BTO2UBERON.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import requests\n",
    "from pprint import pprint\n",
    "import pandas as pd\n",
    "from ontobio.ontol_factory import OntologyFactory"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "350"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# retrieve tissues from BigGIM API (these are BTO Ontology terms with underscores inplace of ' ' and '-')\n",
    "bg_tissues = requests.get('http://biggim.ncats.io/api/metadata/tissue').json()['tissues']\n",
    "len(bg_tissues)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "# use ontobio to get mappings from bto and uberon ontologies\n",
    "ofactory = OntologyFactory()\n",
    "ub_ont = ofactory.create(\"uberon\")\n",
    "bto_ont = ofactory.create(\"bto\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "# create dictionary of bto ids and labels ex: {'brain': BTO:0000142'}\n",
    "bto_nodes = bto_ont.nodes()\n",
    "bto_term_label = dict()\n",
    "for bto in bto_nodes:\n",
    "    bto_term_label[bto_ont.label(bto)] = bto"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'BTO:0000142'"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bto_term_label['brain']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_ont_xref(xref_id, ont_factory):\n",
    "    \"\"\"\n",
    "    search for xref in given ontology and return an object with the node id and label\n",
    "    \"\"\"\n",
    "    ont_nodes = ont_factory.nodes()\n",
    "    result = {'id': None, 'label': None}\n",
    "    for node in ont_nodes:\n",
    "        if xref_id in ont_factory.xrefs(node):\n",
    "            result['id'] = node\n",
    "            result['label'] = ont_factory.label(node)\n",
    "    return result"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "# map bigGIM terms to bto terms/ids, then uberon terms/ids\n",
    "bto2bg = list()\n",
    "for tissue in bg_tissues:\n",
    "    result = {\n",
    "        'bg_label': tissue,\n",
    "        'bto_label': None,\n",
    "        'bto_id': None,\n",
    "        'uberon_id': None,\n",
    "        'uberon_label': None\n",
    "    }\n",
    "    # ex B_lymphocite -> B lymphocite\n",
    "    tissue1 = tissue.replace('_', ' ')\n",
    "    if tissue1 in bto_term_label.keys():\n",
    "        result['bto_label'] = tissue1\n",
    "        result['bto_id'] = bto_term_label[tissue1]\n",
    "        uberon = get_ont_xref(xref_id=bto_term_label[tissue1], ont_factory=ub_ont)\n",
    "        result['uberon_id'] = uberon['id']\n",
    "        result['uberon_label'] = uberon['label']\n",
    "    else:\n",
    "        # ex: B lymphocite -> B-lymphocite\n",
    "        tissue2 = tissue1.replace(' ', '-', 1)\n",
    "        if tissue2 in bto_term_label.keys():\n",
    "            result['bto_label'] = tissue2\n",
    "            result['bto_id'] = bto_term_label[tissue2]\n",
    "            uberon = get_ont_xref(xref_id=bto_term_label[tissue2], ont_factory=ub_ont)\n",
    "            result['uberon_id'] = uberon['id']\n",
    "            result['uberon_label'] = uberon['label']\n",
    "    bto2bg.append(result)\n",
    "with open('bto_uberon_bg.json', 'w') as outfile:\n",
    "    json.dump(bto2bg, outfile)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "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>bto_label</th>\n",
       "      <th>bto_id</th>\n",
       "      <th>bg_label</th>\n",
       "      <th>uberon_id</th>\n",
       "      <th>uberon_label</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>B-lymphocyte</td>\n",
       "      <td>BTO:0000776</td>\n",
       "      <td>B_lymphocyte</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>B-lymphoma cell line</td>\n",
       "      <td>BTO:0001518</td>\n",
       "      <td>B_lymphoma_cell_line</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>T-lymphocyte</td>\n",
       "      <td>BTO:0000782</td>\n",
       "      <td>T_lymphocyte</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>acute myeloid leukemia cell</td>\n",
       "      <td>BTO:0001545</td>\n",
       "      <td>acute_myeloid_leukemia_cell</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>adenocarcinoma cell</td>\n",
       "      <td>BTO:0000604</td>\n",
       "      <td>adenocarcinoma_cell</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>adipose tissue</td>\n",
       "      <td>BTO:0001487</td>\n",
       "      <td>adipose_tissue</td>\n",
       "      <td>UBERON:0001013</td>\n",
       "      <td>adipose tissue</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>adrenal cortex</td>\n",
       "      <td>BTO:0000045</td>\n",
       "      <td>adrenal_cortex</td>\n",
       "      <td>UBERON:0001235</td>\n",
       "      <td>adrenal cortex</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>adrenal gland</td>\n",
       "      <td>BTO:0000047</td>\n",
       "      <td>adrenal_gland</td>\n",
       "      <td>UBERON:0002369</td>\n",
       "      <td>adrenal gland</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>adrenal gland cancer cell</td>\n",
       "      <td>BTO:0000592</td>\n",
       "      <td>adrenal_gland_cancer_cell</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>adrenocortical carcinoma cell</td>\n",
       "      <td>BTO:0002219</td>\n",
       "      <td>adrenocortical_carcinoma_cell</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>adult stem cell</td>\n",
       "      <td>BTO:0002666</td>\n",
       "      <td>adult_stem_cell</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>alimentary canal</td>\n",
       "      <td>BTO:0000058</td>\n",
       "      <td>alimentary_canal</td>\n",
       "      <td>UBERON:0005409</td>\n",
       "      <td>alimentary part of gastrointestinal system</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>amygdala</td>\n",
       "      <td>BTO:0001042</td>\n",
       "      <td>amygdala</td>\n",
       "      <td>UBERON:0001876</td>\n",
       "      <td>amygdala</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>animal</td>\n",
       "      <td>BTO:0000042</td>\n",
       "      <td>animal</td>\n",
       "      <td>UBERON:0000468</td>\n",
       "      <td>multicellular organism</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>aorta</td>\n",
       "      <td>BTO:0000135</td>\n",
       "      <td>aorta</td>\n",
       "      <td>UBERON:0000947</td>\n",
       "      <td>aorta</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>artery</td>\n",
       "      <td>BTO:0000573</td>\n",
       "      <td>artery</td>\n",
       "      <td>UBERON:0001637</td>\n",
       "      <td>artery</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>astroblast</td>\n",
       "      <td>BTO:0000098</td>\n",
       "      <td>astroblast</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>astrocyte</td>\n",
       "      <td>BTO:0000099</td>\n",
       "      <td>astrocyte</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>astrocytoma cell</td>\n",
       "      <td>BTO:0000100</td>\n",
       "      <td>astrocytoma_cell</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>astroglia</td>\n",
       "      <td>BTO:0003852</td>\n",
       "      <td>astroglia</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>astroglial cell</td>\n",
       "      <td>BTO:0002609</td>\n",
       "      <td>astroglial_cell</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>avian pallium</td>\n",
       "      <td>BTO:0003399</td>\n",
       "      <td>avian_pallium</td>\n",
       "      <td>UBERON:0000203</td>\n",
       "      <td>pallium</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>basal ganglion</td>\n",
       "      <td>BTO:0000235</td>\n",
       "      <td>basal_ganglion</td>\n",
       "      <td>UBERON:0002420</td>\n",
       "      <td>basal ganglion</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>basophil</td>\n",
       "      <td>BTO:0000129</td>\n",
       "      <td>basophil</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>bile duct</td>\n",
       "      <td>BTO:0000122</td>\n",
       "      <td>bile_duct</td>\n",
       "      <td>UBERON:0002394</td>\n",
       "      <td>bile duct</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>bile duct epithelium</td>\n",
       "      <td>BTO:0000417</td>\n",
       "      <td>bile_duct_epithelium</td>\n",
       "      <td>UBERON:0004820</td>\n",
       "      <td>bile duct epithelium</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>biliary epithelium</td>\n",
       "      <td>BTO:0001513</td>\n",
       "      <td>biliary_epithelium</td>\n",
       "      <td>UBERON:0034932</td>\n",
       "      <td>epithelium of biliary system</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>bladder</td>\n",
       "      <td>BTO:0000123</td>\n",
       "      <td>bladder</td>\n",
       "      <td>UBERON:0018707</td>\n",
       "      <td>bladder organ</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>blast cell</td>\n",
       "      <td>BTO:0000125</td>\n",
       "      <td>blast_cell</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>blastomere</td>\n",
       "      <td>BTO:0001473</td>\n",
       "      <td>blastomere</td>\n",
       "      <td>None</td>\n",
       "      <td>None</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>320</th>\n",
       "      <td>tooth</td>\n",
       "      <td>BTO:0000397</td>\n",
       "      <td>tooth</td>\n",
       "      <td>UBERON:0001091</td>\n",
       "      <td>calcareous tooth</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>321</th>\n",
       "      <td>trachea</td>\n",
       "      <td>BTO:0001388</td>\n",
       "      <td>trachea</td>\n",
       "      <td>UBERON:0003126</td>\n",
       "      <td>trachea</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>322</th>\n",
       "      <td>trophoblast</td>\n",
       "      <td>BTO:0001079</td>\n",
       "      <td>trophoblast</td>\n",
       "      <td>UBERON:0000088</td>\n",
       "      <td>trophoblast</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>323</th>\n",
       "      <td>trunk</td>\n",
       "      <td>BTO:0001493</td>\n",
       "      <td>trunk</td>\n",
       "      <td>UBERON:0002100</td>\n",
       "      <td>trunk</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>324</th>\n",
       "      <td>umbilical cord</td>\n",
       "      <td>BTO:0001415</td>\n",
       "      <td>umbilical_cord</td>\n",
       "      <td>UBERON:0002331</td>\n",
       "      <td>umbilical cord</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>325</th>\n",
       "      <td>umbilical vein</td>\n",
       "      <td>BTO:0001509</td>\n",
       "      <td>umbilical_vein</td>\n",
       "      <td>UBERON:0002066</td>\n",
       "      <td>umbilical vein</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>326</th>\n",
       "      <td>umbilical vein endothelial cell</td>\n",
       "      <td>BTO:0004296</td>\n",
       "      <td>umbilical_vein_endothelial_cell</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>327</th>\n",
       "      <td>umbilical vein endothelium</td>\n",
       "      <td>BTO:0001416</td>\n",
       "      <td>umbilical_vein_endothelium</td>\n",
       "      <td>UBERON:0007777</td>\n",
       "      <td>umbilical vein endothelium</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>328</th>\n",
       "      <td>urinary bladder</td>\n",
       "      <td>BTO:0001418</td>\n",
       "      <td>urinary_bladder</td>\n",
       "      <td>UBERON:0001255</td>\n",
       "      <td>urinary bladder</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>329</th>\n",
       "      <td>urinary bladder cancer cell</td>\n",
       "      <td>BTO:0000362</td>\n",
       "      <td>urinary_bladder_cancer_cell</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>330</th>\n",
       "      <td>urinary system</td>\n",
       "      <td>BTO:0003092</td>\n",
       "      <td>urinary_system</td>\n",
       "      <td>UBERON:0001008</td>\n",
       "      <td>renal system</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>331</th>\n",
       "      <td>urinary tract</td>\n",
       "      <td>BTO:0001244</td>\n",
       "      <td>urinary_tract</td>\n",
       "      <td>UBERON:0001008</td>\n",
       "      <td>renal system</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>332</th>\n",
       "      <td>uroepithelium</td>\n",
       "      <td>BTO:0003906</td>\n",
       "      <td>uroepithelium</td>\n",
       "      <td>UBERON:0000365</td>\n",
       "      <td>urothelium</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>333</th>\n",
       "      <td>urogenital system</td>\n",
       "      <td>BTO:0003091</td>\n",
       "      <td>urogenital_system</td>\n",
       "      <td>UBERON:0004122</td>\n",
       "      <td>genitourinary system</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>334</th>\n",
       "      <td>uterine cancer cell</td>\n",
       "      <td>BTO:0000257</td>\n",
       "      <td>uterine_cancer_cell</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>335</th>\n",
       "      <td>uterine cervix</td>\n",
       "      <td>BTO:0001421</td>\n",
       "      <td>uterine_cervix</td>\n",
       "      <td>UBERON:0000002</td>\n",
       "      <td>uterine cervix</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>336</th>\n",
       "      <td>uterine endometrium</td>\n",
       "      <td>BTO:0001422</td>\n",
       "      <td>uterine_endometrium</td>\n",
       "      <td>UBERON:0001295</td>\n",
       "      <td>endometrium</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>337</th>\n",
       "      <td>uterine sarcoma cell</td>\n",
       "      <td>BTO:0003596</td>\n",
       "      <td>uterine_sarcoma_cell</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>338</th>\n",
       "      <td>uterus</td>\n",
       "      <td>BTO:0001424</td>\n",
       "      <td>uterus</td>\n",
       "      <td>UBERON:0000995</td>\n",
       "      <td>uterus</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>339</th>\n",
       "      <td>uveal melanoma cell</td>\n",
       "      <td>BTO:0004980</td>\n",
       "      <td>uveal_melanoma_cell</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>340</th>\n",
       "      <td>vascular endothelial cell</td>\n",
       "      <td>BTO:0001854</td>\n",
       "      <td>vascular_endothelial_cell</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>341</th>\n",
       "      <td>vascular endothelium</td>\n",
       "      <td>BTO:0001853</td>\n",
       "      <td>vascular_endothelium</td>\n",
       "      <td>UBERON:0004852</td>\n",
       "      <td>cardiovascular system endothelium</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>342</th>\n",
       "      <td>vascular system</td>\n",
       "      <td>BTO:0001085</td>\n",
       "      <td>vascular_system</td>\n",
       "      <td>UBERON:0007798</td>\n",
       "      <td>vascular system</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>343</th>\n",
       "      <td>vermiform appendix</td>\n",
       "      <td>BTO:0000084</td>\n",
       "      <td>vermiform_appendix</td>\n",
       "      <td>UBERON:0001154</td>\n",
       "      <td>vermiform appendix</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>344</th>\n",
       "      <td>vertebrate muscular system</td>\n",
       "      <td>BTO:0001369</td>\n",
       "      <td>vertebrate_muscular_system</td>\n",
       "      <td>UBERON:0000383</td>\n",
       "      <td>musculature of body</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>345</th>\n",
       "      <td>vestibular labyrinth</td>\n",
       "      <td>BTO:0001856</td>\n",
       "      <td>vestibular_labyrinth</td>\n",
       "      <td>UBERON:0001862</td>\n",
       "      <td>vestibular labyrinth</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>346</th>\n",
       "      <td>vestibular system</td>\n",
       "      <td>BTO:0003381</td>\n",
       "      <td>vestibular_system</td>\n",
       "      <td>UBERON:0004681</td>\n",
       "      <td>vestibular system</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>347</th>\n",
       "      <td>viscus</td>\n",
       "      <td>BTO:0001491</td>\n",
       "      <td>viscus</td>\n",
       "      <td>UBERON:0002075</td>\n",
       "      <td>viscus</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>348</th>\n",
       "      <td>whole body</td>\n",
       "      <td>BTO:0001489</td>\n",
       "      <td>whole_body</td>\n",
       "      <td>UBERON:0013702</td>\n",
       "      <td>body proper</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>349</th>\n",
       "      <td>zygote</td>\n",
       "      <td>BTO:0000854</td>\n",
       "      <td>zygote</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>350 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                           bto_label       bto_id  \\\n",
       "0                       B-lymphocyte  BTO:0000776   \n",
       "1               B-lymphoma cell line  BTO:0001518   \n",
       "2                       T-lymphocyte  BTO:0000782   \n",
       "3        acute myeloid leukemia cell  BTO:0001545   \n",
       "4                adenocarcinoma cell  BTO:0000604   \n",
       "5                     adipose tissue  BTO:0001487   \n",
       "6                     adrenal cortex  BTO:0000045   \n",
       "7                      adrenal gland  BTO:0000047   \n",
       "8          adrenal gland cancer cell  BTO:0000592   \n",
       "9      adrenocortical carcinoma cell  BTO:0002219   \n",
       "10                   adult stem cell  BTO:0002666   \n",
       "11                  alimentary canal  BTO:0000058   \n",
       "12                          amygdala  BTO:0001042   \n",
       "13                            animal  BTO:0000042   \n",
       "14                             aorta  BTO:0000135   \n",
       "15                            artery  BTO:0000573   \n",
       "16                        astroblast  BTO:0000098   \n",
       "17                         astrocyte  BTO:0000099   \n",
       "18                  astrocytoma cell  BTO:0000100   \n",
       "19                         astroglia  BTO:0003852   \n",
       "20                   astroglial cell  BTO:0002609   \n",
       "21                     avian pallium  BTO:0003399   \n",
       "22                    basal ganglion  BTO:0000235   \n",
       "23                          basophil  BTO:0000129   \n",
       "24                         bile duct  BTO:0000122   \n",
       "25              bile duct epithelium  BTO:0000417   \n",
       "26                biliary epithelium  BTO:0001513   \n",
       "27                           bladder  BTO:0000123   \n",
       "28                        blast cell  BTO:0000125   \n",
       "29                        blastomere  BTO:0001473   \n",
       "..                               ...          ...   \n",
       "320                            tooth  BTO:0000397   \n",
       "321                          trachea  BTO:0001388   \n",
       "322                      trophoblast  BTO:0001079   \n",
       "323                            trunk  BTO:0001493   \n",
       "324                   umbilical cord  BTO:0001415   \n",
       "325                   umbilical vein  BTO:0001509   \n",
       "326  umbilical vein endothelial cell  BTO:0004296   \n",
       "327       umbilical vein endothelium  BTO:0001416   \n",
       "328                  urinary bladder  BTO:0001418   \n",
       "329      urinary bladder cancer cell  BTO:0000362   \n",
       "330                   urinary system  BTO:0003092   \n",
       "331                    urinary tract  BTO:0001244   \n",
       "332                    uroepithelium  BTO:0003906   \n",
       "333                urogenital system  BTO:0003091   \n",
       "334              uterine cancer cell  BTO:0000257   \n",
       "335                   uterine cervix  BTO:0001421   \n",
       "336              uterine endometrium  BTO:0001422   \n",
       "337             uterine sarcoma cell  BTO:0003596   \n",
       "338                           uterus  BTO:0001424   \n",
       "339              uveal melanoma cell  BTO:0004980   \n",
       "340        vascular endothelial cell  BTO:0001854   \n",
       "341             vascular endothelium  BTO:0001853   \n",
       "342                  vascular system  BTO:0001085   \n",
       "343               vermiform appendix  BTO:0000084   \n",
       "344       vertebrate muscular system  BTO:0001369   \n",
       "345             vestibular labyrinth  BTO:0001856   \n",
       "346                vestibular system  BTO:0003381   \n",
       "347                           viscus  BTO:0001491   \n",
       "348                       whole body  BTO:0001489   \n",
       "349                           zygote  BTO:0000854   \n",
       "\n",
       "                            bg_label       uberon_id  \\\n",
       "0                       B_lymphocyte            None   \n",
       "1               B_lymphoma_cell_line            None   \n",
       "2                       T_lymphocyte            None   \n",
       "3        acute_myeloid_leukemia_cell            None   \n",
       "4                adenocarcinoma_cell            None   \n",
       "5                     adipose_tissue  UBERON:0001013   \n",
       "6                     adrenal_cortex  UBERON:0001235   \n",
       "7                      adrenal_gland  UBERON:0002369   \n",
       "8          adrenal_gland_cancer_cell            None   \n",
       "9      adrenocortical_carcinoma_cell            None   \n",
       "10                   adult_stem_cell            None   \n",
       "11                  alimentary_canal  UBERON:0005409   \n",
       "12                          amygdala  UBERON:0001876   \n",
       "13                            animal  UBERON:0000468   \n",
       "14                             aorta  UBERON:0000947   \n",
       "15                            artery  UBERON:0001637   \n",
       "16                        astroblast            None   \n",
       "17                         astrocyte            None   \n",
       "18                  astrocytoma_cell            None   \n",
       "19                         astroglia            None   \n",
       "20                   astroglial_cell            None   \n",
       "21                     avian_pallium  UBERON:0000203   \n",
       "22                    basal_ganglion  UBERON:0002420   \n",
       "23                          basophil            None   \n",
       "24                         bile_duct  UBERON:0002394   \n",
       "25              bile_duct_epithelium  UBERON:0004820   \n",
       "26                biliary_epithelium  UBERON:0034932   \n",
       "27                           bladder  UBERON:0018707   \n",
       "28                        blast_cell            None   \n",
       "29                        blastomere            None   \n",
       "..                               ...             ...   \n",
       "320                            tooth  UBERON:0001091   \n",
       "321                          trachea  UBERON:0003126   \n",
       "322                      trophoblast  UBERON:0000088   \n",
       "323                            trunk  UBERON:0002100   \n",
       "324                   umbilical_cord  UBERON:0002331   \n",
       "325                   umbilical_vein  UBERON:0002066   \n",
       "326  umbilical_vein_endothelial_cell            None   \n",
       "327       umbilical_vein_endothelium  UBERON:0007777   \n",
       "328                  urinary_bladder  UBERON:0001255   \n",
       "329      urinary_bladder_cancer_cell            None   \n",
       "330                   urinary_system  UBERON:0001008   \n",
       "331                    urinary_tract  UBERON:0001008   \n",
       "332                    uroepithelium  UBERON:0000365   \n",
       "333                urogenital_system  UBERON:0004122   \n",
       "334              uterine_cancer_cell            None   \n",
       "335                   uterine_cervix  UBERON:0000002   \n",
       "336              uterine_endometrium  UBERON:0001295   \n",
       "337             uterine_sarcoma_cell            None   \n",
       "338                           uterus  UBERON:0000995   \n",
       "339              uveal_melanoma_cell            None   \n",
       "340        vascular_endothelial_cell            None   \n",
       "341             vascular_endothelium  UBERON:0004852   \n",
       "342                  vascular_system  UBERON:0007798   \n",
       "343               vermiform_appendix  UBERON:0001154   \n",
       "344       vertebrate_muscular_system  UBERON:0000383   \n",
       "345             vestibular_labyrinth  UBERON:0001862   \n",
       "346                vestibular_system  UBERON:0004681   \n",
       "347                           viscus  UBERON:0002075   \n",
       "348                       whole_body  UBERON:0013702   \n",
       "349                           zygote            None   \n",
       "\n",
       "                                   uberon_label  \n",
       "0                                          None  \n",
       "1                                          None  \n",
       "2                                          None  \n",
       "3                                          None  \n",
       "4                                          None  \n",
       "5                                adipose tissue  \n",
       "6                                adrenal cortex  \n",
       "7                                 adrenal gland  \n",
       "8                                          None  \n",
       "9                                          None  \n",
       "10                                         None  \n",
       "11   alimentary part of gastrointestinal system  \n",
       "12                                     amygdala  \n",
       "13                       multicellular organism  \n",
       "14                                        aorta  \n",
       "15                                       artery  \n",
       "16                                         None  \n",
       "17                                         None  \n",
       "18                                         None  \n",
       "19                                         None  \n",
       "20                                         None  \n",
       "21                                      pallium  \n",
       "22                               basal ganglion  \n",
       "23                                         None  \n",
       "24                                    bile duct  \n",
       "25                         bile duct epithelium  \n",
       "26                 epithelium of biliary system  \n",
       "27                                bladder organ  \n",
       "28                                         None  \n",
       "29                                         None  \n",
       "..                                          ...  \n",
       "320                            calcareous tooth  \n",
       "321                                     trachea  \n",
       "322                                 trophoblast  \n",
       "323                                       trunk  \n",
       "324                              umbilical cord  \n",
       "325                              umbilical vein  \n",
       "326                                        None  \n",
       "327                  umbilical vein endothelium  \n",
       "328                             urinary bladder  \n",
       "329                                        None  \n",
       "330                                renal system  \n",
       "331                                renal system  \n",
       "332                                  urothelium  \n",
       "333                        genitourinary system  \n",
       "334                                        None  \n",
       "335                              uterine cervix  \n",
       "336                                 endometrium  \n",
       "337                                        None  \n",
       "338                                      uterus  \n",
       "339                                        None  \n",
       "340                                        None  \n",
       "341           cardiovascular system endothelium  \n",
       "342                             vascular system  \n",
       "343                          vermiform appendix  \n",
       "344                         musculature of body  \n",
       "345                        vestibular labyrinth  \n",
       "346                           vestibular system  \n",
       "347                                      viscus  \n",
       "348                                 body proper  \n",
       "349                                        None  \n",
       "\n",
       "[350 rows x 5 columns]"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bto_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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