tissues.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Compute anatomy-disease cooccurrence for Hetionet"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true,
    "jupyter": {
     "outputs_hidden": true
    }
   },
   "outputs": [],
   "source": [
    "import io\n",
    "import gzip\n",
    "\n",
    "import pandas\n",
    "import requests\n",
    "import networkx\n",
    "\n",
    "import eutility\n",
    "import cooccurrence"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Tissues"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false,
    "jupyter": {
     "outputs_hidden": false
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>uberon_id</th>\n",
       "      <th>uberon_name</th>\n",
       "      <th>mesh_id</th>\n",
       "      <th>mesh_name</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>UBERON:0001716</td>\n",
       "      <td>secondary palate</td>\n",
       "      <td>D010159</td>\n",
       "      <td>Palate</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>UBERON:0001908</td>\n",
       "      <td>optic tract</td>\n",
       "      <td>D014795</td>\n",
       "      <td>Visual Pathways</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>UBERON:0002286</td>\n",
       "      <td>third ventricle</td>\n",
       "      <td>D020542</td>\n",
       "      <td>Third Ventricle</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>UBERON:0002349</td>\n",
       "      <td>myocardium</td>\n",
       "      <td>D009206</td>\n",
       "      <td>Myocardium</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>UBERON:0000978</td>\n",
       "      <td>leg</td>\n",
       "      <td>D035002</td>\n",
       "      <td>Lower Extremity</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        uberon_id       uberon_name  mesh_id        mesh_name\n",
       "0  UBERON:0001716  secondary palate  D010159           Palate\n",
       "1  UBERON:0001908       optic tract  D014795  Visual Pathways\n",
       "2  UBERON:0002286   third ventricle  D020542  Third Ventricle\n",
       "3  UBERON:0002349        myocardium  D009206       Myocardium\n",
       "4  UBERON:0000978               leg  D035002  Lower Extremity"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Read MeSH UBERON Anatomical structures\n",
    "url = 'https://raw.githubusercontent.com/dhimmel/uberon/86a9b754871e5ce7d91d2ef15bcc8f6a0ef6cda1/data/hetio-slim.tsv'\n",
    "uberon_df = pandas.read_table(url)\n",
    "uberon_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false,
    "jupyter": {
     "outputs_hidden": false
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "9284 articles for Palate\n",
      "15786 articles for Visual Pathways\n",
      "1359 articles for Third Ventricle\n",
      "139687 articles for Myocardium\n",
      "8596 articles for Lower Extremity\n",
      "39066 articles for Cerebellum\n",
      "2471 articles for Arachnoid\n",
      "382125 articles for Liver\n",
      "3960 articles for Dermis\n",
      "3295 articles for Sweat\n",
      "16125 articles for Optic Nerve\n",
      "13305 articles for Gallbladder\n",
      "11676 articles for Parotid Gland\n",
      "265 articles for Manubrium\n",
      "6438 articles for Vena Cava, Superior\n",
      "47991 articles for Arteries\n",
      "26790 articles for Arm\n",
      "28944 articles for Aorta, Thoracic\n",
      "60440 articles for Pancreas\n",
      "16194 articles for Mesencephalon\n",
      "9469 articles for Common Bile Duct\n",
      "4456 articles for Choroid Plexus\n",
      "5769 articles for Nails\n",
      "13016 articles for Joints\n",
      "399 articles for Bulbourethral Glands\n",
      "158666 articles for Skin\n",
      "530 articles for Incus\n",
      "14579 articles for Forearm\n",
      "8129 articles for Trigeminal Nerve\n",
      "1167 articles for Axillary Vein\n",
      "3943 articles for Peroneal Nerve\n",
      "465 articles for Stapedius\n",
      "20418 articles for Vagus Nerve\n",
      "24984 articles for Femoral Artery\n",
      "7003 articles for Ligaments\n",
      "19976 articles for Extremities\n",
      "7780 articles for Thumb\n",
      "32275 articles for Trachea\n",
      "4117 articles for Subclavian Vein\n",
      "11826 articles for Iris\n",
      "5612 articles for Epiphyses\n",
      "5318 articles for Hemolymph\n",
      "13982 articles for Wrist\n",
      "2056 articles for Sense Organs\n",
      "3271 articles for Sweat Glands\n",
      "2276 articles for Axillary Artery\n",
      "6069 articles for Basilar Artery\n",
      "12065 articles for Lymphoid Tissue\n",
      "16279 articles for Medulla Oblongata\n",
      "7256 articles for Gonads\n",
      "15748 articles for Penis\n",
      "33282 articles for Heart Atria\n",
      "1138 articles for Basilar Membrane\n",
      "212 articles for Zona Reticularis\n",
      "7331 articles for Femoral Vein\n",
      "15273 articles for Tongue\n",
      "9959 articles for Tunica Intima\n",
      "7380 articles for Seminal Vesicles\n",
      "17376 articles for Mouth\n",
      "16444 articles for Thoracic Vertebrae\n",
      "3420 articles for Semicircular Canals\n",
      "754 articles for Ulnar Artery\n",
      "1692 articles for Cranial Sutures\n",
      "12999 articles for Carotid Artery, Internal\n",
      "17868 articles for Cardiovascular System\n",
      "8207 articles for Vertebral Artery\n",
      "7214 articles for Papillary Muscles\n",
      "1566 articles for Palate, Hard\n",
      "11061 articles for Ankle Joint\n",
      "1838 articles for Ethmoid Bone\n",
      "4409 articles for Locus Coeruleus\n",
      "415 articles for Malleus\n",
      "138163 articles for Muscles\n",
      "24440 articles for Maxilla\n",
      "3333 articles for Sebaceous Glands\n",
      "5278 articles for Ganglia, Autonomic\n",
      "1753 articles for Uvea\n",
      "2250 articles for Pia Mater\n",
      "313 articles for Oval Window, Ear\n",
      "62855 articles for Retina\n",
      "2802 articles for Purkinje Fibers\n",
      "10795 articles for Ear, External\n",
      "7283 articles for Prosencephalon\n",
      "15487 articles for Head\n",
      "10011 articles for Submandibular Gland\n",
      "45 articles for Metencephalon\n",
      "11258 articles for Pulmonary Veins\n",
      "4959 articles for Neck Muscles\n",
      "4934 articles for Decidua\n",
      "1974 articles for Loop of Henle\n",
      "2487 articles for Zygoma\n",
      "2774 articles for Intestinal Secretions\n",
      "1151 articles for Eyelashes\n",
      "2388 articles for Brachiocephalic Trunk\n",
      "12103 articles for Umbilical Veins\n",
      "60128 articles for Testis\n",
      "22830 articles for Pulmonary Alveoli\n",
      "28862 articles for Skull\n",
      "368 articles for Geniculate Ganglion\n",
      "1560 articles for Cochlear Nucleus\n",
      "7456 articles for Ganglia\n",
      "53374 articles for Uterus\n",
      "5274 articles for Umbilical Arteries\n",
      "2980 articles for Ethmoid Sinus\n",
      "2110 articles for Stellate Ganglion\n",
      "3345 articles for Palate, Soft\n",
      "5092 articles for Scapula\n",
      "8415 articles for Median Nerve\n",
      "816 articles for Maxillary Artery\n",
      "50886 articles for Thyroid Gland\n",
      "70886 articles for Lymph Nodes\n",
      "9377 articles for Elbow Joint\n",
      "3943 articles for Nipples\n",
      "6072 articles for Atrioventricular Node\n",
      "594 articles for Anterior Cerebral Artery\n",
      "3299 articles for Skull Base\n",
      "38733 articles for Mandible\n",
      "38733 articles for Mandible\n",
      "8666 articles for Endocrine Glands\n",
      "13807 articles for Immune System\n",
      "444 articles for Vestibular Aqueduct\n",
      "22218 articles for Cartilage\n",
      "70968 articles for Spinal Cord\n",
      "2860 articles for Radial Nerve\n",
      "7956 articles for Vas Deferens\n",
      "4298 articles for Vestibulocochlear Nerve\n",
      "1018 articles for Sternoclavicular Joint\n",
      "17244 articles for Mammary Glands, Animal\n",
      "2818 articles for Exocrine Glands\n",
      "3322 articles for Fovea Centralis\n",
      "18490 articles for Aorta, Abdominal\n",
      "3535 articles for Endocrine System\n",
      "4302 articles for Ear Canal\n",
      "848 articles for Bile Canaliculi\n",
      "430 articles for Cochlear Duct\n",
      "49555 articles for Muscle, Smooth\n",
      "23210 articles for Endometrium\n",
      "882 articles for Acromion\n",
      "6664 articles for Lacrimal Apparatus\n",
      "39662 articles for Pulmonary Artery\n",
      "20823 articles for Foot\n",
      "1819 articles for Olfactory Nerve\n",
      "1000 articles for Medial Forebrain Bundle\n",
      "10831 articles for Parathyroid Glands\n",
      "11571 articles for Bile Ducts\n",
      "23513 articles for Neck\n",
      "72662 articles for Bone and Bones\n",
      "2449 articles for Nasal Bone\n",
      "6464 articles for Kidney Medulla\n",
      "5374 articles for Hepatic Veins\n",
      "3782 articles for Masseter Muscle\n",
      "121682 articles for Heart\n",
      "4958 articles for Endothelium, Corneal\n",
      "3739 articles for Tibial Nerve\n",
      "7079 articles for Tears\n",
      "18399 articles for Gastric Juice\n",
      "2475 articles for Musculoskeletal System\n",
      "3679 articles for Hematopoietic System\n",
      "4587 articles for Elastic Tissue\n",
      "1078 articles for Stapes\n",
      "856 articles for Zona Glomerulosa\n",
      "12726 articles for Pericardium\n",
      "7595 articles for Arterioles\n",
      "3811 articles for Myenteric Plexus\n",
      "2157 articles for Enteric Nervous System\n",
      "905 articles for Celiac Plexus\n",
      "21094 articles for Ureter\n",
      "4224 articles for Pulmonary Valve\n",
      "6662 articles for Pyramidal Tracts\n",
      "10362 articles for Kidney Cortex\n",
      "15782 articles for Renal Artery\n",
      "2332 articles for Petrous Bone\n",
      "66514 articles for Epithelium\n",
      "20764 articles for Hair\n",
      "2413 articles for Ophthalmic Artery\n",
      "10484 articles for Fallopian Tubes\n",
      "272 articles for Endolymphatic Duct\n",
      "4235 articles for Epithelium, Corneal\n",
      "10160 articles for Pons\n",
      "1674 articles for Bronchial Arteries\n",
      "5314 articles for Colostrum\n",
      "868 articles for Neuropil\n",
      "21982 articles for Digestive System\n",
      "11662 articles for Eyelids\n",
      "2474 articles for Lumbosacral Plexus\n",
      "158 articles for Truncus Arteriosus\n",
      "7471 articles for Macula Lutea\n",
      "13490 articles for Salivary Glands\n",
      "14568 articles for Elbow\n",
      "222 articles for Acoustic Maculae\n",
      "1188 articles for Sebum\n",
      "41482 articles for Pituitary Gland\n",
      "2389 articles for Femoral Nerve\n",
      "6717 articles for Renal Veins\n",
      "6673 articles for Subclavian Artery\n",
      "3161 articles for Trigeminal Ganglion\n",
      "42968 articles for Embryo, Mammalian\n",
      "18090 articles for Endothelium\n",
      "18347 articles for Portal Vein\n",
      "4601 articles for Clavicle\n",
      "50256 articles for Blood\n",
      "1219 articles for Zygapophyseal Joint\n",
      "1882 articles for Retinal Vein\n",
      "20645 articles for Urethra\n",
      "11286 articles for Synovial Fluid\n",
      "28147 articles for Cervical Vertebrae\n",
      "39275 articles for Central Nervous System\n",
      "887 articles for Sesamoid Bones\n",
      "1766 articles for Otolithic Membrane\n",
      "29346 articles for Prostate\n",
      "8731 articles for Brachial Artery\n",
      "6440 articles for Facial Muscles\n",
      "2580 articles for Cerebellar Nuclei\n",
      "486 articles for Ejaculatory Ducts\n",
      "1676 articles for Nasolacrimal Duct\n",
      "1035 articles for Round Window, Ear\n",
      "67285 articles for Heart Ventricles\n",
      "12568 articles for Ear, Middle\n",
      "20945 articles for Autonomic Nervous System\n",
      "1193 articles for Serous Membrane\n",
      "3208 articles for Cranial Nerves\n",
      "777 articles for Trochlear Nerve\n",
      "2901 articles for Occipital Bone\n",
      "5188 articles for Carotid Artery, Common\n",
      "5890 articles for Paranasal Sinuses\n",
      "2866 articles for Oculomotor Nerve\n",
      "2574 articles for Hepatic Duct, Common\n",
      "11292 articles for Ear, Inner\n",
      "2976 articles for Peripheral Nervous System\n",
      "28343 articles for Hindlimb\n",
      "3319 articles for Sacroiliac Joint\n",
      "7290 articles for Perineum\n",
      "700 articles for Cerumen\n",
      "7040 articles for Tricuspid Valve\n",
      "3474 articles for Seminiferous Tubules\n",
      "14570 articles for Vena Cava, Inferior\n",
      "21373 articles for Tendons\n",
      "3202 articles for Optic Chiasm\n",
      "8320 articles for Parasympathetic Nervous System\n",
      "2226 articles for Follicular Fluid\n",
      "4265 articles for Nephrons\n",
      "9982 articles for Hip\n",
      "8989 articles for Dura Mater\n",
      "33485 articles for Saliva\n",
      "4545 articles for Hair Follicle\n",
      "8669 articles for Kidney Pelvis\n",
      "253 articles for Ultimobranchial Body\n",
      "24382 articles for Cervix Uteri\n",
      "480 articles for Internal Capsule\n",
      "3271 articles for Vestibular Nuclei\n",
      "29115 articles for Eye\n",
      "3742 articles for Celiac Artery\n",
      "8402 articles for Pleura\n",
      "5731 articles for Sinoatrial Node\n",
      "1892 articles for Chromaffin Cells\n",
      "15068 articles for Synovial Membrane\n",
      "715 articles for Spinothalamic Tracts\n",
      "218 articles for Tensor Tympani\n",
      "7331 articles for Reticular Formation\n",
      "56200 articles for Ovary\n",
      "5004 articles for Cerebellar Cortex\n",
      "1606 articles for Trigeminal Nuclei\n",
      "2947 articles for Retinal Artery\n",
      "10206 articles for Shoulder\n",
      "7475 articles for Pancreatic Ducts\n",
      "19257 articles for Epidermis\n",
      "8584 articles for Maxillary Sinus\n",
      "18673 articles for Basement Membrane\n",
      "9330 articles for Nasal Cavity\n",
      "39454 articles for Cornea\n",
      "14737 articles for Respiratory System\n",
      "9830 articles for Temporal Bone\n",
      "10127 articles for Corpus Luteum\n",
      "1571 articles for Superior Cervical Ganglion\n",
      "32909 articles for Face\n",
      "6536 articles for Cheek\n",
      "11521 articles for Hepatic Artery\n",
      "35393 articles for Sympathetic Nervous System\n",
      "391093 articles for Brain\n",
      "16739 articles for Semen\n",
      "8922 articles for Sclera\n",
      "3358 articles for Frontal Sinus\n",
      "5619 articles for Biliary Tract\n",
      "5184 articles for Endocardium\n",
      "892 articles for Meibomian Glands\n",
      "118 articles for Diagonal Band of Broca\n",
      "1575 articles for Intercostal Muscles\n",
      "3514 articles for Sphenoid Bone\n",
      "10040 articles for Genitalia, Female\n",
      "1235 articles for Skeleton\n",
      "429 articles for Scala Tympani\n",
      "29363 articles for Blood Vessels\n",
      "9860 articles for Aqueous Humor\n",
      "33165 articles for Islets of Langerhans\n",
      "161 articles for Para-Aortic Bodies\n",
      "9149 articles for Ribs\n",
      "21783 articles for Hip Joint\n",
      "17297 articles for Sciatic Nerve\n",
      "5419 articles for Spinal Nerves\n",
      "23545 articles for Bile\n",
      "18713 articles for Nose\n",
      "14785 articles for Orbit\n",
      "1947 articles for Glossopharyngeal Nerve\n",
      "2651 articles for Turbinates\n",
      "1034 articles for Diaphyses\n",
      "7338 articles for Jaw\n",
      "23702 articles for Spine\n",
      "12877 articles for Adrenal Cortex\n",
      "7442 articles for Ciliary Body\n",
      "40260 articles for Adrenal Glands\n",
      "1439 articles for Azygos Vein\n",
      "3276 articles for Bundle of His\n",
      "8269 articles for Popliteal Artery\n",
      "823 articles for Stria Vascularis\n",
      "34461 articles for Urine\n",
      "4302 articles for Corneal Stroma\n",
      "23289 articles for Aortic Valve\n",
      "200 articles for Area Postrema\n",
      "387 articles for Neurilemma\n",
      "1886 articles for Axis\n",
      "932 articles for Salivary Ducts\n",
      "17828 articles for Diaphragm\n",
      "181304 articles for Lung\n",
      "2212 articles for Carotid Artery, External\n",
      "3792 articles for Oviducts\n",
      "9569 articles for Growth Plate\n",
      "8384 articles for Facial Nerve\n",
      "50094 articles for Knee\n",
      "4815 articles for Meninges\n",
      "4618 articles for Periosteum\n",
      "27105 articles for Veins\n",
      "7875 articles for Forelimb\n",
      "656 articles for Fourth Ventricle\n",
      "2817 articles for Mesenteric Artery, Superior\n",
      "1790 articles for Abducens Nerve\n",
      "24297 articles for Mitral Valve\n",
      "5586 articles for Telencephalon\n",
      "839 articles for Accessory Nerve\n",
      "1563 articles for Saccule and Utricle\n",
      "4045 articles for Vulva\n",
      "7473 articles for Brachial Plexus\n",
      "1133 articles for Endolymphatic Sac\n",
      "1710 articles for Hyoid Bone\n",
      "693 articles for Trigeminal Nucleus, Spinal\n",
      "234281 articles for Kidney\n",
      "14926 articles for Plasma\n",
      "20874 articles for Peripheral Nerves\n",
      "19503 articles for Nervous System\n",
      "2910 articles for Sphenoid Sinus\n",
      "398 articles for Mesenteric Artery, Inferior\n",
      "1316 articles for Sublingual Gland\n",
      "8982 articles for Ear\n",
      "5827 articles for Adipose Tissue, Brown\n",
      "6326 articles for Ulnar Nerve\n",
      "28976 articles for Brain Stem\n",
      "7950 articles for Pupil\n",
      "25665 articles for Fingers\n",
      "7456 articles for Heart Septum\n",
      "2905 articles for Hypoglossal Nerve\n",
      "11207 articles for Pineal Gland\n",
      "7808 articles for Optic Disk\n",
      "4657 articles for Cochlear Nerve\n",
      "7849 articles for Sternum\n",
      "3487 articles for Splenic Artery\n",
      "2059 articles for Juxtaglomerular Apparatus\n",
      "7755 articles for Scrotum\n",
      "14802 articles for Shoulder Joint\n",
      "1622 articles for Joint Capsule\n",
      "37166 articles for Bronchi\n",
      "34463 articles for Hand\n",
      "29131 articles for Vagina\n",
      "39872 articles for Knee Joint\n",
      "13964 articles for Larynx\n",
      "529 articles for Posterior Cerebral Artery\n",
      "3832 articles for Kidney Tubules, Collecting\n",
      "4097 articles for Tunica Media\n",
      "415 articles for Zona Fasciculata\n",
      "9454 articles for Choroid\n",
      "6330 articles for Myometrium\n",
      "1541 articles for Uvula\n",
      "1377 articles for Clitoris\n",
      "2054 articles for Temporal Muscle\n",
      "4811 articles for Heart Valves\n",
      "21040 articles for Kidney Tubules\n",
      "4609 articles for Radial Artery\n",
      "3766 articles for Middle Cerebral Artery\n",
      "8773 articles for Lip\n",
      "58594 articles for Bone Marrow\n",
      "63407 articles for Adipose Tissue\n",
      "9228 articles for Abdominal Muscles\n",
      "1739 articles for Rectus Abdominis\n",
      "40413 articles for Lumbar Vertebrae\n",
      "4744 articles for Glottis\n",
      "2472 articles for Rhombencephalon\n",
      "15689 articles for Ovarian Follicle\n",
      "72824 articles for Feces\n",
      "6049 articles for Phrenic Nerve\n",
      "25711 articles for Cochlea\n",
      "19935 articles for Connective Tissue\n",
      "1666 articles for Popliteal Vein\n",
      "1473 articles for Lateral Ventricles\n",
      "6089 articles for Urinary Tract\n"
     ]
    }
   ],
   "source": [
    "rows_out = list()\n",
    "\n",
    "for i, row in uberon_df.iterrows():\n",
    "    term_query = '{tissue}[MeSH Terms:noexp]'.format(tissue = row.mesh_name.lower())\n",
    "    payload = {'db': 'pubmed', 'term': term_query}\n",
    "    pmids = eutility.esearch_query(payload, retmax = 5000, sleep=2)\n",
    "    row['term_query'] = term_query\n",
    "    row['n_articles'] = len(pmids)\n",
    "    row['pubmed_ids'] = '|'.join(pmids)\n",
    "    rows_out.append(row)\n",
    "    print('{} articles for {}'.format(len(pmids), row.mesh_name))\n",
    "\n",
    "uberon_pmids_df = pandas.DataFrame(rows_out)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false,
    "jupyter": {
     "outputs_hidden": false
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>uberon_id</th>\n",
       "      <th>uberon_name</th>\n",
       "      <th>mesh_id</th>\n",
       "      <th>mesh_name</th>\n",
       "      <th>term_query</th>\n",
       "      <th>n_articles</th>\n",
       "      <th>pubmed_ids</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>UBERON:0001716</td>\n",
       "      <td>secondary palate</td>\n",
       "      <td>D010159</td>\n",
       "      <td>Palate</td>\n",
       "      <td>palate[MeSH Terms:noexp]</td>\n",
       "      <td>9284</td>\n",
       "      <td>26023113|25975064|25895319|25872295|25869559|2...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>UBERON:0001908</td>\n",
       "      <td>optic tract</td>\n",
       "      <td>D014795</td>\n",
       "      <td>Visual Pathways</td>\n",
       "      <td>visual pathways[MeSH Terms:noexp]</td>\n",
       "      <td>15786</td>\n",
       "      <td>26113723|26089513|26080589|26080584|25972183|2...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>UBERON:0002286</td>\n",
       "      <td>third ventricle</td>\n",
       "      <td>D020542</td>\n",
       "      <td>Third Ventricle</td>\n",
       "      <td>third ventricle[MeSH Terms:noexp]</td>\n",
       "      <td>1359</td>\n",
       "      <td>26120619|26023696|25723723|25723303|25723298|2...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>UBERON:0002349</td>\n",
       "      <td>myocardium</td>\n",
       "      <td>D009206</td>\n",
       "      <td>Myocardium</td>\n",
       "      <td>myocardium[MeSH Terms:noexp]</td>\n",
       "      <td>139687</td>\n",
       "      <td>26072537|26062198|26040042|26040041|26039915|2...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>UBERON:0000978</td>\n",
       "      <td>leg</td>\n",
       "      <td>D035002</td>\n",
       "      <td>Lower Extremity</td>\n",
       "      <td>lower extremity[MeSH Terms:noexp]</td>\n",
       "      <td>8596</td>\n",
       "      <td>26118216|26072540|26062181|26047150|26047149|2...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        uberon_id       uberon_name  mesh_id        mesh_name  \\\n",
       "0  UBERON:0001716  secondary palate  D010159           Palate   \n",
       "1  UBERON:0001908       optic tract  D014795  Visual Pathways   \n",
       "2  UBERON:0002286   third ventricle  D020542  Third Ventricle   \n",
       "3  UBERON:0002349        myocardium  D009206       Myocardium   \n",
       "4  UBERON:0000978               leg  D035002  Lower Extremity   \n",
       "\n",
       "                          term_query  n_articles  \\\n",
       "0           palate[MeSH Terms:noexp]        9284   \n",
       "1  visual pathways[MeSH Terms:noexp]       15786   \n",
       "2  third ventricle[MeSH Terms:noexp]        1359   \n",
       "3       myocardium[MeSH Terms:noexp]      139687   \n",
       "4  lower extremity[MeSH Terms:noexp]        8596   \n",
       "\n",
       "                                          pubmed_ids  \n",
       "0  26023113|25975064|25895319|25872295|25869559|2...  \n",
       "1  26113723|26089513|26080589|26080584|25972183|2...  \n",
       "2  26120619|26023696|25723723|25723303|25723298|2...  \n",
       "3  26072537|26062198|26040042|26040041|26039915|2...  \n",
       "4  26118216|26072540|26062181|26047150|26047149|2...  "
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "with gzip.open('data/uberon-pmids.tsv.gz', 'w') as write_file:\n",
    "    write_file = io.TextIOWrapper(write_file)\n",
    "    uberon_pmids_df.to_csv(write_file, sep='\\t', index=False)\n",
    "\n",
    "uberon_pmids_df.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Tissue-Disease Cooccurrence"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false,
    "jupyter": {
     "outputs_hidden": false
    }
   },
   "outputs": [],
   "source": [
    "uberon_df, uberon_to_pmids = cooccurrence.read_pmids_tsv('data/uberon-pmids.tsv.gz', key='uberon_id')\n",
    "disease_df, disease_to_pmids = cooccurrence.read_pmids_tsv('data/disease-pmids.tsv.gz', key='doid_code')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false,
    "jupyter": {
     "outputs_hidden": false
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Total articles containing a doid_code: 3686312\n",
      "Total articles containing a uberon_id: 4697277\n",
      "Total articles containing both a doid_code and uberon_id: 696252\n",
      "\n",
      "After removing terms without any cooccurences:\n",
      "+ 133 doid_codes remain\n",
      "+ 401 uberon_ids remain\n",
      "\n",
      "Cooccurrence scores calculated for 53333 doid_code -- uberon_id pairs\n"
     ]
    }
   ],
   "source": [
    "cooc_df = cooccurrence.score_pmid_cooccurrence(disease_to_pmids, uberon_to_pmids, 'doid_code', 'uberon_id')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false,
    "jupyter": {
     "outputs_hidden": false
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>doid_code</th>\n",
       "      <th>doid_name</th>\n",
       "      <th>uberon_id</th>\n",
       "      <th>uberon_name</th>\n",
       "      <th>cooccurrence</th>\n",
       "      <th>expected</th>\n",
       "      <th>enrichment</th>\n",
       "      <th>odds_ratio</th>\n",
       "      <th>p_fisher</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>28748</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0000955</td>\n",
       "      <td>brain</td>\n",
       "      <td>11209</td>\n",
       "      <td>1182.634069</td>\n",
       "      <td>9.477995</td>\n",
       "      <td>74.210761</td>\n",
       "      <td>0.000000e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28553</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0001890</td>\n",
       "      <td>forebrain</td>\n",
       "      <td>114</td>\n",
       "      <td>7.326350</td>\n",
       "      <td>15.560272</td>\n",
       "      <td>21.733764</td>\n",
       "      <td>5.971023e-99</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28476</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0002037</td>\n",
       "      <td>cerebellum</td>\n",
       "      <td>303</td>\n",
       "      <td>86.548368</td>\n",
       "      <td>3.500933</td>\n",
       "      <td>3.740149</td>\n",
       "      <td>3.504584e-76</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28541</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0002148</td>\n",
       "      <td>locus ceruleus</td>\n",
       "      <td>97</td>\n",
       "      <td>8.450598</td>\n",
       "      <td>11.478477</td>\n",
       "      <td>14.449700</td>\n",
       "      <td>1.183699e-70</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28708</th>\n",
       "      <td>DOID:10652</td>\n",
       "      <td>Alzheimer's disease</td>\n",
       "      <td>UBERON:0000011</td>\n",
       "      <td>parasympathetic nervous system</td>\n",
       "      <td>103</td>\n",
       "      <td>14.727650</td>\n",
       "      <td>6.993648</td>\n",
       "      <td>7.952412</td>\n",
       "      <td>3.985211e-53</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        doid_code            doid_name       uberon_id  \\\n",
       "28748  DOID:10652  Alzheimer's disease  UBERON:0000955   \n",
       "28553  DOID:10652  Alzheimer's disease  UBERON:0001890   \n",
       "28476  DOID:10652  Alzheimer's disease  UBERON:0002037   \n",
       "28541  DOID:10652  Alzheimer's disease  UBERON:0002148   \n",
       "28708  DOID:10652  Alzheimer's disease  UBERON:0000011   \n",
       "\n",
       "                          uberon_name  cooccurrence     expected  enrichment  \\\n",
       "28748                           brain         11209  1182.634069    9.477995   \n",
       "28553                       forebrain           114     7.326350   15.560272   \n",
       "28476                      cerebellum           303    86.548368    3.500933   \n",
       "28541                  locus ceruleus            97     8.450598   11.478477   \n",
       "28708  parasympathetic nervous system           103    14.727650    6.993648   \n",
       "\n",
       "       odds_ratio      p_fisher  \n",
       "28748   74.210761  0.000000e+00  \n",
       "28553   21.733764  5.971023e-99  \n",
       "28476    3.740149  3.504584e-76  \n",
       "28541   14.449700  1.183699e-70  \n",
       "28708    7.952412  3.985211e-53  "
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cooc_df = uberon_df[['uberon_id', 'uberon_name']].drop_duplicates().merge(cooc_df)\n",
    "cooc_df = disease_df[['doid_code', 'doid_name']].drop_duplicates().merge(cooc_df)\n",
    "cooc_df = cooc_df.sort_values(by=['doid_name', 'p_fisher'])\n",
    "cooc_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": true,
    "jupyter": {
     "outputs_hidden": true
    }
   },
   "outputs": [],
   "source": [
    "cooc_df.to_csv('data/disease-uberon-cooccurrence.tsv', index=False, sep='\\t')"
   ]
  }
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