nxontology_data/mesh/mesh.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Development notebook for creating a MeSH NXOntology via SPARQL queries"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "# type: ignore\n",
    "%load_ext autoreload\n",
    "%autoreload 2\n",
    "\n",
    "import pandas as pd\n",
    "from nxontology_data.mesh.mesh import MeshLoader\n",
    "# from IPython.display import Image\n",
    "# from networkx.drawing.nx_agraph import to_agraph"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## load RDF"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 9min 38s, sys: 10.8 s, total: 9min 49s\n",
      "Wall time: 10min 3s\n"
     ]
    }
   ],
   "source": [
    "%%time\n",
    "mesh_year = \"2022\"\n",
    "rdf = MeshLoader.get_mesh_rdf(mesh_year)"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## subclass graph"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "vocab = MeshLoader.create_vocab_digraph(rdf)\n",
    "# gviz = to_agraph(vocab)\n",
    "# gviz.layout(\"dot\")\n",
    "# Image(gviz.draw(format=\"png\"))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## identifiers"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 17min 23s, sys: 4.46 s, total: 17min 27s\n",
      "Wall time: 17min 28s\n"
     ]
    },
    {
     "data": {
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>mesh_id</th>\n",
       "      <th>mesh_class</th>\n",
       "      <th>mesh_uri</th>\n",
       "      <th>mesh_label</th>\n",
       "      <th>mesh_date_created</th>\n",
       "      <th>mesh_date_revised</th>\n",
       "      <th>mesh_date_established</th>\n",
       "      <th>mesh_frequency</th>\n",
       "      <th>mesh_description</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>C000002</td>\n",
       "      <td>SCR_Chemical</td>\n",
       "      <td>http://id.nlm.nih.gov/mesh/2022/C000002</td>\n",
       "      <td>bevonium</td>\n",
       "      <td>1971-01-01</td>\n",
       "      <td>2018-09-24</td>\n",
       "      <td>None</td>\n",
       "      <td>1.0</td>\n",
       "      <td>structure given in first source</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>C000006</td>\n",
       "      <td>SCR_Chemical</td>\n",
       "      <td>http://id.nlm.nih.gov/mesh/2022/C000006</td>\n",
       "      <td>insulin, neutral</td>\n",
       "      <td>1971-01-01</td>\n",
       "      <td>2017-10-04</td>\n",
       "      <td>None</td>\n",
       "      <td>263.0</td>\n",
       "      <td>a neutral, buffered solution of pork insulin</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   mesh_id    mesh_class                                 mesh_uri  \\\n",
       "0  C000002  SCR_Chemical  http://id.nlm.nih.gov/mesh/2022/C000002   \n",
       "1  C000006  SCR_Chemical  http://id.nlm.nih.gov/mesh/2022/C000006   \n",
       "\n",
       "         mesh_label mesh_date_created mesh_date_revised mesh_date_established  \\\n",
       "0          bevonium        1971-01-01        2018-09-24                  None   \n",
       "1  insulin, neutral        1971-01-01        2017-10-04                  None   \n",
       "\n",
       "   mesh_frequency                              mesh_description  \n",
       "0             1.0               structure given in first source  \n",
       "1           263.0  a neutral, buffered solution of pork insulin  "
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "%%time\n",
    "id_df = MeshLoader.run_query(rdf, \"identifiers\", cache=True)\n",
    "id_df.head(2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Term                      843575\n",
       "Concept                   457296\n",
       "SCR_Chemical              246750\n",
       "SCR_Organism               65233\n",
       "TopicalDescriptor          29607\n",
       "SCR_Disease                 6540\n",
       "SCR_Protocol                1217\n",
       "GeographicalDescriptor       398\n",
       "PublicationType              187\n",
       "Qualifier                     76\n",
       "CheckTag                       2\n",
       "Name: mesh_class, dtype: int64"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "id_df.mesh_class.value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# missing labels\n",
    "# id_df[id_df.mesh_label.isna()]\n",
    "id_df.mesh_label.isna().sum()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "False"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# duplicate rows\n",
    "# id_df[id_df.mesh_id.duplicated(keep=False)]\n",
    "id_df.mesh_id.duplicated().any()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>mesh_id</th>\n",
       "      <th>mesh_class</th>\n",
       "      <th>mesh_uri</th>\n",
       "      <th>mesh_label</th>\n",
       "      <th>mesh_date_created</th>\n",
       "      <th>mesh_date_revised</th>\n",
       "      <th>mesh_date_established</th>\n",
       "      <th>mesh_frequency</th>\n",
       "      <th>mesh_description</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>807230</th>\n",
       "      <td>Q000000981</td>\n",
       "      <td>Qualifier</td>\n",
       "      <td>http://id.nlm.nih.gov/mesh/2022/Q000000981</td>\n",
       "      <td>diagnostic imaging</td>\n",
       "      <td>2016-06-29</td>\n",
       "      <td>2016-06-08</td>\n",
       "      <td>2017-01-01</td>\n",
       "      <td>NaN</td>\n",
       "      <td>subheading only; coordinate with specific  ima...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>807231</th>\n",
       "      <td>Q000002</td>\n",
       "      <td>Qualifier</td>\n",
       "      <td>http://id.nlm.nih.gov/mesh/2022/Q000002</td>\n",
       "      <td>abnormalities</td>\n",
       "      <td>1973-12-27</td>\n",
       "      <td>2015-07-01</td>\n",
       "      <td>1966-01-01</td>\n",
       "      <td>NaN</td>\n",
       "      <td>subhead only; congenital &amp; structural only: do...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "           mesh_id mesh_class                                    mesh_uri  \\\n",
       "807230  Q000000981  Qualifier  http://id.nlm.nih.gov/mesh/2022/Q000000981   \n",
       "807231     Q000002  Qualifier     http://id.nlm.nih.gov/mesh/2022/Q000002   \n",
       "\n",
       "                mesh_label mesh_date_created mesh_date_revised  \\\n",
       "807230  diagnostic imaging        2016-06-29        2016-06-08   \n",
       "807231       abnormalities        1973-12-27        2015-07-01   \n",
       "\n",
       "       mesh_date_established  mesh_frequency  \\\n",
       "807230            2017-01-01             NaN   \n",
       "807231            1966-01-01             NaN   \n",
       "\n",
       "                                         mesh_description  \n",
       "807230  subheading only; coordinate with specific  ima...  \n",
       "807231  subhead only; congenital & structural only: do...  "
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "id_df.query(\"mesh_class=='Qualifier'\").head(2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## tree numbers"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 18.8 s, sys: 4.02 ms, total: 18.8 s\n",
      "Wall time: 18.8 s\n"
     ]
    },
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>mesh_id</th>\n",
       "      <th>tree_number</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>D000001</td>\n",
       "      <td>D03.633.100.221.173</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>D000002</td>\n",
       "      <td>D02.705.400.625.800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>D000002</td>\n",
       "      <td>D02.705.539.345.800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>D000002</td>\n",
       "      <td>D02.886.300.692.800</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
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      ],
      "text/plain": [
       "   mesh_id          tree_number\n",
       "0  D000001  D03.633.100.221.173\n",
       "1  D000002  D02.705.400.625.800\n",
       "2  D000002  D02.705.539.345.800\n",
       "3  D000002  D02.886.300.692.800"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "%%time\n",
    "tree_number_df = MeshLoader.run_query(rdf, \"tree-numbers\", cache=True)\n",
    "tree_number_df.head(4)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## load into networkx\n",
    "\n",
    "Currently, the ontology excludes qualifiers and descriptor-qualifier pairs. Future work should determine how to handle these instances."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%time\n",
    "nxo = MeshLoader.create_nxo(rdf, year_yyyy=mesh_year)\n",
    "nxo.n_nodes, nxo.graph.number_of_edges()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>mesh_id</th>\n",
       "      <th>mesh_class</th>\n",
       "      <th>mesh_uri</th>\n",
       "      <th>mesh_label</th>\n",
       "      <th>in_nxo</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>C000002</td>\n",
       "      <td>SCR_Chemical</td>\n",
       "      <td>http://id.nlm.nih.gov/mesh/2021/C000002</td>\n",
       "      <td>bevonium</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>C000006</td>\n",
       "      <td>SCR_Chemical</td>\n",
       "      <td>http://id.nlm.nih.gov/mesh/2021/C000006</td>\n",
       "      <td>insulin, neutral</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   mesh_id    mesh_class                                 mesh_uri  \\\n",
       "0  C000002  SCR_Chemical  http://id.nlm.nih.gov/mesh/2021/C000002   \n",
       "1  C000006  SCR_Chemical  http://id.nlm.nih.gov/mesh/2021/C000006   \n",
       "\n",
       "         mesh_label  in_nxo  \n",
       "0          bevonium    True  \n",
       "1  insulin, neutral    True  "
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "id_df[\"in_nxo\"] = id_df.mesh_id.isin(set(nxo.graph))\n",
    "id_df.head(2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th>in_nxo</th>\n",
       "      <th>mesh_class</th>\n",
       "      <th>False</th>\n",
       "      <th>True</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>CheckTag</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Concept</td>\n",
       "      <td>454398</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>GeographicalDescriptor</td>\n",
       "      <td>0</td>\n",
       "      <td>397</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>PublicationType</td>\n",
       "      <td>0</td>\n",
       "      <td>187</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Qualifier</td>\n",
       "      <td>76</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>SCR_Chemical</td>\n",
       "      <td>0</td>\n",
       "      <td>245164</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>SCR_Disease</td>\n",
       "      <td>0</td>\n",
       "      <td>6526</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>SCR_Organism</td>\n",
       "      <td>0</td>\n",
       "      <td>65256</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>SCR_Protocol</td>\n",
       "      <td>0</td>\n",
       "      <td>1217</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>Term</td>\n",
       "      <td>835307</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>TopicalDescriptor</td>\n",
       "      <td>0</td>\n",
       "      <td>29331</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "in_nxo              mesh_class   False    True\n",
       "0                     CheckTag       0       2\n",
       "1                      Concept  454398       0\n",
       "2       GeographicalDescriptor       0     397\n",
       "3              PublicationType       0     187\n",
       "4                    Qualifier      76       0\n",
       "5                 SCR_Chemical       0  245164\n",
       "6                  SCR_Disease       0    6526\n",
       "7                 SCR_Organism       0   65256\n",
       "8                 SCR_Protocol       0    1217\n",
       "9                         Term  835307       0\n",
       "10           TopicalDescriptor       0   29331"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.crosstab(id_df.mesh_class, id_df.in_nxo).reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Nodes in graph that are not in the id_df. e.g. Descriptor Qualifier Pairs\n",
    "assert len(set(nxo.graph) - set(id_df.mesh_id)) == 0"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 29.3 s, sys: 172 ms, total: 29.5 s\n",
      "Wall time: 29.5 s\n"
     ]
    },
    {
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       "      <th></th>\n",
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       "      <th>mesh_label</th>\n",
       "      <th>mesh_class</th>\n",
       "      <th>top_mesh_id</th>\n",
       "      <th>top_tree_number</th>\n",
       "      <th>top_mesh_label</th>\n",
       "      <th>top_is_disease</th>\n",
       "      <th>depth</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>466639</th>\n",
       "      <td>D001829</td>\n",
       "      <td>Body Regions</td>\n",
       "      <td>TopicalDescriptor</td>\n",
       "      <td>D001829</td>\n",
       "      <td>A01</td>\n",
       "      <td>Body Regions</td>\n",
       "      <td>False</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>466849</th>\n",
       "      <td>D001940</td>\n",
       "      <td>Breast</td>\n",
       "      <td>TopicalDescriptor</td>\n",
       "      <td>D001829</td>\n",
       "      <td>A01</td>\n",
       "      <td>Body Regions</td>\n",
       "      <td>False</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>472065</th>\n",
       "      <td>D005121</td>\n",
       "      <td>Extremities</td>\n",
       "      <td>TopicalDescriptor</td>\n",
       "      <td>D001829</td>\n",
       "      <td>A01</td>\n",
       "      <td>Body Regions</td>\n",
       "      <td>False</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>473889</th>\n",
       "      <td>D006257</td>\n",
       "      <td>Head</td>\n",
       "      <td>TopicalDescriptor</td>\n",
       "      <td>D001829</td>\n",
       "      <td>A01</td>\n",
       "      <td>Body Regions</td>\n",
       "      <td>False</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>478907</th>\n",
       "      <td>D009333</td>\n",
       "      <td>Neck</td>\n",
       "      <td>TopicalDescriptor</td>\n",
       "      <td>D001829</td>\n",
       "      <td>A01</td>\n",
       "      <td>Body Regions</td>\n",
       "      <td>False</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        mesh_id    mesh_label         mesh_class top_mesh_id top_tree_number  \\\n",
       "466639  D001829  Body Regions  TopicalDescriptor     D001829             A01   \n",
       "466849  D001940        Breast  TopicalDescriptor     D001829             A01   \n",
       "472065  D005121   Extremities  TopicalDescriptor     D001829             A01   \n",
       "473889  D006257          Head  TopicalDescriptor     D001829             A01   \n",
       "478907  D009333          Neck  TopicalDescriptor     D001829             A01   \n",
       "\n",
       "       top_mesh_label  top_is_disease  depth  \n",
       "466639   Body Regions           False      0  \n",
       "466849   Body Regions           False      1  \n",
       "472065   Body Regions           False      1  \n",
       "473889   Body Regions           False      1  \n",
       "478907   Body Regions           False      1  "
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "%%time\n",
    "top_map_df = MeshLoader.create_top_level_map_df(nxo)\n",
    "top_map_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<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>top_mesh_id</th>\n",
       "      <th>top_tree_number</th>\n",
       "      <th>top_mesh_label</th>\n",
       "      <th>top_is_disease</th>\n",
       "      <th>GeographicalDescriptor</th>\n",
       "      <th>SCR_Chemical</th>\n",
       "      <th>SCR_Disease</th>\n",
       "      <th>SCR_Organism</th>\n",
       "      <th>SCR_Protocol</th>\n",
       "      <th>TopicalDescriptor</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>D001829</td>\n",
       "      <td>A01</td>\n",
       "      <td>Body Regions</td>\n",
       "      <td>False</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>266</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>D009141</td>\n",
       "      <td>A02</td>\n",
       "      <td>Musculoskeletal System</td>\n",
       "      <td>False</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>5</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>242</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  top_mesh_id top_tree_number          top_mesh_label  top_is_disease  \\\n",
       "0     D001829             A01            Body Regions           False   \n",
       "1     D009141             A02  Musculoskeletal System           False   \n",
       "\n",
       "   GeographicalDescriptor  SCR_Chemical  SCR_Disease  SCR_Organism  \\\n",
       "0                       0             1            7             0   \n",
       "1                       0             4            5             0   \n",
       "\n",
       "   SCR_Protocol  TopicalDescriptor  \n",
       "0             0                266  \n",
       "1             0                242  "
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# top level terms and the number of descendants by class\n",
    "top_summary_df = (\n",
    "    top_map_df\n",
    "    [[\"top_mesh_id\", \"top_tree_number\", \"top_mesh_label\", \"top_is_disease\"]]\n",
    "    .drop_duplicates()\n",
    "    .merge(\n",
    "        top_map_df\n",
    "        .groupby([\"top_mesh_id\", \"mesh_class\"])\n",
    "        .size()\n",
    "        .reset_index(name='n_descendants')\n",
    "        .pivot_table(index=\"top_mesh_id\", columns=\"mesh_class\", values=\"n_descendants\", fill_value=0)\n",
    "        .reset_index()\n",
    "    )\n",
    ")\n",
    "top_summary_df.head(2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### disease subset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<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>top_mesh_id</th>\n",
       "      <th>top_tree_number</th>\n",
       "      <th>top_mesh_label</th>\n",
       "      <th>top_is_disease</th>\n",
       "      <th>SCR_Chemical</th>\n",
       "      <th>SCR_Disease</th>\n",
       "      <th>TopicalDescriptor</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>D007239</td>\n",
       "      <td>C01</td>\n",
       "      <td>Infections</td>\n",
       "      <td>True</td>\n",
       "      <td>1</td>\n",
       "      <td>119</td>\n",
       "      <td>798</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>D009369</td>\n",
       "      <td>C04</td>\n",
       "      <td>Neoplasms</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "      <td>401</td>\n",
       "      <td>704</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>D009140</td>\n",
       "      <td>C05</td>\n",
       "      <td>Musculoskeletal Diseases</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "      <td>1750</td>\n",
       "      <td>392</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>D004066</td>\n",
       "      <td>C06</td>\n",
       "      <td>Digestive System Diseases</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "      <td>302</td>\n",
       "      <td>321</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>D009057</td>\n",
       "      <td>C07</td>\n",
       "      <td>Stomatognathic Diseases</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "      <td>354</td>\n",
       "      <td>229</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>31</th>\n",
       "      <td>D012140</td>\n",
       "      <td>C08</td>\n",
       "      <td>Respiratory Tract Diseases</td>\n",
       "      <td>True</td>\n",
       "      <td>1</td>\n",
       "      <td>162</td>\n",
       "      <td>247</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32</th>\n",
       "      <td>D010038</td>\n",
       "      <td>C09</td>\n",
       "      <td>Otorhinolaryngologic Diseases</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "      <td>409</td>\n",
       "      <td>132</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>33</th>\n",
       "      <td>D009422</td>\n",
       "      <td>C10</td>\n",
       "      <td>Nervous System Diseases</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "      <td>2335</td>\n",
       "      <td>998</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34</th>\n",
       "      <td>D005128</td>\n",
       "      <td>C11</td>\n",
       "      <td>Eye Diseases</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "      <td>910</td>\n",
       "      <td>270</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35</th>\n",
       "      <td>D052801</td>\n",
       "      <td>C12</td>\n",
       "      <td>Male Urogenital Diseases</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "      <td>434</td>\n",
       "      <td>265</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36</th>\n",
       "      <td>D005261</td>\n",
       "      <td>C13</td>\n",
       "      <td>Female Urogenital Diseases and Pregnancy Compl...</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "      <td>502</td>\n",
       "      <td>395</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>37</th>\n",
       "      <td>D002318</td>\n",
       "      <td>C14</td>\n",
       "      <td>Cardiovascular Diseases</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "      <td>543</td>\n",
       "      <td>451</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>38</th>\n",
       "      <td>D006425</td>\n",
       "      <td>C15</td>\n",
       "      <td>Hemic and Lymphatic Diseases</td>\n",
       "      <td>True</td>\n",
       "      <td>6</td>\n",
       "      <td>433</td>\n",
       "      <td>295</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>39</th>\n",
       "      <td>D009358</td>\n",
       "      <td>C16</td>\n",
       "      <td>Congenital, Hereditary, and Neonatal Diseases ...</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "      <td>4115</td>\n",
       "      <td>788</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>40</th>\n",
       "      <td>D017437</td>\n",
       "      <td>C17</td>\n",
       "      <td>Skin and Connective Tissue Diseases</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "      <td>887</td>\n",
       "      <td>490</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>41</th>\n",
       "      <td>D009750</td>\n",
       "      <td>C18</td>\n",
       "      <td>Nutritional and Metabolic Diseases</td>\n",
       "      <td>True</td>\n",
       "      <td>1</td>\n",
       "      <td>1050</td>\n",
       "      <td>383</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42</th>\n",
       "      <td>D004700</td>\n",
       "      <td>C19</td>\n",
       "      <td>Endocrine System Diseases</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "      <td>508</td>\n",
       "      <td>180</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>43</th>\n",
       "      <td>D007154</td>\n",
       "      <td>C20</td>\n",
       "      <td>Immune System Diseases</td>\n",
       "      <td>True</td>\n",
       "      <td>6</td>\n",
       "      <td>296</td>\n",
       "      <td>271</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44</th>\n",
       "      <td>D007280</td>\n",
       "      <td>C21</td>\n",
       "      <td>Disorders of Environmental Origin</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>45</th>\n",
       "      <td>D000820</td>\n",
       "      <td>C22</td>\n",
       "      <td>Animal Diseases</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "      <td>5</td>\n",
       "      <td>164</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>46</th>\n",
       "      <td>D013568</td>\n",
       "      <td>C23</td>\n",
       "      <td>Pathological Conditions, Signs and Symptoms</td>\n",
       "      <td>True</td>\n",
       "      <td>1</td>\n",
       "      <td>2102</td>\n",
       "      <td>1114</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47</th>\n",
       "      <td>D009784</td>\n",
       "      <td>C24</td>\n",
       "      <td>Occupational Diseases</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "      <td>5</td>\n",
       "      <td>27</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48</th>\n",
       "      <td>D064419</td>\n",
       "      <td>C25</td>\n",
       "      <td>Chemically-Induced Disorders</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "      <td>9</td>\n",
       "      <td>135</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>72</th>\n",
       "      <td>D001523</td>\n",
       "      <td>F03</td>\n",
       "      <td>Mental Disorders</td>\n",
       "      <td>True</td>\n",
       "      <td>1</td>\n",
       "      <td>714</td>\n",
       "      <td>276</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   top_mesh_id top_tree_number  \\\n",
       "26     D007239             C01   \n",
       "27     D009369             C04   \n",
       "28     D009140             C05   \n",
       "29     D004066             C06   \n",
       "30     D009057             C07   \n",
       "31     D012140             C08   \n",
       "32     D010038             C09   \n",
       "33     D009422             C10   \n",
       "34     D005128             C11   \n",
       "35     D052801             C12   \n",
       "36     D005261             C13   \n",
       "37     D002318             C14   \n",
       "38     D006425             C15   \n",
       "39     D009358             C16   \n",
       "40     D017437             C17   \n",
       "41     D009750             C18   \n",
       "42     D004700             C19   \n",
       "43     D007154             C20   \n",
       "44     D007280             C21   \n",
       "45     D000820             C22   \n",
       "46     D013568             C23   \n",
       "47     D009784             C24   \n",
       "48     D064419             C25   \n",
       "72     D001523             F03   \n",
       "\n",
       "                                       top_mesh_label  top_is_disease  \\\n",
       "26                                         Infections            True   \n",
       "27                                          Neoplasms            True   \n",
       "28                           Musculoskeletal Diseases            True   \n",
       "29                          Digestive System Diseases            True   \n",
       "30                            Stomatognathic Diseases            True   \n",
       "31                         Respiratory Tract Diseases            True   \n",
       "32                      Otorhinolaryngologic Diseases            True   \n",
       "33                            Nervous System Diseases            True   \n",
       "34                                       Eye Diseases            True   \n",
       "35                           Male Urogenital Diseases            True   \n",
       "36  Female Urogenital Diseases and Pregnancy Compl...            True   \n",
       "37                            Cardiovascular Diseases            True   \n",
       "38                       Hemic and Lymphatic Diseases            True   \n",
       "39  Congenital, Hereditary, and Neonatal Diseases ...            True   \n",
       "40                Skin and Connective Tissue Diseases            True   \n",
       "41                 Nutritional and Metabolic Diseases            True   \n",
       "42                          Endocrine System Diseases            True   \n",
       "43                             Immune System Diseases            True   \n",
       "44                  Disorders of Environmental Origin            True   \n",
       "45                                    Animal Diseases            True   \n",
       "46        Pathological Conditions, Signs and Symptoms            True   \n",
       "47                              Occupational Diseases            True   \n",
       "48                       Chemically-Induced Disorders            True   \n",
       "72                                   Mental Disorders            True   \n",
       "\n",
       "    SCR_Chemical  SCR_Disease  TopicalDescriptor  \n",
       "26             1          119                798  \n",
       "27             0          401                704  \n",
       "28             0         1750                392  \n",
       "29             0          302                321  \n",
       "30             0          354                229  \n",
       "31             1          162                247  \n",
       "32             0          409                132  \n",
       "33             0         2335                998  \n",
       "34             0          910                270  \n",
       "35             0          434                265  \n",
       "36             0          502                395  \n",
       "37             0          543                451  \n",
       "38             6          433                295  \n",
       "39             0         4115                788  \n",
       "40             0          887                490  \n",
       "41             1         1050                383  \n",
       "42             0          508                180  \n",
       "43             6          296                271  \n",
       "44             0            0                  5  \n",
       "45             0            5                164  \n",
       "46             1         2102               1114  \n",
       "47             0            5                 27  \n",
       "48             0            9                135  \n",
       "72             1          714                276  "
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "top_summary_df.query(\"top_is_disease\").drop(\n",
    "    columns=[\"GeographicalDescriptor\", \"SCR_Organism\", \"SCR_Protocol\"]\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "11251"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "all_diseases = set(top_map_df.query(\"top_is_disease\").mesh_id)\n",
    "len(all_diseases)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## GitHub outputs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "gh_data_url = \"https://github.com/related-sciences/nxontology-data/raw/output/mesh/\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<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>mesh_id</th>\n",
       "      <th>mesh_label</th>\n",
       "      <th>mesh_class</th>\n",
       "      <th>top_mesh_id</th>\n",
       "      <th>top_tree_number</th>\n",
       "      <th>top_mesh_label</th>\n",
       "      <th>top_is_disease</th>\n",
       "      <th>depth</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>36053</th>\n",
       "      <td>C000664754</td>\n",
       "      <td>Calonectria longiramosa</td>\n",
       "      <td>SCR_Organism</td>\n",
       "      <td>D056890</td>\n",
       "      <td>B01</td>\n",
       "      <td>Eukaryota</td>\n",
       "      <td>False</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>420240</th>\n",
       "      <td>C474744</td>\n",
       "      <td>GP90-MC301 protein, rat</td>\n",
       "      <td>SCR_Chemical</td>\n",
       "      <td>D000602</td>\n",
       "      <td>D12</td>\n",
       "      <td>Amino Acids, Peptides, and Proteins</td>\n",
       "      <td>False</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>102707</th>\n",
       "      <td>C543241</td>\n",
       "      <td>Cardiomyopathy, fatal fetal, due to myocardial...</td>\n",
       "      <td>SCR_Disease</td>\n",
       "      <td>D013568</td>\n",
       "      <td>C23</td>\n",
       "      <td>Pathological Conditions, Signs and Symptoms</td>\n",
       "      <td>True</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>146679</th>\n",
       "      <td>C038055</td>\n",
       "      <td>N-nitrosomethyl-N-propylamine</td>\n",
       "      <td>SCR_Chemical</td>\n",
       "      <td>D009930</td>\n",
       "      <td>D02</td>\n",
       "      <td>Organic Chemicals</td>\n",
       "      <td>False</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>572839</th>\n",
       "      <td>C000725016</td>\n",
       "      <td>Sauk-Suiattle Indian Tribe</td>\n",
       "      <td>SCR_Population</td>\n",
       "      <td>D011154</td>\n",
       "      <td>N01</td>\n",
       "      <td>Population Characteristics</td>\n",
       "      <td>False</td>\n",
       "      <td>5</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "           mesh_id                                         mesh_label  \\\n",
       "36053   C000664754                            Calonectria longiramosa   \n",
       "420240     C474744                            GP90-MC301 protein, rat   \n",
       "102707     C543241  Cardiomyopathy, fatal fetal, due to myocardial...   \n",
       "146679     C038055                      N-nitrosomethyl-N-propylamine   \n",
       "572839  C000725016                         Sauk-Suiattle Indian Tribe   \n",
       "\n",
       "            mesh_class top_mesh_id top_tree_number  \\\n",
       "36053     SCR_Organism     D056890             B01   \n",
       "420240    SCR_Chemical     D000602             D12   \n",
       "102707     SCR_Disease     D013568             C23   \n",
       "146679    SCR_Chemical     D009930             D02   \n",
       "572839  SCR_Population     D011154             N01   \n",
       "\n",
       "                                     top_mesh_label  top_is_disease  depth  \n",
       "36053                                     Eukaryota           False      4  \n",
       "420240          Amino Acids, Peptides, and Proteins           False      3  \n",
       "102707  Pathological Conditions, Signs and Symptoms            True      4  \n",
       "146679                            Organic Chemicals           False      3  \n",
       "572839                   Population Characteristics           False      5  "
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.read_json(f\"{gh_data_url}mesh_topical_descriptor_descendants_top_level_map.json.gz\").sample(5, random_state=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>mesh_id</th>\n",
       "      <th>mesh_class</th>\n",
       "      <th>mesh_uri</th>\n",
       "      <th>mesh_label</th>\n",
       "      <th>mesh_date_created</th>\n",
       "      <th>mesh_date_revised</th>\n",
       "      <th>mesh_date_established</th>\n",
       "      <th>mesh_frequency</th>\n",
       "      <th>mesh_description</th>\n",
       "      <th>tree_numbers</th>\n",
       "      <th>in_full_nxo</th>\n",
       "      <th>in_desc_nxo</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>C000002</td>\n",
       "      <td>SCR_Chemical</td>\n",
       "      <td>http://id.nlm.nih.gov/mesh/2023/C000002</td>\n",
       "      <td>bevonium</td>\n",
       "      <td>1971-01-01</td>\n",
       "      <td>2018-09-24</td>\n",
       "      <td>None</td>\n",
       "      <td>1.0</td>\n",
       "      <td>structure given in first source</td>\n",
       "      <td>None</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2346</th>\n",
       "      <td>C000591739</td>\n",
       "      <td>SCR_Disease</td>\n",
       "      <td>http://id.nlm.nih.gov/mesh/2023/C000591739</td>\n",
       "      <td>familial gynecomastia, due to increased aromat...</td>\n",
       "      <td>2014-11-04</td>\n",
       "      <td>2022-11-02</td>\n",
       "      <td>None</td>\n",
       "      <td>5.0</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15848</th>\n",
       "      <td>C000612320</td>\n",
       "      <td>SCR_Organism</td>\n",
       "      <td>http://id.nlm.nih.gov/mesh/2023/C000612320</td>\n",
       "      <td>UR2 sarcoma virus</td>\n",
       "      <td>2017-10-18</td>\n",
       "      <td>2020-09-30</td>\n",
       "      <td>None</td>\n",
       "      <td>0.0</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>93595</th>\n",
       "      <td>C000705129</td>\n",
       "      <td>SCR_Protocol</td>\n",
       "      <td>http://id.nlm.nih.gov/mesh/2023/C000705129</td>\n",
       "      <td>LAMP assay</td>\n",
       "      <td>2020-03-28</td>\n",
       "      <td>2020-03-31</td>\n",
       "      <td>None</td>\n",
       "      <td>930.0</td>\n",
       "      <td>for use of LAMP assay for detecting COVID-19 a...</td>\n",
       "      <td>None</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>98889</th>\n",
       "      <td>C000724254</td>\n",
       "      <td>SCR_Population</td>\n",
       "      <td>http://id.nlm.nih.gov/mesh/2023/C000724254</td>\n",
       "      <td>Big Sandy Rancheria of Western Mono Indians of...</td>\n",
       "      <td>2022-11-29</td>\n",
       "      <td>2022-11-29</td>\n",
       "      <td>None</td>\n",
       "      <td>0.0</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>321747</th>\n",
       "      <td>D000001</td>\n",
       "      <td>TopicalDescriptor</td>\n",
       "      <td>http://id.nlm.nih.gov/mesh/2023/D000001</td>\n",
       "      <td>Calcimycin</td>\n",
       "      <td>1974-11-19</td>\n",
       "      <td>2016-05-27</td>\n",
       "      <td>1984-01-01</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>[D03.633.100.221.173]</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>321964</th>\n",
       "      <td>D000068036</td>\n",
       "      <td>PublicationType</td>\n",
       "      <td>http://id.nlm.nih.gov/mesh/2023/D000068036</td>\n",
       "      <td>Graphic Novel</td>\n",
       "      <td>2015-07-01</td>\n",
       "      <td>2019-07-05</td>\n",
       "      <td>2016-01-01</td>\n",
       "      <td>NaN</td>\n",
       "      <td>This heading is used as a Publication Type. Gr...</td>\n",
       "      <td>[V02.700.415]</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>321965</th>\n",
       "      <td>D000068037</td>\n",
       "      <td>GeographicalDescriptor</td>\n",
       "      <td>http://id.nlm.nih.gov/mesh/2023/D000068037</td>\n",
       "      <td>South Sudan</td>\n",
       "      <td>2015-07-01</td>\n",
       "      <td>2021-01-26</td>\n",
       "      <td>2016-01-01</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>[Z01.058.290.120.745]</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>329835</th>\n",
       "      <td>D005260</td>\n",
       "      <td>CheckTag</td>\n",
       "      <td>http://id.nlm.nih.gov/mesh/2023/D005260</td>\n",
       "      <td>Female</td>\n",
       "      <td>1999-01-01</td>\n",
       "      <td>2015-06-10</td>\n",
       "      <td>1966-01-01</td>\n",
       "      <td>NaN</td>\n",
       "      <td>check tag only for female organs, diseases, ph...</td>\n",
       "      <td>None</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>352201</th>\n",
       "      <td>M0000001</td>\n",
       "      <td>Concept</td>\n",
       "      <td>http://id.nlm.nih.gov/mesh/2023/M0000001</td>\n",
       "      <td>Calcimycin</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>NaN</td>\n",
       "      <td>An ionophorous, polyether antibiotic from Stre...</td>\n",
       "      <td>None</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>812297</th>\n",
       "      <td>Q000000981</td>\n",
       "      <td>Qualifier</td>\n",
       "      <td>http://id.nlm.nih.gov/mesh/2023/Q000000981</td>\n",
       "      <td>diagnostic imaging</td>\n",
       "      <td>2016-06-29</td>\n",
       "      <td>2016-06-08</td>\n",
       "      <td>2017-01-01</td>\n",
       "      <td>NaN</td>\n",
       "      <td>subheading only; coordinate with specific  ima...</td>\n",
       "      <td>[Y04.010]</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>812373</th>\n",
       "      <td>T000001</td>\n",
       "      <td>Term</td>\n",
       "      <td>http://id.nlm.nih.gov/mesh/2023/T000001</td>\n",
       "      <td>A-23187</td>\n",
       "      <td>1990-03-08</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "           mesh_id              mesh_class  \\\n",
       "0          C000002            SCR_Chemical   \n",
       "2346    C000591739             SCR_Disease   \n",
       "15848   C000612320            SCR_Organism   \n",
       "93595   C000705129            SCR_Protocol   \n",
       "98889   C000724254          SCR_Population   \n",
       "321747     D000001       TopicalDescriptor   \n",
       "321964  D000068036         PublicationType   \n",
       "321965  D000068037  GeographicalDescriptor   \n",
       "329835     D005260                CheckTag   \n",
       "352201    M0000001                 Concept   \n",
       "812297  Q000000981               Qualifier   \n",
       "812373     T000001                    Term   \n",
       "\n",
       "                                          mesh_uri  \\\n",
       "0          http://id.nlm.nih.gov/mesh/2023/C000002   \n",
       "2346    http://id.nlm.nih.gov/mesh/2023/C000591739   \n",
       "15848   http://id.nlm.nih.gov/mesh/2023/C000612320   \n",
       "93595   http://id.nlm.nih.gov/mesh/2023/C000705129   \n",
       "98889   http://id.nlm.nih.gov/mesh/2023/C000724254   \n",
       "321747     http://id.nlm.nih.gov/mesh/2023/D000001   \n",
       "321964  http://id.nlm.nih.gov/mesh/2023/D000068036   \n",
       "321965  http://id.nlm.nih.gov/mesh/2023/D000068037   \n",
       "329835     http://id.nlm.nih.gov/mesh/2023/D005260   \n",
       "352201    http://id.nlm.nih.gov/mesh/2023/M0000001   \n",
       "812297  http://id.nlm.nih.gov/mesh/2023/Q000000981   \n",
       "812373     http://id.nlm.nih.gov/mesh/2023/T000001   \n",
       "\n",
       "                                               mesh_label mesh_date_created  \\\n",
       "0                                                bevonium        1971-01-01   \n",
       "2346    familial gynecomastia, due to increased aromat...        2014-11-04   \n",
       "15848                                   UR2 sarcoma virus        2017-10-18   \n",
       "93595                                          LAMP assay        2020-03-28   \n",
       "98889   Big Sandy Rancheria of Western Mono Indians of...        2022-11-29   \n",
       "321747                                         Calcimycin        1974-11-19   \n",
       "321964                                      Graphic Novel        2015-07-01   \n",
       "321965                                        South Sudan        2015-07-01   \n",
       "329835                                             Female        1999-01-01   \n",
       "352201                                         Calcimycin              None   \n",
       "812297                                 diagnostic imaging        2016-06-29   \n",
       "812373                                            A-23187        1990-03-08   \n",
       "\n",
       "       mesh_date_revised mesh_date_established  mesh_frequency  \\\n",
       "0             2018-09-24                  None             1.0   \n",
       "2346          2022-11-02                  None             5.0   \n",
       "15848         2020-09-30                  None             0.0   \n",
       "93595         2020-03-31                  None           930.0   \n",
       "98889         2022-11-29                  None             0.0   \n",
       "321747        2016-05-27            1984-01-01             NaN   \n",
       "321964        2019-07-05            2016-01-01             NaN   \n",
       "321965        2021-01-26            2016-01-01             NaN   \n",
       "329835        2015-06-10            1966-01-01             NaN   \n",
       "352201              None                  None             NaN   \n",
       "812297        2016-06-08            2017-01-01             NaN   \n",
       "812373              None                  None             NaN   \n",
       "\n",
       "                                         mesh_description  \\\n",
       "0                         structure given in first source   \n",
       "2346                                                 None   \n",
       "15848                                                None   \n",
       "93595   for use of LAMP assay for detecting COVID-19 a...   \n",
       "98889                                                None   \n",
       "321747                                               None   \n",
       "321964  This heading is used as a Publication Type. Gr...   \n",
       "321965                                               None   \n",
       "329835  check tag only for female organs, diseases, ph...   \n",
       "352201  An ionophorous, polyether antibiotic from Stre...   \n",
       "812297  subheading only; coordinate with specific  ima...   \n",
       "812373                                               None   \n",
       "\n",
       "                 tree_numbers  in_full_nxo  in_desc_nxo  \n",
       "0                        None         True         True  \n",
       "2346                     None         True         True  \n",
       "15848                    None         True         True  \n",
       "93595                    None         True         True  \n",
       "98889                    None         True         True  \n",
       "321747  [D03.633.100.221.173]         True         True  \n",
       "321964          [V02.700.415]         True        False  \n",
       "321965  [Z01.058.290.120.745]         True        False  \n",
       "329835                   None         True        False  \n",
       "352201                   None        False        False  \n",
       "812297              [Y04.010]        False        False  \n",
       "812373                   None        False        False  "
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.read_json(f\"{gh_data_url}mesh_identifiers.json.gz\").drop_duplicates(\"mesh_class\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>mesh_id</th>\n",
       "      <th>concept_id</th>\n",
       "      <th>term_id</th>\n",
       "      <th>mesh_label</th>\n",
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       "      <th>concept_relation_to_preferred</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>704006</th>\n",
       "      <td>C577955</td>\n",
       "      <td>M0581027</td>\n",
       "      <td>T836700</td>\n",
       "      <td>3-(2-chlorophenyl)-1-(2,4-dihydroxyphenyl)prop...</td>\n",
       "      <td>NPD170</td>\n",
       "      <td>NPD170</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>LAB</td>\n",
       "      <td>2013-02-03</td>\n",
       "      <td>narrower</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>100718</th>\n",
       "      <td>C000674955</td>\n",
       "      <td>M000700981</td>\n",
       "      <td>T001033762</td>\n",
       "      <td>Derxomyces nakasei</td>\n",
       "      <td>Derxomyces nakasei</td>\n",
       "      <td>Bullera nakasei</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>NON</td>\n",
       "      <td>2020-03-26</td>\n",
       "      <td>exact</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>586186</th>\n",
       "      <td>C509465</td>\n",
       "      <td>M0497018</td>\n",
       "      <td>T671283</td>\n",
       "      <td>meso-tetrakis(heptafluoropropyl)porphyrin</td>\n",
       "      <td>meso-tetrakis(heptafluoropropyl)porphyrin</td>\n",
       "      <td>meso-tetrakis(heptafluoropropyl)porphyrin</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>NON</td>\n",
       "      <td>2006-04-13</td>\n",
       "      <td>exact</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>503573</th>\n",
       "      <td>C459630</td>\n",
       "      <td>M0430868</td>\n",
       "      <td>T503918</td>\n",
       "      <td>ent-beyer-15-en-18-O-oxalate</td>\n",
       "      <td>ent-beyer-15-en-18-O-oxalate</td>\n",
       "      <td>ent-beyer-15-en-18-O-oxalate</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>NON</td>\n",
       "      <td>2002-07-14</td>\n",
       "      <td>exact</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>905742</th>\n",
       "      <td>D020526</td>\n",
       "      <td>M0328180</td>\n",
       "      <td>T000952246</td>\n",
       "      <td>Brain Stem Infarctions</td>\n",
       "      <td>Brain Stem Infarctions</td>\n",
       "      <td>Brain Stem Infarcts</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>NON</td>\n",
       "      <td>2019-02-26</td>\n",
       "      <td>exact</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "           mesh_id  concept_id     term_id  \\\n",
       "704006     C577955    M0581027     T836700   \n",
       "100718  C000674955  M000700981  T001033762   \n",
       "586186     C509465    M0497018     T671283   \n",
       "503573     C459630    M0430868     T503918   \n",
       "905742     D020526    M0328180  T000952246   \n",
       "\n",
       "                                               mesh_label  \\\n",
       "704006  3-(2-chlorophenyl)-1-(2,4-dihydroxyphenyl)prop...   \n",
       "100718                                 Derxomyces nakasei   \n",
       "586186          meso-tetrakis(heptafluoropropyl)porphyrin   \n",
       "503573                       ent-beyer-15-en-18-O-oxalate   \n",
       "905742                             Brain Stem Infarctions   \n",
       "\n",
       "                                    concept_label  \\\n",
       "704006                                     NPD170   \n",
       "100718                         Derxomyces nakasei   \n",
       "586186  meso-tetrakis(heptafluoropropyl)porphyrin   \n",
       "503573               ent-beyer-15-en-18-O-oxalate   \n",
       "905742                     Brain Stem Infarctions   \n",
       "\n",
       "                                       term_label  concept_is_preferred  \\\n",
       "704006                                     NPD170                 False   \n",
       "100718                            Bullera nakasei                  True   \n",
       "586186  meso-tetrakis(heptafluoropropyl)porphyrin                  True   \n",
       "503573               ent-beyer-15-en-18-O-oxalate                  True   \n",
       "905742                        Brain Stem Infarcts                  True   \n",
       "\n",
       "        term_is_preferred  term_label_is_preferred term_lexical_tag  \\\n",
       "704006               True                     True              LAB   \n",
       "100718              False                     True              NON   \n",
       "586186               True                     True              NON   \n",
       "503573               True                     True              NON   \n",
       "905742              False                    False              NON   \n",
       "\n",
       "       term_date_created concept_relation_to_preferred  \n",
       "704006        2013-02-03                      narrower  \n",
       "100718        2020-03-26                         exact  \n",
       "586186        2006-04-13                         exact  \n",
       "503573        2002-07-14                         exact  \n",
       "905742        2019-02-26                         exact  "
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.read_json(f\"{gh_data_url}mesh_synonyms.json.gz\").sample(5, random_state=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>pair_label</th>\n",
       "      <th>pair_allowed</th>\n",
       "      <th>pair_type</th>\n",
       "      <th>pair_uri</th>\n",
       "      <th>descriptor_id</th>\n",
       "      <th>qualifier_id</th>\n",
       "      <th>descriptor_label</th>\n",
       "      <th>qualifier_label</th>\n",
       "      <th>use_instead_uri</th>\n",
       "      <th>use_instead_label</th>\n",
       "      <th>use_instead_class</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>45319</th>\n",
       "      <td>Masked Mycotoxins/physiology</td>\n",
       "      <td>NaN</td>\n",
       "      <td>AllowedDescriptorQualifierPair</td>\n",
       "      <td>http://id.nlm.nih.gov/mesh/2023/D000083842Q000502</td>\n",
       "      <td>D000083842</td>\n",
       "      <td>Q000502</td>\n",
       "      <td>Masked Mycotoxins</td>\n",
       "      <td>physiology</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>114717</th>\n",
       "      <td>Chromium Alloys/analysis</td>\n",
       "      <td>NaN</td>\n",
       "      <td>AllowedDescriptorQualifierPair</td>\n",
       "      <td>http://id.nlm.nih.gov/mesh/2023/D002858Q000032</td>\n",
       "      <td>D002858</td>\n",
       "      <td>Q000032</td>\n",
       "      <td>Chromium Alloys</td>\n",
       "      <td>analysis</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>251852</th>\n",
       "      <td>o-Phthalaldehyde/standards</td>\n",
       "      <td>NaN</td>\n",
       "      <td>AllowedDescriptorQualifierPair</td>\n",
       "      <td>http://id.nlm.nih.gov/mesh/2023/D009764Q000592</td>\n",
       "      <td>D009764</td>\n",
       "      <td>Q000592</td>\n",
       "      <td>o-Phthalaldehyde</td>\n",
       "      <td>standards</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>369654</th>\n",
       "      <td>HLA-B8 Antigen/cerebrospinal fluid</td>\n",
       "      <td>NaN</td>\n",
       "      <td>AllowedDescriptorQualifierPair</td>\n",
       "      <td>http://id.nlm.nih.gov/mesh/2023/D015795Q000134</td>\n",
       "      <td>D015795</td>\n",
       "      <td>Q000134</td>\n",
       "      <td>HLA-B8 Antigen</td>\n",
       "      <td>cerebrospinal fluid</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>350916</th>\n",
       "      <td>Vertebral Artery/enzymology</td>\n",
       "      <td>NaN</td>\n",
       "      <td>AllowedDescriptorQualifierPair</td>\n",
       "      <td>http://id.nlm.nih.gov/mesh/2023/D014711Q000201</td>\n",
       "      <td>D014711</td>\n",
       "      <td>Q000201</td>\n",
       "      <td>Vertebral Artery</td>\n",
       "      <td>enzymology</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                pair_label  pair_allowed  \\\n",
       "45319         Masked Mycotoxins/physiology           NaN   \n",
       "114717            Chromium Alloys/analysis           NaN   \n",
       "251852          o-Phthalaldehyde/standards           NaN   \n",
       "369654  HLA-B8 Antigen/cerebrospinal fluid           NaN   \n",
       "350916         Vertebral Artery/enzymology           NaN   \n",
       "\n",
       "                             pair_type  \\\n",
       "45319   AllowedDescriptorQualifierPair   \n",
       "114717  AllowedDescriptorQualifierPair   \n",
       "251852  AllowedDescriptorQualifierPair   \n",
       "369654  AllowedDescriptorQualifierPair   \n",
       "350916  AllowedDescriptorQualifierPair   \n",
       "\n",
       "                                                 pair_uri descriptor_id  \\\n",
       "45319   http://id.nlm.nih.gov/mesh/2023/D000083842Q000502    D000083842   \n",
       "114717     http://id.nlm.nih.gov/mesh/2023/D002858Q000032       D002858   \n",
       "251852     http://id.nlm.nih.gov/mesh/2023/D009764Q000592       D009764   \n",
       "369654     http://id.nlm.nih.gov/mesh/2023/D015795Q000134       D015795   \n",
       "350916     http://id.nlm.nih.gov/mesh/2023/D014711Q000201       D014711   \n",
       "\n",
       "       qualifier_id   descriptor_label      qualifier_label use_instead_uri  \\\n",
       "45319       Q000502  Masked Mycotoxins           physiology            None   \n",
       "114717      Q000032    Chromium Alloys             analysis            None   \n",
       "251852      Q000592   o-Phthalaldehyde            standards            None   \n",
       "369654      Q000134     HLA-B8 Antigen  cerebrospinal fluid            None   \n",
       "350916      Q000201   Vertebral Artery           enzymology            None   \n",
       "\n",
       "       use_instead_label use_instead_class  \n",
       "45319               None              None  \n",
       "114717              None              None  \n",
       "251852              None              None  \n",
       "369654              None              None  \n",
       "350916              None              None  "
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.read_json(f\"{gh_data_url}mesh_descriptor_qualifier_pairs.json.gz\").sample(5, random_state=0)"
   ]
  }
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