src/ontology/MONDO_GO_Phenologs.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/cjm/repos/mondo-build/src/ontology/venv/lib/python3.6/site-packages/cachier/mongo_core.py:24: UserWarning: Cachier warning: pymongo was not found. MongoDB cores will not work.\n",
      "  \"Cachier warning: pymongo was not found. MongoDB cores will not work.\")\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<ontobio.config.Config at 0x1126286d8>"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from ontobio.config import set_config\n",
    "set_config('conf/config.yaml')\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "from ontobio.ontol_factory import OntologyFactory\n",
    "\n",
    "ofactory = OntologyFactory()\n",
    "mondo = ofactory.create(\"mondo.json\") ## interpreted as a json local handle"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "go = ofactory.create(\"go\") ## remote\n",
    "asmap = {}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "h:go g:"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "go"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "LOOKUP: NCBITaxon:4896\n",
      "CACHED\n",
      "LOOKUP: NCBITaxon:4932\n",
      "CACHED\n",
      "LOOKUP: NCBITaxon:7955\n",
      "CACHED\n",
      "LOOKUP: NCBITaxon:10090\n",
      "CACHED\n",
      "LOOKUP: NCBITaxon:9606\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:root:>1 relation: ['not', 'colocalizes_with']\n",
      "WARNING:root:>1 relation: ['not', 'colocalizes_with']\n",
      "WARNING:root:>1 relation: ['not', 'contributes_to']\n",
      "WARNING:root:>1 relation: ['not', 'contributes_to']\n",
      "WARNING:root:>1 relation: ['not', 'colocalizes_with']\n",
      "WARNING:root:>1 relation: ['not', 'colocalizes_with']\n",
      "WARNING:root:>1 relation: ['not', 'colocalizes_with']\n",
      "WARNING:root:>1 relation: ['not', 'colocalizes_with']\n",
      "WARNING:root:>1 relation: ['not', 'colocalizes_with']\n",
      "WARNING:root:>1 relation: ['not', 'colocalizes_with']\n",
      "WARNING:root:>1 relation: ['not', 'colocalizes_with']\n",
      "WARNING:root:>1 relation: ['not', 'colocalizes_with']\n",
      "WARNING:root:>1 relation: ['not', 'colocalizes_with']\n",
      "WARNING:root:>1 relation: ['not', 'colocalizes_with']\n",
      "WARNING:root:>1 relation: ['not', 'contributes_to']\n",
      "WARNING:root:>1 relation: ['not', 'colocalizes_with']\n",
      "WARNING:root:>1 relation: ['not', 'colocalizes_with']\n",
      "WARNING:root:>1 relation: ['not', 'colocalizes_with']\n",
      "WARNING:root:>1 relation: ['not', 'colocalizes_with']\n",
      "WARNING:root:>1 relation: ['not', 'colocalizes_with']\n"
     ]
    }
   ],
   "source": [
    "from ontobio import AssociationSetFactory\n",
    "afactory = AssociationSetFactory()\n",
    "\n",
    "taxa = ['NCBITaxon:4896', 'NCBITaxon:4932', 'NCBITaxon:7955', 'NCBITaxon:10090', 'NCBITaxon:9606']\n",
    "\n",
    "for taxon in taxa:\n",
    "    print(\"LOOKUP: {}\".format(taxon))\n",
    "    if taxon in asmap:\n",
    "        print(\"CACHED\")\n",
    "        continue\n",
    "    aset = afactory.create(ontology=go, subject_category='gene', object_category='function', taxon=taxon)\n",
    "    asmap[taxon] = aset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "from ontobio.golr.golr_associations import bulk_fetch\n",
    "\n",
    "from ontobio.vocabulary.relations import HomologyTypes\n",
    "\n",
    "#results = bulk_fetch(subject_category='gene', object_category='gene', taxon='NCBITaxon:9606', \n",
    "#               relation=HomologyTypes.Ortholog.value)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "[d] = mondo.search('Alzheimers disease')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "df = pd.read_csv('mim2gene_medgen', sep='\\t')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "    }\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>#MIM number</th>\n",
       "      <th>GeneID</th>\n",
       "      <th>type</th>\n",
       "      <th>Source</th>\n",
       "      <th>MedGenCUI</th>\n",
       "      <th>Comment</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>100050</td>\n",
       "      <td>-</td>\n",
       "      <td>phenotype</td>\n",
       "      <td>-</td>\n",
       "      <td>C3149220</td>\n",
       "      <td>-</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>100070</td>\n",
       "      <td>-</td>\n",
       "      <td>phenotype</td>\n",
       "      <td>-</td>\n",
       "      <td>C0162871</td>\n",
       "      <td>-</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>100100</td>\n",
       "      <td>1131</td>\n",
       "      <td>phenotype</td>\n",
       "      <td>GeneMap</td>\n",
       "      <td>C0033770</td>\n",
       "      <td>question</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>100200</td>\n",
       "      <td>-</td>\n",
       "      <td>phenotype</td>\n",
       "      <td>-</td>\n",
       "      <td>C0271355</td>\n",
       "      <td>-</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>100300</td>\n",
       "      <td>57514</td>\n",
       "      <td>phenotype</td>\n",
       "      <td>GeneMap</td>\n",
       "      <td>CN028867</td>\n",
       "      <td>-</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   #MIM number GeneID       type    Source MedGenCUI   Comment\n",
       "0       100050      -  phenotype         -  C3149220         -\n",
       "1       100070      -  phenotype         -  C0162871         -\n",
       "2       100100   1131  phenotype   GeneMap  C0033770  question\n",
       "3       100200      -  phenotype         -  C0271355         -\n",
       "4       100300  57514  phenotype   GeneMap  CN028867         -"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df[0:5]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "df = df.loc[df['type'] == 'phenotype']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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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>#MIM number</th>\n",
       "      <th>GeneID</th>\n",
       "      <th>type</th>\n",
       "      <th>Source</th>\n",
       "      <th>MedGenCUI</th>\n",
       "      <th>Comment</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>100050</td>\n",
       "      <td>-</td>\n",
       "      <td>phenotype</td>\n",
       "      <td>-</td>\n",
       "      <td>C3149220</td>\n",
       "      <td>-</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>100070</td>\n",
       "      <td>-</td>\n",
       "      <td>phenotype</td>\n",
       "      <td>-</td>\n",
       "      <td>C0162871</td>\n",
       "      <td>-</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>100100</td>\n",
       "      <td>1131</td>\n",
       "      <td>phenotype</td>\n",
       "      <td>GeneMap</td>\n",
       "      <td>C0033770</td>\n",
       "      <td>question</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>100200</td>\n",
       "      <td>-</td>\n",
       "      <td>phenotype</td>\n",
       "      <td>-</td>\n",
       "      <td>C0271355</td>\n",
       "      <td>-</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>100300</td>\n",
       "      <td>57514</td>\n",
       "      <td>phenotype</td>\n",
       "      <td>GeneMap</td>\n",
       "      <td>CN028867</td>\n",
       "      <td>-</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>100600</td>\n",
       "      <td>-</td>\n",
       "      <td>phenotype</td>\n",
       "      <td>-</td>\n",
       "      <td>C0000889</td>\n",
       "      <td>-</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>100675</td>\n",
       "      <td>-</td>\n",
       "      <td>phenotype</td>\n",
       "      <td>-</td>\n",
       "      <td>C1863486</td>\n",
       "      <td>-</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>100700</td>\n",
       "      <td>-</td>\n",
       "      <td>phenotype</td>\n",
       "      <td>-</td>\n",
       "      <td>C1332135</td>\n",
       "      <td>-</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>100800</td>\n",
       "      <td>2261</td>\n",
       "      <td>phenotype</td>\n",
       "      <td>GeneMap</td>\n",
       "      <td>C0001080</td>\n",
       "      <td>-</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>100820</td>\n",
       "      <td>-</td>\n",
       "      <td>phenotype</td>\n",
       "      <td>-</td>\n",
       "      <td>C1863416</td>\n",
       "      <td>-</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    #MIM number GeneID       type    Source MedGenCUI   Comment\n",
       "0        100050      -  phenotype         -  C3149220         -\n",
       "1        100070      -  phenotype         -  C0162871         -\n",
       "2        100100   1131  phenotype   GeneMap  C0033770  question\n",
       "3        100200      -  phenotype         -  C0271355         -\n",
       "4        100300  57514  phenotype   GeneMap  CN028867         -\n",
       "5        100600      -  phenotype         -  C0000889         -\n",
       "10       100675      -  phenotype         -  C1863486         -\n",
       "13       100700      -  phenotype         -  C1332135         -\n",
       "20       100800   2261  phenotype   GeneMap  C0001080         -\n",
       "21       100820      -  phenotype         -  C1863416         -"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df[0:10]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "eg = mondo.equiv_graph()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "5623"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tups = []\n",
    "notfound = []\n",
    "for ix,row in df.iterrows():\n",
    "    gid = row['GeneID']\n",
    "    if gid == '-':\n",
    "        continue\n",
    "    if row['Comment'] == 'nondisease':\n",
    "        continue\n",
    "    mim = row['#MIM number']\n",
    "    mim_uri = \"http://purl.obolibrary.org/obo/OMIM_{}\".format(mim)\n",
    "    if mim_uri not in eg:\n",
    "        #print(\"NOT FOUND:{} {}\".format(mim, row['Source']))\n",
    "        notfound.append(row)\n",
    "        continue\n",
    "    for d in eg.neighbors(mim_uri):\n",
    "        tups.append( (d, mondo.label(d), 'NCBIGene:{}'.format(gid)) )\n",
    "\n",
    "len(tups)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[#MIM number       110800\n",
       " GeneID              2651\n",
       " type           phenotype\n",
       " Source           GeneMap\n",
       " MedGenCUI       C1862229\n",
       " Comment                -\n",
       " Name: 440, dtype: object, #MIM number       111150\n",
       " GeneID             10661\n",
       " type           phenotype\n",
       " Source           GeneMap\n",
       " MedGenCUI       C1292231\n",
       " Comment                -\n",
       " Name: 445, dtype: object, #MIM number       111400\n",
       " GeneID             53947\n",
       " type           phenotype\n",
       " Source           GeneMap\n",
       " MedGenCUI       C0599990\n",
       " Comment                -\n",
       " Name: 451, dtype: object, #MIM number       113750\n",
       " GeneID            283652\n",
       " type           phenotype\n",
       " Source           GeneMap\n",
       " MedGenCUI       C2676042\n",
       " Comment                -\n",
       " Name: 528, dtype: object, #MIM number               138900\n",
       " GeneID                      9429\n",
       " type                   phenotype\n",
       " Source                   GeneMap\n",
       " MedGenCUI               C1841837\n",
       " Comment        nondisease; QTL 2\n",
       " Name: 1711, dtype: object, #MIM number       141749\n",
       " GeneID              3043\n",
       " type           phenotype\n",
       " Source           GeneMap\n",
       " MedGenCUI       C1841621\n",
       " Comment                -\n",
       " Name: 1810, dtype: object, #MIM number       141749\n",
       " GeneID              3047\n",
       " type           phenotype\n",
       " Source           GeneMap\n",
       " MedGenCUI       C1841621\n",
       " Comment                -\n",
       " Name: 1811, dtype: object, #MIM number       141749\n",
       " GeneID              3048\n",
       " type           phenotype\n",
       " Source           GeneMap\n",
       " MedGenCUI       C1841621\n",
       " Comment                -\n",
       " Name: 1812, dtype: object, #MIM number       167320\n",
       " GeneID              7415\n",
       " type           phenotype\n",
       " Source           GeneMap\n",
       " MedGenCUI       C1833662\n",
       " Comment                -\n",
       " Name: 3038, dtype: object, #MIM number       180295\n",
       " GeneID             23405\n",
       " type           phenotype\n",
       " Source           GeneMap\n",
       " MedGenCUI       C1867234\n",
       " Comment                -\n",
       " Name: 3623, dtype: object, #MIM number                        266300\n",
       " GeneID                               4157\n",
       " type                            phenotype\n",
       " Source                            GeneMap\n",
       " MedGenCUI                        C1849452\n",
       " Comment        nondisease; susceptibility\n",
       " Name: 5983, dtype: object, #MIM number       276400\n",
       " GeneID              2492\n",
       " type           phenotype\n",
       " Source           GeneMap\n",
       " MedGenCUI       C0220761\n",
       " Comment                -\n",
       " Name: 6223, dtype: object, #MIM number       300087\n",
       " GeneID              7503\n",
       " type           phenotype\n",
       " Source           GeneMap\n",
       " MedGenCUI       C1848138\n",
       " Comment                -\n",
       " Name: 6370, dtype: object, #MIM number            300306\n",
       " GeneID                  11254\n",
       " type                phenotype\n",
       " Source                GeneMap\n",
       " MedGenCUI            C2678155\n",
       " Comment        susceptibility\n",
       " Name: 6574, dtype: object, #MIM number       300537\n",
       " GeneID              2316\n",
       " type           phenotype\n",
       " Source           GeneMap\n",
       " MedGenCUI       C1848213\n",
       " Comment                -\n",
       " Name: 6788, dtype: object, #MIM number       300910\n",
       " GeneID              5358\n",
       " type           phenotype\n",
       " Source           GeneMap\n",
       " MedGenCUI       C3806712\n",
       " Comment                -\n",
       " Name: 7150, dtype: object, #MIM number               300932\n",
       " GeneID                      6906\n",
       " type                   phenotype\n",
       " Source                   GeneMap\n",
       " MedGenCUI               C4310821\n",
       " Comment        nondisease; QTL 2\n",
       " Name: 7172, dtype: object, #MIM number       300997\n",
       " GeneID              8473\n",
       " type           phenotype\n",
       " Source           GeneMap\n",
       " MedGenCUI       CN270121\n",
       " Comment                -\n",
       " Name: 7235, dtype: object, #MIM number       300998\n",
       " GeneID              6134\n",
       " type           phenotype\n",
       " Source           GeneMap\n",
       " MedGenCUI       CN298079\n",
       " Comment                -\n",
       " Name: 7236, dtype: object, #MIM number       301006\n",
       " GeneID              8270\n",
       " type           phenotype\n",
       " Source           GeneMap\n",
       " MedGenCUI       CN570502\n",
       " Comment                -\n",
       " Name: 7244, dtype: object]"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "        \n",
    "notfound[0:20]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[('http://purl.obolibrary.org/obo/MONDO_0007032',\n",
       "  'prune belly syndome',\n",
       "  'NCBIGene:1131'),\n",
       " ('http://purl.obolibrary.org/obo/MONDO_0007034',\n",
       "  'Adams-Oliver syndrome',\n",
       "  'NCBIGene:57514'),\n",
       " ('http://purl.obolibrary.org/obo/MONDO_0007037',\n",
       "  'achondroplasia',\n",
       "  'NCBIGene:2261'),\n",
       " ('http://purl.obolibrary.org/obo/MONDO_0007039',\n",
       "  'neurofibromatosis type 2',\n",
       "  'NCBIGene:4771'),\n",
       " ('http://purl.obolibrary.org/obo/MONDO_0007041',\n",
       "  'Apert syndrome',\n",
       "  'NCBIGene:2263'),\n",
       " ('http://purl.obolibrary.org/obo/MONDO_0007042',\n",
       "  'Saethre-Chotzen syndrome',\n",
       "  'NCBIGene:2263'),\n",
       " ('http://purl.obolibrary.org/obo/MONDO_0007042',\n",
       "  'Saethre-Chotzen syndrome',\n",
       "  'NCBIGene:7291'),\n",
       " ('http://purl.obolibrary.org/obo/MONDO_0007043',\n",
       "  'Pfeiffer syndrome',\n",
       "  'NCBIGene:2260'),\n",
       " ('http://purl.obolibrary.org/obo/MONDO_0007043',\n",
       "  'Pfeiffer syndrome',\n",
       "  'NCBIGene:2263'),\n",
       " ('http://purl.obolibrary.org/obo/MONDO_0007044',\n",
       "  'acrodysostosis 1 with or without hormone resistance',\n",
       "  'NCBIGene:5573'),\n",
       " ('http://purl.obolibrary.org/obo/MONDO_0007048',\n",
       "  'acrokeratosis verruciformis',\n",
       "  'NCBIGene:488'),\n",
       " ('http://purl.obolibrary.org/obo/MONDO_0007049',\n",
       "  'acroleukopathy, symmetric',\n",
       "  'NCBIGene:9049'),\n",
       " ('http://purl.obolibrary.org/obo/MONDO_0007052',\n",
       "  'growth hormone secreting pituitary adenoma',\n",
       "  'NCBIGene:2778'),\n",
       " ('http://purl.obolibrary.org/obo/MONDO_0007052',\n",
       "  'growth hormone secreting pituitary adenoma',\n",
       "  'NCBIGene:9049'),\n",
       " ('http://purl.obolibrary.org/obo/MONDO_0007055',\n",
       "  'acromicric dysplasia',\n",
       "  'NCBIGene:2200'),\n",
       " ('http://purl.obolibrary.org/obo/MONDO_0007057',\n",
       "  'acroosteolysis dominant type',\n",
       "  'NCBIGene:4853'),\n",
       " ('http://purl.obolibrary.org/obo/MONDO_0007060',\n",
       "  'spermatogenic failure 6',\n",
       "  'NCBIGene:83893'),\n",
       " ('http://purl.obolibrary.org/obo/MONDO_0007064',\n",
       "  'adenosine deaminase deficiency',\n",
       "  'NCBIGene:100'),\n",
       " ('http://purl.obolibrary.org/obo/MONDO_0007067',\n",
       "  'pyruvate kinase hyperactivity',\n",
       "  'NCBIGene:5313'),\n",
       " ('http://purl.obolibrary.org/obo/MONDO_0007068',\n",
       "  'Adenylosuccinate lyase deficiency',\n",
       "  'NCBIGene:158')]"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tups[0:20]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "godict = {}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [],
   "source": [
    "from ontobio.golr.golr_query import GolrAssociationQuery\n",
    "msolr = \"https://solr.monarchinitiative.org/solr/golr\"\n",
    "golr = \"http://golr.berkeleybop.org\"\n",
    "from ontobio.vocabulary.relations import HomologyTypes\n",
    "\n",
    "def orthogo(gid):\n",
    "    if gid in godict:\n",
    "        return godict[gid]\n",
    "    terms = set()\n",
    "    hq = GolrAssociationQuery(subject_category='gene', object_category='gene', subject=gid, \n",
    "                              relation=HomologyTypes.Ortholog.value,\n",
    "                              rows=100,\n",
    "                              url=msolr)\n",
    "    #print(\"PARAMS={}\".format(hq.solr_params()))\n",
    "    assocs = hq.exec()\n",
    "    for a in assocs['associations']:\n",
    "        orth = a['object']['id']\n",
    "        #print(\"LOOKUP: {}\".format(orth))\n",
    "        for taxon, aset in asmap.items():\n",
    "            #hq = GolrAssociationQuery(object_category='function', subject=orth, url=golr, rows=1000)\n",
    "            #for fa in hq.exec()['associations']:\n",
    "            for ann in aset.annotations(orth):\n",
    "                terms.add(str(ann))\n",
    "    godict[gid] = terms\n",
    "    return terms\n",
    "\n",
    "terms = orthogo('NCBIGene:5313')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'GO:0000166',\n",
       " 'GO:0000287',\n",
       " 'GO:0001889',\n",
       " 'GO:0003824',\n",
       " 'GO:0004743',\n",
       " 'GO:0005524',\n",
       " 'GO:0005737',\n",
       " 'GO:0005829',\n",
       " 'GO:0005975',\n",
       " 'GO:0006096',\n",
       " 'GO:0006754',\n",
       " 'GO:0008152',\n",
       " 'GO:0009408',\n",
       " 'GO:0010226',\n",
       " 'GO:0016301',\n",
       " 'GO:0016310',\n",
       " 'GO:0016740',\n",
       " 'GO:0030955',\n",
       " 'GO:0032869',\n",
       " 'GO:0033198',\n",
       " 'GO:0042866',\n",
       " 'GO:0046872',\n",
       " 'GO:0051591',\n",
       " 'GO:0051707',\n",
       " 'GO:0070062'}"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "terms"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "http://purl.obolibrary.org/obo/MONDO_0007032 -> {'GO:0003056', 'GO:0004871', 'GO:0045987', 'GO:0016907', 'GO:0007271', 'GO:0045211', 'GO:0007207', 'GO:0007165', 'GO:0005887', 'GO:0004930', 'GO:0007197', 'GO:0005886', 'GO:0030054', 'GO:0016021', 'GO:0007186', 'GO:0016020', 'GO:0046541', 'GO:0045202'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0007204 -> {'GO:0004656', 'GO:0031545'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0007311 -> {'GO:0010977', 'GO:0030154', 'GO:0003674', 'GO:0008150', 'GO:0007050', 'GO:0043218', 'GO:0032060', 'GO:0032288', 'GO:0042552', 'GO:0008219', 'GO:0008285', 'GO:0005886', 'GO:0007049', 'GO:0016021', 'GO:0016020', 'GO:0005923'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0007455 -> {'GO:0003674', 'GO:0031018', 'GO:0055074', 'GO:1990798', 'GO:0005783', 'GO:0000502', 'GO:0042593', 'GO:0016021', 'GO:0016020', 'GO:0003323'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0007631 -> set()\n",
      "http://purl.obolibrary.org/obo/MONDO_0007784 -> {'GO:0043565', 'GO:0004887', 'GO:0043010', 'GO:0006351', 'GO:0001076', 'GO:0000790', 'GO:0003677', 'GO:0046872', 'GO:0005634', 'GO:0070324', 'GO:0048839', 'GO:0008270', 'GO:0002154', 'GO:0003700', 'GO:0006355', 'GO:0043401', 'GO:0003707', 'GO:0005515', 'GO:0046549'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0007954 -> {'GO:0032835', 'GO:0021555', 'GO:0000142', 'GO:0016459', 'GO:0032836', 'GO:0001772', 'GO:0070650', 'GO:0008360', 'GO:0003779', 'GO:0072015', 'GO:0005524', 'GO:0000166', 'GO:0031594', 'GO:0008305', 'GO:0005925', 'GO:0003774', 'GO:0008180', 'GO:0003094', 'GO:0051015', 'GO:0005886', 'GO:0072104', 'GO:0005819'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0008147 -> {'GO:0005581', 'GO:0031101', 'GO:0005576', 'GO:0005578', 'GO:0005737', 'GO:0033333', 'GO:0005201', 'GO:0031012', 'GO:0033339', 'GO:0033334', 'GO:0030278'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0008296 -> {'GO:1904440', 'GO:0032435', 'GO:0009897', 'GO:0045177', 'GO:0048471', 'GO:0010862', 'GO:1900122', 'GO:1900121', 'GO:2000008', 'GO:0060586', 'GO:0048260', 'GO:0030881', 'GO:0055037', 'GO:1904434', 'GO:1904437', 'GO:0016021', 'GO:1990712', 'GO:1990357', 'GO:0090277', 'GO:0002725', 'GO:0042446', 'GO:0055072', 'GO:0006811', 'GO:0030509', 'GO:0071281', 'GO:0005886', 'GO:0010039', 'GO:0045178', 'GO:0031410', 'GO:0002626', 'GO:1904283', 'GO:0032092', 'GO:0006879', 'GO:1990459', 'GO:2000059', 'GO:2001186', 'GO:0005615', 'GO:0010628', 'GO:0039706', 'GO:0005102', 'GO:2000273', 'GO:2000272', 'GO:0098711', 'GO:0005769', 'GO:0016020'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0005090 -> {'GO:0043209', 'GO:0046983', 'GO:0007269', 'GO:0014069', 'GO:0031201', 'GO:0030672', 'GO:0048306', 'GO:0005524', 'GO:0003824', 'GO:0043195', 'GO:0005886', 'GO:0030054', 'GO:0005515', 'GO:0008021', 'GO:0045202'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0008586 -> {'GO:0003674', 'GO:1905168', 'GO:0005634', 'GO:0043240', 'GO:0006974', 'GO:2000042', 'GO:0035690', 'GO:0006281', 'GO:1990414', 'GO:0072757'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0008726 -> {'GO:0006629', 'GO:0055114', 'GO:0032332', 'GO:0070988', 'GO:0090181', 'GO:0005789', 'GO:0004128', 'GO:0050661', 'GO:0090346', 'GO:0047726', 'GO:0008202', 'GO:0005783', 'GO:0043154', 'GO:0016021', 'GO:0009055', 'GO:0060192', 'GO:0005739', 'GO:0003420', 'GO:0050660', 'GO:0016491', 'GO:0043602', 'GO:0043231', 'GO:0006696', 'GO:0032770', 'GO:0018393', 'GO:0016787', 'GO:0005886', 'GO:0019899', 'GO:0008941', 'GO:0003958', 'GO:0045542', 'GO:0016126', 'GO:0005741', 'GO:0010181', 'GO:0019395', 'GO:0045880', 'GO:0043066', 'GO:0016020', 'GO:0090031', 'GO:0006694', 'GO:0046210'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0008871 -> set()\n",
      "http://purl.obolibrary.org/obo/MONDO_0021020 -> {'GO:0052696', 'GO:0016757', 'GO:0052697', 'GO:0016740', 'GO:0043231', 'GO:0008152', 'GO:0016758', 'GO:0016787', 'GO:0016021', 'GO:0015020', 'GO:0016020'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0009180 -> {'GO:0007155', 'GO:0030334', 'GO:0005102', 'GO:0070831', 'GO:0045995', 'GO:0005604', 'GO:0030155', 'GO:0048731'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0009341 -> {'GO:0043565', 'GO:1902748', 'GO:0021846', 'GO:0007417', 'GO:0048066', 'GO:0045636', 'GO:0048598', 'GO:0021766', 'GO:0090243', 'GO:0070412', 'GO:0000790', 'GO:0048668', 'GO:0021957', 'GO:0030177', 'GO:0001755', 'GO:0035622', 'GO:0006355', 'GO:0009953', 'GO:0043507', 'GO:0050772', 'GO:0045944', 'GO:0003677', 'GO:0003676', 'GO:0005730', 'GO:0060028', 'GO:0060030', 'GO:0061373', 'GO:0048023', 'GO:0001843', 'GO:0021540', 'GO:0014029', 'GO:0001205', 'GO:0001756', 'GO:1903056', 'GO:0097324', 'GO:0006351', 'GO:0005829', 'GO:0046872', 'GO:0005634', 'GO:0000122', 'GO:0040037', 'GO:0001227'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0009529 -> {'GO:0045454', 'GO:0005737', 'GO:0055114', 'GO:0006090', 'GO:0005874', 'GO:0006103', 'GO:0045931', 'GO:0034604', 'GO:0005967', 'GO:0004738', 'GO:0006550', 'GO:0051315', 'GO:0034453', 'GO:0008017', 'GO:0006552', 'GO:0009055', 'GO:0005759', 'GO:0005739', 'GO:0006564', 'GO:0050660', 'GO:0016491', 'GO:0006546', 'GO:0004591', 'GO:0060047', 'GO:0007020', 'GO:0004148', 'GO:0032259', 'GO:0042743', 'GO:0045144', 'GO:0006312', 'GO:0009353', 'GO:0006574', 'GO:0008757', 'GO:0005960', 'GO:0042645', 'GO:0016668', 'GO:0004375'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0009668 -> {'GO:0015464', 'GO:0022848', 'GO:0042166'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0009797 -> {'GO:0004588', 'GO:0006207', 'GO:0005737', 'GO:0044205', 'GO:0016757', 'GO:0016740', 'GO:0005634', 'GO:0009116', 'GO:0016829', 'GO:0006221', 'GO:0042802', 'GO:0003824', 'GO:0008152', 'GO:0006222', 'GO:0004590', 'GO:0016831'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0009960 -> {'GO:0005576', 'GO:0006955', 'GO:0005138'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0010134 -> {'GO:0006810', 'GO:0006885', 'GO:0031526', 'GO:0005789', 'GO:0008150', 'GO:0055081', 'GO:0009651', 'GO:0016324', 'GO:0051453', 'GO:0015701', 'GO:0005783', 'GO:0032880', 'GO:0042391', 'GO:0008509', 'GO:0016021', 'GO:1902358', 'GO:0008271', 'GO:0015116', 'GO:0003674', 'GO:0070062', 'GO:0006821', 'GO:0008272', 'GO:0015111', 'GO:0005886', 'GO:0015698', 'GO:0019532', 'GO:0016020', 'GO:0019531', 'GO:1902476', 'GO:0009887', 'GO:0015108', 'GO:0005887', 'GO:0098656', 'GO:0055085', 'GO:0015301', 'GO:0015106', 'GO:0005254'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0010305 -> {'GO:0005328', 'GO:0006810', 'GO:0005308', 'GO:0006811', 'GO:0015293', 'GO:0005309', 'GO:0005887', 'GO:0006814', 'GO:0006836', 'GO:0015881', 'GO:0016021', 'GO:0016020', 'GO:0015220'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0010461 -> {'GO:0000790', 'GO:0061630', 'GO:0031625', 'GO:0005737', 'GO:0000209', 'GO:0043161', 'GO:0005524', 'GO:0006281', 'GO:0033503', 'GO:0016574', 'GO:0000166'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0010622 -> {'GO:0006629', 'GO:0008202', 'GO:0046872', 'GO:0008484', 'GO:0005783', 'GO:0004773', 'GO:0043231', 'GO:0003824', 'GO:0008152', 'GO:0007565', 'GO:0016787', 'GO:0016021', 'GO:0016020'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0010789 -> {'GO:0006810', 'GO:0055114', 'GO:0006397', 'GO:0004519', 'GO:0070469', 'GO:0022904', 'GO:0008380', 'GO:0000372', 'GO:0016021', 'GO:0004518', 'GO:0009055', 'GO:0005739', 'GO:0003723', 'GO:0016491', 'GO:0090305', 'GO:0008121', 'GO:0045275', 'GO:0006122', 'GO:0005743', 'GO:0046872', 'GO:0016020'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0010947 -> {'GO:0019901', 'GO:0004672', 'GO:0005856', 'GO:0005515', 'GO:0071549', 'GO:0034612', 'GO:0045121', 'GO:0030099', 'GO:0060548', 'GO:0070671', 'GO:0000166', 'GO:0014068', 'GO:0045944', 'GO:0016477', 'GO:0007165', 'GO:0007259', 'GO:0045822', 'GO:0050731', 'GO:0030155', 'GO:0046677', 'GO:0097012', 'GO:0031959', 'GO:0005131', 'GO:0046872', 'GO:0006979', 'GO:0016020', 'GO:0043388', 'GO:0007204', 'GO:0051770', 'GO:0033077', 'GO:0010811', 'GO:0046777', 'GO:0004713', 'GO:0033194', 'GO:0009755', 'GO:0045429', 'GO:0007186', 'GO:0032496', 'GO:0042981', 'GO:0005143', 'GO:0031702', 'GO:0097296', 'GO:0018108', 'GO:0007169', 'GO:0016363', 'GO:1904707', 'GO:0060399', 'GO:0046427', 'GO:2001235', 'GO:0042531', 'GO:0002376', 'GO:0045597', 'GO:0050729', 'GO:0048514', 'GO:0043524', 'GO:0043548', 'GO:0006919', 'GO:0004715', 'GO:0030154', 'GO:0050867', 'GO:0060333', 'GO:0005634', 'GO:0005901', 'GO:0042393', 'GO:0020037', 'GO:0006468', 'GO:0022408', 'GO:0045087', 'GO:0008022', 'GO:0000186', 'GO:0008284', 'GO:0016569', 'GO:0030218', 'GO:0048008', 'GO:0032760', 'GO:0097191', 'GO:0016310', 'GO:0032731', 'GO:0038083', 'GO:0033130', 'GO:0051091', 'GO:0007260', 'GO:0007262', 'GO:0005925', 'GO:0008631', 'GO:0035166', 'GO:0042802', 'GO:0060396', 'GO:0008285', 'GO:0005886', 'GO:0030335', 'GO:0042169', 'GO:0034050', 'GO:0051428', 'GO:0060397', 'GO:0032516', 'GO:0032024', 'GO:0043066', 'GO:0035409', 'GO:0042127', 'GO:0005737', 'GO:1902728', 'GO:0042976', 'GO:0061180', 'GO:0031103', 'GO:0016301', 'GO:0006954', 'GO:0031234', 'GO:0035401', 'GO:0010667', 'GO:0007167', 'GO:0005524', 'GO:0033160', 'GO:0071222', 'GO:0030097', 'GO:0002250', 'GO:0033209', 'GO:0050727', 'GO:0005654', 'GO:0035556', 'GO:0043392', 'GO:0060215', 'GO:1904037', 'GO:0035722', 'GO:0043065', 'GO:0043560', 'GO:0036016', 'GO:0005829', 'GO:0016740', 'GO:0005102', 'GO:0030098', 'GO:0019221'}\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "http://purl.obolibrary.org/obo/MONDO_0011122 -> {'GO:0007218', 'GO:0005576', 'GO:0043473', 'GO:2000253', 'GO:0070062', 'GO:0005794', 'GO:0070996', 'GO:0005615', 'GO:0043025', 'GO:0048589', 'GO:0005796', 'GO:0005102', 'GO:0009755', 'GO:0060259', 'GO:0031781', 'GO:0040008', 'GO:0008343', 'GO:0005184', 'GO:0031782', 'GO:0042755'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0011285 -> {'GO:0071711', 'GO:0033334', 'GO:0005509', 'GO:0033333'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0011439 -> {'GO:0005856', 'GO:0004722'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0011585 -> {'GO:0006810', 'GO:0006629', 'GO:0042995', 'GO:0009611', 'GO:0005637', 'GO:0005789', 'GO:0030054', 'GO:0005515', 'GO:0014069', 'GO:0008202', 'GO:0005783', 'GO:0043523', 'GO:0007399', 'GO:0045211', 'GO:0016021', 'GO:0004872', 'GO:0000247', 'GO:0042802', 'GO:0005640', 'GO:0070207', 'GO:0006696', 'GO:0006869', 'GO:0005635', 'GO:0005886', 'GO:0005811', 'GO:0031410', 'GO:0016126', 'GO:0005634', 'GO:0016853', 'GO:0004985', 'GO:0016020', 'GO:0006694', 'GO:0045202'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0011762 -> {'GO:0003674', 'GO:0031225', 'GO:0005576', 'GO:0005578', 'GO:0016324', 'GO:0007605', 'GO:0019226', 'GO:0005886', 'GO:0016021', 'GO:0016020', 'GO:0009986', 'GO:0007160'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0011903 -> {'GO:0005791', 'GO:0043209', 'GO:0005515', 'GO:0016323', 'GO:0098743', 'GO:0042552', 'GO:0098742', 'GO:0005887', 'GO:0005764', 'GO:0005886', 'GO:0016021', 'GO:0045217', 'GO:0043066', 'GO:0016020'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0012037 -> {'GO:0006351', 'GO:0070062', 'GO:0004871', 'GO:0005829', 'GO:0001650', 'GO:0043123', 'GO:0003677', 'GO:0005737', 'GO:0005634', 'GO:0000122', 'GO:0000978', 'GO:0005856', 'GO:0001078', 'GO:0006355', 'GO:0005886', 'GO:0045296', 'GO:0016020'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0012189 -> {'GO:0006486', 'GO:0005794', 'GO:0016757', 'GO:0016740', 'GO:0006688', 'GO:0047291', 'GO:0008373', 'GO:0000139', 'GO:0018279', 'GO:0016021', 'GO:0016020', 'GO:0009311'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0012349 -> {'GO:0045747', 'GO:0051446', 'GO:0007386', 'GO:0001541', 'GO:0033829', 'GO:0008593', 'GO:0055016', 'GO:0016757', 'GO:1902367', 'GO:0007399', 'GO:0030217', 'GO:0016021', 'GO:0036066', 'GO:0005794', 'GO:0007389', 'GO:1903561', 'GO:0007219', 'GO:0001756', 'GO:0032092', 'GO:0030154', 'GO:0031101', 'GO:0016740', 'GO:0046872', 'GO:0045665', 'GO:0014807', 'GO:0007275', 'GO:0002315', 'GO:0030173', 'GO:0016020'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0012506 -> {'GO:0014704', 'GO:0060027', 'GO:0030057', 'GO:0005913', 'GO:0030054', 'GO:0086091', 'GO:0002159', 'GO:0098911', 'GO:0055113', 'GO:0005509', 'GO:0016021', 'GO:0070062', 'GO:0005886', 'GO:0031410', 'GO:0016020', 'GO:0007155', 'GO:0046872', 'GO:0007507', 'GO:0007156', 'GO:0086073', 'GO:0086042', 'GO:0009267'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0021024 -> {'GO:0050715', 'GO:0035325', 'GO:0031526', 'GO:2000379', 'GO:0034121', 'GO:0045177', 'GO:0005515', 'GO:0071221', 'GO:2000505', 'GO:0045121', 'GO:0030169', 'GO:0042593', 'GO:0051092', 'GO:0032735', 'GO:0042755', 'GO:0070538', 'GO:0071447', 'GO:0070053', 'GO:0043231', 'GO:0050731', 'GO:2000334', 'GO:0031623', 'GO:0034694', 'GO:0044130', 'GO:0019915', 'GO:1904646', 'GO:0019395', 'GO:0006910', 'GO:0071813', 'GO:0016020', 'GO:0005622', 'GO:0007204', 'GO:0001676', 'GO:0045429', 'GO:0060907', 'GO:0010629', 'GO:0030299', 'GO:0044539', 'GO:0034381', 'GO:0007263', 'GO:0042742', 'GO:0015909', 'GO:0043619', 'GO:1900227', 'GO:0050892', 'GO:0006631', 'GO:0010628', 'GO:0005901', 'GO:1990000', 'GO:0035634', 'GO:0070374', 'GO:0090208', 'GO:0043410', 'GO:2000121', 'GO:0043234', 'GO:0008289', 'GO:0003085', 'GO:0033993', 'GO:0055096', 'GO:0032760', 'GO:0050431', 'GO:0071223', 'GO:0050702', 'GO:0071726', 'GO:0070542', 'GO:0016021', 'GO:0010744', 'GO:0005739', 'GO:0050830', 'GO:0005794', 'GO:0034383', 'GO:0006641', 'GO:0070892', 'GO:0050909', 'GO:0005886', 'GO:1903428', 'GO:0009986', 'GO:0007155', 'GO:0034197', 'GO:0042383', 'GO:0010886', 'GO:0000122', 'GO:0070543', 'GO:0050766', 'GO:0005041', 'GO:0009897', 'GO:0042953', 'GO:0001954', 'GO:0016525', 'GO:0007166', 'GO:0015908', 'GO:0008035', 'GO:0005783', 'GO:0006955', 'GO:0010942', 'GO:0033552', 'GO:0071222', 'GO:0071404', 'GO:0043497', 'GO:0042992', 'GO:0009612', 'GO:0043235', 'GO:0070508', 'GO:0030194', 'GO:0030301', 'GO:0140052', 'GO:0005615', 'GO:0043123', 'GO:0060100', 'GO:0043277', 'GO:0019934', 'GO:0032755'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0012802 -> {'GO:0043565', 'GO:0045892', 'GO:0043010', 'GO:0006351', 'GO:0003677', 'GO:0000977', 'GO:0005634', 'GO:0000122', 'GO:0007275', 'GO:0006355', 'GO:0060042', 'GO:0001227', 'GO:0046549'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0012975 -> {'GO:0005921', 'GO:0005829', 'GO:0016324', 'GO:0007154', 'GO:0005243', 'GO:0048839', 'GO:0007605', 'GO:0008285', 'GO:0005922', 'GO:0030054', 'GO:0016021', 'GO:0005515', 'GO:0016020', 'GO:0042471', 'GO:0005886'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0013120 -> {'GO:0000792', 'GO:0035064', 'GO:0006351', 'GO:0045137', 'GO:0003677', 'GO:0005654', 'GO:0031519', 'GO:0016569', 'GO:0005634', 'GO:0000122', 'GO:0003682', 'GO:0035102', 'GO:0006355', 'GO:0005515', 'GO:0000791', 'GO:0005694'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0013248 -> {'GO:0048476', 'GO:0004520'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0013372 -> set()\n",
      "http://purl.obolibrary.org/obo/MONDO_0013479 -> {'GO:0051087', 'GO:0032403', 'GO:0008625', 'GO:0005737', 'GO:0007626', 'GO:0071260', 'GO:0097192', 'GO:0045296', 'GO:0005515', 'GO:0030018', 'GO:0050821', 'GO:0046827', 'GO:0097201', 'GO:0000774', 'GO:0043005', 'GO:0006915', 'GO:0034605', 'GO:0060047', 'GO:0005886', 'GO:0010664', 'GO:0042993', 'GO:0005829', 'GO:0005634', 'GO:0007519'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0013593 -> {'GO:0005739', 'GO:0006915', 'GO:0097193', 'GO:0043065', 'GO:0008631', 'GO:0005737', 'GO:0008635', 'GO:0035631', 'GO:0005758', 'GO:0005622', 'GO:0006919', 'GO:0051402', 'GO:0009898'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0013719 -> {'GO:0005929', 'GO:0060271', 'GO:0061055', 'GO:0005737', 'GO:0042995', 'GO:0005856', 'GO:0030991', 'GO:0061512', 'GO:0008406', 'GO:0001701', 'GO:0000902', 'GO:0035721', 'GO:0050877', 'GO:0055123', 'GO:0032391', 'GO:0031076', 'GO:0097730', 'GO:0003674', 'GO:0060831', 'GO:0005654', 'GO:0031514', 'GO:0048701', 'GO:0030326', 'GO:0042471', 'GO:0030030', 'GO:0060830', 'GO:0007224'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0013834 -> {'GO:0009411', 'GO:0000993', 'GO:0006283', 'GO:0006974', 'GO:0016567', 'GO:0006281', 'GO:0005694'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0013949 -> {'GO:0016020', 'GO:0001967', 'GO:0030674', 'GO:0006810', 'GO:0016560', 'GO:1990415', 'GO:0007626', 'GO:0005778', 'GO:0043231', 'GO:0005777', 'GO:0001764', 'GO:0021795', 'GO:0016021', 'GO:0060152', 'GO:1990429', 'GO:0015031', 'GO:0000268', 'GO:0005779', 'GO:0001561'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0014064 -> {'GO:0008121'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0014174 -> {'GO:0005929', 'GO:0060271', 'GO:0004702', 'GO:0005737', 'GO:0001947', 'GO:0042995', 'GO:0004672', 'GO:0051301', 'GO:0008289', 'GO:0005856', 'GO:1904888', 'GO:0005515', 'GO:0061326', 'GO:0042981', 'GO:0016301', 'GO:0016310', 'GO:0097546', 'GO:0005524', 'GO:0035330', 'GO:0048793', 'GO:0016021', 'GO:0000166', 'GO:0032147', 'GO:0005576', 'GO:0061371', 'GO:0072116', 'GO:0006869', 'GO:0097543', 'GO:0004674', 'GO:0031098', 'GO:0009887', 'GO:0016740', 'GO:0046872', 'GO:0042157', 'GO:0007368', 'GO:0006468', 'GO:0007507', 'GO:0007049', 'GO:0007346', 'GO:0016020'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0014276 -> {'GO:0016020', 'GO:0007163', 'GO:0002250', 'GO:0046982', 'GO:0007166', 'GO:0042803', 'GO:0070228', 'GO:0051260', 'GO:0004888', 'GO:0002376', 'GO:0042105', 'GO:0016021', 'GO:0005515', 'GO:0015031'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0014386 -> {'GO:0043547', 'GO:0005737', 'GO:0005085', 'GO:0005829', 'GO:0042995', 'GO:0046872', 'GO:0005509', 'GO:0035556', 'GO:0005886', 'GO:0030054', 'GO:0007264', 'GO:0016020', 'GO:0071277', 'GO:0043005', 'GO:0045202'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0014489 -> {'GO:0004672', 'GO:0030247', 'GO:0005789', 'GO:0043531', 'GO:0016301', 'GO:0016310', 'GO:0016773', 'GO:0007420', 'GO:0005783', 'GO:0005524', 'GO:0001764', 'GO:0006493', 'GO:0016021', 'GO:0046835', 'GO:0000166', 'GO:0019233', 'GO:0061061', 'GO:0019200', 'GO:0016740', 'GO:0050905', 'GO:0006468', 'GO:0007611', 'GO:0016020', 'GO:0036268'}\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "http://purl.obolibrary.org/obo/MONDO_0014592 -> {'GO:0051011'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0014694 -> {'GO:0045892', 'GO:0001757', 'GO:0006351', 'GO:0032525', 'GO:0060349', 'GO:0007219', 'GO:0009880', 'GO:0005634', 'GO:0000122', 'GO:0007368', 'GO:0036342', 'GO:0010468', 'GO:0007275', 'GO:0006355', 'GO:0009798', 'GO:0048641', 'GO:0005515', 'GO:0001503', 'GO:0001756'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0014800 -> {'GO:0044297', 'GO:0030017', 'GO:0005737', 'GO:0005884', 'GO:0048741', 'GO:0043234', 'GO:0005856', 'GO:0005515', 'GO:0072562', 'GO:0005524', 'GO:0030027', 'GO:0000166', 'GO:0090131', 'GO:0070062', 'GO:0030175', 'GO:0001725', 'GO:0015629', 'GO:0005865', 'GO:0005615', 'GO:0010628', 'GO:0035050', 'GO:0030240'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0014902 -> {'GO:0045087', 'GO:0004672', 'GO:0004713', 'GO:0021549', 'GO:0033339', 'GO:0001889', 'GO:0051897', 'GO:0016301', 'GO:0021587', 'GO:0021522', 'GO:0016310', 'GO:0031017', 'GO:0005524', 'GO:0001764', 'GO:0021707', 'GO:0007169', 'GO:0071526', 'GO:0016021', 'GO:0021953', 'GO:0000166', 'GO:0030282', 'GO:0016477', 'GO:0002376', 'GO:0004714', 'GO:0001725', 'GO:0009615', 'GO:0005886', 'GO:0019899', 'GO:0009986', 'GO:0016032', 'GO:0043406', 'GO:0016740', 'GO:0005773', 'GO:0006468', 'GO:0017154', 'GO:0016020'}\n",
      "http://purl.obolibrary.org/obo/MONDO_0015005 -> {'GO:0005739', 'GO:0005575', 'GO:0008150', 'GO:0070062', 'GO:0030170', 'GO:0005737', 'GO:0005634', 'GO:0005622'}\n"
     ]
    }
   ],
   "source": [
    "m2go = {}\n",
    "n = 0\n",
    "for t in tups:\n",
    "    terms = orthogo(t[2])\n",
    "    mid = t[0]\n",
    "    if mid not in m2go:\n",
    "        m2go[mid] = set()\n",
    "    m2go[mid].update(terms)\n",
    "    n += 1\n",
    "    if n % 100 == 1:\n",
    "        print(\"{} -> {}\".format(mid, terms))\n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'GO:0000166',\n",
       " 'GO:0003140',\n",
       " 'GO:0004672',\n",
       " 'GO:0004713',\n",
       " 'GO:0004714',\n",
       " 'GO:0005007',\n",
       " 'GO:0005515',\n",
       " 'GO:0005524',\n",
       " 'GO:0005794',\n",
       " 'GO:0005886',\n",
       " 'GO:0006468',\n",
       " 'GO:0006915',\n",
       " 'GO:0008284',\n",
       " 'GO:0008543',\n",
       " 'GO:0016020',\n",
       " 'GO:0016021',\n",
       " 'GO:0016301',\n",
       " 'GO:0016310',\n",
       " 'GO:0016740',\n",
       " 'GO:0017134',\n",
       " 'GO:0030901',\n",
       " 'GO:0031012',\n",
       " 'GO:0031410',\n",
       " 'GO:0033278',\n",
       " 'GO:0035469',\n",
       " 'GO:0048565',\n",
       " 'GO:0048701',\n",
       " 'GO:0060271',\n",
       " 'GO:0061371',\n",
       " 'GO:0071910'}"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "[apert] = mondo.search('Apert syndrome')\n",
    "m2go[apert]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'http://purl.obolibrary.org/obo/MONDO_0007041'"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "apert"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "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>disease</th>\n",
       "      <th>disease_name</th>\n",
       "      <th>go</th>\n",
       "      <th>go_name</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0007032</td>\n",
       "      <td>prune belly syndome</td>\n",
       "      <td>GO:0003056</td>\n",
       "      <td>regulation of vascular smooth muscle contraction</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0007032</td>\n",
       "      <td>prune belly syndome</td>\n",
       "      <td>GO:0004871</td>\n",
       "      <td>signal transducer activity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0007032</td>\n",
       "      <td>prune belly syndome</td>\n",
       "      <td>GO:0045987</td>\n",
       "      <td>positive regulation of smooth muscle contraction</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0007032</td>\n",
       "      <td>prune belly syndome</td>\n",
       "      <td>GO:0007271</td>\n",
       "      <td>synaptic transmission, cholinergic</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0007032</td>\n",
       "      <td>prune belly syndome</td>\n",
       "      <td>GO:0007207</td>\n",
       "      <td>phospholipase C-activating G-protein coupled a...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                        disease         disease_name  \\\n",
       "0  http://purl.obolibrary.org/obo/MONDO_0007032  prune belly syndome   \n",
       "1  http://purl.obolibrary.org/obo/MONDO_0007032  prune belly syndome   \n",
       "2  http://purl.obolibrary.org/obo/MONDO_0007032  prune belly syndome   \n",
       "3  http://purl.obolibrary.org/obo/MONDO_0007032  prune belly syndome   \n",
       "4  http://purl.obolibrary.org/obo/MONDO_0007032  prune belly syndome   \n",
       "\n",
       "           go                                            go_name  \n",
       "0  GO:0003056   regulation of vascular smooth muscle contraction  \n",
       "1  GO:0004871                         signal transducer activity  \n",
       "2  GO:0045987   positive regulation of smooth muscle contraction  \n",
       "3  GO:0007271                 synaptic transmission, cholinergic  \n",
       "4  GO:0007207  phospholipase C-activating G-protein coupled a...  "
      ]
     },
     "execution_count": 30,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rows = []\n",
    "for d,terms in m2go.items():\n",
    "    for t in terms:\n",
    "        rows.append( {'disease': d, 'disease_name': mondo.label(d), 'go':t, 'go_name': go.label(t)} )\n",
    "\n",
    "df = pd.DataFrame(rows)\n",
    "df.set_index('disease')\n",
    "df.to_csv('mondo-leaves-to-go.tsv', sep='\\t')\n",
    "df[0:5]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 81,
   "metadata": {},
   "outputs": [],
   "source": [
    "mtups = []\n",
    "for d,terms in m2go.items():\n",
    "    for t in terms:\n",
    "        mtups.append( (d, mondo.label(d), t) )\n",
    "        \n",
    "mset = afactory.create_from_tuples(mtups, ontology=go)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "msimple = mondo.subontology(relations='subClassOf')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 89,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'c': 'GO:0006767', 'p': 3.3528193217327691e-09, 'p_uncorrected': 2.6317263121921265e-12, 'n': 'water-soluble vitamin metabolic process', 'disease': 'http://purl.obolibrary.org/obo/MONDO_0001639', 'disease label': 'deficiency anemia'}\n",
      "{'c': 'GO:0050863', 'p': 4.5076412611943789e-08, 'p_uncorrected': 9.042409751643689e-12, 'n': 'regulation of T cell activation', 'disease': 'http://purl.obolibrary.org/obo/MONDO_0015823', 'disease label': 'primary immunodeficiency due to a defect in adaptive immunity'}\n",
      "{'c': 'GO:0007265', 'p': 1.2375779678481437e-07, 'p_uncorrected': 7.9535859116204605e-11, 'n': 'Ras protein signal transduction', 'disease': 'http://purl.obolibrary.org/obo/MONDO_0021060', 'disease label': 'RASopathy'}\n",
      "{'c': 'GO:0035082', 'p': 2.7407890616283519e-28, 'p_uncorrected': 2.4691793348003171e-31, 'n': 'axoneme assembly', 'disease': 'http://purl.obolibrary.org/obo/MONDO_0018395', 'disease label': 'male infertility due to sperm motility disorder'}\n",
      "{'c': 'GO:0050664', 'p': 3.0763569797343126e-09, 'p_uncorrected': 1.7990391694352706e-11, 'n': 'oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor', 'disease': 'http://purl.obolibrary.org/obo/MONDO_0018305', 'disease label': 'chronic granulomatous disease'}\n",
      "{'c': 'GO:0006625', 'p': 5.4094788391193165e-22, 'p_uncorrected': 1.7695383837485498e-25, 'n': 'protein targeting to peroxisome', 'disease': 'http://purl.obolibrary.org/obo/MONDO_0020242', 'disease label': 'genetic macular dystrophy'}\n",
      "{'c': 'GO:0034702', 'p': 1.7725177357621256e-07, 'p_uncorrected': 2.4281064873453775e-10, 'n': 'ion channel complex', 'disease': 'http://purl.obolibrary.org/obo/MONDO_0019171', 'disease label': 'familial long QT syndrome'}\n",
      "{'c': 'GO:0045214', 'p': 6.2086954523834375e-09, 'p_uncorrected': 1.1830593468718441e-12, 'n': 'sarcomere organization', 'disease': 'http://purl.obolibrary.org/obo/MONDO_0020029', 'disease label': 'rare genetic cardiac disease'}\n",
      "{'c': 'GO:0042645', 'p': 5.2542181697443292e-09, 'p_uncorrected': 2.5998110686513256e-12, 'n': 'mitochondrial nucleoid', 'disease': 'http://purl.obolibrary.org/obo/MONDO_0016578', 'disease label': 'mitochondrial oxidative phosphorylation disorder due to nuclear DNA anomalies'}\n",
      "{'c': 'GO:0022839', 'p': 2.7395157735771631e-15, 'p_uncorrected': 1.5826203198019428e-18, 'n': 'ion gated channel activity', 'disease': 'http://purl.obolibrary.org/obo/MONDO_0015110', 'disease label': 'genetic cardiac rhythm disease'}\n",
      "{'c': 'GO:0043574', 'p': 7.6106937826282869e-21, 'p_uncorrected': 1.6860198898157481e-24, 'n': 'peroxisomal transport', 'disease': 'http://purl.obolibrary.org/obo/MONDO_0018928', 'disease label': 'rare hepatic disease'}\n",
      "{'c': 'GO:0008206', 'p': 2.5378436688013758e-08, 'p_uncorrected': 3.094931303416312e-11, 'n': 'bile acid metabolic process', 'disease': 'http://purl.obolibrary.org/obo/MONDO_0017290', 'disease label': 'familial intrahepatic cholestasis'}\n"
     ]
    }
   ],
   "source": [
    "eobjs = []\n",
    "for d in msimple.nodes():\n",
    "    if not d.startswith('http://purl.obolibrary.org/obo/MONDO'):\n",
    "        continue\n",
    "    leafs = msimple.descendants(d)\n",
    "    if len(leafs) < 2:\n",
    "        continue\n",
    "    enr = mset.enrichment_test(subjects=leafs, threshold=0.000005, labels=True)\n",
    "    if len(enr) == 0:\n",
    "        continue\n",
    "    #print('{} {}'.format(d, msimple.label(d)))\n",
    "    for r in enr:\n",
    "       #print('  {}'.format(r))\n",
    "        r['disease'] = d\n",
    "        r['disease label'] = mondo.label(d)\n",
    "        eobjs.append(r)\n",
    "        if len(eobjs) % 1000 == 1:\n",
    "            print('{}'.format(r))\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 90,
   "metadata": {},
   "outputs": [],
   "source": [
    "edf = pd.DataFrame(eobjs)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 99,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>c</th>\n",
       "      <th>disease</th>\n",
       "      <th>disease label</th>\n",
       "      <th>n</th>\n",
       "      <th>p</th>\n",
       "      <th>p_uncorrected</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>3000</th>\n",
       "      <td>GO:0035082</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>axoneme assembly</td>\n",
       "      <td>2.740789e-28</td>\n",
       "      <td>2.469179e-31</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3001</th>\n",
       "      <td>GO:0097711</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>ciliary basal body-plasma membrane docking</td>\n",
       "      <td>2.740789e-28</td>\n",
       "      <td>2.469179e-31</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3002</th>\n",
       "      <td>GO:0042073</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>intraciliary transport</td>\n",
       "      <td>5.141390e-28</td>\n",
       "      <td>4.631883e-31</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3003</th>\n",
       "      <td>GO:0048199</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>vesicle targeting, to, from or within Golgi</td>\n",
       "      <td>7.006935e-28</td>\n",
       "      <td>6.312554e-31</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3004</th>\n",
       "      <td>GO:0001578</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>microtubule bundle formation</td>\n",
       "      <td>8.170072e-28</td>\n",
       "      <td>7.360425e-31</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3005</th>\n",
       "      <td>GO:0044782</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>cilium organization</td>\n",
       "      <td>8.170072e-28</td>\n",
       "      <td>7.360425e-31</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3006</th>\n",
       "      <td>GO:0061512</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>protein localization to cilium</td>\n",
       "      <td>9.518704e-28</td>\n",
       "      <td>8.575409e-31</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3007</th>\n",
       "      <td>GO:0006903</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>vesicle targeting</td>\n",
       "      <td>1.108122e-27</td>\n",
       "      <td>9.983077e-31</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3008</th>\n",
       "      <td>GO:0098840</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>protein transport along microtubule</td>\n",
       "      <td>1.498280e-27</td>\n",
       "      <td>1.349802e-30</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3009</th>\n",
       "      <td>GO:0099118</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>microtubule-based protein transport</td>\n",
       "      <td>1.498280e-27</td>\n",
       "      <td>1.349802e-30</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3010</th>\n",
       "      <td>GO:0140056</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>organelle localization by membrane tethering</td>\n",
       "      <td>2.714208e-27</td>\n",
       "      <td>2.445233e-30</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3011</th>\n",
       "      <td>GO:0022406</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>membrane docking</td>\n",
       "      <td>3.636965e-27</td>\n",
       "      <td>3.276545e-30</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3012</th>\n",
       "      <td>GO:0031503</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>protein complex localization</td>\n",
       "      <td>9.905154e-27</td>\n",
       "      <td>8.923563e-30</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3013</th>\n",
       "      <td>GO:0005929</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>cilium</td>\n",
       "      <td>9.311446e-26</td>\n",
       "      <td>8.388690e-29</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3014</th>\n",
       "      <td>GO:0030990</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>intraciliary transport particle</td>\n",
       "      <td>1.017026e-25</td>\n",
       "      <td>9.162394e-29</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3015</th>\n",
       "      <td>GO:0005930</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>axoneme</td>\n",
       "      <td>2.054014e-25</td>\n",
       "      <td>1.850463e-28</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3016</th>\n",
       "      <td>GO:0097014</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>ciliary plasm</td>\n",
       "      <td>2.054014e-25</td>\n",
       "      <td>1.850463e-28</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3017</th>\n",
       "      <td>GO:0007018</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>microtubule-based movement</td>\n",
       "      <td>5.816744e-25</td>\n",
       "      <td>5.240310e-28</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3018</th>\n",
       "      <td>GO:0048193</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>Golgi vesicle transport</td>\n",
       "      <td>1.916822e-24</td>\n",
       "      <td>1.726866e-27</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3019</th>\n",
       "      <td>GO:0099111</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>microtubule-based transport</td>\n",
       "      <td>2.721016e-24</td>\n",
       "      <td>2.451366e-27</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3020</th>\n",
       "      <td>GO:0010970</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>transport along microtubule</td>\n",
       "      <td>2.721016e-24</td>\n",
       "      <td>2.451366e-27</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3021</th>\n",
       "      <td>GO:0051650</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>establishment of vesicle localization</td>\n",
       "      <td>3.846488e-24</td>\n",
       "      <td>3.465305e-27</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3022</th>\n",
       "      <td>GO:0030705</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>cytoskeleton-dependent intracellular transport</td>\n",
       "      <td>4.833906e-24</td>\n",
       "      <td>4.354870e-27</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3023</th>\n",
       "      <td>GO:0051648</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>vesicle localization</td>\n",
       "      <td>3.144541e-23</td>\n",
       "      <td>2.832920e-26</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3024</th>\n",
       "      <td>GO:0051656</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>establishment of organelle localization</td>\n",
       "      <td>2.196312e-22</td>\n",
       "      <td>1.978660e-25</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3025</th>\n",
       "      <td>GO:0032838</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>plasma membrane bounded cell projection cytoplasm</td>\n",
       "      <td>3.121732e-22</td>\n",
       "      <td>2.812371e-25</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3026</th>\n",
       "      <td>GO:0000226</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>microtubule cytoskeleton organization</td>\n",
       "      <td>2.393154e-20</td>\n",
       "      <td>2.155995e-23</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3027</th>\n",
       "      <td>GO:0051640</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>organelle localization</td>\n",
       "      <td>4.907954e-20</td>\n",
       "      <td>4.421580e-23</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3028</th>\n",
       "      <td>GO:0007017</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>microtubule-based process</td>\n",
       "      <td>3.254176e-19</td>\n",
       "      <td>2.931690e-22</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3029</th>\n",
       "      <td>GO:0036158</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0018395</td>\n",
       "      <td>male infertility due to sperm motility disorder</td>\n",
       "      <td>outer dynein arm assembly</td>\n",
       "      <td>5.452116e-19</td>\n",
       "      <td>4.911817e-22</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4969</th>\n",
       "      <td>GO:0044438</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>microbody part</td>\n",
       "      <td>2.554039e-21</td>\n",
       "      <td>8.986767e-25</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4970</th>\n",
       "      <td>GO:0044439</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>peroxisomal part</td>\n",
       "      <td>2.554039e-21</td>\n",
       "      <td>8.986767e-25</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4971</th>\n",
       "      <td>GO:0031903</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>microbody membrane</td>\n",
       "      <td>4.854400e-21</td>\n",
       "      <td>1.708093e-24</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4972</th>\n",
       "      <td>GO:0005778</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>peroxisomal membrane</td>\n",
       "      <td>4.854400e-21</td>\n",
       "      <td>1.708093e-24</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4973</th>\n",
       "      <td>GO:0007031</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>peroxisome organization</td>\n",
       "      <td>4.967183e-18</td>\n",
       "      <td>1.747777e-21</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4974</th>\n",
       "      <td>GO:0044743</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>protein transmembrane import into intracellula...</td>\n",
       "      <td>1.631016e-17</td>\n",
       "      <td>5.738972e-21</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4975</th>\n",
       "      <td>GO:0005779</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>integral component of peroxisomal membrane</td>\n",
       "      <td>2.087445e-16</td>\n",
       "      <td>7.344987e-20</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4976</th>\n",
       "      <td>GO:0031231</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>intrinsic component of peroxisomal membrane</td>\n",
       "      <td>1.150743e-15</td>\n",
       "      <td>4.049061e-19</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4977</th>\n",
       "      <td>GO:0065002</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>intracellular protein transmembrane transport</td>\n",
       "      <td>2.337442e-15</td>\n",
       "      <td>8.224638e-19</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4978</th>\n",
       "      <td>GO:0042579</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>microbody</td>\n",
       "      <td>9.684572e-15</td>\n",
       "      <td>3.407661e-18</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4979</th>\n",
       "      <td>GO:0005777</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>peroxisome</td>\n",
       "      <td>9.684572e-15</td>\n",
       "      <td>3.407661e-18</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4980</th>\n",
       "      <td>GO:0071806</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>protein transmembrane transport</td>\n",
       "      <td>1.842114e-13</td>\n",
       "      <td>6.481751e-17</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4981</th>\n",
       "      <td>GO:1990415</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>Pex17p-Pex14p docking complex</td>\n",
       "      <td>1.873095e-09</td>\n",
       "      <td>6.590763e-13</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4982</th>\n",
       "      <td>GO:0032402</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>melanosome transport</td>\n",
       "      <td>2.735314e-09</td>\n",
       "      <td>9.624611e-13</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4983</th>\n",
       "      <td>GO:0032401</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>establishment of melanosome localization</td>\n",
       "      <td>2.735314e-09</td>\n",
       "      <td>9.624611e-13</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4984</th>\n",
       "      <td>GO:0006605</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>protein targeting</td>\n",
       "      <td>4.483951e-09</td>\n",
       "      <td>1.577745e-12</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4985</th>\n",
       "      <td>GO:0032400</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>melanosome localization</td>\n",
       "      <td>7.866372e-09</td>\n",
       "      <td>2.767900e-12</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4986</th>\n",
       "      <td>GO:0051904</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>pigment granule transport</td>\n",
       "      <td>1.288762e-08</td>\n",
       "      <td>4.534703e-12</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4987</th>\n",
       "      <td>GO:0006886</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>intracellular protein transport</td>\n",
       "      <td>2.020314e-08</td>\n",
       "      <td>7.108776e-12</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4988</th>\n",
       "      <td>GO:0045046</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>protein import into peroxisome membrane</td>\n",
       "      <td>2.282661e-08</td>\n",
       "      <td>8.031884e-12</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4989</th>\n",
       "      <td>GO:1990429</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>peroxisomal importomer complex</td>\n",
       "      <td>3.824290e-08</td>\n",
       "      <td>1.345633e-11</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4990</th>\n",
       "      <td>GO:0046907</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>intracellular transport</td>\n",
       "      <td>9.166820e-08</td>\n",
       "      <td>3.225482e-11</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4991</th>\n",
       "      <td>GO:0034464</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>BBSome</td>\n",
       "      <td>1.110540e-07</td>\n",
       "      <td>3.907600e-11</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4992</th>\n",
       "      <td>GO:0051905</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>establishment of pigment granule localization</td>\n",
       "      <td>2.483481e-07</td>\n",
       "      <td>8.738497e-11</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4993</th>\n",
       "      <td>GO:0033365</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>protein localization to organelle</td>\n",
       "      <td>3.668101e-07</td>\n",
       "      <td>1.290676e-10</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4994</th>\n",
       "      <td>GO:0051875</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>pigment granule localization</td>\n",
       "      <td>5.097743e-07</td>\n",
       "      <td>1.793717e-10</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4995</th>\n",
       "      <td>GO:0033059</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>cellular pigmentation</td>\n",
       "      <td>1.139999e-06</td>\n",
       "      <td>4.011255e-10</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4996</th>\n",
       "      <td>GO:0031301</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020244</td>\n",
       "      <td>unclassified primitive or secondary maculopathy</td>\n",
       "      <td>integral component of organelle membrane</td>\n",
       "      <td>3.959531e-06</td>\n",
       "      <td>1.393220e-09</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4997</th>\n",
       "      <td>GO:0015919</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020242</td>\n",
       "      <td>genetic macular dystrophy</td>\n",
       "      <td>peroxisomal membrane transport</td>\n",
       "      <td>1.578920e-22</td>\n",
       "      <td>5.164932e-26</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4998</th>\n",
       "      <td>GO:0072663</td>\n",
       "      <td>http://purl.obolibrary.org/obo/MONDO_0020242</td>\n",
       "      <td>genetic macular dystrophy</td>\n",
       "      <td>establishment of protein localization to perox...</td>\n",
       "      <td>5.409479e-22</td>\n",
       "      <td>1.769538e-25</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1999 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "               c                                       disease  \\\n",
       "3000  GO:0035082  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3001  GO:0097711  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3002  GO:0042073  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3003  GO:0048199  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3004  GO:0001578  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3005  GO:0044782  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3006  GO:0061512  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3007  GO:0006903  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3008  GO:0098840  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3009  GO:0099118  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3010  GO:0140056  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3011  GO:0022406  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3012  GO:0031503  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3013  GO:0005929  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3014  GO:0030990  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3015  GO:0005930  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3016  GO:0097014  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3017  GO:0007018  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3018  GO:0048193  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3019  GO:0099111  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3020  GO:0010970  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3021  GO:0051650  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3022  GO:0030705  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3023  GO:0051648  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3024  GO:0051656  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3025  GO:0032838  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3026  GO:0000226  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3027  GO:0051640  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3028  GO:0007017  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "3029  GO:0036158  http://purl.obolibrary.org/obo/MONDO_0018395   \n",
       "...          ...                                           ...   \n",
       "4969  GO:0044438  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4970  GO:0044439  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4971  GO:0031903  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4972  GO:0005778  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4973  GO:0007031  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4974  GO:0044743  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4975  GO:0005779  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4976  GO:0031231  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4977  GO:0065002  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4978  GO:0042579  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4979  GO:0005777  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4980  GO:0071806  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4981  GO:1990415  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4982  GO:0032402  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4983  GO:0032401  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4984  GO:0006605  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4985  GO:0032400  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4986  GO:0051904  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4987  GO:0006886  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4988  GO:0045046  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4989  GO:1990429  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4990  GO:0046907  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4991  GO:0034464  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4992  GO:0051905  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4993  GO:0033365  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4994  GO:0051875  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4995  GO:0033059  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4996  GO:0031301  http://purl.obolibrary.org/obo/MONDO_0020244   \n",
       "4997  GO:0015919  http://purl.obolibrary.org/obo/MONDO_0020242   \n",
       "4998  GO:0072663  http://purl.obolibrary.org/obo/MONDO_0020242   \n",
       "\n",
       "                                        disease label  \\\n",
       "3000  male infertility due to sperm motility disorder   \n",
       "3001  male infertility due to sperm motility disorder   \n",
       "3002  male infertility due to sperm motility disorder   \n",
       "3003  male infertility due to sperm motility disorder   \n",
       "3004  male infertility due to sperm motility disorder   \n",
       "3005  male infertility due to sperm motility disorder   \n",
       "3006  male infertility due to sperm motility disorder   \n",
       "3007  male infertility due to sperm motility disorder   \n",
       "3008  male infertility due to sperm motility disorder   \n",
       "3009  male infertility due to sperm motility disorder   \n",
       "3010  male infertility due to sperm motility disorder   \n",
       "3011  male infertility due to sperm motility disorder   \n",
       "3012  male infertility due to sperm motility disorder   \n",
       "3013  male infertility due to sperm motility disorder   \n",
       "3014  male infertility due to sperm motility disorder   \n",
       "3015  male infertility due to sperm motility disorder   \n",
       "3016  male infertility due to sperm motility disorder   \n",
       "3017  male infertility due to sperm motility disorder   \n",
       "3018  male infertility due to sperm motility disorder   \n",
       "3019  male infertility due to sperm motility disorder   \n",
       "3020  male infertility due to sperm motility disorder   \n",
       "3021  male infertility due to sperm motility disorder   \n",
       "3022  male infertility due to sperm motility disorder   \n",
       "3023  male infertility due to sperm motility disorder   \n",
       "3024  male infertility due to sperm motility disorder   \n",
       "3025  male infertility due to sperm motility disorder   \n",
       "3026  male infertility due to sperm motility disorder   \n",
       "3027  male infertility due to sperm motility disorder   \n",
       "3028  male infertility due to sperm motility disorder   \n",
       "3029  male infertility due to sperm motility disorder   \n",
       "...                                               ...   \n",
       "4969  unclassified primitive or secondary maculopathy   \n",
       "4970  unclassified primitive or secondary maculopathy   \n",
       "4971  unclassified primitive or secondary maculopathy   \n",
       "4972  unclassified primitive or secondary maculopathy   \n",
       "4973  unclassified primitive or secondary maculopathy   \n",
       "4974  unclassified primitive or secondary maculopathy   \n",
       "4975  unclassified primitive or secondary maculopathy   \n",
       "4976  unclassified primitive or secondary maculopathy   \n",
       "4977  unclassified primitive or secondary maculopathy   \n",
       "4978  unclassified primitive or secondary maculopathy   \n",
       "4979  unclassified primitive or secondary maculopathy   \n",
       "4980  unclassified primitive or secondary maculopathy   \n",
       "4981  unclassified primitive or secondary maculopathy   \n",
       "4982  unclassified primitive or secondary maculopathy   \n",
       "4983  unclassified primitive or secondary maculopathy   \n",
       "4984  unclassified primitive or secondary maculopathy   \n",
       "4985  unclassified primitive or secondary maculopathy   \n",
       "4986  unclassified primitive or secondary maculopathy   \n",
       "4987  unclassified primitive or secondary maculopathy   \n",
       "4988  unclassified primitive or secondary maculopathy   \n",
       "4989  unclassified primitive or secondary maculopathy   \n",
       "4990  unclassified primitive or secondary maculopathy   \n",
       "4991  unclassified primitive or secondary maculopathy   \n",
       "4992  unclassified primitive or secondary maculopathy   \n",
       "4993  unclassified primitive or secondary maculopathy   \n",
       "4994  unclassified primitive or secondary maculopathy   \n",
       "4995  unclassified primitive or secondary maculopathy   \n",
       "4996  unclassified primitive or secondary maculopathy   \n",
       "4997                        genetic macular dystrophy   \n",
       "4998                        genetic macular dystrophy   \n",
       "\n",
       "                                                      n             p  \\\n",
       "3000                                   axoneme assembly  2.740789e-28   \n",
       "3001         ciliary basal body-plasma membrane docking  2.740789e-28   \n",
       "3002                             intraciliary transport  5.141390e-28   \n",
       "3003        vesicle targeting, to, from or within Golgi  7.006935e-28   \n",
       "3004                       microtubule bundle formation  8.170072e-28   \n",
       "3005                                cilium organization  8.170072e-28   \n",
       "3006                     protein localization to cilium  9.518704e-28   \n",
       "3007                                  vesicle targeting  1.108122e-27   \n",
       "3008                protein transport along microtubule  1.498280e-27   \n",
       "3009                microtubule-based protein transport  1.498280e-27   \n",
       "3010       organelle localization by membrane tethering  2.714208e-27   \n",
       "3011                                   membrane docking  3.636965e-27   \n",
       "3012                       protein complex localization  9.905154e-27   \n",
       "3013                                             cilium  9.311446e-26   \n",
       "3014                    intraciliary transport particle  1.017026e-25   \n",
       "3015                                            axoneme  2.054014e-25   \n",
       "3016                                      ciliary plasm  2.054014e-25   \n",
       "3017                         microtubule-based movement  5.816744e-25   \n",
       "3018                            Golgi vesicle transport  1.916822e-24   \n",
       "3019                        microtubule-based transport  2.721016e-24   \n",
       "3020                        transport along microtubule  2.721016e-24   \n",
       "3021              establishment of vesicle localization  3.846488e-24   \n",
       "3022     cytoskeleton-dependent intracellular transport  4.833906e-24   \n",
       "3023                               vesicle localization  3.144541e-23   \n",
       "3024            establishment of organelle localization  2.196312e-22   \n",
       "3025  plasma membrane bounded cell projection cytoplasm  3.121732e-22   \n",
       "3026              microtubule cytoskeleton organization  2.393154e-20   \n",
       "3027                             organelle localization  4.907954e-20   \n",
       "3028                          microtubule-based process  3.254176e-19   \n",
       "3029                          outer dynein arm assembly  5.452116e-19   \n",
       "...                                                 ...           ...   \n",
       "4969                                     microbody part  2.554039e-21   \n",
       "4970                                   peroxisomal part  2.554039e-21   \n",
       "4971                                 microbody membrane  4.854400e-21   \n",
       "4972                               peroxisomal membrane  4.854400e-21   \n",
       "4973                            peroxisome organization  4.967183e-18   \n",
       "4974  protein transmembrane import into intracellula...  1.631016e-17   \n",
       "4975         integral component of peroxisomal membrane  2.087445e-16   \n",
       "4976        intrinsic component of peroxisomal membrane  1.150743e-15   \n",
       "4977      intracellular protein transmembrane transport  2.337442e-15   \n",
       "4978                                          microbody  9.684572e-15   \n",
       "4979                                         peroxisome  9.684572e-15   \n",
       "4980                    protein transmembrane transport  1.842114e-13   \n",
       "4981                      Pex17p-Pex14p docking complex  1.873095e-09   \n",
       "4982                               melanosome transport  2.735314e-09   \n",
       "4983           establishment of melanosome localization  2.735314e-09   \n",
       "4984                                  protein targeting  4.483951e-09   \n",
       "4985                            melanosome localization  7.866372e-09   \n",
       "4986                          pigment granule transport  1.288762e-08   \n",
       "4987                    intracellular protein transport  2.020314e-08   \n",
       "4988            protein import into peroxisome membrane  2.282661e-08   \n",
       "4989                     peroxisomal importomer complex  3.824290e-08   \n",
       "4990                            intracellular transport  9.166820e-08   \n",
       "4991                                             BBSome  1.110540e-07   \n",
       "4992      establishment of pigment granule localization  2.483481e-07   \n",
       "4993                  protein localization to organelle  3.668101e-07   \n",
       "4994                       pigment granule localization  5.097743e-07   \n",
       "4995                              cellular pigmentation  1.139999e-06   \n",
       "4996           integral component of organelle membrane  3.959531e-06   \n",
       "4997                     peroxisomal membrane transport  1.578920e-22   \n",
       "4998  establishment of protein localization to perox...  5.409479e-22   \n",
       "\n",
       "      p_uncorrected  \n",
       "3000   2.469179e-31  \n",
       "3001   2.469179e-31  \n",
       "3002   4.631883e-31  \n",
       "3003   6.312554e-31  \n",
       "3004   7.360425e-31  \n",
       "3005   7.360425e-31  \n",
       "3006   8.575409e-31  \n",
       "3007   9.983077e-31  \n",
       "3008   1.349802e-30  \n",
       "3009   1.349802e-30  \n",
       "3010   2.445233e-30  \n",
       "3011   3.276545e-30  \n",
       "3012   8.923563e-30  \n",
       "3013   8.388690e-29  \n",
       "3014   9.162394e-29  \n",
       "3015   1.850463e-28  \n",
       "3016   1.850463e-28  \n",
       "3017   5.240310e-28  \n",
       "3018   1.726866e-27  \n",
       "3019   2.451366e-27  \n",
       "3020   2.451366e-27  \n",
       "3021   3.465305e-27  \n",
       "3022   4.354870e-27  \n",
       "3023   2.832920e-26  \n",
       "3024   1.978660e-25  \n",
       "3025   2.812371e-25  \n",
       "3026   2.155995e-23  \n",
       "3027   4.421580e-23  \n",
       "3028   2.931690e-22  \n",
       "3029   4.911817e-22  \n",
       "...             ...  \n",
       "4969   8.986767e-25  \n",
       "4970   8.986767e-25  \n",
       "4971   1.708093e-24  \n",
       "4972   1.708093e-24  \n",
       "4973   1.747777e-21  \n",
       "4974   5.738972e-21  \n",
       "4975   7.344987e-20  \n",
       "4976   4.049061e-19  \n",
       "4977   8.224638e-19  \n",
       "4978   3.407661e-18  \n",
       "4979   3.407661e-18  \n",
       "4980   6.481751e-17  \n",
       "4981   6.590763e-13  \n",
       "4982   9.624611e-13  \n",
       "4983   9.624611e-13  \n",
       "4984   1.577745e-12  \n",
       "4985   2.767900e-12  \n",
       "4986   4.534703e-12  \n",
       "4987   7.108776e-12  \n",
       "4988   8.031884e-12  \n",
       "4989   1.345633e-11  \n",
       "4990   3.225482e-11  \n",
       "4991   3.907600e-11  \n",
       "4992   8.738497e-11  \n",
       "4993   1.290676e-10  \n",
       "4994   1.793717e-10  \n",
       "4995   4.011255e-10  \n",
       "4996   1.393220e-09  \n",
       "4997   5.164932e-26  \n",
       "4998   1.769538e-25  \n",
       "\n",
       "[1999 rows x 6 columns]"
      ]
     },
     "execution_count": 99,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "edf[3000:4999]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 98,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "11379"
      ]
     },
     "execution_count": 98,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(edf)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 100,
   "metadata": {},
   "outputs": [],
   "source": [
    "edf.to_csv('mondo-to-go-enr.tsv', sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 102,
   "metadata": {},
   "outputs": [],
   "source": [
    "edf = edf[['disease', 'disease label', 'c', 'n', 'p']]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 106,
   "metadata": {},
   "outputs": [],
   "source": [
    "df = edf.set_index('disease')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 104,
   "metadata": {},
   "outputs": [],
   "source": [
    "edf.to_csv('mondo-to-go-enr.tsv', sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 107,
   "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>disease label</th>\n",
       "      <th>c</th>\n",
       "      <th>n</th>\n",
       "      <th>p</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>disease</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>http://purl.obolibrary.org/obo/MONDO_0001639</th>\n",
       "      <td>deficiency anemia</td>\n",
       "      <td>GO:0006767</td>\n",
       "      <td>water-soluble vitamin metabolic process</td>\n",
       "      <td>3.352819e-09</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>http://purl.obolibrary.org/obo/MONDO_0001639</th>\n",
       "      <td>deficiency anemia</td>\n",
       "      <td>GO:0009235</td>\n",
       "      <td>cobalamin metabolic process</td>\n",
       "      <td>6.864751e-09</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>http://purl.obolibrary.org/obo/MONDO_0001639</th>\n",
       "      <td>deficiency anemia</td>\n",
       "      <td>GO:0031419</td>\n",
       "      <td>cobalamin binding</td>\n",
       "      <td>2.047286e-08</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>http://purl.obolibrary.org/obo/MONDO_0001639</th>\n",
       "      <td>deficiency anemia</td>\n",
       "      <td>GO:0019842</td>\n",
       "      <td>vitamin binding</td>\n",
       "      <td>2.959151e-06</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>http://purl.obolibrary.org/obo/MONDO_0000359</th>\n",
       "      <td>spondylocostal dysostosis</td>\n",
       "      <td>GO:0001756</td>\n",
       "      <td>somitogenesis</td>\n",
       "      <td>3.349297e-07</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                          disease label  \\\n",
       "disease                                                                   \n",
       "http://purl.obolibrary.org/obo/MONDO_0001639          deficiency anemia   \n",
       "http://purl.obolibrary.org/obo/MONDO_0001639          deficiency anemia   \n",
       "http://purl.obolibrary.org/obo/MONDO_0001639          deficiency anemia   \n",
       "http://purl.obolibrary.org/obo/MONDO_0001639          deficiency anemia   \n",
       "http://purl.obolibrary.org/obo/MONDO_0000359  spondylocostal dysostosis   \n",
       "\n",
       "                                                       c  \\\n",
       "disease                                                    \n",
       "http://purl.obolibrary.org/obo/MONDO_0001639  GO:0006767   \n",
       "http://purl.obolibrary.org/obo/MONDO_0001639  GO:0009235   \n",
       "http://purl.obolibrary.org/obo/MONDO_0001639  GO:0031419   \n",
       "http://purl.obolibrary.org/obo/MONDO_0001639  GO:0019842   \n",
       "http://purl.obolibrary.org/obo/MONDO_0000359  GO:0001756   \n",
       "\n",
       "                                                                                    n  \\\n",
       "disease                                                                                 \n",
       "http://purl.obolibrary.org/obo/MONDO_0001639  water-soluble vitamin metabolic process   \n",
       "http://purl.obolibrary.org/obo/MONDO_0001639              cobalamin metabolic process   \n",
       "http://purl.obolibrary.org/obo/MONDO_0001639                        cobalamin binding   \n",
       "http://purl.obolibrary.org/obo/MONDO_0001639                          vitamin binding   \n",
       "http://purl.obolibrary.org/obo/MONDO_0000359                            somitogenesis   \n",
       "\n",
       "                                                         p  \n",
       "disease                                                     \n",
       "http://purl.obolibrary.org/obo/MONDO_0001639  3.352819e-09  \n",
       "http://purl.obolibrary.org/obo/MONDO_0001639  6.864751e-09  \n",
       "http://purl.obolibrary.org/obo/MONDO_0001639  2.047286e-08  \n",
       "http://purl.obolibrary.org/obo/MONDO_0001639  2.959151e-06  \n",
       "http://purl.obolibrary.org/obo/MONDO_0000359  3.349297e-07  "
      ]
     },
     "execution_count": 107,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df[0:5]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 108,
   "metadata": {},
   "outputs": [],
   "source": [
    "df.to_csv('mondo-to-go-enr.tsv', sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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