tutorials/Ensmallen_Automatic_graph_retrieval_utilities.ipynb

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   "source": [
    "<a href=\"https://colab.research.google.com/github/AnacletoLAB/grape/blob/main/tutorials/Ensmallen_Automatic_graph_retrieval_utilities.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
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  {
   "cell_type": "markdown",
   "metadata": {
    "id": "sbnz5HFrFPMZ"
   },
   "source": [
    "# Automatic graph retrieval utilities\n",
    "In this tutorial we will explore the utilities available for the automatic graph retrieval."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "nbVWIXSyHhLE"
   },
   "source": [
    "## Installing the library\n",
    "First of all, we install the GRAPE library:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "colab": {
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    "id": "33LIZEHcE5vq",
    "outputId": "312320f8-9b40-4956-8d63-92ee92ce2b83"
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   "outputs": [],
   "source": [
    "!pip install -qU grape"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "EmKq46p6HuGl"
   },
   "source": [
    "## A few of the available methods\n",
    "We will rapidly present the available methods that allow to programmatically retrieve the available datasets."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "2LD6zVrr52Da"
   },
   "source": [
    "Retrieve the list of the available graph repositories, that is the sources from where we can scrape graphs currently"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "vq5-PVbBHspg",
    "outputId": "6da892a6-7b52-4a9c-cdbf-b463a70f839f"
   },
   "outputs": [
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     "data": {
      "text/plain": [
       "['freebase',\n",
       " 'kghub',\n",
       " 'linqs',\n",
       " 'pheknowlatorkg',\n",
       " 'wikidata',\n",
       " 'zenodo',\n",
       " 'jax',\n",
       " 'monarchinitiative',\n",
       " 'string',\n",
       " 'yue',\n",
       " 'kgobo',\n",
       " 'networkrepository',\n",
       " 'wikipedia']"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from grape.datasets import get_available_repositories\n",
    "get_available_repositories()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "-uUlmO8tQrmI"
   },
   "source": [
    "Retrieving the list of graphs available from a given repository"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "no3re2BpIATS",
    "outputId": "2b475618-6803-496a-b1a2-aee8b9b6cfed"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "dict_keys(['SLDB', 'KGMicrobe', 'KGIDG', 'KGPhenio', 'KGCOVID19', 'EcoKG'])"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from grape.datasets import get_available_graphs_from_repository\n",
    "get_available_graphs_from_repository(\"kghub\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "KEJV-Oiw6QYV"
   },
   "source": [
    "Retrieving the list of graph versions available from a given graph and repository"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
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    "id": "eC92v-pP6QrN",
    "outputId": "562b40bc-c57a-4d6e-b850-230ff3d48770"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['20200925',\n",
       " '20200927',\n",
       " '20200929',\n",
       " '20201001',\n",
       " '20201012',\n",
       " '20201101',\n",
       " '20201202',\n",
       " '20210101',\n",
       " '20210128',\n",
       " '20210201',\n",
       " '20210218',\n",
       " '20210301',\n",
       " '20210412',\n",
       " '20210725',\n",
       " '20210726',\n",
       " '20210727',\n",
       " '20210823',\n",
       " '20210902',\n",
       " '20211002',\n",
       " '20211102',\n",
       " '20211202',\n",
       " '20220102',\n",
       " '20220202',\n",
       " '20220217',\n",
       " '20220223',\n",
       " '20220225',\n",
       " '20220228',\n",
       " '20220328',\n",
       " '20220330',\n",
       " '20220402',\n",
       " '20220502',\n",
       " '20220610',\n",
       " '20220702',\n",
       " 'current']"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from grape.datasets import get_available_versions_from_graph_and_repository\n",
    "get_available_versions_from_graph_and_repository(\n",
    "    name=\"KGCOVID19\",\n",
    "    repository=\"kghub\"\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "3x5M1YjLQvOM"
   },
   "source": [
    "Getting all the available datasets dataframe"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "id": "MuaVlU64QuiW"
   },
   "outputs": [],
   "source": [
    "from grape.datasets import get_all_available_graphs_dataframe\n",
    "\n",
    "available_graphs = get_all_available_graphs_dataframe(verbose=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "p-IaAYA8R6oN"
   },
   "source": [
    "Display the available graphs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
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       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>repository</th>\n",
       "      <th>name</th>\n",
       "      <th>version</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>freebase</td>\n",
       "      <td>FreeBase</td>\n",
       "      <td>latest</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>freebase</td>\n",
       "      <td>FreeBase2WikiData</td>\n",
       "      <td>latest</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>kghub</td>\n",
       "      <td>SLDB</td>\n",
       "      <td>20220522</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>kghub</td>\n",
       "      <td>KGMicrobe</td>\n",
       "      <td>20210422</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>kghub</td>\n",
       "      <td>KGMicrobe</td>\n",
       "      <td>20210517</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83639</th>\n",
       "      <td>wikipedia</td>\n",
       "      <td>WikiSourceHR</td>\n",
       "      <td>20220601</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83640</th>\n",
       "      <td>wikipedia</td>\n",
       "      <td>WikiSourceHR</td>\n",
       "      <td>20220620</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83641</th>\n",
       "      <td>wikipedia</td>\n",
       "      <td>WikiSourceHR</td>\n",
       "      <td>20220701</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83642</th>\n",
       "      <td>wikipedia</td>\n",
       "      <td>WikiSourceHR</td>\n",
       "      <td>20220720</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83643</th>\n",
       "      <td>wikipedia</td>\n",
       "      <td>WikiSourceHR</td>\n",
       "      <td>latest</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>83644 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      repository               name   version\n",
       "0       freebase           FreeBase    latest\n",
       "1       freebase  FreeBase2WikiData    latest\n",
       "2          kghub               SLDB  20220522\n",
       "3          kghub          KGMicrobe  20210422\n",
       "4          kghub          KGMicrobe  20210517\n",
       "...          ...                ...       ...\n",
       "83639  wikipedia       WikiSourceHR  20220601\n",
       "83640  wikipedia       WikiSourceHR  20220620\n",
       "83641  wikipedia       WikiSourceHR  20220701\n",
       "83642  wikipedia       WikiSourceHR  20220720\n",
       "83643  wikipedia       WikiSourceHR    latest\n",
       "\n",
       "[83644 rows x 3 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "available_graphs"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "x1fs-bq36wjn"
   },
   "source": [
    "Getting the number of graphs per repository"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "9ci30oGySHyd",
    "outputId": "79249f6f-4919-4714-eab7-0df816408b77"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Counter({'freebase': 2,\n",
       "         'kghub': 92,\n",
       "         'linqs': 3,\n",
       "         'pheknowlatorkg': 116,\n",
       "         'wikidata': 22,\n",
       "         'zenodo': 163,\n",
       "         'jax': 1,\n",
       "         'monarchinitiative': 23,\n",
       "         'string': 75590,\n",
       "         'yue': 7,\n",
       "         'kgobo': 462,\n",
       "         'networkrepository': 1194,\n",
       "         'wikipedia': 5969})"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from collections import Counter\n",
    "\n",
    "Counter(available_graphs[\"repository\"])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "OHA7-b9xQnDD"
   },
   "source": [
    "Programmatically retrieving a graph"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "id": "zvm3GRr1INg4"
   },
   "outputs": [],
   "source": [
    "from grape.datasets import get_dataset\n",
    "dataset_generator = get_dataset(\n",
    "    name=\"KGMicrobe\",\n",
    "    repository=\"kghub\"\n",
    ")"
   ]
  },
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    "outputId": "4706e371-8772-4cbb-8ff5-be550171ae74"
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   "outputs": [],
   "source": [
    "dataset_generator()"
   ]
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