PubMed_Articles_Extraction.ipynb

{
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  "metadata": {
    "colab": {
      "provenance": [],
      "authorship_tag": "ABX9TyMi+0iQsCJUakZW8a7XojHJ",
      "include_colab_link": true
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    },
    "language_info": {
      "name": "python"
    }
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/github/RehanKhan-007/NLP/blob/main/PubMed_Articles_Extraction.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 1,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "ay9Xe6dr0n32",
        "outputId": "8ea9d17d-95ec-46e2-ff0a-275cecb25a54"
      },
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
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            "Successfully installed Levenshtein-0.20.9 coloredlogs-15.0.1 cssselect-1.2.0 distlib-0.3.6 docopt-0.6.2 eutils-0.6.0 habanero-1.2.3 humanfriendly-10.0 metapub-0.5.5 python-Levenshtein-0.20.9 rapidfuzz-2.13.7 tox-3.12.1 unidecode-1.3.6 virtualenv-20.21.0\n"
          ]
        }
      ],
      "source": [
        "!pip install metapub"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "import pandas as pd"
      ],
      "metadata": {
        "id": "NZF3FD750uPv"
      },
      "execution_count": 2,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "#initialise the keyword to be searched and number of articles to be retrieved\n",
        "\n",
        "keyword=\"medicinal plants and phytocompounds\"\n",
        "num_of_articles=10"
      ],
      "metadata": {
        "id": "YL7CU7zV06nc"
      },
      "execution_count": 3,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "from metapub import PubMedFetcher\n",
        "fetch = PubMedFetcher()\n",
        "\n",
        "# get the  PMID for first 3 articles with keyword medicinal plants and phytocompounds\n",
        "pmids = fetch.pmids_for_query(keyword, retmax=num_of_articles)\n",
        "\n",
        "# get  articles\n",
        "articles = {}\n",
        "for pmid in pmids:\n",
        "    articles[pmid] = fetch.article_by_pmid(pmid)"
      ],
      "metadata": {
        "id": "j_6h-RRT1BEx"
      },
      "execution_count": 5,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "# get title for each article:\n",
        "titles = {}\n",
        "for pmid in pmids:\n",
        "    titles[pmid] = fetch.article_by_pmid(pmid).title\n",
        "Title = pd.DataFrame(list(titles.items()),columns = ['pmid','Title'])\n",
        "Title\n",
        "\n",
        "# get abstract for each article:\n",
        "abstracts = {}\n",
        "for pmid in pmids:\n",
        "    abstracts[pmid] = fetch.article_by_pmid(pmid).abstract\n",
        "Abstract = pd.DataFrame(list(abstracts.items()),columns = ['pmid','Abstract'])\n",
        "Abstract"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 363
        },
        "id": "AyvP-yIS1LsY",
        "outputId": "5f6df162-5a80-4e55-be1e-f8478d12f478"
      },
      "execution_count": 6,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "       pmid                                           Abstract\n",
              "0  36866556  BACKGROUND: Candidiasis is a common oral and v...\n",
              "1  36839737                                               None\n",
              "2  36837862  Inflammatory bowel diseases (IBDs) are related...\n",
              "3  36771738  The island of Grande-Terre is a French oversea...\n",
              "4  36771558  Antioxidants are important supplements for the...\n",
              "5  36747936  Herbal medications are gaining popularity due ...\n",
              "6  36675191  Paulownia spp. is a genus of trees in the Paul...\n",
              "7  36672732  Cancer is one of the main causes of death worl...\n",
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              "9  36644848                                               None"
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    },
    {
      "cell_type": "code",
      "source": [
        "import pandas as pd\n",
        "#initialise the keyword to be searched and number of articles to be retrieved\n",
        "\n",
        "keyword=\"medicinal plants and phytocompounds\"\n",
        "num_of_articles=10\n",
        "\n",
        "from metapub import PubMedFetcher\n",
        "fetch = PubMedFetcher()\n",
        "\n",
        "# get the  PMID for first 3 articles with keyword medicinal plants and phytocompounds\n",
        "pmids = fetch.pmids_for_query(keyword, retmax=num_of_articles)\n",
        "\n",
        "# get  articles\n",
        "articles = {}\n",
        "for pmid in pmids:\n",
        "    articles[pmid] = fetch.article_by_pmid(pmid)\n",
        "\n",
        "# get title for each article:\n",
        "titles = {}\n",
        "for pmid in pmids:\n",
        "    titles[pmid] = fetch.article_by_pmid(pmid).title\n",
        "Title = pd.DataFrame(list(titles.items()),columns = ['pmid','Title'])\n",
        "Title\n",
        "\n",
        "# get abstract for each article:\n",
        "abstracts = {}\n",
        "for pmid in pmids:\n",
        "    abstracts[pmid] = fetch.article_by_pmid(pmid).abstract\n",
        "Abstract = pd.DataFrame(list(abstracts.items()),columns = ['pmid','Abstract'])\n",
        "Abstract\n",
        "\n",
        "# get author for each article:\n",
        "authors = {}\n",
        "for pmid in pmids:\n",
        "    authors[pmid] = fetch.article_by_pmid(pmid).authors\n",
        "Author = pd.DataFrame(list(authors.items()),columns = ['pmid','Author'])\n",
        "Author\n",
        "\n",
        "# get year for each article:\n",
        "years = {}\n",
        "for pmid in pmids:\n",
        "    years[pmid] = fetch.article_by_pmid(pmid).year\n",
        "Year = pd.DataFrame(list(years.items()),columns = ['pmid','Year'])\n",
        "Year\n",
        "\n",
        "# get volume for each article:\n",
        "volumes = {}\n",
        "for pmid in pmids:\n",
        "    volumes[pmid] = fetch.article_by_pmid(pmid).volume\n",
        "Volume = pd.DataFrame(list(volumes.items()),columns = ['pmid','Volume'])\n",
        "Volume\n",
        "\n",
        "# get issue for each article:\n",
        "issues = {}\n",
        "for pmid in pmids:\n",
        "    issues[pmid] = fetch.article_by_pmid(pmid).issue\n",
        "Issue = pd.DataFrame(list(issues.items()),columns = ['pmid','Issue'])\n",
        "Issue\n",
        "\n",
        "# get journal for each article:\n",
        "journals = {}\n",
        "for pmid in pmids:\n",
        "    journals[pmid] = fetch.article_by_pmid(pmid).journal\n",
        "Journal = pd.DataFrame(list(journals.items()),columns = ['pmid','Journal'])\n",
        "Journal\n",
        "\n",
        "# get citation for each article:\n",
        "citations = {}\n",
        "for pmid in pmids:\n",
        "    citations[pmid] = fetch.article_by_pmid(pmid).citation\n",
        "Citation = pd.DataFrame(list(citations.items()),columns = ['pmid','Citation'])\n",
        "Citation\n",
        "\n",
        "links={}\n",
        "for pmid in pmids:\n",
        "    links[pmid] = \"https://pubmed.ncbi.nlm.nih.gov/\"+pmid+\"/\"\n",
        "Link = pd.DataFrame(list(links.items()),columns = ['pmid','Link'])\n",
        "Link\n",
        "\n",
        "data_frames = [Title,Abstract,Author,Year,Volume,Issue,Journal,Citation,Link]\n",
        "from functools import reduce\n",
        "df_merged = reduce(lambda  left,right: pd.merge(left,right,on=['pmid'],\n",
        "                                            how='outer'), data_frames)\n",
        "df_merged"
      ],
      "metadata": {
        "id": "yP7AiOWO1eXP",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 650
        },
        "outputId": "d402d153-c97d-4386-ce8d-ccd00f31adcd"
      },
      "execution_count": 7,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "       pmid                                              Title  \\\n",
              "0  36866556  Anti-Candida and Antibiofilm Activity of Selec...   \n",
              "1  36839737  Polyphenolic Profile of Herniaria hemistemon A...   \n",
              "2  36837862  Effects of Medicinal Plants and Phytochemicals...   \n",
              "3  36771738  Medicinal Plants and Plant-Based Remedies in G...   \n",
              "4  36771558  Quali-Quantitative Fingerprinting of the Fruit...   \n",
              "5  36747936  In vitro antioxidant activities of Carissa edu...   \n",
              "6  36675191  Paulownia Organs as Interesting New Sources of...   \n",
              "7  36672732  An Overview of Potential Natural Photosensitiz...   \n",
              "8  36671402  Bioactivity and In Silico Studies of Isoquinol...   \n",
              "9  36644848  Discovery of potential phytochemicals as inhib...   \n",
              "\n",
              "                                            Abstract  \\\n",
              "0  BACKGROUND: Candidiasis is a common oral and v...   \n",
              "1                                               None   \n",
              "2  Inflammatory bowel diseases (IBDs) are related...   \n",
              "3  The island of Grande-Terre is a French oversea...   \n",
              "4  Antioxidants are important supplements for the...   \n",
              "5  Herbal medications are gaining popularity due ...   \n",
              "6  Paulownia spp. is a genus of trees in the Paul...   \n",
              "7  Cancer is one of the main causes of death worl...   \n",
              "8  Viruses are widely recognized as the primary c...   \n",
              "9                                               None   \n",
              "\n",
              "                                              Author  Year Volume Issue  \\\n",
              "0  [Karpiński TM, Ożarowski M, Seremak-Mrozikiewi...  2023     28     2   \n",
              "1  [Ghareeb MA, Sobeh M, Aboushousha T, Esmat M, ...  2023     15     2   \n",
              "2  [Laurindo LF, de Maio MC, Minniti G, de Góes C...  2023     13     2   \n",
              "3  [Courric E, Brinvilier D, Couderc P, Ponce-Mor...  2023     12     3   \n",
              "4  [Rakotonirina FMV, Donno D, Razafindrakoto ZR,...  2023     12     3   \n",
              "5        [Muruthi CW, Ngugi MP, Runo SM, Mwitari PG]  2023      9     1   \n",
              "6                     [Sławińska N, Zając J, Olas B]  2023     24     2   \n",
              "7  [Aziz B, Aziz I, Khurshid A, Raoufi E, Esfahan...  2023     11     1   \n",
              "8  [Sharma D, Sharma N, Manchanda N, Prasad SK, S...  2022     13     1   \n",
              "9  [Alamri MA, Tariq MH, Tahir Ul Qamar M, Alabba...  2023   None  None   \n",
              "\n",
              "                      Journal  \\\n",
              "0  Front Biosci (Landmark Ed)   \n",
              "1               Pharmaceutics   \n",
              "2                 Metabolites   \n",
              "3              Plants (Basel)   \n",
              "4              Plants (Basel)   \n",
              "5                     Heliyon   \n",
              "6               Int J Mol Sci   \n",
              "7                Biomedicines   \n",
              "8                Biomolecules   \n",
              "9         J Biomol Struct Dyn   \n",
              "\n",
              "                                            Citation  \\\n",
              "0  Karpiński TM, et al. Anti-Candida and Antibiof...   \n",
              "1  Ghareeb MA, et al. Polyphenolic Profile of Her...   \n",
              "2  Laurindo LF, et al. Effects of Medicinal Plant...   \n",
              "3  Courric E, et al. Medicinal Plants and Plant-B...   \n",
              "4  Rakotonirina FMV, et al. Quali-Quantitative Fi...   \n",
              "5  Muruthi CW, et al. In vitro antioxidant activi...   \n",
              "6  Sławińska N, et al. Paulownia Organs as Intere...   \n",
              "7  Aziz B, et al. An Overview of Potential Natura...   \n",
              "8  Sharma D, et al. Bioactivity and In Silico Stu...   \n",
              "9  Alamri MA, et al. Discovery of potential phyto...   \n",
              "\n",
              "                                        Link  \n",
              "0  https://pubmed.ncbi.nlm.nih.gov/36866556/  \n",
              "1  https://pubmed.ncbi.nlm.nih.gov/36839737/  \n",
              "2  https://pubmed.ncbi.nlm.nih.gov/36837862/  \n",
              "3  https://pubmed.ncbi.nlm.nih.gov/36771738/  \n",
              "4  https://pubmed.ncbi.nlm.nih.gov/36771558/  \n",
              "5  https://pubmed.ncbi.nlm.nih.gov/36747936/  \n",
              "6  https://pubmed.ncbi.nlm.nih.gov/36675191/  \n",
              "7  https://pubmed.ncbi.nlm.nih.gov/36672732/  \n",
              "8  https://pubmed.ncbi.nlm.nih.gov/36671402/  \n",
              "9  https://pubmed.ncbi.nlm.nih.gov/36644848/  "
            ],
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              "      <td>[Karpiński TM, Ożarowski M, Seremak-Mrozikiewi...</td>\n",
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              "      <td>28</td>\n",
              "      <td>2</td>\n",
              "      <td>Front Biosci (Landmark Ed)</td>\n",
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              "      <td>https://pubmed.ncbi.nlm.nih.gov/36866556/</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>1</th>\n",
              "      <td>36839737</td>\n",
              "      <td>Polyphenolic Profile of Herniaria hemistemon A...</td>\n",
              "      <td>None</td>\n",
              "      <td>[Ghareeb MA, Sobeh M, Aboushousha T, Esmat M, ...</td>\n",
              "      <td>2023</td>\n",
              "      <td>15</td>\n",
              "      <td>2</td>\n",
              "      <td>Pharmaceutics</td>\n",
              "      <td>Ghareeb MA, et al. Polyphenolic Profile of Her...</td>\n",
              "      <td>https://pubmed.ncbi.nlm.nih.gov/36839737/</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>2</th>\n",
              "      <td>36837862</td>\n",
              "      <td>Effects of Medicinal Plants and Phytochemicals...</td>\n",
              "      <td>Inflammatory bowel diseases (IBDs) are related...</td>\n",
              "      <td>[Laurindo LF, de Maio MC, Minniti G, de Góes C...</td>\n",
              "      <td>2023</td>\n",
              "      <td>13</td>\n",
              "      <td>2</td>\n",
              "      <td>Metabolites</td>\n",
              "      <td>Laurindo LF, et al. Effects of Medicinal Plant...</td>\n",
              "      <td>https://pubmed.ncbi.nlm.nih.gov/36837862/</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>3</th>\n",
              "      <td>36771738</td>\n",
              "      <td>Medicinal Plants and Plant-Based Remedies in G...</td>\n",
              "      <td>The island of Grande-Terre is a French oversea...</td>\n",
              "      <td>[Courric E, Brinvilier D, Couderc P, Ponce-Mor...</td>\n",
              "      <td>2023</td>\n",
              "      <td>12</td>\n",
              "      <td>3</td>\n",
              "      <td>Plants (Basel)</td>\n",
              "      <td>Courric E, et al. Medicinal Plants and Plant-B...</td>\n",
              "      <td>https://pubmed.ncbi.nlm.nih.gov/36771738/</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>4</th>\n",
              "      <td>36771558</td>\n",
              "      <td>Quali-Quantitative Fingerprinting of the Fruit...</td>\n",
              "      <td>Antioxidants are important supplements for the...</td>\n",
              "      <td>[Rakotonirina FMV, Donno D, Razafindrakoto ZR,...</td>\n",
              "      <td>2023</td>\n",
              "      <td>12</td>\n",
              "      <td>3</td>\n",
              "      <td>Plants (Basel)</td>\n",
              "      <td>Rakotonirina FMV, et al. Quali-Quantitative Fi...</td>\n",
              "      <td>https://pubmed.ncbi.nlm.nih.gov/36771558/</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>5</th>\n",
              "      <td>36747936</td>\n",
              "      <td>In vitro antioxidant activities of Carissa edu...</td>\n",
              "      <td>Herbal medications are gaining popularity due ...</td>\n",
              "      <td>[Muruthi CW, Ngugi MP, Runo SM, Mwitari PG]</td>\n",
              "      <td>2023</td>\n",
              "      <td>9</td>\n",
              "      <td>1</td>\n",
              "      <td>Heliyon</td>\n",
              "      <td>Muruthi CW, et al. In vitro antioxidant activi...</td>\n",
              "      <td>https://pubmed.ncbi.nlm.nih.gov/36747936/</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>6</th>\n",
              "      <td>36675191</td>\n",
              "      <td>Paulownia Organs as Interesting New Sources of...</td>\n",
              "      <td>Paulownia spp. is a genus of trees in the Paul...</td>\n",
              "      <td>[Sławińska N, Zając J, Olas B]</td>\n",
              "      <td>2023</td>\n",
              "      <td>24</td>\n",
              "      <td>2</td>\n",
              "      <td>Int J Mol Sci</td>\n",
              "      <td>Sławińska N, et al. Paulownia Organs as Intere...</td>\n",
              "      <td>https://pubmed.ncbi.nlm.nih.gov/36675191/</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>7</th>\n",
              "      <td>36672732</td>\n",
              "      <td>An Overview of Potential Natural Photosensitiz...</td>\n",
              "      <td>Cancer is one of the main causes of death worl...</td>\n",
              "      <td>[Aziz B, Aziz I, Khurshid A, Raoufi E, Esfahan...</td>\n",
              "      <td>2023</td>\n",
              "      <td>11</td>\n",
              "      <td>1</td>\n",
              "      <td>Biomedicines</td>\n",
              "      <td>Aziz B, et al. An Overview of Potential Natura...</td>\n",
              "      <td>https://pubmed.ncbi.nlm.nih.gov/36672732/</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>8</th>\n",
              "      <td>36671402</td>\n",
              "      <td>Bioactivity and In Silico Studies of Isoquinol...</td>\n",
              "      <td>Viruses are widely recognized as the primary c...</td>\n",
              "      <td>[Sharma D, Sharma N, Manchanda N, Prasad SK, S...</td>\n",
              "      <td>2022</td>\n",
              "      <td>13</td>\n",
              "      <td>1</td>\n",
              "      <td>Biomolecules</td>\n",
              "      <td>Sharma D, et al. Bioactivity and In Silico Stu...</td>\n",
              "      <td>https://pubmed.ncbi.nlm.nih.gov/36671402/</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>9</th>\n",
              "      <td>36644848</td>\n",
              "      <td>Discovery of potential phytochemicals as inhib...</td>\n",
              "      <td>None</td>\n",
              "      <td>[Alamri MA, Tariq MH, Tahir Ul Qamar M, Alabba...</td>\n",
              "      <td>2023</td>\n",
              "      <td>None</td>\n",
              "      <td>None</td>\n",
              "      <td>J Biomol Struct Dyn</td>\n",
              "      <td>Alamri MA, et al. Discovery of potential phyto...</td>\n",
              "      <td>https://pubmed.ncbi.nlm.nih.gov/36644848/</td>\n",
              "    </tr>\n",
              "  </tbody>\n",
              "</table>\n",
              "</div>\n",
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              "\n",
              "    .colab-df-convert {\n",
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              "  "
            ]
          },
          "metadata": {},
          "execution_count": 7
        }
      ]
    }
  ]
}