{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 19,
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "huggingface/tokenizers: The current process just got forked, after parallelism has already been used. Disabling parallelism to avoid deadlocks...\n",
      "To disable this warning, you can either:\n",
      "\t- Avoid using `tokenizers` before the fork if possible\n",
      "\t- Explicitly set the environment variable TOKENIZERS_PARALLELISM=(true | false)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Requirement already satisfied: pandas in ./.venv/lib/python3.11/site-packages (2.2.2)\r\n",
      "Requirement already satisfied: pyarrow in ./.venv/lib/python3.11/site-packages (17.0.0)\r\n",
      "Requirement already satisfied: tqdm in ./.venv/lib/python3.11/site-packages (4.66.4)\r\n",
      "Requirement already satisfied: nltk in ./.venv/lib/python3.11/site-packages (3.8.1)\r\n",
      "Requirement already satisfied: sentence-transformers in ./.venv/lib/python3.11/site-packages (3.0.1)\r\n",
      "Requirement already satisfied: huggingface_hub in ./.venv/lib/python3.11/site-packages (0.24.3)\r\n",
      "Requirement already satisfied: pyyaml in ./.venv/lib/python3.11/site-packages (6.0.1)\r\n",
      "Requirement already satisfied: numpy>=1.23.2 in ./.venv/lib/python3.11/site-packages (from pandas) (2.0.1)\r\n",
      "Requirement already satisfied: python-dateutil>=2.8.2 in ./.venv/lib/python3.11/site-packages (from pandas) (2.9.0.post0)\r\n",
      "Requirement already satisfied: pytz>=2020.1 in ./.venv/lib/python3.11/site-packages (from pandas) (2024.1)\r\n",
      "Requirement already satisfied: tzdata>=2022.7 in ./.venv/lib/python3.11/site-packages (from pandas) (2024.1)\r\n",
      "Requirement already satisfied: click in ./.venv/lib/python3.11/site-packages (from nltk) (8.1.7)\r\n",
      "Requirement already satisfied: joblib in ./.venv/lib/python3.11/site-packages (from nltk) (1.4.2)\r\n",
      "Requirement already satisfied: regex>=2021.8.3 in ./.venv/lib/python3.11/site-packages (from nltk) (2024.7.24)\r\n",
      "Requirement already satisfied: transformers<5.0.0,>=4.34.0 in ./.venv/lib/python3.11/site-packages (from sentence-transformers) (4.43.3)\r\n",
      "Requirement already satisfied: torch>=1.11.0 in ./.venv/lib/python3.11/site-packages (from sentence-transformers) (2.4.0)\r\n",
      "Requirement already satisfied: scikit-learn in ./.venv/lib/python3.11/site-packages (from sentence-transformers) (1.5.1)\r\n",
      "Requirement already satisfied: scipy in ./.venv/lib/python3.11/site-packages (from sentence-transformers) (1.14.0)\r\n",
      "Requirement already satisfied: Pillow in ./.venv/lib/python3.11/site-packages (from sentence-transformers) (10.4.0)\r\n",
      "Requirement already satisfied: filelock in ./.venv/lib/python3.11/site-packages (from huggingface_hub) (3.15.4)\r\n",
      "Requirement already satisfied: fsspec>=2023.5.0 in ./.venv/lib/python3.11/site-packages (from huggingface_hub) (2024.6.1)\r\n",
      "Requirement already satisfied: packaging>=20.9 in ./.venv/lib/python3.11/site-packages (from huggingface_hub) (24.1)\r\n",
      "Requirement already satisfied: requests in ./.venv/lib/python3.11/site-packages (from huggingface_hub) (2.32.3)\r\n",
      "Requirement already satisfied: typing-extensions>=3.7.4.3 in ./.venv/lib/python3.11/site-packages (from huggingface_hub) (4.12.2)\r\n",
      "Requirement already satisfied: six>=1.5 in ./.venv/lib/python3.11/site-packages (from python-dateutil>=2.8.2->pandas) (1.16.0)\r\n",
      "Requirement already satisfied: sympy in ./.venv/lib/python3.11/site-packages (from torch>=1.11.0->sentence-transformers) (1.13.1)\r\n",
      "Requirement already satisfied: networkx in ./.venv/lib/python3.11/site-packages (from torch>=1.11.0->sentence-transformers) (3.3)\r\n",
      "Requirement already satisfied: jinja2 in ./.venv/lib/python3.11/site-packages (from torch>=1.11.0->sentence-transformers) (3.1.4)\r\n",
      "Requirement already satisfied: safetensors>=0.4.1 in ./.venv/lib/python3.11/site-packages (from transformers<5.0.0,>=4.34.0->sentence-transformers) (0.4.3)\r\n",
      "Requirement already satisfied: tokenizers<0.20,>=0.19 in ./.venv/lib/python3.11/site-packages (from transformers<5.0.0,>=4.34.0->sentence-transformers) (0.19.1)\r\n",
      "Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv/lib/python3.11/site-packages (from requests->huggingface_hub) (3.3.2)\r\n",
      "Requirement already satisfied: idna<4,>=2.5 in ./.venv/lib/python3.11/site-packages (from requests->huggingface_hub) (3.7)\r\n",
      "Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv/lib/python3.11/site-packages (from requests->huggingface_hub) (2.2.2)\r\n",
      "Requirement already satisfied: certifi>=2017.4.17 in ./.venv/lib/python3.11/site-packages (from requests->huggingface_hub) (2024.7.4)\r\n",
      "Requirement already satisfied: threadpoolctl>=3.1.0 in ./.venv/lib/python3.11/site-packages (from scikit-learn->sentence-transformers) (3.5.0)\r\n",
      "Requirement already satisfied: MarkupSafe>=2.0 in ./.venv/lib/python3.11/site-packages (from jinja2->torch>=1.11.0->sentence-transformers) (2.1.5)\r\n",
      "Requirement already satisfied: mpmath<1.4,>=1.1.0 in ./.venv/lib/python3.11/site-packages (from sympy->torch>=1.11.0->sentence-transformers) (1.3.0)\r\n",
      "\r\n",
      "\u001B[1m[\u001B[0m\u001B[34;49mnotice\u001B[0m\u001B[1;39;49m]\u001B[0m\u001B[39;49m A new release of pip is available: \u001B[0m\u001B[31;49m24.0\u001B[0m\u001B[39;49m -> \u001B[0m\u001B[32;49m24.2\u001B[0m\r\n",
      "\u001B[1m[\u001B[0m\u001B[34;49mnotice\u001B[0m\u001B[1;39;49m]\u001B[0m\u001B[39;49m To update, run: \u001B[0m\u001B[32;49mpip install --upgrade pip\u001B[0m\r\n"
     ]
    }
   ],
   "source": [
    "!pip install pandas pyarrow tqdm nltk sentence-transformers huggingface_hub pyyaml\n"
   ],
   "metadata": {
    "collapsed": false,
    "ExecuteTime": {
     "end_time": "2024-07-30T17:30:02.287615Z",
     "start_time": "2024-07-30T17:29:59.759060Z"
    }
   },
   "id": "7c4973586542f9f0"
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "[nltk_data] Downloading package punkt to /Users/jtr4v/nltk_data...\n",
      "[nltk_data]   Package punkt is already up-to-date!\n"
     ]
    },
    {
     "data": {
      "text/plain": "True"
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Import necessary libraries\n",
    "from huggingface_hub import HfApi, create_repo\n",
    "import yaml\n",
    "import nltk\n",
    "\n",
    "import requests\n",
    "from tqdm import tqdm\n",
    "from xml.etree import ElementTree as ET\n",
    "import pandas as pd\n",
    "from nltk.tokenize import sent_tokenize\n",
    "from sentence_transformers import SentenceTransformer\n",
    "import warnings\n",
    "\n",
    "# Download NLTK data\n",
    "nltk.download('punkt')\n"
   ],
   "metadata": {
    "collapsed": false,
    "ExecuteTime": {
     "end_time": "2024-07-30T17:30:02.408371Z",
     "start_time": "2024-07-30T17:30:02.291039Z"
    }
   },
   "id": "829144ba3dfd450a"
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "outputs": [],
   "source": [
    "# Read the PMIDs from the file\n",
    "pmid_file_path = './pmids.txt'\n",
    "with open(pmid_file_path, 'r') as f:\n",
    "    pmids = f.read().splitlines()\n"
   ],
   "metadata": {
    "collapsed": false,
    "ExecuteTime": {
     "end_time": "2024-07-30T17:30:02.412528Z",
     "start_time": "2024-07-30T17:30:02.405680Z"
    }
   },
   "id": "363e4cd840e6d77e"
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "outputs": [],
   "source": [
    "# Function to fetch a PubMed article in XML format by its PMID\n",
    "def fetch_pubmed_article(pmid):\n",
    "    url = f\"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id={pmid}&retmode=xml\"\n",
    "    response = requests.get(url, headers={\"Accept-Encoding\": \"identity\"})\n",
    "    if response.status_code == 200:\n",
    "        return response.content\n",
    "    else:\n",
    "        return None"
   ],
   "metadata": {
    "collapsed": false,
    "ExecuteTime": {
     "end_time": "2024-07-30T17:30:02.412760Z",
     "start_time": "2024-07-30T17:30:02.410489Z"
    }
   },
   "id": "82ba593571b15599"
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "outputs": [],
   "source": [
    "# Initialize the sentence transformer model\n",
    "model = SentenceTransformer('all-MiniLM-L6-v2')\n"
   ],
   "metadata": {
    "collapsed": false,
    "ExecuteTime": {
     "end_time": "2024-07-30T17:30:03.403884Z",
     "start_time": "2024-07-30T17:30:02.413859Z"
    }
   },
   "id": "82bcb60f882f9c64"
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Downloading PubMed Articles:   1%|          | 69/6593 [00:24<32:04,  3.39it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:28187491 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:   1%|          | 73/6593 [00:25<31:16,  3.47it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:2143909 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:   2%|▏         | 106/6593 [00:38<48:29,  2.23it/s] /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:1016976 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:   2%|▏         | 137/6593 [00:52<41:05,  2.62it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:11942911 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:   5%|▍         | 319/6593 [01:53<29:38,  3.53it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:2908603 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:   5%|▌         | 332/6593 [01:58<42:48,  2.44it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:3074131 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:   5%|▌         | 343/6593 [02:00<28:15,  3.69it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:3570023 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:   5%|▌         | 346/6593 [02:02<46:46,  2.23it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:4060747 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:   5%|▌         | 348/6593 [02:02<41:12,  2.53it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:4365448 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:   5%|▌         | 349/6593 [02:02<33:57,  3.06it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:4835320 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:   6%|▌         | 370/6593 [02:16<1:23:10,  1.25it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:7772169 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:   6%|▌         | 374/6593 [02:18<47:20,  2.19it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:7947003 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:   6%|▌         | 377/6593 [02:19<40:05,  2.58it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:8142059 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:   7%|▋         | 432/6593 [02:38<39:07,  2.62it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:14022451 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:   7%|▋         | 457/6593 [02:44<20:18,  5.03it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:12436453 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:   7%|▋         | 471/6593 [02:48<27:08,  3.76it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:13678886 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:   8%|▊         | 538/6593 [03:11<36:50,  2.74it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:31987274 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:   8%|▊         | 540/6593 [03:11<25:18,  3.99it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:35593795 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:   8%|▊         | 551/6593 [03:14<27:31,  3.66it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:33410889 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:   9%|▊         | 562/6593 [03:20<58:04,  1.73it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:35553753 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:   9%|▊         | 564/6593 [03:21<36:03,  2.79it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:35556797 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  10%|▉         | 629/6593 [03:42<56:36,  1.76it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:20799915 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  10%|▉         | 637/6593 [03:44<24:29,  4.05it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:15656346 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  10%|▉         | 655/6593 [03:49<29:30,  3.35it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:6076978 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  10%|▉         | 657/6593 [03:49<21:30,  4.60it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:6896473 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  10%|█         | 660/6593 [03:49<16:30,  5.99it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:11765729 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  11%|█         | 699/6593 [04:04<38:42,  2.54it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:13644254 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  11%|█▏        | 748/6593 [04:19<36:40,  2.66it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:33390801 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  12%|█▏        | 798/6593 [04:38<35:33,  2.72it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:31824318 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  13%|█▎        | 837/6593 [04:50<22:12,  4.32it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:7563172 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  13%|█▎        | 860/6593 [04:58<24:45,  3.86it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:26935538 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  13%|█▎        | 872/6593 [05:03<37:54,  2.52it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:31565830 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  14%|█▍        | 926/6593 [05:22<24:14,  3.90it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:34900981 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  15%|█▍        | 980/6593 [05:38<31:58,  2.93it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:33854437 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  15%|█▌        | 989/6593 [05:41<28:38,  3.26it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:34490047 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  15%|█▌        | 996/6593 [05:43<22:24,  4.16it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:31592109 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  16%|█▌        | 1044/6593 [05:59<28:02,  3.30it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:34751591 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  16%|█▌        | 1060/6593 [06:04<33:44,  2.73it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:3131240 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  16%|█▌        | 1069/6593 [06:07<22:03,  4.17it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:26935012 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  17%|█▋        | 1136/6593 [06:28<31:24,  2.90it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32707827 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  18%|█▊        | 1170/6593 [06:38<20:50,  4.34it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:15642182 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  18%|█▊        | 1171/6593 [06:38<20:15,  4.46it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:20030877 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  19%|█▉        | 1239/6593 [06:57<24:19,  3.67it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32136111 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  19%|█▉        | 1246/6593 [06:58<20:26,  4.36it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:34860884 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  19%|█▉        | 1255/6593 [07:01<26:21,  3.38it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32120753 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  19%|█▉        | 1258/6593 [07:01<16:24,  5.42it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32436244 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  19%|█▉        | 1260/6593 [07:02<14:30,  6.12it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:33300953 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  19%|█▉        | 1264/6593 [07:02<20:10,  4.40it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:34628993 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  19%|█▉        | 1266/6593 [07:03<15:42,  5.65it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:34867401 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  19%|█▉        | 1275/6593 [07:06<31:36,  2.80it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:20032127 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  20%|██        | 1349/6593 [07:33<33:09,  2.64it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:29665663 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  21%|██        | 1363/6593 [07:37<20:09,  4.32it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:36476018 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  21%|██        | 1385/6593 [07:45<29:37,  2.93it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:9260607 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  21%|██        | 1393/6593 [07:46<24:32,  3.53it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:6810311 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  22%|██▏       | 1429/6593 [08:00<22:57,  3.75it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:5083054 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  23%|██▎       | 1489/6593 [08:31<51:28,  1.65it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:11668120 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  23%|██▎       | 1518/6593 [08:42<20:13,  4.18it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:12968098 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  23%|██▎       | 1523/6593 [08:43<17:54,  4.72it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:14668813 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  23%|██▎       | 1542/6593 [08:48<22:59,  3.66it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:15769928 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  24%|██▎       | 1557/6593 [08:51<16:38,  5.04it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:15996830 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  24%|██▍       | 1569/6593 [08:54<24:24,  3.43it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:16341095 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  24%|██▍       | 1570/6593 [08:54<20:58,  3.99it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:16380226 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  24%|██▍       | 1578/6593 [08:56<30:20,  2.75it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:16740543 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  24%|██▍       | 1596/6593 [09:01<23:24,  3.56it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:17114665 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  24%|██▍       | 1602/6593 [09:03<33:11,  2.51it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:17239269 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  24%|██▍       | 1604/6593 [09:04<28:31,  2.92it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:17307082 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  25%|██▍       | 1618/6593 [09:07<22:07,  3.75it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:17685248 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  25%|██▍       | 1627/6593 [09:10<20:47,  3.98it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:18037293 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  25%|██▍       | 1646/6593 [09:19<50:11,  1.64it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:18455358 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  25%|██▌       | 1652/6593 [09:21<23:34,  3.49it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:18565752 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  26%|██▌       | 1716/6593 [09:40<22:50,  3.56it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:20727234 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  27%|██▋       | 1770/6593 [09:56<21:50,  3.68it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:22265695 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  28%|██▊       | 1826/6593 [10:13<27:12,  2.92it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:23867125 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  28%|██▊       | 1855/6593 [10:24<22:13,  3.55it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:24624538 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  29%|██▉       | 1910/6593 [10:54<55:59,  1.39it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:26370026 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  29%|██▉       | 1921/6593 [10:57<43:07,  1.81it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:2679845 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  29%|██▉       | 1937/6593 [11:10<1:05:50,  1.18it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:27165143 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  29%|██▉       | 1944/6593 [11:13<47:25,  1.63it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:27268511 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  30%|██▉       | 1950/6593 [11:16<56:38,  1.37it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:27599035 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  30%|██▉       | 1956/6593 [11:20<45:27,  1.70it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:27790931 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  30%|███       | 1989/6593 [11:36<53:14,  1.44it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:28727864 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  30%|███       | 1990/6593 [11:36<41:38,  1.84it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:28727870 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  30%|███       | 1991/6593 [11:37<33:04,  2.32it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:28727878 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  30%|███       | 1998/6593 [11:40<58:05,  1.32it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:28947566 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  31%|███▏      | 2075/6593 [12:21<1:24:29,  1.12s/it]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:31188955 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  32%|███▏      | 2099/6593 [12:38<40:43,  1.84it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32018570 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  32%|███▏      | 2112/6593 [12:42<21:06,  3.54it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32560000 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  32%|███▏      | 2123/6593 [12:45<22:38,  3.29it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32924570 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  32%|███▏      | 2125/6593 [12:45<16:01,  4.64it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32924574 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  33%|███▎      | 2165/6593 [13:03<19:50,  3.72it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:9376202 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  33%|███▎      | 2180/6593 [13:13<1:09:00,  1.07it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:10326711 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  33%|███▎      | 2190/6593 [13:19<58:38,  1.25it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32136135 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  33%|███▎      | 2194/6593 [13:19<23:29,  3.12it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:33859534 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  33%|███▎      | 2203/6593 [13:26<52:20,  1.40it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:27805627 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  33%|███▎      | 2204/6593 [13:26<40:19,  1.81it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:23335549 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  33%|███▎      | 2208/6593 [13:26<16:19,  4.48it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32084882 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  34%|███▎      | 2221/6593 [13:33<35:57,  2.03it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:33173241 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  34%|███▍      | 2226/6593 [13:36<54:30,  1.34it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:33704214 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  34%|███▍      | 2233/6593 [13:39<53:35,  1.36it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:34296283 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  35%|███▍      | 2294/6593 [14:11<22:51,  3.13it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:19127686 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  35%|███▍      | 2303/6593 [14:17<54:52,  1.30it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:10463993 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  42%|████▏     | 2744/6593 [18:54<42:13,  1.52it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:26069790 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  42%|████▏     | 2745/6593 [18:55<33:20,  1.92it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:28840064 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  42%|████▏     | 2757/6593 [19:02<31:48,  2.01it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:35030448 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  42%|████▏     | 2767/6593 [19:08<38:24,  1.66it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:34946256 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  45%|████▌     | 2982/6593 [21:13<54:05,  1.11it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:33332187 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  46%|████▋     | 3054/6593 [21:50<19:01,  3.10it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32385136 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  47%|████▋     | 3114/6593 [22:24<44:46,  1.29it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:21070449 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  47%|████▋     | 3130/6593 [22:32<25:01,  2.31it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:17443004 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  51%|█████     | 3341/6593 [24:35<32:05,  1.69it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:7169949 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  51%|█████     | 3342/6593 [24:35<25:47,  2.10it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:7438125 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  51%|█████▏    | 3385/6593 [24:55<20:31,  2.61it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:21482991 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  54%|█████▍    | 3549/6593 [26:32<37:43,  1.34it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:20166671 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  55%|█████▌    | 3649/6593 [27:32<32:57,  1.49it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:9733482 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  63%|██████▎   | 4148/6593 [32:35<26:10,  1.56it/s]  /var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:29673161 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  64%|██████▍   | 4247/6593 [33:30<33:44,  1.16it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:25482841 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  67%|██████▋   | 4438/6593 [35:18<14:40,  2.45it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:31338934 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  68%|██████▊   | 4513/6593 [36:01<15:57,  2.17it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:14826937 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  68%|██████▊   | 4514/6593 [36:02<17:23,  1.99it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:5240363 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  68%|██████▊   | 4515/6593 [36:02<13:53,  2.49it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:14151168 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  69%|██████▉   | 4546/6593 [36:15<15:18,  2.23it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:31962547 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  69%|██████▉   | 4547/6593 [36:15<12:17,  2.77it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:31971005 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  69%|██████▉   | 4550/6593 [36:16<07:34,  4.50it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32018484 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  69%|██████▉   | 4553/6593 [36:16<05:28,  6.21it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32057255 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  69%|██████▉   | 4555/6593 [36:17<11:14,  3.02it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32067691 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  69%|██████▉   | 4557/6593 [36:18<10:17,  3.30it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32084729 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  69%|██████▉   | 4561/6593 [36:18<05:52,  5.76it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32137961 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  70%|██████▉   | 4593/6593 [36:42<25:18,  1.32it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:33275459 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  70%|██████▉   | 4611/6593 [36:51<15:24,  2.14it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:34039694 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  71%|███████   | 4652/6593 [37:12<13:17,  2.43it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:35291664 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  71%|███████   | 4677/6593 [37:30<19:54,  1.60it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:36300423 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  71%|███████▏  | 4700/6593 [37:42<17:28,  1.81it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:16841595 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  72%|███████▏  | 4725/6593 [37:56<13:30,  2.31it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:31114373 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  72%|███████▏  | 4729/6593 [38:00<28:17,  1.10it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:16905272 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  73%|███████▎  | 4817/6593 [38:42<11:35,  2.56it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:30856079 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  73%|███████▎  | 4820/6593 [38:43<08:56,  3.31it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:401125 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  73%|███████▎  | 4822/6593 [38:43<06:35,  4.48it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:13415910 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  73%|███████▎  | 4824/6593 [38:44<05:40,  5.19it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:13561240 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  75%|███████▍  | 4942/6593 [39:54<10:50,  2.54it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:7933037 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  75%|███████▌  | 4951/6593 [39:57<11:09,  2.45it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32018912 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  76%|███████▌  | 4994/6593 [40:32<17:13,  1.55it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:31023512 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  81%|████████  | 5322/6593 [43:53<08:04,  2.62it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:4094894 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  81%|████████  | 5343/6593 [44:03<09:21,  2.22it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:6831481 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  81%|████████  | 5345/6593 [44:04<08:07,  2.56it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:7438127 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  82%|████████▏ | 5386/6593 [44:29<15:06,  1.33it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:18487580 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  82%|████████▏ | 5392/6593 [44:32<15:36,  1.28it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:4112005 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  82%|████████▏ | 5413/6593 [44:45<15:51,  1.24it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:22931505 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  82%|████████▏ | 5427/6593 [44:50<07:27,  2.60it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:684253 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  82%|████████▏ | 5429/6593 [44:51<04:58,  3.90it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:4649687 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  83%|████████▎ | 5454/6593 [45:05<14:01,  1.35it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:31428132 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  84%|████████▎ | 5508/6593 [45:35<09:32,  1.89it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:197089 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  85%|████████▍ | 5573/6593 [46:25<18:51,  1.11s/it]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:18905572 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  86%|████████▋ | 5693/6593 [47:41<05:46,  2.59it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:11356100 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  86%|████████▋ | 5699/6593 [47:43<05:13,  2.85it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:18457385 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  87%|████████▋ | 5713/6593 [47:54<07:55,  1.85it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:13909997 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  87%|████████▋ | 5720/6593 [47:57<09:27,  1.54it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:5865975 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  88%|████████▊ | 5772/6593 [48:23<06:31,  2.10it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:22082638 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  88%|████████▊ | 5800/6593 [48:40<06:21,  2.08it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:78345 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  88%|████████▊ | 5801/6593 [48:40<05:09,  2.56it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:79122 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  88%|████████▊ | 5806/6593 [48:43<05:49,  2.25it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:6107740 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  88%|████████▊ | 5809/6593 [48:45<09:34,  1.37it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:22716953 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  89%|████████▊ | 5839/6593 [49:00<06:00,  2.09it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:5968627 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  89%|████████▊ | 5841/6593 [49:00<03:45,  3.33it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:14427350 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  89%|████████▊ | 5844/6593 [49:01<02:17,  5.43it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:13528212 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  89%|████████▉ | 5855/6593 [49:08<14:04,  1.14s/it]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32120682 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  89%|████████▉ | 5881/6593 [49:20<07:39,  1.55it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:22621397 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  89%|████████▉ | 5896/6593 [49:33<09:47,  1.19it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:5956633 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  90%|████████▉ | 5906/6593 [49:37<04:38,  2.46it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:24541335 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  90%|█████████ | 5956/6593 [50:08<06:01,  1.76it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:34911912 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  91%|█████████ | 5985/6593 [50:22<09:33,  1.06it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32138101 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  91%|█████████ | 5986/6593 [50:22<07:12,  1.40it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32145769 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  91%|█████████ | 5988/6593 [50:25<09:02,  1.11it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32286699 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  91%|█████████ | 5989/6593 [50:25<06:48,  1.48it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32579834 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  91%|█████████ | 5990/6593 [50:25<06:03,  1.66it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32579835 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  91%|█████████ | 5995/6593 [50:29<07:34,  1.32it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:35417251 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  92%|█████████▏| 6038/6593 [50:54<04:07,  2.24it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:12973858 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  92%|█████████▏| 6052/6593 [51:02<04:17,  2.10it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32138028 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  92%|█████████▏| 6074/6593 [51:14<04:31,  1.91it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32171753 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  92%|█████████▏| 6080/6593 [51:16<03:27,  2.48it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32351879 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  92%|█████████▏| 6091/6593 [51:23<03:34,  2.34it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:32966831 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  93%|█████████▎| 6103/6593 [51:27<03:34,  2.29it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:34795691 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  93%|█████████▎| 6104/6593 [51:27<02:56,  2.77it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:34867360 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  93%|█████████▎| 6139/6593 [51:48<03:53,  1.94it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:36066779 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  93%|█████████▎| 6147/6593 [51:53<05:07,  1.45it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:36386788 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  94%|█████████▎| 6171/6593 [52:05<03:20,  2.10it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:8279774 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  96%|█████████▌| 6328/6593 [53:38<01:58,  2.24it/s]/var/folders/vc/lfqgrrhn56d9yj5fbxbw6qr00000gt/T/ipykernel_48032/3008939645.py:22: UserWarning: PMID PMID:25483671 has an empty abstract\n",
      "  warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
      "Downloading PubMed Articles:  97%|█████████▋| 6387/6593 [54:10<02:00,  1.71it/s]"
     ]
    }
   ],
   "source": [
    "# Initialize the sentence transformer model\n",
    "model = SentenceTransformer('all-MiniLM-L6-v2')\n",
    "\n",
    "# Fetch articles and process them\n",
    "pmid_list = []\n",
    "sentence_list = []\n",
    "embedding_list = []\n",
    "\n",
    "for pmid in tqdm(pmids, desc=\"Downloading PubMed Articles\"):\n",
    "    article_xml = fetch_pubmed_article(pmid)\n",
    "    if article_xml:\n",
    "        # Parse the XML to extract the abstract\n",
    "        root = ET.fromstring(article_xml)\n",
    "        abstract_texts = root.findall(\".//AbstractText\")\n",
    "        try:\n",
    "            abstract = \" \".join(abstract_text.text for abstract_text in abstract_texts if abstract_text.text is not None)\n",
    "        except TypeError:\n",
    "            warnings.warn(f\"PMID {pmid} has no abstract\")\n",
    "            continue\n",
    "        \n",
    "        if not abstract.strip():\n",
    "            warnings.warn(f\"PMID {pmid} has an empty abstract\")\n",
    "            continue\n",
    "\n",
    "        # Tokenize the abstract into sentences\n",
    "        sentences = sent_tokenize(abstract)\n",
    "        \n",
    "        if not sentences:\n",
    "            warnings.warn(f\"PMID {pmid} resulted in empty sentences after tokenization\")\n",
    "            continue\n",
    "\n",
    "        # Generate embeddings for each sentence\n",
    "        embeddings = model.encode(sentences)\n",
    "        \n",
    "        # Store the PMIDs, sentences, and embeddings\n",
    "        pmid_list.extend([pmid] * len(sentences))\n",
    "        sentence_list.extend(sentences)\n",
    "        embedding_list.extend(embeddings)\n",
    "\n",
    "# Create a DataFrame with PMIDs, sentences, and embeddings\n",
    "data = {'PMID': pmid_list, 'sentence': sentence_list, 'embedding': embedding_list}\n",
    "df = pd.DataFrame(data)\n",
    "\n",
    "# Save the DataFrame to Parquet format\n",
    "parquet_file_path = './data/sentence_embeddings.parquet'\n",
    "df.to_parquet(parquet_file_path, engine='pyarrow', index=False)\n",
    "\n",
    "print(f\"Embeddings saved to {parquet_file_path}\")\n"
   ],
   "metadata": {
    "collapsed": false,
    "is_executing": true,
    "ExecuteTime": {
     "start_time": "2024-07-30T17:30:03.407508Z"
    }
   },
   "id": "7802adc94111daf7"
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "outputs": [],
   "source": [
    "# Generate metadata in venomx format\n",
    "metadata = {\n",
    "    'description': 'Embeddings of each sentence in the abstracts of about 6000 selected PubMed articles. Github repo with jupyter notebook and data files is here: https://github.com/justaddcoffee/embed_pubmed',\n",
    "    'prefixes': {\n",
    "        'PMID': 'https://pubmed.ncbi.nlm.nih.gov/PMID_'\n",
    "    },\n",
    "    'model': {\n",
    "        'name': 'all-MiniLM-L6-v2'\n",
    "    },\n",
    "    'dataset': {\n",
    "        'name': 'Pubmed July 2024',\n",
    "        'url': 'https://huggingface.co/biomedical-translator/pubmed_sentence_embeddings'\n",
    "    }\n",
    "}\n",
    "\n",
    "# Save the metadata to a YAML file\n",
    "metadata_file_path = './data/metadata.yaml'\n",
    "with open(metadata_file_path, 'w') as f:\n",
    "    yaml.dump(metadata, f)\n",
    "\n",
    "print(f\"Metadata saved to {metadata_file_path}\")"
   ],
   "metadata": {
    "collapsed": false,
    "is_executing": true
   },
   "id": "eea4fe2a4bdae560"
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "3ca37dc6",
   "metadata": {
    "is_executing": true
   },
   "outputs": [],
   "source": [
    "# Upload to Hugging Face\n",
    "repo_id = \"biomedical-translator/pubmed_sentence_embeddings\"\n",
    "create_repo(repo_id, repo_type=\"dataset\")\n",
    "\n",
    "this_notebook_path = \"pubmed_sentence_embeddings.ipynb\"\n",
    "\n",
    "api = HfApi()\n",
    "files_to_upload = [parquet_file_path, metadata_file_path, this_notebook_path]\n",
    "\n",
    "for file in files_to_upload:\n",
    "    api.upload_file(\n",
    "        path_or_fileobj=file,\n",
    "        path_in_repo=file,\n",
    "        repo_id=repo_id,\n",
    "        repo_type=\"dataset\"\n",
    "    )\n",
    "\n",
    "print(f\"Files uploaded to Hugging Face in repository: {repo_id}\")\n"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "name": "python3",
   "language": "python",
   "display_name": "Python 3 (ipykernel)"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}