonzález-palacios' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.736626Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'leyre notario-barandiaran' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.736796Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'alejandro oncina-cánovas' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.736959Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'jesús vioque' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.737123Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'manuela garcía-de la hera' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.737288Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'journal' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.737436Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'nutrients 2021' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.737591Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'study' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.737782Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'valencia nutrition study' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.738030Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'eureye-spain' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.738267Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'valencia nutrition survey' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.738422Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'demographic' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.738578Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'participants aged 20 years and above' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.738743Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'health metric' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.739188Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'age' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.739521Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'education level' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.739834Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'body mass index (bmi)' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.740034Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'waist circumference' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.740213Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'smoking status' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.740388Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'diabetes' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.740719Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'physical activity' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.740905Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'tv watching' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.741075Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'sleeping time' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.741375Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'rmed index' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.741550Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for '6 years follow-up mortality' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.741725Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for '12 years follow-up mortality' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.741889Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for '18 years follow-up mortality' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.742134Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'population' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.742306Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'mediterranean population' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.742479Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'health behavior' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.742802Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'beverage' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.743001Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'caffeinated coffee' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.743187Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'health outcome' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.743374Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'cancer mortality' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.743543Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'all-cause mortality' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.743722Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'cvd mortality' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.743892Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'country' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.744058Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'spain' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.744231Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'decaffeinated coffee' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.744483Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'scientific concept' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.744647Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'biological mechanisms' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.744831Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'research participants' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.745001Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'chemical' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.745162Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'caffeine' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.745435Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'torres-collado, l.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.745639Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'garcia-de-la-hera, m.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.745808Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'navarrete-muñoz, e.m.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.746008Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'notario-barandiaran, l.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.746185Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'gonzalez-palacios, s.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.746657Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'zurriaga, o.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.746868Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'melchor, i.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.747422Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'vioque, j.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.747692Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'navarro, a.m.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.747904Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'martinez-gonzalez, m.á.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.748081Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'gea, a.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.748254Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'grosso, g.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.748421Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'ruggiero, e.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.748580Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'di castelnuovo, a.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.748758Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'costanzo, s.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.748926Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'persichillo, m.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.749109Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'de curtis, a.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.749301Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'cerletti, c.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.749494Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'donati, m.b.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.749667Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'de gaetano, g.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.749845Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'iacoviello, l.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.750035Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'bonaccio, m.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.750210Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'harlow, s.d.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.750388Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'linet, m.s.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.750567Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'malerba, s.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.750830Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'dinu, m.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.751026Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'yu, x.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.751207Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'gonzalez de mejia, e.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.751368Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'yamagata, k.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.751619Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'gökcen, b.b.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.751870Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'machado-fragua, m.d.' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.752101Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'date' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.752294Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for '2018-01-01' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.752469Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for '2021-01-01' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.752651Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'coffee consumption and mortality from all causes' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.752821Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'coffee consumption and total mortality in mediterranean cohort' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.753004Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'coffee drinking and lower risks of mortality' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.753181Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'validity of food frequency questionnaire' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.753343Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'adherence to mediterranean diet and coronary heart disease risk' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.753526Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'diet and overall survival in elderly people' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.753701Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'adherence to mediterranean diet and survival' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.753964Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'database' in category 'classes'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.754204Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'usda national nutrient database' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.754391Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'coffee consumption and mortality meta-analysis' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:31:53.754580Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mNo close match found for 'mediterranean diet and multiple health outcomes' in category 'individuals'\u001B[0m [\u001B[0m\u001B[1m\u001B[34mOntologyAdapter\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:32:00.293116Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task started: `summarize_text`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m16:32:00 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m16:32:00 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m16:32:00 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m16:32:00 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m16:32:00 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m16:32:00 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m\n",
      "\u001B[2m2025-04-09T14:32:05.162204Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task started: `add_data_points`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:32:10.432940Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task completed: `add_data_points`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:32:10.433399Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task completed: `summarize_text`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:32:10.433585Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task completed: `extract_graph_from_data`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:32:10.433749Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mAsync generator task completed: `extract_chunks_from_documents`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:32:10.433973Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task completed: `check_permissions_on_documents`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:32:10.434164Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mCoroutine task completed: `classify_documents`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T14:32:10.434368Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mPipeline run completed: `af81ab41-8243-522f-a10a-b7b5febcc577`\u001B[0m [\u001B[0m\u001B[1m\u001B[34mrun_tasks(tasks: [Task], data)\u001B[0m]\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m16:32:12 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m16:32:16 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m16:32:20 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0m"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\u001B[92m16:32:23 - LiteLLM:INFO\u001B[0m: utils.py:2784 - \n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[1m\n",
      "LiteLLM completion() model= gpt-4o-mini; provider = openai\u001B[0mQ: What are common risk factors for Type 2 Diabetes?\n",
      "A: ['Common risk factors for Type 2 Diabetes include obesity, physical inactivity, and poor diet. Additionally, coffee consumption may be related to lower mortality rates, which could indirectly influence diabetes risk. Participants aged 20 years and above are also considered in health metrics related to diabetes.']\n",
      "\n",
      "Q: What preventive measures reduce the risk of Hypertension?\n",
      "A: ['Preventive measures that reduce the risk of hypertension include moderate coffee consumption, which is linked to reduced cardiovascular disease mortality and potentially lower risks for hypertension, cholesterol issues, heart failure, and atrial fibrillation. Additionally, antioxidants may also provide a preventative effect on cardiovascular health.']\n",
      "\n",
      "Q: What symptoms indicate possible Cardiovascular Disease?\n",
      "A: ['Symptoms that may indicate possible Cardiovascular Disease include hypertension, heart failure, and atrial fibrillation. Additionally, high cholesterol levels can also be a sign of cardiovascular issues.']\n",
      "\n",
      "Q: What diseases are associated with Obesity?\n",
      "A: ['Diseases associated with obesity include cardiovascular disease (CVD) and diabetes mellitus.']\n",
      "\n"
     ]
    }
   ],
   "execution_count": 23
  },
  {
   "metadata": {},
   "cell_type": "markdown",
   "source": [
    "## Visualizing the Knowledge Graph\n",
    "\n",
    "Let's visualize how our ontology connects different medical concepts:"
   ],
   "id": "c60533d2423acdb0"
  },
  {
   "metadata": {
    "ExecuteTime": {
     "end_time": "2025-04-09T15:25:33.512697Z",
     "start_time": "2025-04-09T15:25:33.471854Z"
    }
   },
   "cell_type": "code",
   "source": [
    "from cognee.api.v1.visualize import visualize_graph\n",
    "await visualize_graph()"
   ],
   "id": "36ee2a360f47a054",
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "\u001B[2m2025-04-09T15:25:33.504468Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mGraph visualization saved as /Users/vasilije/graph_visualization.html\u001B[0m [\u001B[0m\u001B[1m\u001B[34mcognee.shared.logging_utils\u001B[0m]\u001B[0m\n",
      "\u001B[2m2025-04-09T15:25:33.505762Z\u001B[0m [\u001B[32m\u001B[1minfo     \u001B[0m] \u001B[1mThe HTML file has been stored on your home directory! Navigate there with cd ~\u001B[0m [\u001B[0m\u001B[1m\u001B[34mcognee.shared.logging_utils\u001B[0m]\u001B[0m"
     ]
    },
    {
     "data": {
      "text/plain": [
       "'\\n    <!DOCTYPE html>\\n    <html>\\n    <head>\\n        <meta charset=\"utf-8\">\\n        <script src=\"https://d3js.org/d3.v5.min.js\"></script>\\n        <style>\\n            body, html { margin: 0; padding: 0; width: 100%; height: 100%; overflow: hidden; background: linear-gradient(90deg, #101010, #1a1a2e); color: white; font-family: \\'Inter\\', sans-serif; }\\n\\n            svg { width: 100vw; height: 100vh; display: block; }\\n            .links line { stroke: rgba(255, 255, 255, 0.4); stroke-width: 2px; }\\n            .nodes circle { stroke: white; stroke-width: 0.5px; filter: drop-shadow(0 0 5px rgba(255,255,255,0.3)); }\\n            .node-label { font-size: 5px; font-weight: bold; fill: white; text-anchor: middle; dominant-baseline: middle; font-family: \\'Inter\\', sans-serif; pointer-events: none; }\\n            .edge-label { font-size: 3px; fill: rgba(255, 255, 255, 0.7); text-anchor: middle; dominant-baseline: middle; font-family: \\'Inter\\', sans-serif; pointer-events: none; }\\n        </style>\\n    </head>\\n    <body>\\n        <svg></svg>\\n        <script>\\n            var nodes = [{\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"text\"]}, \"type\": \"DocumentChunk\", \"text\": \"REVIEWSANDCONTEMPORARYUPDATES\\\\nOchsner Journal 23:152\\\\u2013158, 2023\\\\n\\\\u00a92023 by the author(s); Creative Commons Attribution License (CC BY)\\\\nDOI: 10.31486/toj.22.0073\\\\nImpact of Coffee Consumption on Cardiovascular Health\\\\nMichael F. Mendoza, MD,1Ralf Martz Sulague, MD,2Therese Posas-Mendoza, MD,3Carl J. Lavie, MD4,5\\\\n1The Gayle and Tom Benson Cancer Center, Ochsner Clinic Foundation, New Orleans, LA2School of Health, Georgetown University,\\\\nWashington, DC3Department of Rheumatology, Ochsner Clinic Foundation, Covington, LA4Department of Cardiology, Ochsner Clinic\\\\nFoundation, New Orleans, LA5The University of Queensland Medical School, Ochsner Clinical School, New Orleans, LA\\\\nBackground: Coffeeisawidelyavailablebeveragethatisenjoyedbyindividualsofmanycultures.Thepublicationofnewstudies\\\\npromptsareviewoftheclinicalupdatesregardingtheassociationbetweencoffeeconsumptionandcardiovasculardisease.Methods: Wepresentanarrativereviewoftheliteraturerelatedtocoffeeconsumptionandcardiovasculardisease.\\\\nResults:Recent(2000-2021)studieshaveshownthatregularcoffeeconsumptionisassociatedwithadecreasedriskofdeveloping\\\\nhypertension,heartfailure,andatrialfibrillation.However,resultsareinconsistentwithregardtocoffeeconsumptionandriskofdevelopingcoronaryheartdisease.MoststudiesshowaJ-shapedassociation,whereinmoderatecoffeeconsumptionresultedindecreasedriskofcoronaryheartdiseaseandheavycoffeeconsumptionresultedinincreasedrisk.Inaddition,boiledorunfilteredcoffeeismoreatherogenicthanfilteredcoffeebecauseofitsrichditerpenecontentthatinhibitsbileacidsynthesisandultimatelyaffectslipidmetabolism.Ontheotherhand,filteredcoffee,whichisessentiallydevoidoftheaforementionedcompounds,exertsantiatherogenic properties by increasing high-density lipoprotein\\\\u2013mediated cholesterol efflux from macrophages through theinfluenceofplasmaphenolicacid.Assuch,cholesterollevelsareprincipallyinfluencedbythemannerofcoffeepreparation(boiledvsfiltered).\\\\nConclusion: Ourfindingssuggestthatmoderatecoffeeconsumptionleadstoadecreaseinall-causeandcardiovascular-related\\\\nmortality,hypertension,cholesterol,heartfailure,andatrialfibrillation.However,noconclusiverelationshipbetweencoffeeandcoronaryheartdiseaseriskhasbeenconsistentlyidentified.\\\\nKeywords: Atrialfibrillation ,cholesterol ,coffee,coronarydisease ,diterpenes ,heartfailure ,hypertension ,lipids,phenolicacid\\\\nAddress correspondence to Michael F. Mendoza, MD, The Gayle and Tom Benson Cancer Center, Ochsner Clinic Foundation, 1514 Jefferson\\\\nHwy., New Orleans, LA 70121. Tel: (504) 842-4482. Email: michael.mendoza@ochsner.org\\\\nINTRODUCTION\\\\nCoffee, one of the most popular beverages in the world,\\\\nis widely enjoyed regardless of individuals\\\\u2019 ethnicity, sex,\\\\nor cultural background because of its psychoactive effects,\\\\nincluding mental alertness, vigilance, reaction time, andproductivity. Its accessibility and extensive consumption\\\\nhave generated great interest regarding its overall impact\\\\non health. Concerns have been raised about the ability ofcoffee to induce cardiac arrhythmias and increase blood\\\\npressure.\\\\n1,2Inthe1960s,coffeeconsumptionwaslabeledas\\\\na cardiovascular risk factor associated with coronary heartdisease.\\\\n3\\\\nAmericans, similar to Europeans, are estimated to con-\\\\nsume approximately 5.1 kg of coffee per person per year.4\\\\nTheamountofcaffeine,amajorcomponentofcoffee,varies\\\\nbetween 30 mg and 175 mg in a single home-prepared cup\\\\nof coffee.4The stimulant effect of caffeine is caused by\\\\nthe antagonism of adenosine receptors, effectively inhibit-\\\\ning the effects of adenosine, a well-known inhibitory neu-\\\\nromodulator. However, caffeine is not a completely benigncompound, as it can cross the placenta during pregnancy\\\\nand may potentially cause conditions such as sponta-neous abortion and impaired fetal growth. Therefore, cof-\\\\nfee consumption for females who are pregnant or plan-ning to become pregnant should be limited to a moder-\\\\nate level that does not exceed 300 mg of caffeine per\\\\nday.\\\\n5\\\\nGiven the publication of recent (2000-2021) studies\\\\nregarding coffee consumption, we review clinical updates\\\\nregarding the impact of coffee consumption on cardio-vascular health. This review focuses on the association\\\\nbetween coffee consumption and cardiovascular disease\\\\u2013\\\\nrelated mortality and morbidity.\\\\nMETHODS\\\\nWe conducted a literature search of the PubMed/\\\\nMEDLINE database for relevant articles using a combina-\\\\ntion of key terms such as \\\\u201ccoffee,\\\\u201d \\\\u201ccoffee consumption,\\\\u201d\\\\u201ccardiovascular diseases,\\\\u201d \\\\u201chypertension,\\\\u201d \\\\u201ccholesterol,\\\\u201d\\\\n\\\\u201cmyocardial infarct,\\\\u201d and \\\\u201catrial fibrillation.\\\\u201d We included\\\\nstudiesthatinvestigatedtheassociationofcoffeeconsump-tion and various cardiac conditions. This narrative review\\\\nsynthesizesfindingsfrompreviousresearchandrecentstud-\\\\nies on the topic.\\\\n152 OchsnerJournal Mendoza, MF\\\\nCOFFEE CONSUMPTION AND HYPERTENSION\\\\nA 1999 meta-analysis of clinical trials by Jee et al\\\\nthat included 11 eligible studies (n =522) revealed a direct\\\\nincreased relationship between coffee consumption and\\\\nblood pressure readings after a 56-day median follow-up.6\\\\nAnoldercohortstudybyJenneretal(1988)thatincluded340\\\\nworking males aged 20 to 45 years old who were not on any\\\\nantihypertensivemedicationfora6-yearperiodrevealedthatsystolic and diastolic changes in blood pressure were both\\\\npositively related to baseline age and weight.\\\\n7In the Jenner\\\\netalstudy,areductionincoffeeconsumptionwasnegativelyassociated with systolic changes in blood pressure.\\\\n7\\\\nHowever, more recent studies have reported contrast-\\\\ning findings. A large cohort study (n =8,780) of middle-\\\\naged adults from Brazil by Miranda et al (2021) showed\\\\nthat those who consumed moderate (1 to 3 cups per day)\\\\namounts of coffee had less risk of developing hyperten-sion than those who never or almost never drank coffee\\\\n(relative risk [RR] =0.82, 95% CI 0.68 to 0.97, P=0.018).\\\\n8\\\\nNotably, these benefits were only observed in those who\\\\nhad never smoked (RR =0.79, 95% CI 0.64 to 0.98) as\\\\nopposed to current and former smokers who did not showa statistically significant reduction in relative risk.\\\\n8In a pilot\\\\ncrossover randomized study by Revuelta-Iniesta and Al-\\\\nDujaili(2014),greencoffeewasfoundtosignificantlyreducesystolic blood pressure ( P=0.02) by a mean of 2.65 \\\\u00b1\\\\n1.37 mm Hg compared to baseline.\\\\n9\\\\nA 2018 review by Fan et al proposed several possible\\\\nmechanisms underlying these results: (1) the augmentation\\\\nofcytochromeP4501A2(CYP1A2)activity(themainenzyme\\\\nfor metabolizing caffeine), which is inversely correlated withblood pressure levels in coffee drinkers who are nonsmok-\\\\ners; (2) the inhibition of sodium and water reabsorption;\\\\nand (3) the inhibition of inflammation, oxidative stress, andtherenin-angiotensin-aldosteronesystem(RAAS)viachloro-\\\\ngenicacid,whichisfoundinhighconcentrationsincoffee.\\\\n10\\\\nIn 2009, the Hypertension and Ambulatory Recording VEne-\\\\ntiaSTudy(HARVEST)foundthattheriskofdevelopinghyper-\\\\ntensionwasdirectlyassociatedwithcoffeeconsumptionbut\\\\nonly in people who possessed the allele CYP1A2 variantfor slow metabolizers (59% of the population); whereas in\\\\nthose who were rapid CYP1A2 metabolizers, coffee con-\\\\nsumption was inversely related to the risk of developinghypertension.\\\\n11\\\\nCOFFEE CONSUMPTION AND CHOLESTEROL\\\\nAs stated previously, boiled or unfiltered coffee is more\\\\natherogenicthanfilteredcoffeebecauseofitsditerpenecon-\\\\ntent. Cafestol and kahweol are 2 diterpenes in coffee bever-ages, with approximately 7.2 mg of each substance per cup\\\\nof boiled coffee.\\\\n12However, paper-filtering coffee removes\\\\nmost of these oils, with only about 0.02 mg of each sub-stance retained per cup.\\\\n12-14Post et al (1997) found that\\\\nditerpenes inhibit bile acid synthesis which leads to atten-\\\\nuated catabolism of lipids.15The researchers observed that\\\\ncafestol suppressed cholesterol 7 \\\\u03b1-hydroxylase and sterol\\\\n27-hydroxylase in rat hepatocytes, while kahweol had less\\\\nsuppressive effects.15\\\\nBecauseboiledcoffeeisknowntohaveatherogeniccapa-\\\\nbilities through cafestol and kahweol, filtered coffee that is\\\\nvirtually devoid of these compounds can exert antiathero-genic properties by increasing high-density lipoprotein\\\\u2013mediated cholesterol efflux from macrophages through the\\\\ninfluenceofplasmaphenolicacid,anothermajorcomponentin coffee beverages. Uto-Kondo et al (2010) concluded that\\\\nplasma phenolic acid is capable of increasing ATP-binding\\\\ncassette transporter ABCG1 and scavenger receptor classB type I (SR-BI) expression, which are responsible for high-\\\\ndensity lipoprotein\\\\u2013mediated cellular cholesterol efflux.\\\\n16\\\\nFurthermore, coffee consumption was observed to have\\\\na direct linear relationship with total cholesterol levels.17\\\\nResearchers later (in 1987 and 1989) found that between\\\\nunfiltered (boiled) and filtered coffee, only boiled coffee\\\\nwas directly associated with an increase in total cholesterol\\\\nlevels.18,19Acrossover,randomized,controlledstudybySar-\\\\nri\\\\u00e1 et al (2018) of 25 normocholesterolemic and 27 hyper-\\\\ncholesterolemic males and females aged 18 to 45 years\\\\nwith body mass index 18 to 25 kg/m2found significant\\\\ndecreases in systolic and diastolic blood pressure ( P=0.001\\\\nandP<0.001,respectively)inbothgroups,aswellasinper-\\\\ncentage of body fat ( P=0.001) after 3 servings per day of a\\\\ngreen/roastedcoffeeblend,providing510.6mghydroxycin-\\\\nnamicacidsand121.2mgcaffeineperday,vsacontroldrink\\\\n(8 weeks each).20Concurrent significant decreases were\\\\nseen in leptin ( P=0.001), plasminogen activator inhibitor 1\\\\n(P<0.001), and resistin ( P=0.034) levels, as well as glucose\\\\nconcentration ( P=0.030), insulin resistance ( P=0.011), and\\\\ntriglyceride levels ( P=0.017) in the 2 groups after coffee\\\\nconsumption, with a notably greater reduction in the hyper-\\\\ncholesterolemic cohort (group effect, P=0.027).20Currently,\\\\nno specific recommendations on the type and ideal amount\\\\nof coffee consumption take advantage of these findings.\\\\nCOFFEE CONSUMPTION, CORONARY HEART\\\\nDISEASE, AND CARDIOVASCULAR DISEASE\\\\nDespite evidence that cholesterol levels seem to be\\\\nincreased by boiled coffee consumption,18,19the associa-\\\\ntion with coronary heart disease seems to be different. In\\\\na prospective cohort study by Lopez-Garcia et al (2006),groups with varying coffee consumption had insignificant\\\\nRRs for coronary heart disease.\\\\n21However, results across\\\\nstudies are inconsistent. In an Italian study by Grioni et al\\\\n(2015) ,the consumption of more than 2 cups per day of\\\\nItalian-style coffee was associated with an increased riskof coronary heart disease.\\\\n12Additionally, a meta-analysis of\\\\n13 case-control and 10 cohort studies by Sofi et al (2007)\\\\nshowed a significant association between high coffee con-sumption and risk of coronary heart disease in the case-\\\\ncontrol studies: >4 cups per day (odds ratio [OR] 1.83, 95%\\\\nCI1.49to2.24, P<0.0001)and3to4cupsperday(OR1.33,\\\\n95% CI 1.04 to 1.71, P<0.0001).\\\\n22In the long-term follow-\\\\nup cohort studies, however, the risk of developing coronary\\\\nheart disease was insignificant for those drinking >4c u p s\\\\nper day (RR 1.16, 95% CI 0.95 to 1.41, P=0.14), 3 to 4 cups\\\\nperday(RR1.05,95%CI0.90to1.22, P=0.57),and /22642cups\\\\nper day (RR 1.04, 95% CI 0.90 to 1.19, P=0.60).22\\\\nInastudybyRodriguez-ArtalejoandL\\\\u00f3pez-Garcia(2018),\\\\nmoderatelevelsofcoffeeconsumption(3to5cupsper day)\\\\nwere associated with a 15% reduction in the risk of car-diovascular disease, and higher levels of intake were not\\\\nshown to increase risk.\\\\n23In a study by Zhou and Hypp\\\\u00f6-\\\\nnen(2019),thosewho didnotdrinkcoffee,thosewho drankdecaffeinatedcoffee,andheavycoffeedrinkers( >6cupsper\\\\nday) had higher odds of developing cardiovascular disease\\\\nVolume23,Number2,Summer2023 153 Coffee Consumption and Cardiovascular Health\\\\nby11%,7%,and22%,respectively( P=0.013)comparedto\\\\nthose who consumed 1 to 2 cups of coffee per day.24\\\\nIn a meta-analysis of 17 studies involving 233,617 partici-\\\\npants,Moetal(2018)notedanincreaseinmyocardialinfarc-\\\\ntionamongmaleswhoconsumed >3cupsofcoffeeperday;\\\\nthis effect was not observed in females.25Inconsistencies\\\\nhave also been seen among elderly males and females. A\\\\nstudybyvanWoudenberghetal(2008)revealedasignificant\\\\nreductionincoronarycalcificationinelderly(meanageof64\\\\nyears) females with moderate (3 to 4 cups per day) and high(>4 cups per day) coffee intake compared to those with a\\\\ndaily intake of /22643c u p s .\\\\n26The investigators speculated that\\\\nthe phytoestrogens in coffee could partly replace estrogenstores in postmenopausal females, leading to a decreased\\\\nincidence of atherosclerosis. This function of phytoestro-\\\\ngen may explain the lack of protective effect of coffee foratherosclerotic calcification in males.\\\\n26\\\\nCornelis et al (2006) shed some light on why these stud-\\\\nies commonly reported a dose-dependent J- or U-shapedcurve.\\\\n27According to their study, the increased risk of coro-\\\\nnary heart disease among boiled (unfiltered) coffee con-\\\\nsumers is associated with diterpenes that increase choles-terol levels and ultimately the risk of coronary heart dis-\\\\nease. However, Cornelis et al noted that the risk of devel-\\\\noping myocardial infarction was not obviated by filteringditerpenoids.\\\\n27Variations in CYP1A2 activity among coffee\\\\nconsumers determined the risk of cardiovascular disease,\\\\nand because CYP1A2 does not metabolize anything else infiltered coffee other than caffeine, the investigators were led\\\\nto believe that caffeine is the major component of filtered\\\\ncoffee that increases the risk of myocardial infarction. Theyproposed that the inhibition of the vasodilatory effects of\\\\nadenosine may play a role in the development of cardio-\\\\nvascular disease. This hypothesis is noteworthy, as coffeedoesnotincreasetheriskofhypertension,possiblyowingto\\\\nits other antihypertensive effects (diuresis, RAAS inhibition,\\\\nand antioxidant properties). Cornelis et al reported that theriskofnonfatalmyocardialinfarctiondependedontheability\\\\nof an individual to metabolize caffeine.\\\\n27CYP1A2 accounts\\\\nfor approximately 95% of caffeine metabolism, and great\\\\nvariability in enzyme activity is observed in individuals. The\\\\ncarriers of the variant allele CYPA12*1F are slow caffeinemetabolizers, while those who are homozygous with the\\\\nCYP1A2*1A allele are rapid metabolizers.\\\\n27This genetic dif-\\\\nference could potentially explain the variable results notedacross studies. The Cornelis et al study indicated a posi-\\\\ntive correlation between increased coffee consumption and\\\\nthe risk of nonfatal myocardial infarction but only in thosewho were slow metabolizers of caffeine.\\\\n27However, when\\\\nsmoking was involved, the results were once again conflict-\\\\ningbecausesmokinginducesCYP1A2activity,andthemag-nitude of CYP1A2 induction was less pronounced in those\\\\nwho had the variant allele CYPA12*IF. The risk of myocar-\\\\ndial infarction was higher in those who were slow caffeinemetabolizers regardless of smoking status. While smoking\\\\nmay appear to decrease the risk of myocardial infarction\\\\nby induction of the homozygous allele, smokers with theCYP1A2*1A allele do not necessarily bode better than slow\\\\nmetabolizers because smoking is an established indepen-\\\\ndentcardiovasculardiseaseriskfactorwithotherpathologicmechanisms beyond the protective effects of CYP1A2 on\\\\ncaffeine regulation.\\\\n27ThegeneticassociationsidentifiedbyCornelisetal27were\\\\nnot observed in the large prospective analysis by Zhou and\\\\nHypp\\\\u00f6nen (2019).24\\\\nResultsfromthesestudiesconflict,andthestudydesigns\\\\ninclude many possible confounders. The standardization of\\\\ncoffee preparation and intake is an important issue becausethe definition of light, moderate, and heavy consumption is\\\\nnot consistent across studies. As such, more studies are\\\\nneeded to reach a solid consensus about the impact of cof-fee consumption on cardiovascular disease, specifically at\\\\nhigher intake levels.\\\\nCOFFEE CONSUMPTION AND\\\\nCARDIOVASCULAR DISEASE POST\\\\nMYOCARDIAL INFARCTION\\\\nIn a study by Silletta et al (2007), no association was\\\\nfound between moderate coffee consumption and cardio-vascular disease events in patients who had had a myocar-\\\\ndial infarction.\\\\n28After a mean follow-up of 3.5 years, coffee\\\\nconsumption did not change the risk of developing coro-nary heart disease, stroke, or sudden cardiac death in those\\\\nwho had previous myocardial infarction. These results are\\\\nnot substantially reliable because the trend finding acrosscategories of coffee consumption was not statistically sig-\\\\nnificant ( P=0.18).\\\\n28A meta-analysis by Brown et al (2016)\\\\nfound a statistically significant inverse correlation betweencoffee consumption and mortality (n =3,271).\\\\n29Light coffee\\\\ndrinkers (1 to 2 cups per day) vs those who did not drink\\\\ncoffeewereassociated withariskratioof0.79(95%CI0.66\\\\nto 0.94, P=0.008), while heavy coffee drinkers ( >2c u p sp e r\\\\nday) vs those who did not drink coffee were associated witha risk ratio of 0.54 (95% CI 0.45 to 0.65, P<0.00001). Heavy\\\\ncoffee drinkers vs light coffee drinkers had a risk ratio of\\\\n0.69 (95% CI 0.58 to 0.83, P<0.0001).\\\\n29These results were\\\\nsupported by a 2020 meta-analysis of 6 prospective stud-\\\\nies showing that coffee consumption was associated with\\\\nlowerriskofcardiovascularmortality(hazardratio[HR]0.70,95% CI 0.54 to 0.91, I\\\\n2=0%; 2 studies) and not associated\\\\nwith an increased risk of all-cause mortality (HR 0.85, 95%\\\\nCI 0.63 to 1.13, I2=50%; 3 studies), recurrent myocardial\\\\ninfarction (HR 0.99, 95% CI 0.80 to 1.22, I2=0%; 3 stud-\\\\nies), or stroke (HR =0.97, 95% CI 0.63 to 1.49, I2=39%;\\\\n2 studies).30\\\\nCOFFEE CONSUMPTION AND HEART FAILURE\\\\nData on diet and food intake from the Framingham Heart\\\\nStudy (FHS), the Cardiovascular Health Study (CHS), and\\\\nthe Atherosclerosis Risk in Communities (ARIC) study werestudied to identify potential lifestyle and behavioral factors\\\\nassociated with heart failure. Stevens et al (2021) showed\\\\naninverseassociationbetweencoffeeconsumptionandtheriskofheartfailureinall3studies.\\\\n31DatafromtheFHS,CHS,\\\\nandARICshowedthathighercoffeeconsumptionwasasso-\\\\nciated with a lower long-term risk of heart failure.31Mostof-\\\\nsky et al (2012) also observed a statistically significant J-\\\\nshaped relationship between coffee consumption and heart\\\\nfailure; those who consumed up to 4 servings of coffee per\\\\nday had a strong inverse relationship with the development\\\\nof heart failure.32Those who tended to consume coffee at\\\\nmuch higher levels (starting at 9 to 10 servings per day) had\\\\na potentially higher risk of heart failure.32Mostofsky et al\\\\nfound no evidence that sex, baseline history of myocardial\\\\n154 OchsnerJournal\", \"chunk_size\": 7134, \"chunk_index\": 0, \"cut_type\": \"sentence_cut\", \"id\": \"38ca4cb2-e6b1-5a03-a313-4b9d66ff16d8\", \"color\": \"#801212\", \"name\": \"38ca4cb2-e6b1-5a03-a313-4b9d66ff16d8\"}, 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\"metadata\": {\"index_fields\": [\"name\"]}, \"type\": \"Entity\", \"name\": \"therese posas-mendoza\", \"description\": \"Co-author of the study on coffee consumption and cardiovascular health.\", \"id\": \"f3c82751-703d-598c-9f2c-332c08ebbb1d\", \"color\": \"#f47710\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"text\"]}, \"type\": \"DocumentChunk\", \"text\": \"Mendoza, MF\\\\ninfarction, or diabetes mellitus affected outcomes.32From\\\\ntheCoronaryArteryRiskDevelopmentinYoungAdultsstudy\\\\n(n=2,735) published by the European Society of Cardiol-\\\\nogy(2020),lowtomoderatecoffeeconsumptionfromyoung\\\\nadulthoodtomiddleagewasassociatedwithbetterleftven-\\\\ntricular systolic and diastolic function.33\\\\nAlthoughresultsseemtobeconsistentacrossstudies,the\\\\npotential mechanisms causing reduction in heart failure risk\\\\nare not well understood. A close look into the biomolecularprocesses is warranted to strengthen causality.\\\\nCOFFEE CONSUMPTION AND ATRIAL\\\\nFIBRILLATION\\\\nBodar et al (2019) found that consumption of 1 to 3\\\\ncups of coffee per day was associated with lower rates of\\\\natrial fibrillation.34After adjusting for age, smoking status,\\\\nalcohol intake, and exercise, those who consumed /22641\\\\ncup per week, 2 to 4 cups per week, and 5 to 6 cups per\\\\nweek were analyzed. In these subgroups, HRs were 0.85(95% CI 0.71 to 1.02), 1.07 (95% CI 0.88 to 1.30), and\\\\n0.93 (95% CI 0.74 to 1.17), respectively. Among those who\\\\nconsumed 1 cup per day, 2 to 3 cups per day, and >4c u p s\\\\nper day, corresponding HRs were 0.85 (95% CI 0.74 to\\\\n0.98), 0.86 (95% CI 0.76 to 0.97), and 0.96 (95% CI 0.80 to\\\\n1.14), respectively, after adjusting for age, smoking, alcohol\\\\nintake, and exercise ( Pfor nonlinear trend =0.01). These\\\\nresults indicate that those who drank 1 to 3 cups of coffeeper day had less risk of atrial fibrillation compared to other\\\\nintakefrequencies.\\\\n34Ameta-analysisofprospectivecohorts\\\\nby Cheng et al (2014) showed an 11% reduction in atrialfibrillation risk for low coffee consumption equivalent to\\\\n<500 mg of caffeine per day (RR 0.89, 95% CI 0.80 to 0.99,\\\\nP=0.032, I\\\\n2=30.9%, P=0.227) and 16% for high coffee\\\\nconsumption equivalent to /2265500 mg of caffeine per day (RR\\\\n0.84, 95% CI 0.75 to 0.94, P=0.002, I2=24.1%, P=0.267)\\\\nafter pooling of results from studies with adjustment ofpotentialconfounders.\\\\n35Atheoryproposedtoexplainthese\\\\nresults is that coffee promotes anti-inflammatory processes\\\\nthrough its high levels of antioxidants such as cafestol,polyphenol, trigonelline, chlorogenic acid, and quinine.\\\\n34,36\\\\nA meta-analysis of 23 randomized controlled trials byAli-Hassan-Sayegh et al (2014) reported that antioxidantssuch as N-acetylcysteine and polyunsaturated fatty acids\\\\nhave a protective role in the prevention of atrial fibrillation\\\\nafter cardiac surgery.\\\\n37Patients who were infused with\\\\nthese antioxidant compounds experienced less incidence\\\\nof atrial fibrillation after cardiac surgery.37These results may\\\\nsuggest that coffee consumption, especially in moderation,may induce anti-inflammatory effects that may attenuate\\\\nthe risk of developing atrial fibrillation.\\\\nCOFFEE CONSUMPTION AND MORTALITY\\\\nA large pool of data indicates that coffee consumption\\\\nis not associated with increased cardiovascular diseasemortality. Results presented by Ding et al (2015) from 3\\\\nwell-known large prospective cohort studies, the Nurses\\\\u2019\\\\nHealthStudy,theHealthProfessionalsFollow-upStudy,and\\\\nthe Nurses\\\\u2019 Health Study-II, showed a nonlinear associa-\\\\ntion between cardiovascular disease mortality and coffeeconsumption.\\\\n38Intheanalysisoftheaforementionedcohort\\\\nstudies, moderate coffee consumption was associated with\\\\nlessmortality,andhigherlevelsofconsumptiondidnotresultin increased deaths after removing the confounding effects\\\\nof smoking history. As such, the nonlinear relationship wasstrengthenedbyremovingtheresidualconfoundingeffectof\\\\nsmoking status. The authors concluded from their analysis\\\\nthat the results extracted from these 3 large cohort studiesindicate that coffee consumption can be incorporated into a\\\\nhealthy lifestyle.\\\\n38\\\\nThe cohort study of Lopez-Garcia et al (2008) revealed\\\\naninverserelationshipbetweencoffeeconsumptionandall-\\\\ncause mortality, principally because of a moderate reduc-tion in risk for cardiovascular disease\\\\u2013related mortality in\\\\nboth males ( Pfor trend =0.008) and females ( Pfor trend\\\\n<0.001).\\\\n39The authors noted that a possible mechanism\\\\nfor such an outcome was the strong antioxidant capacity of\\\\ncoffee compounds other than caffeine such as chlorogenic\\\\nacid,ferulicacid,andp-Coumaricacid.Theyalsonotedthatother substances in coffee such as magnesium, trigonelline,\\\\nand quinides improve insulin sensitivity. Despite the poten-\\\\ntial harmful effects of caffeine and its ability to releaseepinephrine(astronginhibitorofinsulin),theaforementioned\\\\ncompoundsappeartocounterbalancethiseffect.\\\\n39Inalarge\\\\nprospective cohort study conducted by de Koning Ganset al (2010), the consumption of black tea and coffee was\\\\nassociated with a lower incidence of coronary heart disease\\\\nmortality.\\\\n40Andersen et al (2006) reported that consump-\\\\ntion of 1 to 3 cups of coffee per day was associated with\\\\na lower incidence of cardiovascular disease\\\\u2013related mortal-\\\\nity(HR0.76,95%CI0.64to0.91, P=0.005)infemalescom-\\\\nparedtoconsumptionof >4cupsperday .41Anearlierstudy\\\\nby Kleemola et al (2000) noted a decrease in total mortal-\\\\nity among females drinking >7c u p so fc o f f e ep e rd a y( r i s k\\\\nratio0.62,95%CI0.44to0.87),evenafteradjustingforage,\\\\nsmoking status, serum cholesterol level, blood pressure,\\\\nand history of myocardial infarction.42Lopez-Garcia et al\\\\n(2008)foundareductioninRRforall-causemortalityamong\\\\nfemales: RR of 0.93 (95% CI 0.87 to 0.98) for those drink-\\\\ning 5 to 7 cups per week; RR of 0.82 (95% CI 0.77 to 0.87)for those drinking 2 to 3 cups per day; RR of 0.74 (95% CI\\\\n0.68to0.81)forthosedrinking4to5cupsperday;andRRof\\\\n0.83(95%CI0.73to0.95)forthosedrinking /22656cupsperday\\\\n(Pfor trend <0.001).\\\\n39In fact, most studies show an overall\\\\nreductioninmortality,althoughsomestudieshaveproducedconflicting results. The FHS showed that coffee consump-\\\\ntion in the elderly population was associated with a 43%\\\\nreduction in coronary heart disease\\\\u2013related deaths.\\\\n31Fur-\\\\nthermore, a large meta-analysis (40 studies, n =3,852,651)\\\\nby Kim et al (2019) revealed that coffee consumption was\\\\ninverselyrelatedtoall-causemortality.43Thetotalnumberof\\\\ndeaths from all categories was 450,256; among coffee con-\\\\nsumers, the intakes with the lowest RRs were 3.5 cups per\\\\ndayforall-causemortality(RR0.85,95%CI0.82to0.89),2.5cups per day for cardiovascular disease mortality (RR 0.83,\\\\n95% CI 0.80 to 0.87), and 2 cups per day for cancer mortal-\\\\nity (RR0.96, 95% CI, 0.94 to 0.99). The inverse relationshipbetween mortality and coffee consumption in nonsmokers\\\\n(RR 0.95, 95% CI 0.93 to 0.97) was slightly stronger than in\\\\nsmokers (RR 0.97, 95% CI 0.96 to 0.99), although the differ-ence was not statistically significant ( P=0.33). No additional\\\\nbenefit was seen with additional caffeine intake. In conclu-\\\\nsion, moderate coffee consumption was deemed beneficialto overall health. However, the associations were stronger\\\\nin Europeans and Asians compared to Americans living in\\\\nVolume23,Number2,Summer2023 155 Coffee Consumption and Cardiovascular Health\\\\ntheUnitedStates.43Studiesareneededtounderstandthese\\\\ndemographic differences.\\\\nDISCUSSION\\\\nCoffee has the physiologic effect of raising blood pres-\\\\nsure, although the effect appears to be transient and doesnot affect the propensity to develop overt hypertension.\\\\nLikewise, data have shown that moderate consumption\\\\nof coffee is associated with less risk of hypertension butprincipally in those who never smoked or do not smoke and\\\\nin those who are fast metabolizers of caffeine. Boiled coffee\\\\nis atherogenic because of its rich diterpene content, namelycafestol and kahweol, that inhibits bile acid synthesis and\\\\nultimately affects lipid metabolism. On the other hand,\\\\nfiltered coffee, which is essentially devoid of the aforemen-tioned compounds, exerts antiatherogenic properties by\\\\nincreasing high density lipoprotein\\\\u2013mediated cholesterol\\\\nefflux from macrophages through the influence of plasmaphenolic acid. As such, cholesterol levels are influenced\\\\nby the manner of coffee preparation (boiled vs filtered).\\\\nIn terms of the risk of developing cardiovascular disease,studies are inconsistent with regard to coffee consumption\\\\nand risk of coronary heart disease, with discrepancies\\\\nnoted depending on sex, genetics, and smoking status. Themajority of studies showed a J-shape association in which\\\\nmoderate coffee consumption was associated with a lower\\\\nrisk of coronary heart disease compared to heavy coffee\\\\nconsumption which was associated with an increased\\\\nrisk of coronary heart disease. These findings point to theimportance of moderate coffee consumption because of\\\\nthe potential risk of cardiovascular disease. Regarding heart\\\\nfailure, results appear to be consistent across studies. TheFHS,CHS,andARICstudiesshowedthathighcoffeeintake\\\\nwas associated with a decrease in long-term risk of heart\\\\nfailure independent of sex, baseline history of myocardialinfarction, and diabetes. Because of the lack of understand-\\\\ningofpotentialmechanismsbehindreductioninheartfailure\\\\nrisk, more studies are needed. Moderate coffee consump-tion was also found to attenuate the risk of atrial fibrillation,\\\\npossibly owing to its strong anti-inflammatory components\\\\nsuch as cafestol, polyphenol, trigonelline, chlorogenic acid,and quinide. Studies have shown moderate coffee con-\\\\nsumption to be associated with a reduction in all-cause\\\\nand cardiovascular disease\\\\u2013related mortality, whereashigher amounts of coffee consumption were detrimental\\\\nto health.\\\\nCONCLUSION\\\\nOur review suggests that moderate coffee consumption\\\\nis associated with a decrease in all-cause and cardiovas-\\\\ncular disease\\\\u2013related mortality, hypertension, cholesterol,heartfailure,andatrialfibrillation,whileconsensusislacking\\\\nregarding the association between coffee consumption and\\\\ntheriskofdevelopingcardiovasculardisease.Despiteprevi-ous concerns about coffee consumption being a significant\\\\ncoronaryheartdiseaseriskfactor,mostmodernprospective\\\\ncohort meta-analyses found no association between coffee\\\\nconsumption and coronary heart disease. However, results\\\\nare inconsistent across studies. Most favorable outcomesareassociatedwithmoderatecoffeeconsumption;however,\\\\nthere is no current consensus on the definition of moderate\\\\ncoffee consumption. Further, genetics possibly play a largeroleindetermininghypertensionandcardiovasculardisease\\\\noutcomes. This review illustrates that coffee is a complexmixture of compounds that may cause both harm and ben-\\\\nefit. As such, additional studies are needed to further eluci-\\\\ndate the ideal way to consume coffee, not only as a drinkto be enjoyed, but also as a drink with protective health\\\\nbenefits.\\\\nACKNOWLEDGMENTS\\\\nThe authors have no \\\\ufb01nancial or proprietary interest in the\\\\nsubject matter of this article.\\\\nREFERENCES\\\\n1. RobertsonD,Fr\\\\u00f6lichJC,CarrRK,etal.Effectsofcaffeineon\\\\nplasmareninactivity,catecholaminesandbloodpressure. N\\\\nEnglJMed .1978;298(4):181-186.\\\\ndoi:10.1056/NEJM197801262980403\\\\n2. 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BrownOI,AllgarV,WongKY.Coffeereducestheriskofdeath\\\\nafteracutemyocardialinfarction:ameta-analysis. CoronArtery\\\\nDis.2016;27(7):566-572.doi:10.1097/MCA.000000000000039730. RibeiroEM,AlvesM,CostaJ,FerreiraJJ,PintoFJ,CaldeiraD.\\\\nSafetyofcoffeeconsumptionaftermyocardialinfarction:asystematicreviewandmeta-analysis. NutrMetabCardiovasc\\\\nDis.2020;30(12):2146-2158.doi:10.1016/j.numecd.2020.07.016\\\\n31. StevensLM,LinsteadE,HallJL,KaoDP.Associationbetween\\\\ncoffeeintakeandincidentheartfailurerisk:amachinelearning\\\\nanalysisoftheFHS,theARICstudy,andtheCHS. CircHeartFail .\\\\n2021;14(2):e006799.doi:10.1161/CIRCHEARTFAILURE.119.006799\\\\n32. MostofskyE,RiceMS,LevitanEB,MittlemanMA.Habitual\\\\ncoffeeconsumptionandriskofheartfailure:adose-response\\\\nmeta-analysis. CircHeartFail .2012;5(4):401-405.\\\\ndoi:10.1161/CIRCHEARTFAILURE.112.967299\\\\n33. NwabuoCC,BetokoAS,ReisJP,etal.Coffeeandtea\\\\nconsumptionintheearlyadultlifespanandleftventricularfunctioninmiddleage:theCARDIAstudy. ESCHeartFail .\\\\n2020;7(4):1510-1519.doi:10.1002/ehf2.12684\\\\n34. BodarV,ChenJ,GazianoJM,AlbertC,Djouss\\\\u00e9L.Coffee\\\\nconsumptionandriskofatrialfibrillationinthePhysicians\\\\u2019\\\\nHealthStudy. JAmHeartAssoc .2019;8(15):e011346.\\\\ndoi:10.1161/JAHA.118.011346\\\\n35. ChengM,HuZ,LuX,HuangJ,GuD.Caffeineintakeandatrial\\\\nfibrillationincidence:doseresponsemeta-analysisof\\\\nprospectivecohortstudies. CanJCardiol .2014;30(4):448-454.\\\\ndoi:10.1016/j.cjca.2013.12.026\\\\n36. HabauzitV,MorandC.Evidenceforaprotectiveeffectof\\\\npolyphenols-containingfoodsoncardiovascularhealth:an\\\\nupdateforclinicians. TherAdvChronicDis .2012;3(2):87-106.\\\\ndoi:10.1177/2040622311430006\\\\n37. Ali-Hassan-SayeghS,MirhosseiniSJ,RezaeisadrabadiM,etal.\\\\nAntioxidantsupplementationsforpreventionofatrialfibrillationaftercardiacsurgery:anupdatedcomprehensive\\\\nsystematicreviewandmeta-analysisof23randomized\\\\ncontrolledtrials. InteractCardiovascThoracSurg .\\\\n2014;18(5):646-654.doi:10.1093/icvts/ivu020\\\\n38. DingM,SatijaA,BhupathirajuSN,etal.Associationofcoffee\\\\nconsumptionwithtotalandcause-specificmortalityin3largeprospectivecohorts. Circulation .2015;132(24):2305-2315.\\\\ndoi:10.1161/CIRCULATIONAHA.115.017341\\\\n39. Lopez-GarciaE,vanDamRM,LiTY,Rodriguez-ArtalejoF,Hu\\\\nFB.Therelationshipofcoffeeconsumptionwithmortality. Ann\\\\nInternMed .2008;148(12):904-914.\\\\ndoi:10.7326/0003-4819-148-12-200806170-00003\\\\n40. deKoningGansJM,UiterwaalCS,vanderSchouwYT,etal.Tea\\\\nandcoffeeconsumptionandcardiovascularmorbidityand\\\\nmortality. ArteriosclerThrombVascBiol .2010;30(8):1665-1671.\\\\ndoi:10.1161/ATVBAHA.109.201939\\\\n41. AndersenLF,JacobsDRJr,CarlsenMH,BlomhoffR.\\\\nConsumptionofcoffeeisassociatedwithreducedriskofdeath\\\\nattributedtoinflammatoryandcardiovasculardiseasesintheIowaWomen\\\\u2019sHealthStudy. AmJClinNutr .\\\\n2006;83(5):1039-1046.doi:10.1093/ajcn/83.5.1039\\\\n42. KleemolaP,JousilahtiP,PietinenP,VartiainenE,TuomilehtoJ.\\\\nCoffeeconsumptionandtheriskofcoronaryheartdiseaseanddeath.ArchInternMed .2000;160(22):3393-3400.\\\\ndoi:10.1001/archinte.160.22.3393\\\\n43. KimY,JeY,GiovannucciE.Coffeeconsumptionandall-cause\\\\nandcause-specificmortality:ameta-analysisbypotential\\\\nmodifiers. EurJEpidemiol .2019;34(8):731-752.\\\\ndoi:10.1007/s10654-019-00524-3\\\\nVolume23,Number2,Summer2023 157 Coffee Consumption and Cardiovascular Health\\\\nThis article meets the Accreditation Council for Graduate Medical Education and the American Board of Medical\\\\nSpecialties Maintenance of Certi\\\\ufb01cation competencies for Patient Care and Medical Knowledge.\\\\n\\\\u00a92023 by the author(s); licensee Ochsner Journal, Ochsner Clinic Foundation, New Orleans, LA. This article is an open\\\\naccess article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license\\\\n(creativecommons.org/licenses/by/4.0/legalcode) that permits unrestricted use, distribution, and reproduction inany medium, provided the original author(s) and source are credited.\\\\n158 OchsnerJournal\", \"chunk_size\": 7998, \"chunk_index\": 1, \"cut_type\": \"sentence_cut\", \"id\": \"7099f518-eb15-5a5d-9b82-863650115f7e\", \"color\": \"#801212\", \"name\": \"7099f518-eb15-5a5d-9b82-863650115f7e\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"name\"]}, \"type\": \"Entity\", \"name\": \"mortality\", \"description\": \"The state of being subject to death; often used in relation to cause-specific death rates.\", \"id\": \"9e22bd5f-12ad-58c0-9298-903b1b5cff4a\", \"color\": \"#f47710\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"name\"]}, \"type\": \"Entity\", \"name\": \"diabetes mellitus\", \"description\": \"A chronic condition that affects how the body processes blood sugar (glucose).\", \"id\": \"d5371db8-e657-54e2-9d0b-010b5d066f6b\", \"color\": \"#f47710\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"name\"]}, \"type\": \"Entity\", \"name\": \"meta-analysis\", \"description\": \"A statistical analysis that combines the results of multiple scientific studies to provide a more robust conclusion.\", \"id\": \"d55fc944-aaf8-5e42-842a-8e4f82df5853\", \"color\": \"#f47710\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"name\"]}, \"type\": \"EntityType\", \"name\": \"research methodology\", \"description\": \"research methodology\", \"id\": \"e4b65bec-0973-5c51-a6b8-2ddeeddcd80f\", \"color\": \"#6510f4\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"name\"]}, \"type\": \"Entity\", \"name\": \"antioxidants\", \"description\": \"Molecules that inhibit the oxidation of other molecules, potentially preventing cellular damage and various diseases.\", \"id\": \"794ae1c2-a7fc-5dce-a8be-cc0caf0652dc\", \"color\": \"#f47710\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"name\"]}, \"type\": \"Entity\", \"name\": \"infarction\", \"description\": \"Tissue death due to a lack of blood supply, often referring to myocardial infarction (heart attack).\", \"id\": \"21f02456-6126-5fa6-b037-93f64bf7359c\", \"color\": \"#f47710\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"name\"]}, \"type\": \"Entity\", \"name\": \"mendoza, mf\", \"description\": \"Author contributing to the study on coffee consumption and cardiovascular health.\", \"id\": \"e1031297-63ce-5f88-bafc-b457dcb264b3\", \"color\": \"#f47710\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"name\"]}, \"type\": \"Entity\", \"name\": \"oxidative stress\", \"description\": \"An imbalance between free radicals and antioxidants in the body, which can contribute to various diseases.\", \"id\": \"8d0d2ce2-2056-5577-aae7-25568c4991cf\", \"color\": \"#f47710\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"name\"]}, \"type\": \"Entity\", \"name\": \"left ventricular function\", \"description\": \"The performance of the left ventricle of the heart, crucial for effective blood circulation.\", \"id\": \"5e753c37-5f3f-5a9b-b24d-501a87148cc9\", \"color\": \"#f47710\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"text\"]}, \"type\": \"DocumentChunk\", \"text\": \"nutrients\\\\nArticle\\\\nCoffee Consumption and All-Cause, Cardiovascular, and\\\\nCancer Mortality in an Adult Mediterranean Population\\\\nLaura Torres-Collado1,2,3\\\\n, Laura Mar \\\\u00eda Compa\\\\u00f1-Gabucio1,2,3\\\\n, Sandra Gonz \\\\u00e1lez-Palacios1,2,3\\\\n,\\\\nLeyre Notario-Barandiaran1,2,3, Alejandro Oncina-C \\\\u00e1novas1,2,3\\\\n, Jes\\\\u00fas Vioque1,2,3,*\\\\nand Manuela Garc \\\\u00eda-de la Hera1,2,3\\\\n/gid00030/gid00035/gid00032/gid00030/gid00038/gid00001/gid00033/gid00042/gid00045 /gid00001\\\\n/gid00048/gid00043/gid00031/gid00028/gid00047/gid00032/gid00046\\\\nCitation: Torres-Collado, L.;\\\\nCompa\\\\u00f1-Gabucio, L.M.;\\\\nGonz\\\\u00e1lez-Palacios, S.;\\\\nNotario-Barandiaran, L.;\\\\nOncina-C\\\\u00e1novas, A.; Vioque, J.;\\\\nGarc\\\\u00eda-de la Hera, M. Coffee\\\\nConsumption and All-Cause,\\\\nCardiovascular, and Cancer Mortality\\\\nin an Adult Mediterranean\\\\nPopulation. Nutrients 2021 ,13, 1241.\\\\nhttps://doi.org/10.3390/nu13041241\\\\nAcademic Editor: Stefano Realdon\\\\nReceived: 17 March 2021\\\\nAccepted: 7 April 2021\\\\nPublished: 9 April 2021\\\\nPublisher\\\\u2019s Note: MDPI stays neutral\\\\nwith regard to jurisdictional claims in\\\\npublished maps and institutional af\\\\ufb01l-\\\\niations.\\\\nCopyright: \\\\u00a9 2021 by the authors.\\\\nLicensee MDPI, Basel, Switzerland.\\\\nThis article is an open access article\\\\ndistributed under the terms and\\\\nconditions of the Creative Commons\\\\nAttribution (CC BY) license (https://\\\\ncreativecommons.org/licenses/by/\\\\n4.0/).1Instituto de Investigaci \\\\u00f3n Sanitaria y Biom \\\\u00e9dica de Alicante, ISABIAL-UMH, 03010 Alicante, Spain;\\\\nl.torres@umh.es (L.T.-C.); lcompan@umh.es (L.M.C.-G.); sandra.gonzalezp@umh.es (S.G.-P .);\\\\nlnotario@umh.es (L.N.-B.); aoncina@umh.es (A.O.-C.); manoli@umh.es (M.G.-d.l.H.)\\\\n2Unidad de Epidemiolog \\\\u00eda de la Nutrici \\\\u00f3n, Departamento de Salud P \\\\u00fablica, Historia de la Ciencia y\\\\nGinecolog \\\\u00eda, Universidad Miguel Hern \\\\u00e1ndez (UMH), 03550 Alicante, Spain\\\\n3CIBER Epidemiolog \\\\u00eda y Salud P \\\\u00fablica (CIBERESP), Instituto de Salud Carlos III, 28034 Madrid, Spain\\\\n*Correspondence: vioque@umh.es; Tel.: +34-965-919-517\\\\nAbstract: We assessed the association between usual coffee consumption and all-cause, cardiovascu-\\\\nlar (CV), and cancer mortality in an adult population in Spain, taking into account both the amount\\\\nand type of coffee consumed. We used baseline data on coffee consumption and other personal\\\\nvariables, and the number of deaths during an 18-year follow-up period, for 1567 participants aged\\\\n20 years and older from the Valencia Nutrition Study in Spain. Total, caffeinated, and decaffeinated\\\\ncoffee consumption was assessed using a validated food frequency questionnaire. Cox regression\\\\nmodels were used to estimate adjusted hazard ratios (HRs) and 95% con\\\\ufb01dence intervals (CIs).\\\\nDuring the 18-year follow-up period, 317 died; 115 due to CV disease and 82 due to cancer. Com-\\\\npared with no-consumption, the consumption of \\\\u22641 cup per day and >1 cup per day of coffee was\\\\nassociated with a lower risk of all-cause mortality, HR = 0.73 (95% CI: 0.56\\\\u20130.97) and HR 0.56 (95% CI:\\\\n0.41\\\\u20130.77), respectively. A lower cancer mortality was observed among drinkers of more than 1 cup\\\\nper day compared with nondrinkers, HR 0.41 (95% CI 0.20\\\\u20130.86). Regarding the type of coffee, only\\\\nthe overall consumption of caffeinated coffee was associated with lower all-cause mortality at 12 and\\\\n18 years of follow-up, HR = 0.66 (95% CI:0.46\\\\u20130.94) and HR = 0.59 (95% CI: 0.44\\\\u20130.79), respectively.\\\\nIn conclusion, this study suggests that the moderate consumption of coffee, particularly caffeinated\\\\ncoffee (range 1\\\\u20136.5 cups per day), is associated with a lower all-cause and cancer mortality after\\\\na long follow-up period. No signi\\\\ufb01cant association was found between coffee consumption and\\\\nCVD mortality.\\\\nKeywords: coffee; caffeinated; decaffeinated; mortality; cardiovascular disease; cancer\\\\n1. Introduction\\\\nCoffee consumption is very prevalent worldwide and it has been associated with\\\\nlower total mortality, although the association is not fully consistent and the evidence\\\\nfrom Mediterranean countries is still scarce [ 1]. Coffee consumption has been associated\\\\nwith increased low-density lipoprotein (LDL-c) concentration [ 2], insulin resistance [ 3],\\\\nincreased blood pressure [ 4] and higher risk of some cardiovascular diseases (CVD) [ 4,5],\\\\nalthough no long-term adverse effects have been consistently found with its consumption.\\\\nMost of the recently published studies have reported inverse associations between habitual\\\\ncoffee consumption and the incidence of some diseases such as type 2 diabetes [ 6,7], mental\\\\nillness [ 8,9], cardiovascular diseases [ 10\\\\u201312], and cancer [ 10,13,14], all of which are major\\\\ncauses of mortality.\\\\nThese \\\\ufb01ndings are in agreement with the results obtained by Kim et al. [ 1] in a recent\\\\nmeta-analysis that included 40 studies and 3,852,651 subjects from different countries. In\\\\nNutrients 2021 ,13, 1241. https://doi.org/10.3390/nu13041241 https://www.mdpi.com/journal/nutrients Nutrients 2021 ,13, 1241 2 of 13\\\\nthis meta-analysis, a non-linear association between coffee consumption and mortality\\\\nfrom all causes, CVD, and cancer mortality was shown, with the lowest cancer mortality\\\\nobserved for the intake of two cups per day (RR = 0.96), the lowest CVD mortality for\\\\n2.5 cups per day (RR = 0.83), and the lowest all-cause mortality for 3.5 cups per day\\\\n(RR = 0.85), with no additional reduction or increase in mortality with increasing coffee\\\\nconsumption [1].\\\\nThe mechanisms by which coffee may reduce the risk of death are not well known,\\\\nalthough it could be due to the antioxidant and anti-in\\\\ufb02ammatory effects of some of their\\\\ncomponents [ 10,11]. Coffee is rich in polyphenols, a group of compounds with antiox-\\\\nidant and anti-in\\\\ufb02ammatory activity which can be divided according to their chemical\\\\nstructure into \\\\ufb02avonoids and non-\\\\ufb02avonoids [ 15,16]. Some meta-analyses have shown that\\\\n\\\\ufb02avonoids and some non-\\\\ufb02avonoids such as lignans with weak estrogen-like activity may\\\\nhave bene\\\\ufb01cial effects against cardiovascular disease and some cancers [ 15], although more\\\\nevidence on speci\\\\ufb01c compounds is still needed.\\\\nEvidence found in the few studies that have examined the role of coffee consump-\\\\ntion on all-cause, CVD, and cancer mortality in Mediterranean populations with high\\\\nlife-expectancy and healthy diets is still insuf\\\\ufb01cient. To the best of our knowledge, only\\\\ntwo studies have speci\\\\ufb01cally evaluated the association between coffee consumption and\\\\nmortality in adults in Spain [ 17,18], and both have shown an inverse association between\\\\ncoffee consumption and total and CVD mortality [ 17,18]. In addition, in a recently pub-\\\\nlished study with adults in Italy, a moderate consumption of 3\\\\u20134 cups/day of coffee was\\\\nassociated with lower risk of all-cause and CVD mortality [ 19]. Thus, we assessed the\\\\nassociation between coffee consumption and all-cause, CVD, and cancer mortality in a\\\\nrepresentative sample of an adult population in Valencia, Spain, taking into account both\\\\nthe amount and type of coffee.\\\\n2. Materials and Methods\\\\n2.1. Study Design and Population\\\\nData for this study came from Valencia Nutrition Survey (VNS) conducted in 1994.\\\\nSurvey methods have been described in detail elsewhere [ 20]. Brie\\\\ufb02y, the VNS was a\\\\nhealth, nutrition, and examination survey based on a representative sample, which en-\\\\nrolled 1811 adults in the Valencia Region aged 15 years and older (74.4% participation\\\\nrate). Participants younger than 20 years and those with no information regarding cof-\\\\nfee consumption were excluded from the present analysis. Thus, the \\\\ufb01nal analysis was\\\\nconducted with 1567 participants aged 20 years and above with complete information\\\\n(718 men ,849 women ). We obtained written informed consent from all participants, and\\\\nthe Ethical Committees of the Hospital of San Juan and the Miguel Hernandez University\\\\napproved the study.\\\\n2.2. Coffee and Dietary Assessment\\\\nWe collected the dietary information using a validated semi-quantitative food fre-\\\\nquency questionnaire (FFQ). This FFQ was similar to the Willett questionnaire [ 21], which\\\\nwas adapted and validated in adult and elderly populations in Spain [ 22]. We used the FFQ\\\\nin the VNS that had 93 food items and included nine sections for the main food groups:\\\\ndairy, eggs, meat and \\\\ufb01sh, vegetables, fruits, breads and cereals, oils and fats, sweets and\\\\npastry, beverages, and processed foods. The validity and reproducibility of the FFQ has\\\\nbeen described previously [ 22], which showed satisfactory reproducibility and validity. We\\\\ncompared the nutrients and food intake estimates in the adult population with those from\\\\nfour one-week dietary records. The average correlation coef\\\\ufb01cients for one-year validity\\\\nand reproducibility of nutrient intakes were 0.47 and 0.40, respectively. We observed a\\\\ngood reproducibility for total coffee consumption, with a correlation coef\\\\ufb01cient of 0.60.\\\\nWe asked subjects in our study how often, on average, they had consumed a standard\\\\nportion size of each food item during the previous year. The FFQ had nine possible con-\\\\nsumption frequencies, ranging from \\\\u201cnever or less than once per month\\\\u201d to \\\\u201csix or more per Nutrients 2021 ,13, 1241 3 of 13\\\\nday\\\\u201d. Two items were included to collect information about coffee consumption: one item\\\\nfor caffeinated coffee, and another item for decaffeinated coffee. We de\\\\ufb01ned a cup of coffee\\\\nusing typical sizes (50 mL for espresso, or 125\\\\u2013150 mL for instant/brewed/ground coffee)\\\\nand we calculated total coffee consumption in cups per day as the sum of decaffeinated and\\\\ncaffeinated coffee. We classi\\\\ufb01ed participants according to their total coffee consumption as\\\\nnon-drinkers, drinkers of \\\\u22641 cup/day, and drinkers of >1 cup/day.\\\\nAdherence to a Mediterranean diet (MD) was estimated for each subject using the\\\\nrelative Mediterranean diet score (rMED) [ 23], which is a variation of the original Mediter-\\\\nranean diet score [ 24,25]. Instead of using the median to score each component, in the rMED,\\\\nthe intake in grams of each component (except for alcohol) is referred to per 1000 kcals/day\\\\nand divided into tertiles. We assigned values of 0, 1, and 2 to the \\\\ufb01rst, second, and third\\\\ntertiles of intake, respectively, for the six components that form the MD. The six categories\\\\nincluded fruits (including seeds and nuts), vegetables (excluding potatoes), \\\\ufb01sh, legumes,\\\\nolive oil, and cereals (including whole grain). Dairy products and total meat (including\\\\nprocessed meat) were negatively scored, probably because these components do not \\\\ufb01t\\\\nthe MD (lower scoring for the higher intakes). Owing to the assumed bene\\\\ufb01cial effects of\\\\nmoderate alcohol consumption, we calculated it as a dichotomous variable: 2 points for\\\\nmoderate consumption (5\\\\u201325 g/day for women and 10\\\\u201350 g/day for men), and 0 points for\\\\nhigher or lower consumption. Finally, the rMED score was estimated for each participant\\\\nby adding up the points of the 9 components. The scores ranged from 0\\\\u20136 points (low\\\\nadherence), 7\\\\u201310 (medium adherence), to 11\\\\u201318 points (high adherence). Nutrient values\\\\nand energy intake were obtained from food composition tables from the U.S. Department\\\\nof Agriculture [26] and other published Spanish sources [27].\\\\n2.3. Assessment of Mortality\\\\nWe checked the information on the date and cause of deaths through the National\\\\nDeath Index from the Spanish Statistical Of\\\\ufb01ce and the Mortality Registry in the Valencia\\\\nRegion during the 18-year follow-up period.\\\\nWe coded all causes of death according to version 10 of the International Classi\\\\ufb01ca-\\\\ntion of Diseases (ICD \\\\u221210). Due to the small number of deaths, we grouped deaths in\\\\nthree major categories, which included cardiovascular disease (ICD \\\\u221210: I00\\\\u2013I99), cancer\\\\n(ICD\\\\u221210 codes: C00\\\\u2013D49 ), and all-cause mortality. All-cause mortality category included\\\\ndeaths occurring from any cause as well as the \\\\ufb01rst two categories.\\\\n2.4. Other Variables\\\\nTrained \\\\ufb01eldworkers collected baseline information from all participants on socio-\\\\ndemographic and other lifestyles variables, including smoking habits, alcohol consumption,\\\\nhealth status, physical activity, and chronic diseases, using structured questionnaires.\\\\nThe following variables were considered in the analyses: sex (men, women), age\\\\n(in years), educational level (<primary school; \\\\u2265primary school), body mass index (BMI)\\\\nmeasured as weight in kilograms divided by the square of measured height in meters\\\\n(<25 kg/m2, 25\\\\u201330 kg/m2,\\\\u226530 kg/m2), waist circumference (healthy range: 78\\\\u201394 cm in\\\\nmen and 64\\\\u201380 cm in women; moderate risk: 94\\\\u2013102 cm in men and 80\\\\u201388 cm in women;\\\\nand increased risk: >102 cm in men and >88 cm in women) [ 28], smoking status (never,\\\\nex-smoker, current), self-reported main physical activity at leisure-time (low, moderate\\\\n\\\\u2013vigorous), total hours of TV watching per day, and total sleeping time in hours per day.\\\\nWe also collected the presence of pre-existing chronic disease at baseline, diabetes (no/yes),\\\\nhigh blood cholesterol (no/yes), and high blood pressure(no/yes). In the adult population,\\\\nprevious studies have shown that a high level of agreement has been observed between\\\\nself-reported diseases and those documented in the medical records [29,30]. Nutrients 2021 ,13, 1241 4 of 13\\\\n2.5. Statistical Analysis\\\\nStatistical tests were bilateral, and signi\\\\ufb01cation was established at 0.05. We performed\\\\nthe analysis with the statistical software R.3.3.2 (R Foundation for Statistical Computing,\\\\nVienna, Austria, http://www.r-project.org, accessed on 1 April 2020)\\\\nWe classi\\\\ufb01ed participants according to their total coffee consumption as non-drinkers,\\\\ndrinkers of up to 1 cup per day (range 0.1\\\\u20131.0 cups), and drinkers of more than 1 cup per day\\\\n(range 1.1\\\\u20136.5). We also classi\\\\ufb01ed participants by the type of coffee in no coffee consump-\\\\ntion, caffeinated, or decaffeinated consumption. Descriptive analysis of socio-demographic\\\\nfactors was performed between different coffee consumption using percentages and Chi-\\\\nsquared tests to describe and compare categorical variables, and for continuous variables,\\\\nwe used means, standard deviations, and ANOVA tests.\\\\nWe estimated person-years for each participant of follow-up from the date of the\\\\ninterview at baseline to the date of death or completion of the 6-, 12- and 18-year follow-up,\\\\nwhichever came \\\\ufb01rst. We analyzed the association and risk of mortality at 6, 12 and 18 years\\\\nof follow-up (ad hoc division) and total, caffeinated, and decaffeinated coffee consumption\\\\nto explore the potential short, medium, and long-term effects of coffee, adjusting for other\\\\nvariables. We obtained hazard ratios (HRs) and 95% con\\\\ufb01dence intervals (95%CI) by Cox\\\\u2019s\\\\nproportional hazard for each category of coffee consumption in comparison to the lower\\\\ncategory (no consumption, \\\\u22641 cup/day, >1 cup/day) from all causes of mortality, CVD,\\\\nand cancer mortality.\\\\nTwo models were presented, one adjusted for age and sex, and multivariable analyses\\\\nwere performed, in which we further adjusted for several factors considered as potential\\\\nconfounders established in the literature and those variables showing p-values < 0.20 in\\\\nbivariate analysis. We adjusted by: sex, age (in years), education level (<primary school;\\\\n\\\\u2265primary school), BMI (<25 kg/m2, 25\\\\u201330 kg/m2,\\\\u226530 kg/m2), waist circumference\\\\n(healthy range: 78\\\\u201394 cm in men and 64\\\\u201380 cm in women; moderate risk: 94\\\\u2013102 cm in men\\\\nand 80\\\\u201388 cm in women; and increased risk: >102 cm in men and >88 cm in women) [ 28],\\\\nsmoking (never, ex-smoker, current), self-reported main physical activity at leisure-time\\\\n(very low, mostly sitting position; low, moderate\\\\u2013vigorous), adherence to a Mediterranean\\\\ndiet (rMED), hours of TV watching per day, total sleeping time in hours per day, and\\\\ndiabetes (no/yes), high blood cholesterol (no/yes), and high blood pressure (no/yes).\\\\nThe non-zero slope of the scaled Schoenfeld residuals on the time function suggested\\\\nthat the proportional hazard assumption was met. We calculated the likelihood ratio test\\\\n(LRT) to estimate the overall signi\\\\ufb01cance of coffee consumption as a categorical variable,\\\\nand we calculated trend tests to evaluate the dose\\\\u2013response for total coffee consumption as\\\\na continuous term.\\\\n3. Results\\\\nThe main characteristics of the study population according to coffee consumption\\\\nare shown in Table 1. Of 1567 participants, 78% were coffee drinkers, of whom 37.7%\\\\nwere drinkers of up to 1 cup per day, and 40.3% reported drinking more than one cup of\\\\ncoffee per day. In general, participants who consumed >1 cup/daily were more likely to be\\\\ncurrent smokers, have a higher education, spend less time watching television, and have a\\\\nlower prevalence of self-reported diabetes and hypertension.\", \"chunk_size\": 6764, \"chunk_index\": 0, \"cut_type\": \"sentence_end\", \"id\": \"66f8c67a-fe9c-5d4d-8590-5defa26d1f33\", \"color\": \"#801212\", \"name\": \"66f8c67a-fe9c-5d4d-8590-5defa26d1f33\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"name\"]}, \"type\": \"Entity\", \"name\": \"nutrients 2021\", \"description\": \"Academic journal where the study was published\", \"id\": \"06403b84-b61d-5f12-b91d-b71a183ff0fd\", \"color\": \"#f47710\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"name\"]}, \"type\": \"EntityType\", \"name\": \"journal\", \"description\": \"journal\", \"id\": \"4c392db7-7706-5777-97c1-1800245a9825\", \"color\": \"#6510f4\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"name\"]}, \"type\": \"Entity\", \"name\": \"laura mar\\\\u00eda compa\\\\u00f1-gabucio\", \"description\": \"Author of the study on coffee consumption and mortality\", \"id\": \"f9eb3495-af5a-5a9c-bb0c-2ce8b1438d16\", \"color\": \"#f47710\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"name\"]}, \"type\": \"Entity\", \"name\": \"leyre notario-barandiaran\", \"description\": \"Author of the study on coffee consumption and mortality\", \"id\": \"99108d40-2e45-51f8-bda7-724b8a85a88d\", \"color\": \"#f47710\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"name\"]}, \"type\": \"Entity\", \"name\": \"manuela garc\\\\u00eda-de la hera\", \"description\": \"Author of the study on coffee consumption and mortality\", \"id\": \"4c8196cb-690c-596a-b1d2-190773bcfc0d\", \"color\": \"#f47710\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"name\"]}, \"type\": \"Entity\", \"name\": \"alejandro oncina-c\\\\u00e1novas\", \"description\": \"Author of the study on coffee consumption and mortality\", \"id\": \"6db389ac-54c5-5955-95c7-fa3adc77efcb\", \"color\": \"#f47710\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"name\"]}, \"type\": \"Entity\", \"name\": \"laura torres-collado\", \"description\": \"Author of the study on coffee consumption and mortality\", \"id\": \"426b61ad-65cd-5d67-8cab-afcc8c6d098f\", \"color\": \"#f47710\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"name\"]}, \"type\": \"PdfDocument\", \"name\": \"nutrients-13-01241\", \"raw_data_location\": \"/Users/vasilije/cognee/examples/data/scientific_papers/nutrients-13-01241.pdf\", \"external_metadata\": \"{}\", \"mime_type\": \"application/pdf\", \"id\": \"7bb0e18a-ac4b-56cf-80eb-644f176b0363\", \"color\": \"#D3D3D3\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"name\"]}, \"type\": \"Entity\", \"name\": \"valencia nutrition study\", \"description\": \"Study assessing the association between coffee consumption and mortality\", \"id\": \"66a2fbcc-95e5-5290-8d62-d71dd5c51128\", \"color\": \"#f47710\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"name\"]}, \"type\": \"EntityType\", \"name\": \"study\", \"description\": \"study\", \"id\": \"96c859b6-e408-58e5-9be8-92bb84908325\", \"color\": \"#6510f4\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"name\"]}, \"type\": \"Entity\", \"name\": \"sandra gonz\\\\u00e1lez-palacios\", \"description\": \"Author of the study on coffee consumption and mortality\", \"id\": \"03d5df54-a749-5694-931b-20d6c69fac62\", \"color\": \"#f47710\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"name\"]}, \"type\": \"Entity\", \"name\": \"jes\\\\u00fas vioque\", \"description\": \"Author of the study on coffee consumption and mortality\", \"id\": \"ebd7537b-8a59-57dc-8908-d7bc7d092f25\", \"color\": \"#f47710\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"text\"]}, \"type\": \"DocumentChunk\", \"text\": \"Nutrients 2021 ,13, 1241 5 of 13\\\\nTable 1. Socio-demographic and lifestyle characteristics according to total coffee consumption among participants aged\\\\n20 years and above of the EUREYE-Spain and the Valencia Nutrition Study in Spain ( n= 1567).\\\\nCoffee Consumption\\\\nTotal No. \\\\u22641 Cup/Day >1 Cup/Day p1\\\\nStudy, n(%) 1567 (100.0) 345 (22.0) 591 (37.7) 631 (40.3) <0.001\\\\nSex, n(%)\\\\nMen 718 (45.8) 147 (42.6) 274 (46.4) 297 (47.1)\\\\nWomen 849 (54.2) 198 (57.4) 317 (53.6) 334 (52.9) 0.39\\\\nAge, mean (SD) 45.9 (18.0) 48.6 (20.6) 46.0 (18.8) 44.4 (15.5) 0.002\\\\nEducation Level, n(%)\\\\n<Primary school 714 (45.6) 177 (51.3) 290 (49.1) 247 (39.1)\\\\n\\\\u2265Primary school 853 (54.4) 168 (48.7) 301 (50.9) 384 (60.9) <0.001\\\\nBody Mass Index kg/m2,n(%)\\\\n<25 kg/m2650 (41.7) 139 (40.4) 254 (43.3) 257 (40.9)\\\\n25\\\\u201330 kg/m2623 (40.0) 126 (36.6) 232 (39.5) 265 (42.2)\\\\n\\\\u226530 kg/m2286 (18.3) 79 (23.0) 101 (17.2) 106 (16.9) 0.11\\\\nWaist circumference *, n(%)\\\\nHealthy range 582 (37.6) 122 (36.0) 222 (37.9) 238 (38.2)\\\\nModerate risk 373 (24.1) 68 (20.1) 137 (23.4) 168 (27.0)\\\\nIncreased risk 592 (38.3) 149 (44.0) 226 (38.6) 217 (34.8) 0.05\\\\nSmoking Status, n(%)\\\\nNever 775 (49.5) 223 (64.6) 308 (52.1) 244 (38.7)\\\\nEx-smoker 262 (16.7) 44 (12.8) 101 (17.1) 117 (18.5)\\\\nCurrent 550 (33.8) 78 (22.6) 182 (30.8) 270 (42.8) <0.001\\\\nDiabetes3(yes), n(%) 121 (7.7) 41 (11.9) 43 (7.3) 37 (5.9) 0.003\\\\nCholesterol3(yes), n(%) 207 (13.2) 50 (14.5) 65 (11.0) 92 (14.6) 0.13\\\\nHypertension3(yes), n(%) 280 (17.9) 92 (26.7) 100 (16.9) 88 (13.9) <0.001\\\\nPhysical activity at leisure time, n(%)\\\\nLow 609 (39.6) 139 (41.4) 218 (37.4) 252 (40.6)\\\\nModerate\\\\u2013vigorous 930 (60.4) 197 (58.6) 365 (62.6) 368 (59.4) 0.38\\\\nTV watching, hours/day, mean (SD) 2.5 (1.77) 2.7 (2.0) 2.5 (1.6) 2.3 (1.7) 0.03\\\\nSleeping time, hours/day, mean (SD) 7.5 (1.4) 7.5 (1.6) 7.5 (1.4) 7.4 (1.3) 0.57\\\\nrMED, mean (SD) 8.2 (2.6) 8.3 (2.6) 8.3 (2.6) 8.1 (2.6) 0.41\\\\nAbbreviations: VNS, Valencia Nutrition Survey; SD, standard deviation; BMI, body mass index; rMED, relative Mediterranean dietary\\\\nindex.1p-value ( p) from chi-squared test (categorical variables) and ANOVA (continuous variables).*Waist circumference: healthy range\\\\n(78\\\\u201394 cm in men and 64\\\\u201380 cm in women), moderate risk (94\\\\u2013102 cm in men and 80\\\\u201388 cm in women), increased risk (>102 cm in men and\\\\n>88 cm in women).3Self-reported diabetes (no/yes), high cholesterol (no/yes) and hypertension (no/yes).\\\\nAs shown in Table 2, during the \\\\ufb01rst six years of follow-up (9169.4 person-years),\\\\n85 deaths occurred. Of these deaths, 31 (36.4%) were from CV diseases and 25 (29.4%)\\\\nwere due to cancer. In the 12 years of follow-up (17,693.7 person-years), we documented\\\\n216 deaths; 77 (35.6%) due to CV diseases, and 56 (25.9%) to cancer. Finally, during\\\\nthe total 18 years of follow-up (25,526.9 person-years), we documented 317 deaths; 115\\\\n(36.3%) due to CVD, and 82 (25.9%) to cancer. Curves of cumulative incidence for all-cause\\\\nmortality during the study period according to coffee consumption are shown in Figure 1 .\\\\nCoffee drinkers showed lower incidence of mortality than nondrinkers in cumulative\\\\nincidence curves. Nutrients 2021 ,13, 1241 6 of 13\\\\nTable 2. Associations between the level of total coffee consumption and all-cause, cardiovascular disease, and cancer\\\\nmortality among participants of the Valencia Nutrition Survey in Spain.\\\\nCoffee Consumption\\\\nNo. \\\\u22641 Cup/Day >1 Cup/Day p-Value2p-Trend3\\\\nFollow-up at 6 Years\\\\nAll-cause mortality ( n, %) 345 (22.0) 591 (37.7) 631 (40.3)\\\\nDeaths, n 33 37 15\\\\nPerson-years 1971.3 3450.5 3747.6\\\\nHR (95% CI)\\\\nAge and sex adjusted 1.00 0.72 (0.45\\\\u20131.15) 0.38 (0.20\\\\u20130.72)\\\\nMultivariable11.00 0.78 (0.46\\\\u20131.30) 0.44 (0.22\\\\u20130.85) 0.01 0.04\\\\nCVD ( n, %) 325 (21.5) 566 (37.4) 622 (41.1)\\\\nDeaths, n 13 12 6\\\\nPerson-years 1918.8 3369.9 3713.5\\\\nHR (95% CI)\\\\nAge and sex adjusted 1.00 0.66 (0.30\\\\u20131.46) 0.44 (0.17\\\\u20131.20)\\\\nMultivariable11.00 0.76 (0.32\\\\u20131.83) 0.42 (0.14\\\\u20131.26) 0.11 0.27\\\\nCancer ( n, %) 319 569 619\\\\nDeaths, n 7 15 3\\\\nPerson-years 1891.8 3371.8 3711.0\\\\nHR (95% CI)\\\\nAge and sex adjusted 1.00 1.36 (0.54\\\\u20133.35) 0.34 (0.09\\\\u20131.34)\\\\nMultivariable11.00 1.54 (0.58\\\\u20134.08) 0.45 (0.10\\\\u20131.90) 0.35 0.10\\\\nFollow-up at 12 Years\\\\nAll-cause mortality ( n, %) 345 (22.0) 591 (37.7) 631 (40.3)\\\\nDeaths, n 70 84 62\\\\nPerson-years 3734.7 6633.5 7325.5\\\\nHR (95% CI)\\\\nAge and sex adjusted 1.00 0.76 (0.55\\\\u20131.05) 0.70 (0.49\\\\u20131.00)\\\\nMultivariable11.00 0.75 (0.53\\\\u20131.06) 0.67 (0.46\\\\u20130.98) 0.04 0.10\\\\nCVD ( n, %) 302 (21.1) 530 (37.1) 596 (41.7)\\\\nDeaths, n 27 23 27\\\\nPerson-years 3475.2 6229.7 7048.4\\\\nHR (95% CI)\\\\nAge and sex adjusted 1.00 0.62 (0.35\\\\u20131.09) 1.03 (0.59\\\\u20131.79)\\\\nMultivariable11.00 0.63 (0.34\\\\u20131.19) 1.00 (0.54\\\\u20131.89) 0.99 0.23\\\\nCancer ( n, %) 289 (20.5) 537 (38.2) 581 (41.3)\\\\nDeaths, n 14 30 12\\\\nPerson-years 3385.2 6268.7 6927.5\\\\nHR (95% CI)\\\\nAge and sex adjusted 1.00 1.34 (0.70\\\\u20132.55) 0.70 (0.32\\\\u20131.54)\\\\nMultivariable11.00 1.37 (0.69\\\\u20132.72) 0.51 (0.20\\\\u20131.27) 0.16 0.03\\\\nFollow-up at 18 Years\\\\nAll-cause mortality ( n, %) 345 (22.0) 458 (37.7) 631 (40.3)\\\\nDeaths, n 107 126 84\\\\nPerson-years 5273.3 9575.5 10,678.1\\\\nHR (95% CI)\\\\nAge and sex adjusted 1.00 0.72 (0.56\\\\u20130.94) 0.58 (0.43\\\\u20130.79)\\\\nMultivariable11.00 0.73 (0.56\\\\u20130.97) 0.56 (0.41\\\\u20130.77) <0.001 0.001\\\\nCVD ( n, %) 276 (20.2) 504 (36.9) 585 (42.9)\\\\nDeaths, n 38 39 38\\\\nPerson-years 4621.5 8764.2 10,242.5\\\\nHR (95% CI)\\\\nAge and sex adjusted 1.00 0.61 (0.38\\\\u20130.96) 0.80 (0.49\\\\u20131.27)\\\\nMultivariable11.00 0.66 (0.40\\\\u20131.07) 0.71 (0.41\\\\u20131.20) 0.19 0.22\\\\nCancer ( n, %) 259 (19.4) 508 (38.1) 565 (42.4)\\\\nDeaths, n 21 43 18\\\\nPerson-years 4472.8 8759.7 10,027.4\\\\nHR (95% CI)\\\\nAge and sex adjusted 1.00 0.93 (0.55\\\\u20131.58) 0.47 (0.25\\\\u20130.90)\\\\nMultivariable11.00 1.01 (0.57\\\\u20131.79) 0.41 (0.20\\\\u20130.86) 0.01 0.01\\\\n1Cox regression model adjusted for age, sex, educational level (<Primary, \\\\u2265Primary), BMI (<25, 25.0\\\\u201329.9, \\\\u226530), waist circumference\\\\n(healthy, moderate and increased risk), sleeping time (h/day), smoking status (current; past and never), self-reported diabetes (no/yes),\\\\nhigh cholesterol (no/yes), hypertension (no/yes), relative Mediterranean diet, physical activity at leisure time (low, moderate\\\\u2013high) and\\\\nTV watching (h/day).2p-value from the likelihood ratio test.3p-value from the p-trend test. Nutrients 2021 ,13, 1241 7 of 13\\\\nNutrients 2021 , 13, x FOR PEER REVIEW 7 of 13 \\\\n  \\\\nFigure 1.  Cumulative incidence curves of death after 18 years of follow-up, according to total cof-\\\\nfee consumption for all-cause mortality in particip ants from the Valencia Nutritional Survey in \\\\nSpain ( n = 1567). \\\\nTable 2 shows the HRs of all-cause, CVD,  and cancer mortality for coffee consump-\\\\ntion. Coffee consumption was inve rsely associated with all-ca use mortality during the fol-\\\\nlow-up period. After six years of follow-up, compared with non-drinkers, drinkers of \\\\u22641 \\\\ncup of regular coffee had a 22% non-significan t lower risk of death, and those who con-\\\\nsumed more than one cup/day showed a 56% reduced risk of death, HR = 0.44 (95% CI: \\\\n0.22\\\\u20130.85). Similarly, at 12 years of follow-up, lower all-cause mortality was observed \\\\namong drinkers of more than one cup per day, HR = 0.67 (95% CI: 0.46\\\\u20130.98). After 18 \\\\nyears of follow-up, drinkers of up to one cu p per day and those of more than one cup per \\\\nday showed a lower risk of all-cause mortality compared with non-drinkers, HR = 0.73 (95% CI: 0.56\\\\u20130.97) and HR = 0.56 (95% CI: 0.41\\\\u20130.77), respectively, with a significant dose\\\\u2013\\\\nresponse trend ( p-trend = 0.001). The number of deaths by cancer and CV diseases after 6 \\\\nand 12 years of follow-up was too low, although after 18 years of follow-up, an inverse \\\\nassociation was observed for cancer mortalit y among those who consumed more than one \\\\ncup per day, HR 0.41 (95%CI: 0.20\\\\u20130.86). \\\\nThe association between type of coffee consumption and mortality at 6, 12 and 18 \\\\nyears of follow-up is shown in Table 3. Compared with non-drinkers, drinkers of caffein-\\\\nated coffee at 12 and 18 years of follow-up showed lower risks of all-cause mortality; HR = 0.66 (95% CI: 0.46\\\\u20130.94) and HR = 0.59 (95%  CI: 0.44\\\\u20130.79), respectively. There was some \\\\nevidence for an inverse association between ca ffeinated coffee and cancer mortality at 18 \\\\nyears of follow-up ( p = 0.10). No statistically significant association was observed between \\\\ndecaffeinated coffee consumption and all-caus e, CVD, or cancer mortality during the \\\\nstudy period. \\\\nTable 3. Associations between type of coffee consumption and all-cause, cardiovascular disease, and cancer mortality \\\\namong participants of the Valencia Nutrition Survey in Spain. \\\\nCoffee Consumption \\\\n No. Decaffeinated Coffee 2 \\\\n(Range 0.1\\\\u20136.5 Cups/Day) Caffeinated Coffee 2 \\\\n(Range 0.1\\\\u20136.5 Cups/Day) p-Value 3 \\\\n Follow-up at 6 years  \\\\nAll-cause mortality ( n, %) 345 (22.0) 308 (19.7) 914 (58.3)  \\\\nDeaths, n 33 24 28  \\\\nPerson-years 1971.3 1783.4 5414.7  \\\\nFigure 1. Cumulative incidence curves of death after 18 years of follow-up, according to total coffee\\\\nconsumption for all-cause mortality in participants from the Valencia Nutritional Survey in Spain\\\\n(n= 1567).\\\\nTable 2 shows the HRs of all-cause, CVD, and cancer mortality for coffee consumption.\\\\nCoffee consumption was inversely associated with all-cause mortality during the follow-up\\\\nperiod. After six years of follow-up, compared with non-drinkers, drinkers of \\\\u22641 cup of\\\\nregular coffee had a 22% non-signi\\\\ufb01cant lower risk of death, and those who consumed\\\\nmore than one cup/day showed a 56% reduced risk of death, HR = 0.44 (95% CI: 0.22\\\\u20130.85).\\\\nSimilarly, at 12 years of follow-up, lower all-cause mortality was observed among drinkers\\\\nof more than one cup per day, HR = 0.67 (95% CI: 0.46\\\\u20130.98). After 18 years of follow-up,\\\\ndrinkers of up to one cup per day and those of more than one cup per day showed a lower\\\\nrisk of all-cause mortality compared with non-drinkers, HR = 0.73 (95% CI: 0.56\\\\u20130.97)\\\\nand HR = 0.56 (95% CI: 0.41\\\\u20130.77), respectively, with a signi\\\\ufb01cant dose\\\\u2013response trend\\\\n(p-trend = 0.001 ). The number of deaths by cancer and CV diseases after 6 and 12 years of\\\\nfollow-up was too low, although after 18 years of follow-up, an inverse association was\\\\nobserved for cancer mortality among those who consumed more than one cup per day, HR\\\\n0.41 (95% CI: 0.20\\\\u20130.86).\\\\nThe association between type of coffee consumption and mortality at 6, 12 and 18 years\\\\nof follow-up is shown in Table 3. Compared with non-drinkers, drinkers of caffeinated\\\\ncoffee at 12 and 18 years of follow-up showed lower risks of all-cause mortality; HR = 0.66\\\\n(95% CI: 0.46\\\\u20130.94) and HR = 0.59 (95% CI: 0.44\\\\u20130.79), respectively. There was some\\\\nevidence for an inverse association between caffeinated coffee and cancer mortality at\\\\n18 years of follow-up ( p= 0.10). No statistically signi\\\\ufb01cant association was observed\\\\nbetween decaffeinated coffee consumption and all-cause, CVD, or cancer mortality during\\\\nthe study period. Nutrients 2021 ,13, 1241 8 of 13\\\\nTable 3. Associations between type of coffee consumption and all-cause, cardiovascular disease, and cancer mortality\\\\namong participants of the Valencia Nutrition Survey in Spain.\\\\nCoffee Consumption\\\\nNo.Decaffeinated Coffee2\\\\n(Range 0.1\\\\u20136.5 Cups/Day)Caffeinated Coffee2\\\\n(Range 0.1\\\\u20136.5 Cups/Day)p-Value3\\\\nFollow-up at 6 years\\\\nAll-cause mortality ( n, %) 345 (22.0) 308 (19.7) 914 (58.3)\\\\nDeaths, n 33 24 28\\\\nPerson-years 1971.3 1783.4 5414.7\\\\nHR (95% CI)\\\\nAge and sex adjusted 1.00 0.61 (0.36\\\\u20131.04) 0.55 (0.33\\\\u20130.94)\\\\nMultivariable11.00 0.66 (0.37\\\\u20131.18) 0.62 (0.35\\\\u20131.10) 0.20\\\\nCVD ( n, %) 325 (21.5) 295 (19.5) 893 (59.0)\\\\nDeaths, n 13 11 7\\\\nPerson-years 1918.8 1741.8 5341.6\\\\nHR (95% CI)\\\\nAge and sex adjusted 1.00 0.72 (0.32\\\\u20131.63) 0.42 (0.16\\\\u20131.08)\\\\nMultivariable11.00 0.66 (0.26\\\\u20131.65) 0.55 (0.20\\\\u20131.52) 0.46\\\\nCancer ( n,%) 319 (21.2) 293 (19.4) 895 (59.4)\\\\nDeaths, n 7 9 9\\\\nPerson-years 1891.8 1736.6 5346.1\\\\nHR (95% CI)\\\\nAge and sex adjusted 1.00 1.03 (0.38\\\\u20132.80) 0.81 (0.38\\\\u20132.81)\\\\nMultivariable11.00 1.42 (0.50\\\\u20134.09) 0.89 (0.29\\\\u20132.69) 0.65\\\\nFollow-up at 12 years\\\\nAll-cause mortality ( n, %) 345 (22.0) 308 (19.7) 914 (58.3)\\\\nDeaths, n 70 65 81\\\\nPerson-years 3734.7 3361.1 10,598.0\\\\nHR (95% CI)\\\\nAge and sex adjusted 1.00 0.81 (0.58\\\\u20131.14) 0.68 (0.49\\\\u20130.95)\\\\nMultivariable11.00 0.80 (0.55\\\\u20131.15) 0.66 (0.46\\\\u20130.94) 0.08\\\\nCVD ( n, %) 302 (21.1) 271 (19.0) 855 (59.9)\\\\nDeaths, n 27 28 22\\\\nPerson-years 3475.2 3112.1 10,165.9\\\\nHR (95% CI)\\\\nAge and sex adjusted 1.00 0.92 (0.54\\\\u20131.56) 0.64 (0.35\\\\u20131.15)\\\\nMultivariable11.00 0.83 (0.45\\\\u20131.51) 0.71 (0.35\\\\u20131.41) 0.60\\\\nCancer ( n, %) 289 (20.5) 261 (18.6) 857 (60.9)\\\\nDeaths, n 14 18 24\\\\nPerson-years 3385.2 3029.4 10,166.8\\\\nHR (95% CI)\\\\nAge and sex adjusted 1.00 1.16 (0.58\\\\u20132.35) 1.01 (0.51\\\\u20132.00)\\\\nMultivariable11.00 1.24 (0.58\\\\u20132.69) 0.88 (0.41\\\\u20131.87) 0.65\\\\nFollow-up at 18 years\\\\nAll-cause mortality ( n, %) 345 (22.0) 308 (19.7) 914 (58.3)\\\\nDeaths, n 107 95 115\\\\nPerson-years 5273.3 4746.4 15,507.1\\\\nHR (95% CI)\\\\nAge and sex adjusted 1.00 0.77 (0.58\\\\u20131.01) 0.59 (0.45\\\\u20130.77)\\\\nMultivariable11.00 0.76 (0.56\\\\u20131.03) 0.59 (0.44\\\\u20130.79) 0.002\\\\nCVD ( n, %) 276 (20.2) 255 (18.7) 834 (61.1)\\\\nDeaths, n 38 42 35\\\\nPerson-years 4621.5 4255.6 14,751.1\\\\nHR (95% CI)\\\\nAge and sex adjusted 1.00 0.80 (0.51\\\\u20131.24) 0.57 (0.35\\\\u20130.92)\\\\nMultivariable11.00 0.69 (0.42\\\\u20131.14) 0.70 (0.38\\\\u20131.14) 0.23\\\\nCancer ( n, %) 259 (19.4) 242 (18.2) 831 (62.4)\\\\nDeaths, n 21 29 32\\\\nPerson-years 4472.8 4113.1 14,674.085\\\\nHR (95% CI)\\\\nAge and sex adjusted 1.00 0.95 (0.54\\\\u20131.69) 0.59 (0.33\\\\u20131.03)\\\\nMultivariable11.00 1.01 (0.54\\\\u20131.87) 0.57 (0.31\\\\u20131.08) 0.11\\\\nAbbreviations: HR, hazard ratio; CI, con\\\\ufb01dence interval; CVD, cardiovascular disease.1Cox regression model adjusted for age, sex,\\\\neducational level (<Primary, \\\\u2265Primary), BMI (<25, 25.0\\\\u201329.9, \\\\u226530), waist circumference (healthy range, moderate risk and increased risk),\\\\nsleeping time (h/day), smoking status (current; past and never), self-reported diabetes (no/yes), high cholesterol (no/yes), hypertension\\\\n(no/yes), relative Mediterranean diet, physical activity at leisure time (low, moderate\\\\u2013high) and TV watching (h/day).2Any coffee\\\\nconsumption.3p-value from the likelihood ratio test.\", \"chunk_size\": 7244, \"chunk_index\": 1, \"cut_type\": \"sentence_end\", \"id\": \"15dd8ff7-b8d1-5e42-a22b-517828d53ed0\", \"color\": \"#801212\", \"name\": \"15dd8ff7-b8d1-5e42-a22b-517828d53ed0\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"name\"]}, 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\"smoking status\", \"description\": \"Categorization of participants\\' smoking habits.\", \"id\": \"738d11f1-f585-56f1-ae43-e004f2b516de\", \"color\": \"#f47710\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"name\"]}, \"type\": \"Entity\", \"name\": \"participants aged 20 years and above\", \"description\": \"Participants in the studies who are 20 years old or older.\", \"id\": \"011951eb-277e-55f5-993d-dfe64d50f5b0\", \"color\": \"#f47710\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"name\"]}, \"type\": \"EntityType\", \"name\": \"demographic\", \"description\": \"demographic\", \"id\": \"47ca38e1-f0e3-5cd4-a96b-01a66ad86557\", \"color\": \"#6510f4\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"text\"]}, \"type\": \"DocumentChunk\", \"text\": \"Nutrients 2021 ,13, 1241 9 of 13\\\\n4. Discussion\\\\nIn this study, we have shown an inverse association between baseline coffee consump-\\\\ntion and all-cause and cancer mortality in an adult Mediterranean population after 18 years\\\\nof follow-up. Compared with no-consumption, coffee consumption of one or fewer cups\\\\nper day was associated with a 27% reduction in all-cause mortality, and the consumption\\\\nof more than one cup/day (range 2\\\\u20136.5 cups/day) was associated with a 44% reduction\\\\nin all-cause mortality. The consumption of more than one cup of coffee per day was also\\\\nassociated with a 59% reduction in cancer mortality after 18 years of follow-up. We did not\\\\nobserve this protective effect for CVD mortality. Regarding the type of coffee, the protective\\\\neffect was observed only between caffeinated coffee and all causes of mortality after 12 and\\\\n18 years of follow-up.\\\\nThe inverse association between coffee consumption and all-cause mortality observed\\\\nin our study is consistent with the results from previous meta-analyses in adult popula-\\\\ntions [11,31\\\\u201334], and also with results observed in subsequent prospective studies carried\\\\nout in the United States [ 12,35], Europe [ 36,37], and Asia [ 38]. Nevertheless, this association\\\\nhas scarcely been evaluated in adult populations from Mediterranean countries, where\\\\nthe high adherence to a Mediterranean dietary pattern may reduce mortality from all\\\\ncauses [ 39]. Although our results may not seem fully innovative with respect to other\\\\nstudies that have previously reported a protective effect of coffee consumption, the interest\\\\nand the novelty of this study may still be sustained by the fact that it is the \\\\ufb01rst study\\\\nto evaluate the association between coffee consumption and all-cause, CVD, and cancer\\\\nmortality in adults aged 20 years and older of a Mediterranean country, i.e., Spain. As far\\\\nas we know, only three studies have speci\\\\ufb01cally explored the association between coffee\\\\nconsumption and total mortality with Mediterranean populations. In one previous study\\\\ncarried out by our group with an elderly population in Valencia, an inverse association\\\\nwas observed with CVD but not for all causes of mortality [ 17]. In the SUN study, a\\\\nprospective cohort study with university graduate participants, an inverse association was\\\\nalso observed for all-cause mortality among participants who consumed \\\\u22654 cups/day\\\\nof coffee [ 18]. Finally, a recently published prospective cohort study with Italian adults\\\\nreported that moderate consumption of 3\\\\u20134 cups/day of Italian-style coffee was associated\\\\nwith lower risk of all-cause and, speci\\\\ufb01cally, of CVD mortality [19].\\\\nMost studies examining the association between coffee consumption and CV diseases\\\\nhave reported inverse associations [ 12,17,36,37], although in some studies the association\\\\nwas non-statistically signi\\\\ufb01cant [ 31,40]. In this study, we have found evidence of an inverse\\\\nassociation, which is also consistent with a study we carried out in elderly population [ 17].\\\\nRegarding cancer mortality, the inverse association we found is consistent with previous\\\\nstudies in different populations [ 35,37,38], although there are some studies showing no\\\\nassociation [ 12,36]. Other studies have shown an inverse association with speci\\\\ufb01c types\\\\nof cancer [ 41,42]; however, two recently published meta-analyses provided evidence for\\\\nan inverse association with cancer mortality [ 1,11]. Overall, the present evidence suggests\\\\nthat moderate coffee consumption may reduce cancer mortality, as shown in our study that\\\\nthe consumption of more than one cup per day was associated with a 59% decreased risk\\\\nof cancer mortality.\\\\nWhen we explored the association by type of coffee, we found an inverse association\\\\nbetween caffeinated coffee and all-cause mortality at 12 and 18 years of follow-up. Although\\\\nsome studies show that caffeine contained in coffee may produce some adverse effects in\\\\nthe central nervous system and cardiovascular system [ 4,5,43], several cohort studies have\\\\nfound that moderate caffeine consumption is associated with a decreased risk of all-cause\\\\nmortality in adult populations [ 12,35]. Most of these studies have also reported an inverse\\\\nassociation with decaffeinated coffee consumption, which we did not observe in our study,\\\\nalthough our study had the lack of power to detect an association because the number of\\\\nevents by categories of decaffeinated coffee was small, and decaffeinated coffee was also\\\\nless frequently consumed than caffeinated coffee. Nutrients 2021 ,13, 1241 10 of 13\\\\nSeveral biological mechanisms have been proposed to explain why coffee may de-\\\\ncrease the risk of mortality. Coffee is a rich source of antioxidant components such as\\\\ncaffeine, chlorogenic acid, melanoidins, cafestol, kahweol, and trigonelline, as well as other\\\\npolyphenol compounds that may have important bene\\\\ufb01cial effects on in\\\\ufb02ammation, and\\\\nbene\\\\ufb01cial effects have been shown against total mortality, cardiovascular disease and some\\\\ncancers [ 15]. Firstly, caffeine and chlorogenic acid contents in coffee produce an inhibition\\\\nof peroxidation of LDL-c which prevents the development of atherosclerosis and decreases\\\\noxidative stress, preventing endothelial dysfunction [ 44,45]. Moreover, other phenolic com-\\\\npounds and substances such as trigonelline or magnesium may improve insulin sensitivity\\\\nand glucose resistance [ 7]. Finally, coffee may produce biological anticarcinogenic effects,\\\\nincluding inhibition of the enzyme responsible for carcinogen activation, the stimulation\\\\nof intracellular antioxidant defense mechanisms, and inhibition of DNA methylation that\\\\nmanages the inactivation of tumorigenic process and apoptosis [ 45]. Thus, compounds of\\\\ncoffee might play a bene\\\\ufb01cial role in health, mediating not only the association between\\\\nlong-term coffee consumption and risk of all-cause mortality, but also with cancer mortality.\\\\nThe current study has several limitations. Firstly, we were not able to control for possi-\\\\nble changes in coffee consumption during the follow-up; however, coffee consumption is a\\\\nhabit adopted in adult life that rarely changes over time, and the self-reported consumption\\\\ncould be a valid method to assess usual long-term coffee consumption [ 12,46]. Secondly,\\\\nit is possible that pre-existing chronic illness at baseline might cause higher mortality\\\\nand be also associated with lower or non-coffee consumption. When we repeated the\\\\nanalyses excluding deaths in the \\\\ufb01rst and second year of the follow-up and adjusted for the\\\\nself-reported pre-existing chronic diseases at baseline, the associations remained basically\\\\nunchanged (data not shown). Thirdly, although participants were volunteers in a nutrition\\\\nsurvey and some response bias may be possible, it is unlikely that coffee consumption\\\\nwas in\\\\ufb02uential in the participation rate in the study, and coffee consumption among our\\\\nparticipants was similar to that found in other Spanish studies [ 17,18]. Additionally, we\\\\ndid not collect information on the method of coffee preparation, but a previous study\\\\nshowed that un\\\\ufb01ltered coffee is the most widely consumed in Spain [ 47]. Lastly, a point to\\\\nconsider is the small sample size, which may have limited the statistical power to detect\\\\nsome associations as signi\\\\ufb01cant (e.g., CV diseases); however, the follow-up period was\\\\nlong enough to detect signi\\\\ufb01cant associations with all-cause and cancer mortality.\\\\nOur study has several strengths, however. We used a well-de\\\\ufb01ned population com-\\\\nprising participants aged 20 or above from a well-de\\\\ufb01ned Mediterranean area from which\\\\nhigh-quality information was collected at baseline by trained \\\\ufb01eldworkers using stan-\\\\ndardized protocols and validated questionnaires. In addition, the information on coffee\\\\nconsumption was collected before the outcome occurred; thus, any misclassi\\\\ufb01cation in\\\\ncoffee consumption categories, if any, should be non-differential, and could therefore lead\\\\nto an underestimation of the effects of coffee on mortality.\\\\n5. Conclusions\\\\nIn conclusion, this study suggests that the moderate consumption of coffee, partic-\\\\nularly caffeinated coffee (range 1\\\\u20136.5 cups per day), is associated with a lower all-cause\\\\nand cancer mortality after a long follow-up period. These \\\\ufb01ndings are consistent with\\\\nprevious studies, although they add new evidence from a Mediterranean adult population.\\\\nThus, coffee consumption could be promoted as part of a healthy Mediterranean lifestyle,\\\\nalthough further long-term longitudinal studies collecting information on the amount and\\\\ntype of coffee should add valuable information regarding its bene\\\\ufb01cial effects.\\\\nAuthor Contributions: Conceptualization, J.V . and M.G.-d.l.H.; formal analysis, L.T.-C.; data curation ,\\\\nL.T.-C. and J.V .; writing\\\\u2014original draft preparation, L.T.-C.; writing\\\\u2014review and editing, L.T.-C.,\\\\nL.M.C.-G., S.G.-P ., L.N.-B., and A.O.-C.; supervision, J.V . and M.G.-d.l.H. All authors have read and\\\\nagreed to the published version of the manuscript. Nutrients 2021 ,13, 1241 11 of 13\\\\nFunding: The VNS study was supported by a grant from the Direcci \\\\u00f3n General de Salud P \\\\u00fablica,\\\\nGeneralitat Valenciana 1994 and the Fondo Investigacion Sanitaria (FIS 00/0985). This study has also\\\\nreceived support from the Instituto de Salud Carlos III and FEDER funds (FIS PI13/00654).\\\\nInstitutional Review Board Statement: The study was conducted according to the guidelines of the\\\\nDeclaration of Helsinki, and approved by the local Ethical Committees of the Hospital of San Juan\\\\nand the Miguel Hernandez University.\\\\nInformed Consent Statement: Informed consent was obtained from all subjects involved in the study.\\\\nData Availability Statement: The data presented in this study are available on request from the\\\\ncorresponding author. The data are not publicly available due to con\\\\ufb01dentiality and ethical reasons.\\\\nAcknowledgments: The authors thank the VNS participants for their valuable contribution to this\\\\nresearch. We appreciate the English revision of the manuscript made by Jessica Gorlin.\\\\nCon\\\\ufb02icts of Interest: The authors declare no con\\\\ufb02ict of interest. The funders had no role in the design\\\\nof the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or\\\\nin the decision to publish the results.\\\\nReferences\\\\n1. Kim, Y.; Je, Y.; Giovannucci, E. Coffee Consumption and All-Cause and Cause-Speci\\\\ufb01c Mortality: A Meta-Analysis by Potential\\\\nModi\\\\ufb01ers. Eur. J. Epidemiol. 2019 . [CrossRef] [PubMed]\\\\n2. Cai, L.; Ma, D.; Zhang, Y.; Liu, Z.; Wang, P . The Effect of Coffee Consumption on Serum Lipids: A Meta-Analysis of Randomized\\\\nControlled Trials. Eur. J. Clin. Nutr. 2012 ,66, 872\\\\u2013877. 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Impact of Caffeine and Coffee on Our Health. Trends Endocrinol. Metab. 2014 ,25,\\\\n489\\\\u2013492. [CrossRef] [PubMed]\\\\n44. Yamagata, K. Do Coffee Polyphenols Have a Preventive Action on Metabolic Syndrome Associated Endothelial Dysfunctions?\\\\nAn Assessment of the Current Evidence. Antioxidants 2018 ,7, 26. [CrossRef] [PubMed]\\\\n45. G\\\\u00f6kcen, B.B.; \\\\u00b8 Sanlier, N. Coffee Consumption and Disease Correlations. Crit. Rev. Food Sci. Nutr. 2019 ,59, 336\\\\u2013348. [CrossRef]\\\\n[PubMed]\\\\n46. Penolazzi, B.; Natale, V .; Leone, L.; Russo, P .M. Individual Differences Affecting Caffeine Intake. Analysis of Consumption\\\\nBehaviours for Different Times of Day and Caffeine Sources. Appetite 2012 ,58, 971\\\\u2013977. [CrossRef]\\\\n47. Machado-Fragua, M.D.; Struijk, E.A.; Graciani, A.; Guallar-Castillon, P .; Rodr \\\\u00edguez-Artalejo, F.; Lopez-Garcia, E. Coffee Con-\\\\nsumption and Risk of Physical Function Impairment, Frailty and Disability in Older Adults. 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The findings indicate that coffee drinkers have lower overall mortality compared to non-drinkers over various follow-up periods, showing significant reductions in risk, particularly for cardiovascular diseases and cancer. Additionally, the type of coffee consumed (caffeinated vs decaffeinated) and its association with mortality outcomes reveal nuanced differences, suggesting that caffeinated coffee intake may confer protective benefits while decaffeinated does not show significant effects.\", \"id\": \"58434918-8a80-5d40-9c90-18d07cbe2e79\", \"color\": \"#1077f4\", \"name\": \"58434918-8a80-5d40-9c90-18d07cbe2e79\"}, {\"ontology_valid\": false, \"version\": 1, \"topological_rank\": 0, \"metadata\": {\"index_fields\": [\"text\"]}, \"type\": \"TextSummary\", \"text\": \"This research indicates a negative correlation between initial coffee intake and overall and cancer mortality in adults from a Mediterranean region over an 18-year span. 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    "## Understanding the Results\n",
    "\n",
    "The demonstration above shows how ontologies enhance our analysis by:\n",
    "\n",
    "1. **Making Connections**: \n",
    "   - Linking related medical concepts even when not explicitly stated\n",
    "   - Identifying relationships between symptoms, diseases, and risk factors\n",
    "\n",
    "2. **Standardizing Terms**: \n",
    "   - Unifying different ways of referring to the same medical condition\n",
    "   - Ensuring consistent terminology across documents\n",
    "\n",
    "3. **Enabling Inference**: \n",
    "   - Drawing conclusions based on ontological relationships\n",
    "   - Discovering implicit connections in the data\n",
    "\n",
    "## Next Steps\n",
    "\n",
    "To learn more about Cognee and ontologies:\n",
    "1. Check out the [Cognee documentation](https://docs.cognee.ai/)\n",
    "2. Explore more examples in the `examples` directory\n",
    "3. Try creating your own domain-specific ontology\n",
    "\n",
    "Remember to:\n",
    "- Place your scientific papers in the appropriate directory\n",
    "- Update the ontology path to point to your .owl file\n",
    "- Replace the API key with your own OpenAI key"
   ],
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