retrieve-tags.ipynb

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   "cell_type": "code",
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   "source": [
    "import pandas\n",
    "import psycopg2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
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   "source": [
    "# Read database connection info\n",
    "with open('dsn.txt') as read_file:\n",
    "    dsn = read_file.read()\n",
    "\n",
    "# Connect to database\n",
    "con = psycopg2.connect(dsn)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
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   "outputs": [],
   "source": [
    "# Retreive and save all tags\n",
    "tag_df = pandas.read_sql('SELECT * FROM tag', con)\n",
    "tag_df.to_csv('download/tag.tsv', sep='\\t', index=False)"
   ]
  },
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   "cell_type": "code",
   "execution_count": 4,
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   "outputs": [],
   "source": [
    "# # Retreive DO slim diseases and subsumed diseases\n",
    "# url = 'https://raw.githubusercontent.com/dhimmel/disease-ontology/72614ade9f1cc5a5317b8f6836e1e464b31d5587/data/slim-terms-prop.tsv'\n",
    "# do_df = pandas.read_table(url).rename(columns={'subsumed_id': 'doid_id', 'subsumed_name': 'doid_name'})\n",
    "# do_df = do_df[['doid_id', 'doid_name', 'min_distance']].sort(['min_distance', 'doid_name'])\n",
    "# do_df = do_df.drop_duplicates(['doid_id', 'doid_name'])\n",
    "# do_df.to_csv('download/disease-ontology-terms.tsv', sep='\\t', index=False)\n",
    "# do_df.head()"
   ]
  }
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