1184 lines
99 KiB
Text
Vendored
1184 lines
99 KiB
Text
Vendored
{
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"cells": [
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{
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"cell_type": "markdown",
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"id": "25cf0a40e669a70",
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"metadata": {},
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"source": [
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"# Understanding Ontologies with Cognee\n",
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"\n",
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"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",
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"\n",
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"## What is an Ontology?\n",
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"\n",
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"An ontology is a formal representation of knowledge that defines:\n",
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"- Concepts within a domain\n",
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"- Relationships between concepts\n",
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"- Properties and attributes\n",
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"- Rules and constraints\n",
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"\n",
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"Key terms:\n",
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"- **Classes**: Categories or types (e.g., Disease, Symptom)\n",
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"- **Instances**: Specific examples of classes (e.g., Type 2 Diabetes)\n",
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"- **Properties**: Relationships between classes/instances (e.g., hasSymptom)\n",
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"- **Axioms**: Logical statements defining relationships"
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]
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},
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{
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"cell_type": "markdown",
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"id": "441248da37f2b901",
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"metadata": {},
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"source": [
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"## Setup\n",
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"\n",
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"First, let's install the required packages and set up our environment:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "8cf7ba29f9a150af",
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"metadata": {},
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"outputs": [],
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"source": [
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"# Install required package\n",
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"# !pip install cognee"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"id": "abb86851",
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"metadata": {},
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"outputs": [],
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"source": [
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"import os\n",
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"\n",
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"# Set up OpenAI API key (required for Cognee's LLM functionality)\n",
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"if \"LLM_API_KEY\" not in os.environ:\n",
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" os.environ[\"LLM_API_KEY\"] = \"your-api-key-here\" # Replace with your API key"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"id": "d825d126b3a0ec26",
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"metadata": {},
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"\n",
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"\u001b[2m2025-10-07T20:40:15.192965\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mDeleted old log file: /Users/daulet/Desktop/dev/cognee-claude/logs/2025-10-07_21-25-04.log\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.shared.logging_utils\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:15.894155\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mLogging initialized \u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.shared.logging_utils\u001b[0m]\u001b[0m \u001b[36mcognee_version\u001b[0m=\u001b[35m0.3.5-local\u001b[0m \u001b[36mdatabase_path\u001b[0m=\u001b[35m/Users/daulet/Desktop/dev/cognee-claude/cognee/.cognee_system/databases\u001b[0m \u001b[36mgraph_database_name\u001b[0m=\u001b[35m\u001b[0m \u001b[36mos_info\u001b[0m=\u001b[35m'Darwin 24.5.0 (Darwin Kernel Version 24.5.0: Tue Apr 22 19:54:43 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T8132)'\u001b[0m \u001b[36mpython_version\u001b[0m=\u001b[35m3.10.11\u001b[0m \u001b[36mrelational_config\u001b[0m=\u001b[35mcognee_db\u001b[0m \u001b[36mstructlog_version\u001b[0m=\u001b[35m25.4.0\u001b[0m \u001b[36mvector_config\u001b[0m=\u001b[35mlancedb\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:15.894641\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mDatabase storage: /Users/daulet/Desktop/dev/cognee-claude/cognee/.cognee_system/databases\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.shared.logging_utils\u001b[0m]\u001b[0m\n",
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"/Users/daulet/Desktop/dev/cognee-claude/.venv/lib/python3.10/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
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" from .autonotebook import tqdm as notebook_tqdm\n"
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]
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},
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"0.3.5-local\n"
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]
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}
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],
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"source": [
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"# Import required libraries\n",
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"import cognee\n",
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"print(cognee.__version__)\n",
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"from cognee.shared.logging_utils import get_logger\n",
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"\n",
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"cognee.config.set_llm_model(\"gpt-4o-mini\")\n",
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"cognee.config.set_llm_provider(\"openai\")\n",
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"from cognee.api.v1.search import SearchType\n",
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"\n",
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"logger = get_logger()"
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]
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},
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{
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"cell_type": "markdown",
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"id": "6af350837e86b7a1",
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"metadata": {},
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"source": [
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"## Creating the Pipeline\n",
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"\n",
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"Let's create a pipeline that will:\n",
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"1. Clean existing data\n",
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"2. Process scientific papers\n",
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"3. Apply ontological knowledge"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"id": "4d0e4a58e4207a7d",
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"metadata": {},
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"outputs": [],
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"source": [
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"async def run_pipeline(config=None):\n",
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" # Clean existing data\n",
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" await cognee.prune.prune_data()\n",
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" await cognee.prune.prune_system(metadata=True)\n",
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" \n",
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" # Set up path to scientific papers\n",
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" scientific_papers_dir = os.path.join(\n",
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" os.path.dirname(os.path.dirname(os.path.abspath(\".\"))), \n",
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" \"cognee\",\n",
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" \"examples\",\n",
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" \"data\", \n",
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" \"scientific_papers/\"\n",
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" )\n",
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" \n",
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" # Add papers to the system\n",
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" await cognee.add(scientific_papers_dir)\n",
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" \n",
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" # Cognify with optional ontology\n",
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" return await cognee.cognify(config=config)\n",
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"\n",
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"async def query_pipeline(questions):\n",
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" answers = []\n",
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" for question in questions:\n",
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" search_results = await cognee.search(\n",
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" query_type=SearchType.GRAPH_COMPLETION,\n",
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" query_text=question,\n",
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" )\n",
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" answers.append(search_results)\n",
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" return answers"
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]
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},
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{
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"cell_type": "markdown",
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"id": "c87c21a75d6f4d79",
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"metadata": {},
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"source": [
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"## Running the Demo\n",
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"\n",
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"Let's test our system with some medical questions, comparing results with and without ontological knowledge:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"id": "1363772d2b48f5c0",
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"metadata": {},
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"\n",
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"\u001b[2m2025-10-07T20:40:24.236015\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mOntology loaded successfully from file: ../examples/python/ontology_input_example/enriched_medical_ontology_with_classes.owl\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:24.236931\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mLookup built: 4 classes, 50 individuals\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:24.348030\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mJSON extension already loaded or unavailable: Binder exception: Extension: JSON is already loaded. You can check loaded extensions by `CALL SHOW_LOADED_EXTENSIONS() RETURN *`.\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.shared.logging_utils\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:24.387417\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mDeleted Kuzu database files at /Users/daulet/Desktop/dev/cognee-claude/cognee/.cognee_system/databases/cognee_graph_kuzu\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.shared.logging_utils\u001b[0m]\u001b[0m\n"
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]
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},
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"\n",
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"--- Results WITH ontology ---\n",
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"\n"
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]
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},
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"\n",
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"\u001b[2m2025-10-07T20:40:26.930731\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[0m\n",
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"\n",
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"\u001b[1mStorage manager absolute path: /Users/daulet/Desktop/dev/cognee-claude/cognee/.cognee_cache\u001b[0m\n",
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"\n",
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"\u001b[1mDeleting cache... \u001b[0m\n",
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"\n",
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"\u001b[1m✓ Cache deleted successfully! \u001b[0m\n"
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]
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},
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"User ddfe2676-fa68-430d-981e-1d335a6fdb1b has registered.\n"
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]
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},
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"\n",
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"\u001b[1mEmbeddingRateLimiter initialized: enabled=False, requests_limit=60, interval_seconds=60\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:28.202666\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mPipeline run started: `00128a51-0bd2-5512-9865-851caf7251ba`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_with_telemetry()\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:28.203107\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task started: `resolve_data_directories`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:28.203471\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task started: `ingest_data`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:28.204254\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mPipeline run started: `00128a51-0bd2-5512-9865-851caf7251ba`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_with_telemetry()\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:28.204491\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task started: `resolve_data_directories`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:28.204812\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task started: `ingest_data`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:28.219424\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mRegistered loader: pypdf_loader\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.infrastructure.loaders.LoaderEngine\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:28.219844\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mRegistered loader: text_loader\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.infrastructure.loaders.LoaderEngine\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:28.220221\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mRegistered loader: image_loader\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.infrastructure.loaders.LoaderEngine\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:28.220433\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mRegistered loader: audio_loader\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.infrastructure.loaders.LoaderEngine\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:28.220712\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mRegistered loader: unstructured_loader\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.infrastructure.loaders.LoaderEngine\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:28.220947\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mRegistered loader: advanced_pdf_loader\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.infrastructure.loaders.LoaderEngine\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:28.221361\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mProcessing PDF: /Users/daulet/Desktop/dev/cognee/examples/data/scientific_papers/nutrients-13-01241.pdf\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.infrastructure.loaders.external.advanced_pdf_loader\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[1mpikepdf C++ to Python logger bridge initialized\u001b[0m\n"
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]
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},
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Warning: No languages specified, defaulting to English.\n"
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]
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},
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"\n",
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"\u001b[1mReading PDF for file: /Users/daulet/Desktop/dev/cognee/examples/data/scientific_papers/nutrients-13-01241.pdf ...\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:35.976082\u001b[0m [\u001b[33m\u001b[1mwarning \u001b[0m] \u001b[1mFailed to process PDF with AdvancedPdfLoader: Unable to get page count. Is poppler installed and in PATH?\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.infrastructure.loaders.external.advanced_pdf_loader\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:35.977344\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mFalling back to PyPDF loader for /Users/daulet/Desktop/dev/cognee/examples/data/scientific_papers/nutrients-13-01241.pdf\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.infrastructure.loaders.external.advanced_pdf_loader\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:35.979542\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mReading PDF: /Users/daulet/Desktop/dev/cognee/examples/data/scientific_papers/nutrients-13-01241.pdf\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.infrastructure.loaders.external.pypdf_loader\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:36.323535\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mProcessing PDF: /Users/daulet/Desktop/dev/cognee/examples/data/scientific_papers/TOJ-22-0073_152Mendoza.pdf\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.infrastructure.loaders.external.advanced_pdf_loader\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[1mReading PDF for file: /Users/daulet/Desktop/dev/cognee/examples/data/scientific_papers/TOJ-22-0073_152Mendoza.pdf ...\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:36.627761\u001b[0m [\u001b[33m\u001b[1mwarning \u001b[0m] \u001b[1mFailed to process PDF with AdvancedPdfLoader: Unable to get page count. Is poppler installed and in PATH?\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.infrastructure.loaders.external.advanced_pdf_loader\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:36.628591\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mFalling back to PyPDF loader for /Users/daulet/Desktop/dev/cognee/examples/data/scientific_papers/TOJ-22-0073_152Mendoza.pdf\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.infrastructure.loaders.external.advanced_pdf_loader\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:36.629517\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mReading PDF: /Users/daulet/Desktop/dev/cognee/examples/data/scientific_papers/TOJ-22-0073_152Mendoza.pdf\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.infrastructure.loaders.external.pypdf_loader\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:36.747011\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task completed: `ingest_data`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:36.747398\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task completed: `resolve_data_directories`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:36.747660\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mPipeline run completed: `00128a51-0bd2-5512-9865-851caf7251ba`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_with_telemetry()\u001b[0m]\u001b[0m\n",
|
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"\n",
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"\u001b[2m2025-10-07T20:40:36.750279\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task completed: `ingest_data`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:36.750549\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task completed: `resolve_data_directories`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:36.750821\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mPipeline run completed: `00128a51-0bd2-5512-9865-851caf7251ba`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_with_telemetry()\u001b[0m]\u001b[0m\n",
|
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"\n",
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"\u001b[2m2025-10-07T20:40:36.772492\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mPipeline run started: `325268f2-318a-5318-8570-3616626129ed`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_with_telemetry()\u001b[0m]\u001b[0m\n",
|
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"\n",
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"\u001b[2m2025-10-07T20:40:36.772995\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task started: `classify_documents`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
|
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"\n",
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"\u001b[2m2025-10-07T20:40:36.773865\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task started: `check_permissions_on_dataset`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:40:36.774764\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mPipeline run started: `325268f2-318a-5318-8570-3616626129ed`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_with_telemetry()\u001b[0m]\u001b[0m\n",
|
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"\n",
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"\u001b[2m2025-10-07T20:40:36.775056\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task started: `classify_documents`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:40:36.775718\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task started: `check_permissions_on_dataset`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
|
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"\n",
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"\u001b[2m2025-10-07T20:40:36.783240\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_base\u001b[0m]\u001b[0m\n",
|
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"\n",
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"\u001b[2m2025-10-07T20:40:36.809815\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_base\u001b[0m]\u001b[0m\n"
|
|
]
|
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},
|
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{
|
|
"name": "stdout",
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"output_type": "stream",
|
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"text": [
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"Warning: No languages specified, defaulting to English.\n"
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]
|
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},
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{
|
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"name": "stderr",
|
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"output_type": "stream",
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"text": [
|
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"\n",
|
|
"\u001b[2m2025-10-07T20:40:36.849367\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_base\u001b[0m]\u001b[0m\n",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:40:36.863627\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_base\u001b[0m]\u001b[0m\n",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:40:55.726911\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mLoaded JSON extension \u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.shared.logging_utils\u001b[0m]\u001b[0m\n",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:40:55.757864\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",
|
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"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.758561\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",
|
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"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.759088\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",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:40:55.759456\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",
|
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"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.759801\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",
|
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"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.760065\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.760398\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",
|
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"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.760701\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",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:40:55.760968\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mhttp://example.org/ontology#Hypertension match was found for found for 'hypertension' node\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:40:55.763146\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mhttp://example.org/ontology#HighCholesterol match was found for found for 'cholesterol' node\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:40:55.763622\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mhttp://example.org/ontology#AtrialFibrillation match was found for found for 'atrial fibrillation' node\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
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"\u001b[2m2025-10-07T20:40:55.764459\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mhttp://example.org/ontology#HeartFailure match was found for found for 'heart failure' node\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
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"\u001b[2m2025-10-07T20:40:55.765517\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mhttp://example.org/ontology#CoronaryArteryDisease match was found for found for 'coronary heart disease' node\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.765914\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",
|
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"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.766214\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'filtered coffee' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.766546\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'boiled coffee' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.766895\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.767142\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.767407\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for '2023' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.767784\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.768084\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'coffee' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.768319\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.768618\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mhttp://example.org/ontology#CardiovascularDisease match was found for found for 'cardiovascular disease' node\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.769313\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.769628\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.769899\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'chemical compound' in category 'classes'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.770226\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.770777\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'smoking history' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.771177\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.771432\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'research method' in category 'classes'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.771696\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.771952\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'cohort study' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.772202\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:40:55.772565\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mhttp://example.org/ontology#ModerateCoffeeConsumption match was found for found for 'moderate coffee consumption' node\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:40:58.393172\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task started: `summarize_text`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.885405\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.886605\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.887338\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.888151\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.888781\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.889249\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.889792\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.890369\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.890717\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.891286\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.891705\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.892208\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.892732\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.893359\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.893834\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.894316\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.894743\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'methodology' in category 'classes'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.895096\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'cox regression models' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.895355\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.895772\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for '2021-04-09' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.896129\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'nutrients 2021, 13, 1241' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.896884\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.897158\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'dietary habit' in category 'classes'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.897435\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.897846\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mhttp://example.org/ontology#CardiovascularDisease match was found for found for 'cardiovascular disease (cvd)' node\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.899072\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mhttp://example.org/ontology#Cancer match was found for found for 'cancer' node\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.900268\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.900642\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.901014\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.901370\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.901726\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'research finding' in category 'classes'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.902070\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'coffee death association' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.902364\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'coffee type' in category 'classes'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.902739\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'coffee consumption types' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.903068\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.903419\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.903728\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'chemical compound' in category 'classes'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.904073\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.904441\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'chlorogenic acid' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.904846\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'trigonelline' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.905223\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'melanoidins' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.905559\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'health benefit' in category 'classes'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.905871\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'coffee consumption mortality reduction' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.906210\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.906508\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'coffee' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.906740\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.907285\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.907833\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'adult population' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.908178\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'lifestyle' in category 'classes'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.908658\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mhttp://example.org/ontology#MediterraneanDiet match was found for found for 'mediterranean lifestyle' node\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.909236\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'chronic illness' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.909603\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.909852\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'research study' in category 'classes'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.910155\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'nutritional study' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.910525\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'study participants' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.910775\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'institution' in category 'classes'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.911136\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'ethics committee' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:00.911403\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'data type' in category 'classes'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:00.911738\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'data contribution' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:03.240933\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task started: `add_data_points`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:04.242533\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task started: `summarize_text`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:05.771183\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task completed: `add_data_points`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:05.771815\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task completed: `summarize_text`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:05.772143\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_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:05.772389\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_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:05.772610\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task completed: `check_permissions_on_dataset`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:05.772909\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task completed: `classify_documents`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:05.773236\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mPipeline run completed: `325268f2-318a-5318-8570-3616626129ed`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_with_telemetry()\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:11.284104\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task started: `add_data_points`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:15.335459\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task completed: `add_data_points`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:15.336033\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task completed: `summarize_text`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:15.336293\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_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:15.336526\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_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:15.336901\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task completed: `check_permissions_on_dataset`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:15.337200\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task completed: `classify_documents`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:15.337497\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mPipeline run completed: `325268f2-318a-5318-8570-3616626129ed`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_with_telemetry()\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:15.351757\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mGraph projection completed: 126 nodes, 264 edges in 0.00s\u001b[0m [\u001b[0m\u001b[1m\u001b[34mCogneeGraph\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:15.656347\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mVector collection retrieval completed: Retrieved distances from 6 collections in 0.09s\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.shared.logging_utils\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:17.595983\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mGraph projection completed: 126 nodes, 264 edges in 0.01s\u001b[0m [\u001b[0m\u001b[1m\u001b[34mCogneeGraph\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:18.045113\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mVector collection retrieval completed: Retrieved distances from 6 collections in 0.09s\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.shared.logging_utils\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:19.425864\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mGraph projection completed: 126 nodes, 264 edges in 0.01s\u001b[0m [\u001b[0m\u001b[1m\u001b[34mCogneeGraph\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:19.711301\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mVector collection retrieval completed: Retrieved distances from 6 collections in 0.08s\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.shared.logging_utils\u001b[0m]\u001b[0m\n",
|
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"\n",
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"\u001b[2m2025-10-07T20:41:21.796373\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mGraph projection completed: 126 nodes, 264 edges in 0.01s\u001b[0m [\u001b[0m\u001b[1m\u001b[34mCogneeGraph\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:22.366335\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mVector collection retrieval completed: Retrieved distances from 6 collections in 0.09s\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.shared.logging_utils\u001b[0m]\u001b[0m\n"
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]
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},
|
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{
|
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"name": "stdout",
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"output_type": "stream",
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"text": [
|
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"Q: What are common risk factors for Type 2 Diabetes?\n",
|
|
"A: ['Common risk factors for Type 2 Diabetes include:\\n1. Obesity\\n2. Hypertension (high blood pressure)\\n3. High cholesterol\\n4. Smoking\\n5. Cardiovascular disease\\n6. Heart failure']\n",
|
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"\n",
|
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"Q: What preventive measures reduce the risk of Hypertension?\n",
|
|
"A: ['Preventive measures to reduce the risk of hypertension include:\\n1. Low sodium diet\\n2. Moderate coffee consumption\\n3. Regular exercise\\n4. Maintaining a healthy lifestyle']\n",
|
|
"\n",
|
|
"Q: What symptoms indicate possible Cardiovascular Disease?\n",
|
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"A: ['Symptoms indicating possible cardiovascular disease include:\\n1. Chest pain\\n2. Shortness of breath\\n3. Fatigue']\n",
|
|
"\n",
|
|
"Q: What diseases are associated with Obesity?\n",
|
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"A: ['Diseases associated with obesity include cardiovascular disease, diabetes, hypertension, high cholesterol, and high blood pressure.']\n",
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"\n"
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]
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},
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"\n",
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"\u001b[2m2025-10-07T20:41:48.134301\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mLoaded JSON extension \u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.shared.logging_utils\u001b[0m]\u001b[0m\n"
|
|
]
|
|
}
|
|
],
|
|
"source": [
|
|
"from cognee.modules.ontology.rdf_xml.RDFLibOntologyResolver import RDFLibOntologyResolver\n",
|
|
"from cognee.modules.ontology.ontology_config import Config\n",
|
|
"# 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",
|
|
"config: Config = {\n",
|
|
" \"ontology_config\": {\n",
|
|
" \"ontology_resolver\": RDFLibOntologyResolver(ontology_file=ontology_path)\n",
|
|
" }\n",
|
|
" }\n",
|
|
"\n",
|
|
"# Run with ontology\n",
|
|
"print(\"\\n--- Results WITH ontology ---\\n\")\n",
|
|
"await run_pipeline(config=config)\n",
|
|
"answers_with = await query_pipeline(questions)\n",
|
|
"for q, a in zip(questions, answers_with):\n",
|
|
" print(f\"Q: {q}\\nA: {a}\\n\")"
|
|
]
|
|
},
|
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{
|
|
"cell_type": "code",
|
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"execution_count": 5,
|
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"id": "3aa18f4cdd5ceff6",
|
|
"metadata": {},
|
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"outputs": [
|
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{
|
|
"name": "stderr",
|
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"output_type": "stream",
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"text": [
|
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"\n",
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"\u001b[2m2025-10-07T20:41:23.957345\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mDeleted Kuzu database files at /Users/daulet/Desktop/dev/cognee-claude/cognee/.cognee_system/databases/cognee_graph_kuzu\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.shared.logging_utils\u001b[0m]\u001b[0m\n"
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]
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},
|
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{
|
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"name": "stdout",
|
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"output_type": "stream",
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"text": [
|
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"\n",
|
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"--- Results WITHOUT ontology ---\n",
|
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"\n"
|
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]
|
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},
|
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"\n",
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"\u001b[2m2025-10-07T20:41:25.980678\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[0m\n",
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"\n",
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"\u001b[1mDeleting cache... \u001b[0m\n",
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"\n",
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"\u001b[1m✓ Cache deleted successfully! \u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:26.100988\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mPipeline run started: `d7e0340c-b6c6-568f-856c-b9f4347628d4`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_with_telemetry()\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:26.101412\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task started: `resolve_data_directories`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:26.101746\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task started: `ingest_data`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:26.102449\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mPipeline run started: `d7e0340c-b6c6-568f-856c-b9f4347628d4`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_with_telemetry()\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:26.102713\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task started: `resolve_data_directories`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:26.103039\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task started: `ingest_data`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
|
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"\n",
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"\u001b[2m2025-10-07T20:41:26.115879\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mProcessing PDF: /Users/daulet/Desktop/dev/cognee/examples/data/scientific_papers/TOJ-22-0073_152Mendoza.pdf\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.infrastructure.loaders.external.advanced_pdf_loader\u001b[0m]\u001b[0m\n"
|
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]
|
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},
|
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{
|
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"name": "stdout",
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"output_type": "stream",
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"text": [
|
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"User 215612a9-f107-44d8-9263-d680872182c9 has registered.\n"
|
|
]
|
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},
|
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{
|
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"\n",
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"\u001b[1mReading PDF for file: /Users/daulet/Desktop/dev/cognee/examples/data/scientific_papers/TOJ-22-0073_152Mendoza.pdf ...\u001b[0m\n",
|
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"\n",
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"\u001b[2m2025-10-07T20:41:26.605043\u001b[0m [\u001b[33m\u001b[1mwarning \u001b[0m] \u001b[1mFailed to process PDF with AdvancedPdfLoader: Unable to get page count. Is poppler installed and in PATH?\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.infrastructure.loaders.external.advanced_pdf_loader\u001b[0m]\u001b[0m\n",
|
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"\n",
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"\u001b[2m2025-10-07T20:41:26.605986\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mFalling back to PyPDF loader for /Users/daulet/Desktop/dev/cognee/examples/data/scientific_papers/TOJ-22-0073_152Mendoza.pdf\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.infrastructure.loaders.external.advanced_pdf_loader\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:26.606982\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mReading PDF: /Users/daulet/Desktop/dev/cognee/examples/data/scientific_papers/TOJ-22-0073_152Mendoza.pdf\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.infrastructure.loaders.external.pypdf_loader\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:26.714728\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mProcessing PDF: /Users/daulet/Desktop/dev/cognee/examples/data/scientific_papers/nutrients-13-01241.pdf\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.infrastructure.loaders.external.advanced_pdf_loader\u001b[0m]\u001b[0m\n"
|
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]
|
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},
|
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{
|
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"name": "stdout",
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"output_type": "stream",
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"text": [
|
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"Warning: No languages specified, defaulting to English.\n"
|
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]
|
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},
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"\n",
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"\u001b[1mReading PDF for file: /Users/daulet/Desktop/dev/cognee/examples/data/scientific_papers/nutrients-13-01241.pdf ...\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:27.139496\u001b[0m [\u001b[33m\u001b[1mwarning \u001b[0m] \u001b[1mFailed to process PDF with AdvancedPdfLoader: Unable to get page count. Is poppler installed and in PATH?\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.infrastructure.loaders.external.advanced_pdf_loader\u001b[0m]\u001b[0m\n",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:41:27.140291\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mFalling back to PyPDF loader for /Users/daulet/Desktop/dev/cognee/examples/data/scientific_papers/nutrients-13-01241.pdf\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.infrastructure.loaders.external.advanced_pdf_loader\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:27.142512\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mReading PDF: /Users/daulet/Desktop/dev/cognee/examples/data/scientific_papers/nutrients-13-01241.pdf\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.infrastructure.loaders.external.pypdf_loader\u001b[0m]\u001b[0m\n",
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"\n",
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"\u001b[2m2025-10-07T20:41:27.289235\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task completed: `ingest_data`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:41:27.289621\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task completed: `resolve_data_directories`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:41:27.289895\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mPipeline run completed: `d7e0340c-b6c6-568f-856c-b9f4347628d4`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_with_telemetry()\u001b[0m]\u001b[0m\n",
|
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"\n",
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"\u001b[2m2025-10-07T20:41:27.291659\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task completed: `ingest_data`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:41:27.291909\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task completed: `resolve_data_directories`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:41:27.292199\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mPipeline run completed: `d7e0340c-b6c6-568f-856c-b9f4347628d4`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_with_telemetry()\u001b[0m]\u001b[0m\n",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:41:27.298546\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mOntology file 'None' not found. No owl ontology will be attached to the graph.\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
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"\u001b[2m2025-10-07T20:41:27.315361\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mPipeline run started: `8919119c-bee5-5ff1-bc01-794e8a1015ad`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_with_telemetry()\u001b[0m]\u001b[0m\n",
|
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"\n",
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"\u001b[2m2025-10-07T20:41:27.315730\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task started: `classify_documents`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
|
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"\n",
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"\u001b[2m2025-10-07T20:41:27.316096\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task started: `check_permissions_on_dataset`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:41:27.316653\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mPipeline run started: `8919119c-bee5-5ff1-bc01-794e8a1015ad`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_with_telemetry()\u001b[0m]\u001b[0m\n",
|
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"\n",
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"\u001b[2m2025-10-07T20:41:27.316910\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task started: `classify_documents`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
|
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"\n",
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"\u001b[2m2025-10-07T20:41:27.317200\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task started: `check_permissions_on_dataset`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:41:27.323905\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_base\u001b[0m]\u001b[0m\n"
|
|
]
|
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},
|
|
{
|
|
"name": "stdout",
|
|
"output_type": "stream",
|
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"text": [
|
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"Warning: No languages specified, defaulting to English.\n"
|
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]
|
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},
|
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{
|
|
"name": "stderr",
|
|
"output_type": "stream",
|
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"text": [
|
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"\n",
|
|
"\u001b[2m2025-10-07T20:41:27.349508\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_base\u001b[0m]\u001b[0m\n",
|
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"\n",
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"\u001b[2m2025-10-07T20:41:27.387202\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_base\u001b[0m]\u001b[0m\n",
|
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"\n",
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"\u001b[2m2025-10-07T20:41:27.398908\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_base\u001b[0m]\u001b[0m\n",
|
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"\n",
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"\u001b[2m2025-10-07T20:41:48.152674\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",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:41:48.153506\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",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:41:48.154051\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",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:41:48.154641\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",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:41:48.155119\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",
|
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"\n",
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"\u001b[2m2025-10-07T20:41:48.155502\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",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:41:48.155919\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",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:41:48.156428\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",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:41:48.156854\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'location' in category 'classes'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:41:48.157224\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",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:41:48.157532\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",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:41:48.157904\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",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:41:48.158267\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",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:41:48.158702\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'nutrients' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:41:48.159018\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",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:41:48.159393\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for '2021-03-17' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:41:48.159738\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for '2021-04-07' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
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"\n",
|
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"\u001b[2m2025-10-07T20:41:48.160058\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for '2021-04-09' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
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"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.160442\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.160809\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'coffee' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.161047\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.161404\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.161735\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'cancer' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.162033\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'license' in category 'classes'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.162473\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'cc by' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.162946\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.163295\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.163722\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.164014\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.164319\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.164705\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.165120\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.165394\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.165657\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'statistical measure' in category 'classes'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.165990\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'coffees hazard ratio' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.166280\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'medical condition' in category 'classes'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.166547\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.166889\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'measurement' in category 'classes'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.167111\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'person years' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.167340\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.167630\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'person' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.167945\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.169055\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.169486\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'moderate coffee consumption' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.169838\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.170109\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'spanish population' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.170432\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.170773\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'study design' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.171027\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'self-reported data' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.171340\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'chronic illness' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.171649\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'nutrition survey' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.171924\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.172150\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'ethical committee' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.172534\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'health outcomes' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.172825\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'coffee preparation method' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.173190\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'statistical power' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.173499\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'informed consent' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:48.173800\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'sample size' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.669259\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.669912\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'michael f. mendoza, md' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.670464\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'ralf martz sulague, md' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.670996\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'therese posas-mendoza, md' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.671558\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'carl j. lavie, md' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.671838\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.672203\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.672619\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.672998\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.673312\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.673566\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.673909\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.674199\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.674587\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.674834\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.675105\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.675428\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.675730\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'study period 2000-2021' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.676116\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'coffee consumption effects' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.676405\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'research type' in category 'classes'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.676642\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.676924\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'pilot study' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.677362\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.677669\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'coffee' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.678008\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'chemicalcompound' in category 'classes'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.678326\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.678644\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'medicalcondition' in category 'classes'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.678986\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.679278\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.679582\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",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.679851\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'smoking' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.680130\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'chlorogenic acid' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.680382\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'moderate coffee consumption' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.680667\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'researchstudy' in category 'classes'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.680968\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'health studies' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.681265\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'researchmethod' in category 'classes'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.681565\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'medicalprocedure' in category 'classes'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.681841\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mNo close match found for 'cardiac surgery' in category 'individuals'\u001b[0m [\u001b[0m\u001b[1m\u001b[34mOntologyAdapter\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:50.725265\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task started: `summarize_text`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:53.910668\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task started: `summarize_text`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:57.080341\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task started: `add_data_points`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:59.770067\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task started: `add_data_points`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:59.803614\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task completed: `add_data_points`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:59.804032\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task completed: `summarize_text`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:59.804279\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_base\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:59.804531\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_base\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:59.804800\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task completed: `check_permissions_on_dataset`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:59.805061\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task completed: `classify_documents`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:41:59.805294\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mPipeline run completed: `8919119c-bee5-5ff1-bc01-794e8a1015ad`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_with_telemetry()\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:42:02.709736\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task completed: `add_data_points`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:42:02.710292\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task completed: `summarize_text`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:42:02.710708\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_base\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:42:02.711324\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_base\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:42:02.711677\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task completed: `check_permissions_on_dataset`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:42:02.712008\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mCoroutine task completed: `classify_documents`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_base\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:42:02.712225\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mPipeline run completed: `8919119c-bee5-5ff1-bc01-794e8a1015ad`\u001b[0m [\u001b[0m\u001b[1m\u001b[34mrun_tasks_with_telemetry()\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:42:02.725796\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mGraph projection completed: 97 nodes, 209 edges in 0.00s\u001b[0m [\u001b[0m\u001b[1m\u001b[34mCogneeGraph\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:42:03.005337\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mVector collection retrieval completed: Retrieved distances from 6 collections in 0.07s\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.shared.logging_utils\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:42:05.945308\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mGraph projection completed: 97 nodes, 209 edges in 0.00s\u001b[0m [\u001b[0m\u001b[1m\u001b[34mCogneeGraph\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:42:07.476846\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mVector collection retrieval completed: Retrieved distances from 6 collections in 0.08s\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.shared.logging_utils\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:42:11.047320\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mGraph projection completed: 97 nodes, 209 edges in 0.01s\u001b[0m [\u001b[0m\u001b[1m\u001b[34mCogneeGraph\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:42:11.394591\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mVector collection retrieval completed: Retrieved distances from 6 collections in 0.08s\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.shared.logging_utils\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:42:14.634449\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mGraph projection completed: 97 nodes, 209 edges in 0.01s\u001b[0m [\u001b[0m\u001b[1m\u001b[34mCogneeGraph\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:42:14.913245\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mVector collection retrieval completed: Retrieved distances from 6 collections in 0.07s\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.shared.logging_utils\u001b[0m]\u001b[0m\n"
|
|
]
|
|
},
|
|
{
|
|
"name": "stdout",
|
|
"output_type": "stream",
|
|
"text": [
|
|
"Q: What are common risk factors for Type 2 Diabetes?\n",
|
|
"A: ['Common risk factors for Type 2 Diabetes include obesity (as indicated by a body mass index of 25 kg/m² or more), sedentary lifestyle, poor dietary habits, smoking habits, and the presence of chronic conditions such as hypertension and high blood cholesterol. Additionally, waist circumference measurement can indicate risk levels, with increased risk seen in men with a waist over 102 cm and women over 88 cm.']\n",
|
|
"\n",
|
|
"Q: What preventive measures reduce the risk of Hypertension?\n",
|
|
"A: ['Preventive measures to reduce the risk of hypertension include:\\n1. **Moderate Coffee Consumption**: Regular moderate coffee consumption (1-4 cups per day) is associated with a decreased risk of developing hypertension.\\n2. **Dietary Antioxidants**: Coffee contains antioxidants, such as chlorogenic acid, which may inhibit inflammation and support cardiovascular health.\\n3. **Healthy Preparation Methods**: Choosing filtered coffee over boiled coffee can reduce cholesterol levels and promote better heart health.\\n4. **Lifestyle Factors**: Maintaining overall cardiovascular health through lifestyle choices can also contribute to lowering the risk of hypertension.']\n",
|
|
"\n",
|
|
"Q: What symptoms indicate possible Cardiovascular Disease?\n",
|
|
"A: ['Possible symptoms indicating cardiovascular disease include:\\n1. Chest pain or discomfort\\n2. Shortness of breath\\n3. Fatigue or weakness\\n4. Irregular heartbeat\\n5. Swelling in the legs, ankles, or feet \\n6. Lightheadedness or dizziness \\n7. Nausea or cold sweat \\n\\nIt is important to consult a healthcare professional for proper diagnosis and treatment.']\n",
|
|
"\n",
|
|
"Q: What diseases are associated with Obesity?\n",
|
|
"A: ['Diseases associated with obesity include cardiovascular disease, diabetes, and hypertension. Obesity is a significant risk factor for these health conditions, often leading to increased mortality and other health complications.']\n",
|
|
"\n"
|
|
]
|
|
}
|
|
],
|
|
"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\")"
|
|
]
|
|
},
|
|
{
|
|
"cell_type": "markdown",
|
|
"id": "c60533d2423acdb0",
|
|
"metadata": {},
|
|
"source": [
|
|
"## Visualizing the Knowledge Graph\n",
|
|
"\n",
|
|
"Let's visualize how our ontology connects different medical concepts:"
|
|
]
|
|
},
|
|
{
|
|
"cell_type": "code",
|
|
"execution_count": 6,
|
|
"id": "36ee2a360f47a054",
|
|
"metadata": {},
|
|
"outputs": [
|
|
{
|
|
"name": "stderr",
|
|
"output_type": "stream",
|
|
"text": [
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:42:22.959024\u001b[0m [\u001b[32m\u001b[1minfo \u001b[0m] \u001b[1mGraph visualization saved as /Users/daulet/graph_visualization.html\u001b[0m [\u001b[0m\u001b[1m\u001b[34mcognee.shared.logging_utils\u001b[0m]\u001b[0m\n",
|
|
"\n",
|
|
"\u001b[2m2025-10-07T20:42:22.959720\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\n"
|
|
]
|
|
},
|
|
{
|
|
"data": {
|
|
"text/plain": [
|
|
"'/Users/daulet/graph_visualization.html'"
|
|
]
|
|
},
|
|
"metadata": {},
|
|
"output_type": "display_data"
|
|
},
|
|
{
|
|
"data": {
|
|
"text/plain": [
|
|
"True"
|
|
]
|
|
},
|
|
"execution_count": 6,
|
|
"metadata": {},
|
|
"output_type": "execute_result"
|
|
}
|
|
],
|
|
"source": [
|
|
"import webbrowser\n",
|
|
"import os\n",
|
|
"from cognee.api.v1.visualize.visualize import visualize_graph\n",
|
|
"html = await visualize_graph()\n",
|
|
"home_dir = os.path.expanduser(\"~\")\n",
|
|
"html_file = os.path.join(home_dir, \"graph_visualization.html\")\n",
|
|
"display(html_file)\n",
|
|
"webbrowser.open(f\"file://{html_file}\")"
|
|
]
|
|
},
|
|
{
|
|
"cell_type": "markdown",
|
|
"id": "ff39326921b75273",
|
|
"metadata": {},
|
|
"source": [
|
|
"## 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"
|
|
]
|
|
},
|
|
{
|
|
"cell_type": "code",
|
|
"execution_count": null,
|
|
"id": "8d2a0fe555a7bc0f",
|
|
"metadata": {},
|
|
"outputs": [
|
|
{
|
|
"ename": "",
|
|
"evalue": "",
|
|
"output_type": "error",
|
|
"traceback": [
|
|
"\u001b[1;31mThe Kernel crashed while executing code in the current cell or a previous cell. \n",
|
|
"\u001b[1;31mPlease review the code in the cell(s) to identify a possible cause of the failure. \n",
|
|
"\u001b[1;31mClick <a href='https://aka.ms/vscodeJupyterKernelCrash'>here</a> for more info. \n",
|
|
"\u001b[1;31mView Jupyter <a href='command:jupyter.viewOutput'>log</a> for further details."
|
|
]
|
|
}
|
|
],
|
|
"source": [
|
|
"# Only exit in interactive mode, not during GitHub Actions\n",
|
|
"import os\n",
|
|
"\n",
|
|
"# Skip exit if we're running in GitHub Actions\n",
|
|
"if not os.environ.get('GITHUB_ACTIONS'):\n",
|
|
" print(\"Exiting kernel to clean up resources...\")\n",
|
|
" os._exit(0)\n",
|
|
"else:\n",
|
|
" print(\"Skipping kernel exit - running in GitHub Actions\")"
|
|
]
|
|
},
|
|
{
|
|
"cell_type": "code",
|
|
"execution_count": null,
|
|
"id": "adb6601890237b6a",
|
|
"metadata": {},
|
|
"outputs": [],
|
|
"source": []
|
|
}
|
|
],
|
|
"metadata": {
|
|
"kernelspec": {
|
|
"display_name": ".venv",
|
|
"language": "python",
|
|
"name": "python3"
|
|
},
|
|
"language_info": {
|
|
"codemirror_mode": {
|
|
"name": "ipython",
|
|
"version": 3
|
|
},
|
|
"file_extension": ".py",
|
|
"mimetype": "text/x-python",
|
|
"name": "python",
|
|
"nbconvert_exporter": "python",
|
|
"pygments_lexer": "ipython3",
|
|
"version": "3.10.11"
|
|
}
|
|
},
|
|
"nbformat": 4,
|
|
"nbformat_minor": 5
|
|
}
|