descriptors.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import os\n",
    "import gzip\n",
    "import io\n",
    "import json\n",
    "\n",
    "import xml.etree.ElementTree as ET\n",
    "\n",
    "import networkx\n",
    "import pandas"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "#!wget --timestamping --directory-prefix download/ ftp://nlmpubs.nlm.nih.gov/online/mesh/.xmlmesh/desc2015.gz"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# Read MeSH xml release\n",
    "xml_path = os.path.join('download', 'desc2015.gz')\n",
    "with gzip.open(xml_path) as xml_file:\n",
    "    tree = ET.parse(xml_file)\n",
    "root = tree.getroot()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "# Extract mesh terms\n",
    "term_dicts = list()\n",
    "for descriptor in root:\n",
    "    for concept in descriptor.findall('ConceptList/Concept'):\n",
    "        for term in concept.findall('TermList/Term'):\n",
    "            term_dict = {\n",
    "                'DescriptorUI': descriptor.findtext('DescriptorUI'),\n",
    "                'ConceptUI': concept.findtext('ConceptUI'),\n",
    "                'TermUI': term.findtext('TermUI'),\n",
    "                'TermName': term.findtext('String')\n",
    "            }\n",
    "            term_dict.update(concept.attrib)\n",
    "            term_dict.update(term.attrib)\n",
    "            term_dicts.append(term_dict)\n",
    "\n",
    "columns = ['DescriptorUI', 'ConceptUI', 'PreferredConceptYN', 'TermUI', 'TermName',\n",
    "           'ConceptPreferredTermYN', 'IsPermutedTermYN', 'LexicalTag', 'PrintFlagYN', 'RecordPreferredTermYN']\n",
    "term_df = pandas.DataFrame(term_dicts)[columns]\n",
    "term_df.to_csv('data/descriptor-terms.tsv', index=False, sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Test whether MeSH term names are unique\n",
    "len(term_df) == len(set(term_df.TermName))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "# Parse MeSH xml release\n",
    "terms = list()\n",
    "\n",
    "for elem in root:\n",
    "    term = dict()\n",
    "    term['mesh_id'] = elem.findtext('DescriptorUI')\n",
    "    term['mesh_name'] = elem.findtext('DescriptorName/String')\n",
    "    term['semantic_types'] = list({x.text for x in elem.findall(\n",
    "        'ConceptList/Concept/SemanticTypeList/SemanticType/SemanticTypeUI')})\n",
    "    term['tree_numbers'] = [x.text for x in elem.findall('TreeNumberList/TreeNumber')]\n",
    "    terms.append(term)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "# Determine ontology parents\n",
    "tree_number_to_id = {tn: term['mesh_id'] for term in terms for tn in term['tree_numbers']}\n",
    "\n",
    "for term in terms:\n",
    "    parents = set()\n",
    "    for tree_number in term['tree_numbers']:\n",
    "        try:\n",
    "            parent_tn, self_tn = tree_number.rsplit('.', 1)\n",
    "            parents.add(tree_number_to_id[parent_tn])\n",
    "        except ValueError:\n",
    "            pass\n",
    "    term['parents'] = list(parents)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "path = os.path.join('data', 'mesh.json')\n",
    "with open(path, 'w') as write_file:\n",
    "    json.dump(terms, write_file, indent=2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "# Create a newtorkx directed graph represented mesh\n",
    "network = networkx.DiGraph()\n",
    "\n",
    "# add nodes\n",
    "for term in terms:\n",
    "    network.add_node(term['mesh_id'], name=term['mesh_name'])\n",
    "\n",
    "# add edges\n",
    "for term in terms:\n",
    "    for parent in term['parents']:\n",
    "        network.add_edge(parent, term['mesh_id'])\n",
    "\n",
    "assert networkx.is_directed_acyclic_graph(network)\n",
    "\n",
    "networkx.write_gexf(network, 'data/ontology.gexf.gz')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# Read mesh\n",
    "path = os.path.join('data', 'mesh.json')\n",
    "with open(path) as read_file:\n",
    "    mesh = json.load(read_file)\n",
    "\n",
    "mesh_df = pandas.DataFrame.from_dict(mesh)[['mesh_id', 'mesh_name']]\n",
    "mesh_df.to_csv('data/terms.tsv', sep='\\t', index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# Extract (mesh_id, mesh_tree_number) pairs\n",
    "rows = []\n",
    "for term in mesh:\n",
    "    mesh_id = term['mesh_id']\n",
    "    mesh_name = term['mesh_name']\n",
    "    for tree_number in term['tree_numbers']:\n",
    "        rows.append([mesh_id, mesh_name, tree_number])\n",
    "\n",
    "tn_df = pandas.DataFrame(rows, columns=['mesh_id', 'mesh_name', 'mesh_tree_number'])\n",
    "tn_df.to_csv('data/tree-numbers.tsv', sep='\\t', index=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Diseases"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 79,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def is_human_disease(tn):\n",
    "    \"\"\"Given a tree number, return whether the heirarchical path suggests a human disease.\"\"\"\n",
    "    # F03 (mental disorders)\n",
    "    if tn.startswith('F03'):\n",
    "        return True\n",
    "    # C01 though C21 and C24 -- C26\n",
    "    for i in list(range(1, 22)) + ['C24', 'C25', 'C26']:\n",
    "        if tn.startswith('C' + str(i).zfill(2)):\n",
    "            return True\n",
    "    # C23 exlcuding C23.888 (Symptoms and Signs)\n",
    "    if tn.startswith('C23') and not tn.startswith('C23.888'):\n",
    "        return True\n",
    "    return False"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 80,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "4501"
      ]
     },
     "execution_count": 80,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "diseases = {term['mesh_id'] for term in terms if any(map(is_human_disease, term['tree_numbers']))}\n",
    "len(diseases)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Symptoms"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 70,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# Read HSDN symptoms\n",
    "url = 'https://raw.githubusercontent.com/LABrueggs/HSDN/master/Symptom-Occurence-Output.tsv'\n",
    "hsdn_symptom_df = pandas.read_table(url, index_col=0)\n",
    "hsdn_symptoms = hsdn_symptom_df['MeSH Symptom ID']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 71,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "319"
      ]
     },
     "execution_count": 71,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# find MeSH symptoms\n",
    "symptoms = networkx.descendants(network, 'D012816') # signs and symptoms\n",
    "symptom_df = mesh_df[mesh_df.mesh_id.isin(symptoms)]\n",
    "pandas.options.mode.chained_assignment = None\n",
    "symptom_df['in_hsdn'] = symptom_df.mesh_id.isin(hsdn_symptoms).astype(int)\n",
    "symptom_df.to_csv('data/symptoms.tsv', index=False, sep='\\t')\n",
    "sum(symptom_df.in_hsdn)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Side Effects"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "side_effects = networkx.descendants(network, 'D064420') # Drug-Related Side Effects and Adverse Reactions\n",
    "side_effect_df = mesh_df[mesh_df.mesh_id.isin(side_effects)]\n",
    "len(side_effect_df)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 93,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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