{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "d7a838ab-eccb-48a0-bfda-bb9fecbe1dec",
   "metadata": {},
   "outputs": [],
   "source": [
    "%reset -f"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "450a2da2-b889-4fcc-a6f0-90cf71d78c7a",
   "metadata": {},
   "outputs": [],
   "source": [
    "user = \"jtr4v\"\n",
    "db = f\"/Users/{user}/.data/oaklib/phenio.db\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "b955bde6-60c8-4ba7-83ed-4383f3161176",
   "metadata": {},
   "outputs": [],
   "source": [
    "%reload_ext sql\n",
    "%sql sqlite:///{db}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "96a7a5a6-a3c4-4242-9ed6-2be7c31efd81",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " * sqlite:////Users/jtr4v/.data/oaklib/phenio.db\n",
      "Done.\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<table>\n",
       "    <thead>\n",
       "        <tr>\n",
       "            <th>id</th>\n",
       "            <th>subject</th>\n",
       "            <th>predicate</th>\n",
       "            <th>object</th>\n",
       "            <th>evidence_type</th>\n",
       "            <th>publication</th>\n",
       "            <th>source</th>\n",
       "        </tr>\n",
       "    </thead>\n",
       "    <tbody>\n",
       "        <tr>\n",
       "            <td>uuid:70269c5a-42a9-11ee-be37-31ef105c25ea</td>\n",
       "            <td>MONDO:0023659</td>\n",
       "            <td>biolink:has_phenotype</td>\n",
       "            <td>HP:0011097</td>\n",
       "            <td>ECO:0000269</td>\n",
       "            <td>PMID:31675180</td>\n",
       "            <td>infores:hpo-annotations</td>\n",
       "        </tr>\n",
       "        <tr>\n",
       "            <td>uuid:70269c5b-42a9-11ee-be37-31ef105c25ea</td>\n",
       "            <td>MONDO:0023659</td>\n",
       "            <td>biolink:has_phenotype</td>\n",
       "            <td>HP:0002187</td>\n",
       "            <td>ECO:0000269</td>\n",
       "            <td>PMID:31675180</td>\n",
       "            <td>infores:hpo-annotations</td>\n",
       "        </tr>\n",
       "        <tr>\n",
       "            <td>uuid:70269c5c-42a9-11ee-be37-31ef105c25ea</td>\n",
       "            <td>MONDO:0023659</td>\n",
       "            <td>biolink:has_phenotype</td>\n",
       "            <td>HP:0001518</td>\n",
       "            <td>ECO:0000269</td>\n",
       "            <td>PMID:31675180</td>\n",
       "            <td>infores:hpo-annotations</td>\n",
       "        </tr>\n",
       "        <tr>\n",
       "            <td>uuid:70269c5d-42a9-11ee-be37-31ef105c25ea</td>\n",
       "            <td>MONDO:0023659</td>\n",
       "            <td>biolink:has_phenotype</td>\n",
       "            <td>HP:0032792</td>\n",
       "            <td>ECO:0000269</td>\n",
       "            <td>PMID:31675180</td>\n",
       "            <td>infores:hpo-annotations</td>\n",
       "        </tr>\n",
       "        <tr>\n",
       "            <td>uuid:70269c5e-42a9-11ee-be37-31ef105c25ea</td>\n",
       "            <td>MONDO:0023659</td>\n",
       "            <td>biolink:has_phenotype</td>\n",
       "            <td>HP:0011451</td>\n",
       "            <td>ECO:0000269</td>\n",
       "            <td>PMID:31675180</td>\n",
       "            <td>infores:hpo-annotations</td>\n",
       "        </tr>\n",
       "    </tbody>\n",
       "</table>"
      ],
      "text/plain": [
       "[('uuid:70269c5a-42a9-11ee-be37-31ef105c25ea', 'MONDO:0023659', 'biolink:has_phenotype', 'HP:0011097', 'ECO:0000269', 'PMID:31675180', 'infores:hpo-annotations'),\n",
       " ('uuid:70269c5b-42a9-11ee-be37-31ef105c25ea', 'MONDO:0023659', 'biolink:has_phenotype', 'HP:0002187', 'ECO:0000269', 'PMID:31675180', 'infores:hpo-annotations'),\n",
       " ('uuid:70269c5c-42a9-11ee-be37-31ef105c25ea', 'MONDO:0023659', 'biolink:has_phenotype', 'HP:0001518', 'ECO:0000269', 'PMID:31675180', 'infores:hpo-annotations'),\n",
       " ('uuid:70269c5d-42a9-11ee-be37-31ef105c25ea', 'MONDO:0023659', 'biolink:has_phenotype', 'HP:0032792', 'ECO:0000269', 'PMID:31675180', 'infores:hpo-annotations'),\n",
       " ('uuid:70269c5e-42a9-11ee-be37-31ef105c25ea', 'MONDO:0023659', 'biolink:has_phenotype', 'HP:0011451', 'ECO:0000269', 'PMID:31675180', 'infores:hpo-annotations')]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "%sql SELECT * FROM term_association LIMIT 5;"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "dba6b3e5-d637-48fb-a7b1-c29356c1f3ef",
   "metadata": {},
   "source": [
    "### Python"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "723d28cb-8ac6-4eb2-bea8-a1626677bc51",
   "metadata": {},
   "outputs": [],
   "source": [
    "import sqlite3\n",
    "import pandas as pd\n",
    "import numpy as np\n",
    "# Set the option to None to display all rows\n",
    "# pd.set_option('display.max_rows', None)\n",
    "\n",
    "from semsimian import Semsimian"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "ebd327bb-e641-459d-bd37-7d96a9036f67",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[('term_association',),\n",
       " ('has_oio_synonym_statement',),\n",
       " ('anonymous_expression',),\n",
       " ('anonymous_class_expression',),\n",
       " ('anonymous_property_expression',),\n",
       " ('anonymous_individual_expression',),\n",
       " ('owl_restriction',),\n",
       " ('owl_complex_axiom',),\n",
       " ('prefix',),\n",
       " ('rdf_list_statement',),\n",
       " ('rdf_level_summary_statistic',),\n",
       " ('relation_graph_construct',),\n",
       " ('subgraph_query',),\n",
       " ('entailed_edge',),\n",
       " ('repair_action',),\n",
       " ('problem',),\n",
       " ('lexical_problem',),\n",
       " ('statements',)]"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "conn = sqlite3.connect(db)\n",
    "res = conn.execute(\"SELECT name FROM sqlite_master WHERE type='table';\")\n",
    "tables = res.fetchall()\n",
    "\n",
    "tables"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "08aac28f-997f-4864-8bff-6ffcc5ae73c4",
   "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>id</th>\n",
       "      <th>subject</th>\n",
       "      <th>predicate</th>\n",
       "      <th>object</th>\n",
       "      <th>evidence_type</th>\n",
       "      <th>publication</th>\n",
       "      <th>source</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>uuid:70269c5a-42a9-11ee-be37-31ef105c25ea</td>\n",
       "      <td>MONDO:0023659</td>\n",
       "      <td>biolink:has_phenotype</td>\n",
       "      <td>HP:0011097</td>\n",
       "      <td>ECO:0000269</td>\n",
       "      <td>PMID:31675180</td>\n",
       "      <td>infores:hpo-annotations</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>uuid:70269c5b-42a9-11ee-be37-31ef105c25ea</td>\n",
       "      <td>MONDO:0023659</td>\n",
       "      <td>biolink:has_phenotype</td>\n",
       "      <td>HP:0002187</td>\n",
       "      <td>ECO:0000269</td>\n",
       "      <td>PMID:31675180</td>\n",
       "      <td>infores:hpo-annotations</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>uuid:70269c5c-42a9-11ee-be37-31ef105c25ea</td>\n",
       "      <td>MONDO:0023659</td>\n",
       "      <td>biolink:has_phenotype</td>\n",
       "      <td>HP:0001518</td>\n",
       "      <td>ECO:0000269</td>\n",
       "      <td>PMID:31675180</td>\n",
       "      <td>infores:hpo-annotations</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>uuid:70269c5d-42a9-11ee-be37-31ef105c25ea</td>\n",
       "      <td>MONDO:0023659</td>\n",
       "      <td>biolink:has_phenotype</td>\n",
       "      <td>HP:0032792</td>\n",
       "      <td>ECO:0000269</td>\n",
       "      <td>PMID:31675180</td>\n",
       "      <td>infores:hpo-annotations</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>uuid:70269c5e-42a9-11ee-be37-31ef105c25ea</td>\n",
       "      <td>MONDO:0023659</td>\n",
       "      <td>biolink:has_phenotype</td>\n",
       "      <td>HP:0011451</td>\n",
       "      <td>ECO:0000269</td>\n",
       "      <td>PMID:31675180</td>\n",
       "      <td>infores:hpo-annotations</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                          id        subject  \\\n",
       "0  uuid:70269c5a-42a9-11ee-be37-31ef105c25ea  MONDO:0023659   \n",
       "1  uuid:70269c5b-42a9-11ee-be37-31ef105c25ea  MONDO:0023659   \n",
       "2  uuid:70269c5c-42a9-11ee-be37-31ef105c25ea  MONDO:0023659   \n",
       "3  uuid:70269c5d-42a9-11ee-be37-31ef105c25ea  MONDO:0023659   \n",
       "4  uuid:70269c5e-42a9-11ee-be37-31ef105c25ea  MONDO:0023659   \n",
       "\n",
       "               predicate      object evidence_type    publication  \\\n",
       "0  biolink:has_phenotype  HP:0011097   ECO:0000269  PMID:31675180   \n",
       "1  biolink:has_phenotype  HP:0002187   ECO:0000269  PMID:31675180   \n",
       "2  biolink:has_phenotype  HP:0001518   ECO:0000269  PMID:31675180   \n",
       "3  biolink:has_phenotype  HP:0032792   ECO:0000269  PMID:31675180   \n",
       "4  biolink:has_phenotype  HP:0011451   ECO:0000269  PMID:31675180   \n",
       "\n",
       "                    source  \n",
       "0  infores:hpo-annotations  \n",
       "1  infores:hpo-annotations  \n",
       "2  infores:hpo-annotations  \n",
       "3  infores:hpo-annotations  \n",
       "4  infores:hpo-annotations  "
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_term_association = pd.read_sql_query(\"SELECT * FROM term_association\", conn)\n",
    "df_term_association.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "f19aa997-02db-4d3a-9c2b-437e77430a61",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array(['MONDO', 'HGNC', 'WB', 'MGI', 'RGD', 'Xenbase', 'ZFIN'],\n",
       "      dtype=object)"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_term_association['subject'].str.split(\":\").str[0].unique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "f0aefb13-1a00-48d2-a68f-d660bb393ec0",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array(['HP', 'WBPhenotype', 'MP', 'XPO', 'ZP'], dtype=object)"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_term_association['object'].str.split(\":\").str[0].unique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "e1755b79-d6b9-4ce6-9bb7-1ee2a331e11e",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "\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>id</th>\n",
       "      <th>subject</th>\n",
       "      <th>predicate</th>\n",
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       "      <td>uuid:70269c5c-42a9-11ee-be37-31ef105c25ea</td>\n",
       "      <td>MONDO:0023659</td>\n",
       "      <td>biolink:has_phenotype</td>\n",
       "      <td>HP:0001518</td>\n",
       "      <td>ECO:0000269</td>\n",
       "      <td>PMID:31675180</td>\n",
       "      <td>infores:hpo-annotations</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>uuid:70269c5d-42a9-11ee-be37-31ef105c25ea</td>\n",
       "      <td>MONDO:0023659</td>\n",
       "      <td>biolink:has_phenotype</td>\n",
       "      <td>HP:0032792</td>\n",
       "      <td>ECO:0000269</td>\n",
       "      <td>PMID:31675180</td>\n",
       "      <td>infores:hpo-annotations</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>uuid:70269c5e-42a9-11ee-be37-31ef105c25ea</td>\n",
       "      <td>MONDO:0023659</td>\n",
       "      <td>biolink:has_phenotype</td>\n",
       "      <td>HP:0011451</td>\n",
       "      <td>ECO:0000269</td>\n",
       "      <td>PMID:31675180</td>\n",
       "      <td>infores:hpo-annotations</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>240650</th>\n",
       "      <td>uuid:7e6fe369-42a9-11ee-be37-31ef105c25ea</td>\n",
       "      <td>MONDO:0009033</td>\n",
       "      <td>biolink:has_phenotype</td>\n",
       "      <td>HP:0001831</td>\n",
       "      <td>ECO:0000304</td>\n",
       "      <td>orphanet:1777</td>\n",
       "      <td>infores:hpo-annotations</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>240651</th>\n",
       "      <td>uuid:7e6fe36a-42a9-11ee-be37-31ef105c25ea</td>\n",
       "      <td>MONDO:0009033</td>\n",
       "      <td>biolink:has_phenotype</td>\n",
       "      <td>HP:0002970</td>\n",
       "      <td>ECO:0000304</td>\n",
       "      <td>orphanet:1777</td>\n",
       "      <td>infores:hpo-annotations</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>240652</th>\n",
       "      <td>uuid:7e6fe36b-42a9-11ee-be37-31ef105c25ea</td>\n",
       "      <td>MONDO:0009033</td>\n",
       "      <td>biolink:has_phenotype</td>\n",
       "      <td>HP:0004209</td>\n",
       "      <td>ECO:0000304</td>\n",
       "      <td>orphanet:1777</td>\n",
       "      <td>infores:hpo-annotations</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>240653</th>\n",
       "      <td>uuid:7e6fe36c-42a9-11ee-be37-31ef105c25ea</td>\n",
       "      <td>MONDO:0009033</td>\n",
       "      <td>biolink:has_phenotype</td>\n",
       "      <td>HP:0005692</td>\n",
       "      <td>ECO:0000304</td>\n",
       "      <td>orphanet:1777</td>\n",
       "      <td>infores:hpo-annotations</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>240654</th>\n",
       "      <td>uuid:7e6fe36d-42a9-11ee-be37-31ef105c25ea</td>\n",
       "      <td>MONDO:0009033</td>\n",
       "      <td>biolink:has_phenotype</td>\n",
       "      <td>HP:0007370</td>\n",
       "      <td>ECO:0000304</td>\n",
       "      <td>orphanet:1777</td>\n",
       "      <td>infores:hpo-annotations</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>240643 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                               id        subject  \\\n",
       "0       uuid:70269c5a-42a9-11ee-be37-31ef105c25ea  MONDO:0023659   \n",
       "1       uuid:70269c5b-42a9-11ee-be37-31ef105c25ea  MONDO:0023659   \n",
       "2       uuid:70269c5c-42a9-11ee-be37-31ef105c25ea  MONDO:0023659   \n",
       "3       uuid:70269c5d-42a9-11ee-be37-31ef105c25ea  MONDO:0023659   \n",
       "4       uuid:70269c5e-42a9-11ee-be37-31ef105c25ea  MONDO:0023659   \n",
       "...                                           ...            ...   \n",
       "240650  uuid:7e6fe369-42a9-11ee-be37-31ef105c25ea  MONDO:0009033   \n",
       "240651  uuid:7e6fe36a-42a9-11ee-be37-31ef105c25ea  MONDO:0009033   \n",
       "240652  uuid:7e6fe36b-42a9-11ee-be37-31ef105c25ea  MONDO:0009033   \n",
       "240653  uuid:7e6fe36c-42a9-11ee-be37-31ef105c25ea  MONDO:0009033   \n",
       "240654  uuid:7e6fe36d-42a9-11ee-be37-31ef105c25ea  MONDO:0009033   \n",
       "\n",
       "                    predicate      object evidence_type    publication  \\\n",
       "0       biolink:has_phenotype  HP:0011097   ECO:0000269  PMID:31675180   \n",
       "1       biolink:has_phenotype  HP:0002187   ECO:0000269  PMID:31675180   \n",
       "2       biolink:has_phenotype  HP:0001518   ECO:0000269  PMID:31675180   \n",
       "3       biolink:has_phenotype  HP:0032792   ECO:0000269  PMID:31675180   \n",
       "4       biolink:has_phenotype  HP:0011451   ECO:0000269  PMID:31675180   \n",
       "...                       ...         ...           ...            ...   \n",
       "240650  biolink:has_phenotype  HP:0001831   ECO:0000304  orphanet:1777   \n",
       "240651  biolink:has_phenotype  HP:0002970   ECO:0000304  orphanet:1777   \n",
       "240652  biolink:has_phenotype  HP:0004209   ECO:0000304  orphanet:1777   \n",
       "240653  biolink:has_phenotype  HP:0005692   ECO:0000304  orphanet:1777   \n",
       "240654  biolink:has_phenotype  HP:0007370   ECO:0000304  orphanet:1777   \n",
       "\n",
       "                         source  \n",
       "0       infores:hpo-annotations  \n",
       "1       infores:hpo-annotations  \n",
       "2       infores:hpo-annotations  \n",
       "3       infores:hpo-annotations  \n",
       "4       infores:hpo-annotations  \n",
       "...                         ...  \n",
       "240650  infores:hpo-annotations  \n",
       "240651  infores:hpo-annotations  \n",
       "240652  infores:hpo-annotations  \n",
       "240653  infores:hpo-annotations  \n",
       "240654  infores:hpo-annotations  \n",
       "\n",
       "[240643 rows x 7 columns]"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_term_association[df_term_association['subject'].str.startswith(\"MONDO:\")]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "81556e70-f889-483f-b496-ddbd51baab08",
   "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>id</th>\n",
       "      <th>subject</th>\n",
       "      <th>predicate</th>\n",
       "      <th>object</th>\n",
       "      <th>evidence_type</th>\n",
       "      <th>publication</th>\n",
       "      <th>source</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>uuid:70269c5a-42a9-11ee-be37-31ef105c25ea</td>\n",
       "      <td>MONDO:0023659</td>\n",
       "      <td>biolink:has_phenotype</td>\n",
       "      <td>HP:0011097</td>\n",
       "      <td>ECO:0000269</td>\n",
       "      <td>PMID:31675180</td>\n",
       "      <td>infores:hpo-annotations</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>uuid:70269c5b-42a9-11ee-be37-31ef105c25ea</td>\n",
       "      <td>MONDO:0023659</td>\n",
       "      <td>biolink:has_phenotype</td>\n",
       "      <td>HP:0002187</td>\n",
       "      <td>ECO:0000269</td>\n",
       "      <td>PMID:31675180</td>\n",
       "      <td>infores:hpo-annotations</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>uuid:70269c5c-42a9-11ee-be37-31ef105c25ea</td>\n",
       "      <td>MONDO:0023659</td>\n",
       "      <td>biolink:has_phenotype</td>\n",
       "      <td>HP:0001518</td>\n",
       "      <td>ECO:0000269</td>\n",
       "      <td>PMID:31675180</td>\n",
       "      <td>infores:hpo-annotations</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>uuid:70269c5d-42a9-11ee-be37-31ef105c25ea</td>\n",
       "      <td>MONDO:0023659</td>\n",
       "      <td>biolink:has_phenotype</td>\n",
       "      <td>HP:0032792</td>\n",
       "      <td>ECO:0000269</td>\n",
       "      <td>PMID:31675180</td>\n",
       "      <td>infores:hpo-annotations</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>uuid:70269c5e-42a9-11ee-be37-31ef105c25ea</td>\n",
       "      <td>MONDO:0023659</td>\n",
       "      <td>biolink:has_phenotype</td>\n",
       "      <td>HP:0011451</td>\n",
       "      <td>ECO:0000269</td>\n",
       "      <td>PMID:31675180</td>\n",
       "      <td>infores:hpo-annotations</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                          id        subject  \\\n",
       "0  uuid:70269c5a-42a9-11ee-be37-31ef105c25ea  MONDO:0023659   \n",
       "1  uuid:70269c5b-42a9-11ee-be37-31ef105c25ea  MONDO:0023659   \n",
       "2  uuid:70269c5c-42a9-11ee-be37-31ef105c25ea  MONDO:0023659   \n",
       "3  uuid:70269c5d-42a9-11ee-be37-31ef105c25ea  MONDO:0023659   \n",
       "4  uuid:70269c5e-42a9-11ee-be37-31ef105c25ea  MONDO:0023659   \n",
       "\n",
       "               predicate      object evidence_type    publication  \\\n",
       "0  biolink:has_phenotype  HP:0011097   ECO:0000269  PMID:31675180   \n",
       "1  biolink:has_phenotype  HP:0002187   ECO:0000269  PMID:31675180   \n",
       "2  biolink:has_phenotype  HP:0001518   ECO:0000269  PMID:31675180   \n",
       "3  biolink:has_phenotype  HP:0032792   ECO:0000269  PMID:31675180   \n",
       "4  biolink:has_phenotype  HP:0011451   ECO:0000269  PMID:31675180   \n",
       "\n",
       "                    source  \n",
       "0  infores:hpo-annotations  \n",
       "1  infores:hpo-annotations  \n",
       "2  infores:hpo-annotations  \n",
       "3  infores:hpo-annotations  \n",
       "4  infores:hpo-annotations  "
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "condition_1 = df_term_association['subject'].str.startswith(\"MONDO:\")\n",
    "condition_2 = df_term_association['object'].str.startswith(\"HP:\")\n",
    "\n",
    "df = df_term_association[condition_1 & condition_2]\n",
    "\n",
    "df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "81d9f3fe-1f76-4bae-af5e-d9c47da0e13d",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'HP:0000042',\n",
       " 'HP:0002453',\n",
       " 'HP:0004233',\n",
       " 'HP:0007041',\n",
       " 'HP:0007734',\n",
       " 'HP:0008523',\n",
       " 'HP:0010037',\n",
       " 'HP:0011193',\n",
       " 'HP:0011787',\n",
       " 'HP:0410275'}"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Set seed for random\n",
    "np.random.seed(0)\n",
    "random_hp_1 = np.random.choice(df['object'].unique(), size = 10, replace=False)\n",
    "set(random_hp_1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "5f698837-f6c0-4627-b3f1-bf27007c3b61",
   "metadata": {},
   "outputs": [],
   "source": [
    "# # Set seed for random\n",
    "# np.random.seed(10)\n",
    "# random_hp_2 = np.random.choice(df['object'].unique(), size = 10, replace=False)\n",
    "# set(random_hp_2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "66f86458-52cc-419b-a629-55615e9b5687",
   "metadata": {},
   "outputs": [],
   "source": [
    "hp_1 = [\"HP:0003394\",\n",
    "\"HP:0003771\",\n",
    "\"HP:0012378\",\n",
    "\"HP:0012450\",\n",
    "\"HP:0000974\",\n",
    "\"HP:0001027\",\n",
    "\"HP:0001030\",\n",
    "\"HP:0001065\",\n",
    "\"HP:0001073\",\n",
    "\"HP:0001075\",\n",
    "\"HP:0002761\",\n",
    "\"HP:0001386\",\n",
    "\"HP:0001537\",\n",
    "\"HP:0001622\",\n",
    "\"HP:0001760\",\n",
    "\"HP:0001762\",\n",
    "\"HP:0001763\",\n",
    "\"HP:0001788\",\n",
    "\"HP:0002035\",\n",
    "\"HP:0002036\",\n",
    "\"HP:0002616\",\n",
    "\"HP:0002650\",\n",
    "\"HP:0002758\",\n",
    "\"HP:0002827\",\n",
    "\"HP:0002829\",\n",
    "\"HP:0002999\",\n",
    "\"HP:0003010\",\n",
    "\"HP:0003083\",\n",
    "\"HP:0003834\",\n",
    "\"HP:0000938\",\n",
    "\"HP:0001058\",\n",
    "\"HP:0001252\",\n",
    "\"HP:0001324\",\n",
    "\"HP:0002013\",\n",
    "\"HP:0002018\",\n",
    "\"HP:0002020\",\n",
    "\"HP:0000015\",\n",
    "\"HP:0000023\",\n",
    "\"HP:0000139\",\n",
    "\"HP:0000286\",\n",
    "\"HP:0000481\",\n",
    "\"HP:0000978\",\n",
    "\"HP:0000993\",\n",
    "\"HP:0001063\",\n",
    "\"HP:0004872\",\n",
    "\"HP:0004944\",\n",
    "\"HP:0004947\",\n",
    "\"HP:0001270\",\n",
    "\"HP:0005294\",\n",
    "\"HP:0006243\",\n",
    "\"HP:0007495\",\n",
    "\"HP:0009763\",\n",
    "\"HP:0010749\",\n",
    "\"HP:0010750\",\n",
    "\"HP:0010754\",\n",
    "\"HP:0025014\",\n",
    "\"HP:0025019\",\n",
    "\"HP:0025509\",\n",
    "\"HP:0030009\",\n",
    "\"HP:0031364\",\n",
    "\"HP:0031653\",\n",
    "\"HP:0001278\",\n",
    "\"HP:0001634\",\n",
    "\"HP:0001653\",\n",
    "\"HP:0001704\",\n",
    "\"HP:0002315\"]\n",
    "\n",
    "hp_2 = [\"HP:0003645\",\n",
    "\"HP:0005261\",\n",
    "\"HP:0002758\",\n",
    "\"HP:0003125\",\n",
    "\"HP:0001892\",\n",
    "\"HP:0001934\",\n",
    "\"HP:0000967\",\n",
    "\"HP:0000978\",\n",
    "\"HP:0000979\",\n",
    "\"HP:0040242\",\n",
    "\"HP:0007420\",\n",
    "\"HP:0030140\",\n",
    "\"HP:0001386\",\n",
    "\"HP:0002829\",\n",
    "\"HP:0002239\",\n",
    "\"HP:0011889\",\n",
    "\"HP:0001907\",\n",
    "\"HP:0012223\",\n",
    "\"HP:0009811\",\n",
    "\"HP:0012233\",\n",
    "\"HP:0030746\",\n",
    "\"HP:0002170\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "f7cd8388-abc3-4fc9-913e-6c79d8f1d7ad",
   "metadata": {},
   "outputs": [],
   "source": [
    "mondo = set(df['subject'].drop_duplicates())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "5072b5ad-b7ae-4a31-aa2d-f7c22cd0b7d6",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 43.5 s, sys: 1.89 s, total: 45.4 s\n",
      "Wall time: 46.4 s\n"
     ]
    }
   ],
   "source": [
    "%%time\n",
    "predicates = [\"rdfs:subClassOf\",\"BFO:0000050\", \"UPHENO:0000001\"]\n",
    "rss = Semsimian(spo=None, predicates=predicates, pairwise_similarity_attributes=None, resource_path=db)\n",
    "all_x_all = rss.all_by_all_pairwise_similarity(subject_terms=set(hp_1), object_terms=set(hp_2), minimum_jaccard_threshold=0, minimum_resnik_threshold=0)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "104d7245-044e-4696-8f7b-51c65b1806fa",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 1.61 ms, sys: 241 µs, total: 1.85 ms\n",
      "Wall time: 2 ms\n"
     ]
    }
   ],
   "source": [
    "%%time\n",
    "\n",
    "rows_list = []\n",
    "for term1_key, values in all_x_all.items():\n",
    "    for term2_key, result in values.items():\n",
    "        jaccard, resnik, phenodigm, _, _ = result\n",
    "        row_dict = {\"subject\": term1_key, \"object\": term2_key, \"jaccard\": jaccard, \"aic\": resnik, \"phenodigm\": phenodigm}\n",
    "        rows_list.append(row_dict)\n",
    "\n",
    "new_df = pd.DataFrame(rows_list)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "id": "40ef069a-6b31-4b5c-a749-93ebfeb5dc8d",
   "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>subject</th>\n",
       "      <th>object</th>\n",
       "      <th>jaccard</th>\n",
       "      <th>aic</th>\n",
       "      <th>phenodigm</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>HP:0001386</td>\n",
       "      <td>HP:0001386</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>18.008877</td>\n",
       "      <td>4.243687</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>HP:0000978</td>\n",
       "      <td>HP:0000978</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>18.008877</td>\n",
       "      <td>4.243687</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>HP:0002829</td>\n",
       "      <td>HP:0002829</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>17.008877</td>\n",
       "      <td>4.124182</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>HP:0002758</td>\n",
       "      <td>HP:0002758</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>14.838952</td>\n",
       "      <td>3.852136</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HP:0031364</td>\n",
       "      <td>HP:0000967</td>\n",
       "      <td>0.975309</td>\n",
       "      <td>16.423915</td>\n",
       "      <td>4.002298</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1447</th>\n",
       "      <td>HP:0003083</td>\n",
       "      <td>HP:0002239</td>\n",
       "      <td>0.116751</td>\n",
       "      <td>4.134184</td>\n",
       "      <td>0.694745</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1448</th>\n",
       "      <td>HP:0006243</td>\n",
       "      <td>HP:0002829</td>\n",
       "      <td>0.112583</td>\n",
       "      <td>4.010992</td>\n",
       "      <td>0.671989</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1449</th>\n",
       "      <td>HP:0006243</td>\n",
       "      <td>HP:0003125</td>\n",
       "      <td>0.111111</td>\n",
       "      <td>4.134184</td>\n",
       "      <td>0.677756</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1450</th>\n",
       "      <td>HP:0003083</td>\n",
       "      <td>HP:0002829</td>\n",
       "      <td>0.106250</td>\n",
       "      <td>4.010992</td>\n",
       "      <td>0.652815</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1451</th>\n",
       "      <td>HP:0003083</td>\n",
       "      <td>HP:0003125</td>\n",
       "      <td>0.106061</td>\n",
       "      <td>4.134184</td>\n",
       "      <td>0.662174</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1452 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "         subject      object   jaccard        aic  phenodigm\n",
       "0     HP:0001386  HP:0001386  1.000000  18.008877   4.243687\n",
       "1     HP:0000978  HP:0000978  1.000000  18.008877   4.243687\n",
       "2     HP:0002829  HP:0002829  1.000000  17.008877   4.124182\n",
       "3     HP:0002758  HP:0002758  1.000000  14.838952   3.852136\n",
       "4     HP:0031364  HP:0000967  0.975309  16.423915   4.002298\n",
       "...          ...         ...       ...        ...        ...\n",
       "1447  HP:0003083  HP:0002239  0.116751   4.134184   0.694745\n",
       "1448  HP:0006243  HP:0002829  0.112583   4.010992   0.671989\n",
       "1449  HP:0006243  HP:0003125  0.111111   4.134184   0.677756\n",
       "1450  HP:0003083  HP:0002829  0.106250   4.010992   0.652815\n",
       "1451  HP:0003083  HP:0003125  0.106061   4.134184   0.662174\n",
       "\n",
       "[1452 rows x 5 columns]"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "new_df_sorted = new_df.sort_values(by=[\"jaccard\", \"aic\"], ascending=False).reset_index()\n",
    "new_df_sorted.drop(\"index\", axis=1, inplace=True)\n",
    "new_df_sorted"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "id": "195afbdc-6c10-4313-9514-573afe5feabc",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0       18.008877\n",
       "2       17.008877\n",
       "3       14.838952\n",
       "4       16.423915\n",
       "5       15.686949\n",
       "          ...    \n",
       "1079     5.079804\n",
       "1124     4.253051\n",
       "1194     4.403398\n",
       "1204     4.217714\n",
       "1256     6.722319\n",
       "Name: aic, Length: 63, dtype: float64"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "new_df_sorted['aic'].drop_duplicates()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "41bf2bfa-6ea1-4067-b8c4-0274a6ad3ed6",
   "metadata": {},
   "outputs": [],
   "source": [
    "import matplotlib.pyplot as plt\n",
    "\n",
    "df_subset = new_df_sorted.head(10)\n",
    "\n",
    "# Create a figure and a set of subplots\n",
    "fig, ax = plt.subplots()\n",
    "\n",
    "# Set the bar width\n",
    "bar_width = 0.35\n",
    "\n",
    "# Get the positions of the bars\n",
    "positions = list(range(len(df_subset)))\n",
    "\n",
    "# Plot bars for 'jaccard' in one color\n",
    "plt.bar([p - bar_width/2 for p in positions], df_subset['jaccard'], width=bar_width, color='blue', label='jaccard')\n",
    "\n",
    "# Plot bars for 'aic' in another color\n",
    "plt.bar([p + bar_width/2 for p in positions], df_subset['aic'], width=bar_width, color='green', label='aic')\n",
    "\n",
    "# Set the x ticks with names\n",
    "plt.xticks(positions, df_subset['subject'], rotation='vertical')\n",
    "\n",
    "# Show object values on top of the bars\n",
    "for i in range(len(df_subset)):\n",
    "    plt.text(x = i, y = df_subset['jaccard'].iloc[i], s = df_subset['object'].iloc[i], size = 10, ha = 'center', va = 'bottom', rotation='vertical')\n",
    "\n",
    "\n",
    "# Add legend\n",
    "plt.legend()\n",
    "\n",
    "# Add labels and title\n",
    "plt.xlabel('Subject')\n",
    "plt.ylabel('Values')\n",
    "plt.title('Top 10 Subjects vs Corresponding Objects')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "8a08cea9-9c94-42fa-a25f-720c77339c6c",
   "metadata": {},
   "outputs": [],
   "source": [
    "df_subset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "3a215cf0-7895-4d9f-bfff-c4f32d84ffce",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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