{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": 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": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": []
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Tissues"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"
\n",
"
\n",
" \n",
" \n",
" | \n",
" uberon_id | \n",
" uberon_name | \n",
" mesh_tree_number | \n",
" mesh_id | \n",
" mesh_name | \n",
"
\n",
" \n",
" \n",
" \n",
" 0 | \n",
" UBERON:0001577 | \n",
" facial muscle | \n",
" A02.633.567.400 | \n",
" D005152 | \n",
" Facial Muscles | \n",
"
\n",
" \n",
" 1 | \n",
" UBERON:0001681 | \n",
" nasal bone | \n",
" A02.835.232.781.324.665 | \n",
" D009295 | \n",
" Nasal Bone | \n",
"
\n",
" \n",
" 2 | \n",
" UBERON:0001264 | \n",
" pancreas | \n",
" A03.734 | \n",
" D010179 | \n",
" Pancreas | \n",
"
\n",
" \n",
" 3 | \n",
" UBERON:0002356 | \n",
" perineum | \n",
" A01.719 | \n",
" D010502 | \n",
" Perineum | \n",
"
\n",
" \n",
" 4 | \n",
" UBERON:0001688 | \n",
" incus bone | \n",
" A09.246.397.247.362 | \n",
" D007188 | \n",
" Incus | \n",
"
\n",
" \n",
"
\n",
"
"
],
"text/plain": [
" uberon_id uberon_name mesh_tree_number mesh_id \\\n",
"0 UBERON:0001577 facial muscle A02.633.567.400 D005152 \n",
"1 UBERON:0001681 nasal bone A02.835.232.781.324.665 D009295 \n",
"2 UBERON:0001264 pancreas A03.734 D010179 \n",
"3 UBERON:0002356 perineum A01.719 D010502 \n",
"4 UBERON:0001688 incus bone A09.246.397.247.362 D007188 \n",
"\n",
" mesh_name \n",
"0 Facial Muscles \n",
"1 Nasal Bone \n",
"2 Pancreas \n",
"3 Perineum \n",
"4 Incus "
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# Read MeSH UBERON Anatomical structures\n",
"url = 'https://raw.githubusercontent.com/dhimmel/uberon/7de0ed6238c26ea82accae6fc57accd1b845111d/data/mesh-map.tsv'\n",
"uberon_df = pandas.read_table(url)\n",
"uberon_df.head()"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"6400 articles for Facial Muscles\n",
"2401 articles for Nasal Bone\n",
"60200 articles for Pancreas\n",
"7214 articles for Perineum\n",
"527 articles for Incus\n",
"3083 articles for Chromaffin System\n",
"7501 articles for Pressoreceptors\n",
"4298 articles for Vestibulocochlear Nerve\n",
"8645 articles for Kidney Pelvis\n",
"841 articles for Epigastric Arteries\n",
"46609 articles for Muscle, Smooth, Vascular\n",
"2461 articles for Vibrissae\n",
"11188 articles for Pineal Gland\n",
"26993 articles for Veins\n",
"764 articles for Meningeal Arteries\n",
"180254 articles for Lung\n",
"328 articles for Comb and Wattles\n",
"9237 articles for Palate\n",
"2849 articles for Mandibular Nerve\n",
"1324 articles for Brachiocephalic Veins\n",
"4018 articles for Vulva\n",
"2186 articles for Splenic Vein\n",
"23061 articles for Aortic Valve\n",
"7307 articles for Femoral Vein\n",
"595 articles for Beak\n",
"32153 articles for Trachea\n",
"9315 articles for Exudates and Transudates\n",
"9315 articles for Exudates and Transudates\n",
"6947 articles for Ligaments\n",
"2008 articles for Cisterna Magna\n",
"1592 articles for Circle of Willis\n",
"19116 articles for Epidermis\n",
"1552 articles for Descemet Membrane\n",
"59875 articles for Testis\n",
"1486 articles for Spiral Ganglion\n",
"9307 articles for Pigment Epithelium of Eye\n",
"7200 articles for Gonads\n",
"6079 articles for Tail\n",
"2241 articles for Pia Mater\n",
"4572 articles for Elastic Tissue\n",
"8941 articles for Ear\n",
"1132 articles for Basilar Membrane\n",
"3310 articles for Feathers\n",
"11958 articles for Blastocyst\n",
"782 articles for Laryngeal Mucosa\n",
"1607 articles for Joint Capsule\n",
"1650 articles for Chordae Tendineae\n",
"674 articles for Ophthalmic Nerve\n",
"7327 articles for Reticular Formation\n",
"3453 articles for Nerve Tissue\n",
"4803 articles for Meninges\n",
"1878 articles for Chromaffin Cells\n",
"2336 articles for Splanchnic Nerves\n",
"429 articles for Cochlear Duct\n",
"3331 articles for Frontal Sinus\n",
"19871 articles for Extremities\n",
"1311 articles for Sublingual Gland\n",
"810 articles for Maxillary Artery\n",
"6633 articles for Lacrimal Apparatus\n",
"3026 articles for Anterior Eye Segment\n",
"50166 articles for Blood\n",
"11234 articles for Synovial Fluid\n",
"9921 articles for Nerve Endings\n",
"263 articles for Manubrium\n",
"3835 articles for Cavernous Sinus\n",
"15589 articles for Ovarian Follicle\n",
"1589 articles for Recurrent Laryngeal Nerve\n",
"8158 articles for Vertebral Artery\n",
"962 articles for Subdural Space\n",
"6057 articles for Atrioventricular Node\n",
"11579 articles for Eyelids\n",
"7428 articles for Pancreatic Ducts\n",
"49546 articles for Knee\n",
"17165 articles for Mammary Glands, Animal\n",
"72259 articles for Feces\n",
"3921 articles for Peroneal Nerve\n",
"2333 articles for Thoracic Arteries\n",
"25579 articles for Cochlea\n",
"1144 articles for Thoracic Nerves\n",
"1144 articles for Thoracic Nerves\n",
"4587 articles for Periosteum\n",
"2126 articles for Enteric Nervous System\n",
"6784 articles for Gills\n",
"3722 articles for Celiac Artery\n",
"9105 articles for Ribs\n",
"868 articles for Acromion\n",
"104 articles for Paraganglia, Chromaffin\n",
"7425 articles for Ciliary Body\n",
"11741 articles for Mesenteric Arteries\n",
"1013 articles for Sternoclavicular Joint\n",
"6379 articles for Venoms\n",
"5579 articles for Telencephalon\n",
"3440 articles for Trabecular Meshwork\n",
"5779 articles for Adipose Tissue, Brown\n",
"12029 articles for Lymphoid Tissue\n",
"3295 articles for Fovea Centralis\n",
"23474 articles for Bile\n",
"2056 articles for Juxtaglomerular Apparatus\n",
"8667 articles for Brachial Artery\n",
"3720 articles for Tibial Nerve\n",
"7613 articles for Mandibular Condyle\n",
"40189 articles for Adrenal Glands\n",
"881 articles for Sesamoid Bones\n",
"23954 articles for Maxilla\n",
"9514 articles for Growth Plate\n",
"145 articles for Anal Sacs\n",
"12932 articles for Joints\n",
"8373 articles for Pleura\n",
"49432 articles for Muscle, Smooth\n",
"688 articles for Submucous Plexus\n",
"1565 articles for Superior Cervical Ganglion\n",
"1940 articles for Glossopharyngeal Nerve\n",
"39373 articles for Knee Joint\n",
"19878 articles for Connective Tissue\n",
"1874 articles for Retinal Vein\n",
"1692 articles for Hyoid Bone\n",
"1146 articles for Eyelashes\n",
"7420 articles for Macula Lutea\n",
"158 articles for Truncus Arteriosus\n",
"4778 articles for Urogenital System\n",
"2757 articles for Temporal Arteries\n",
"55662 articles for Leg\n",
"2022 articles for Temporal Muscle\n",
"2426 articles for Atlanto-Axial Joint\n",
"2564 articles for Ependyma\n",
"2564 articles for Ependyma\n",
"98 articles for Sternocostal Joints\n",
"1173 articles for Fascia Lata\n",
"889 articles for Apocrine Glands\n",
"619 articles for Bodily Secretions\n",
"295 articles for Omasum\n",
"5401 articles for Spinal Nerves\n",
"394 articles for Mesenteric Artery, Inferior\n",
"2485 articles for Sinus of Valsalva\n",
"268 articles for Gastroepiploic Artery\n",
"1746 articles for Otolithic Membrane\n",
"1551 articles for Cochlear Nucleus\n",
"940 articles for Fibrillar Collagens\n",
"189 articles for Interrenal Gland\n",
"6446 articles for Kidney Medulla\n",
"6446 articles for Kidney Medulla\n",
"4431 articles for Choroid Plexus\n",
"4991 articles for Cerebellar Cortex\n",
"3912 articles for Dermis\n",
"1520 articles for Pubic Symphysis\n",
"11465 articles for Kidney Tubules, Proximal\n",
"12620 articles for Pericardium\n",
"1434 articles for Azygos Vein\n",
"902 articles for Celiac Plexus\n",
"6999 articles for Tricuspid Valve\n",
"7442 articles for Heart Septum\n",
"748 articles for Harderian Gland\n",
"363 articles for Geniculate Ganglion\n",
"734 articles for Ganglia, Sensory\n",
"10367 articles for Axilla\n",
"198 articles for Area Postrema\n",
"1828 articles for Posterior Cruciate Ligament\n",
"591 articles for Salt Gland\n",
"7449 articles for Ganglia\n",
"4086 articles for Tunica Media\n",
"89 articles for Spiral Lamina\n",
"700 articles for Cerumen\n",
"15319 articles for Head\n",
"1789 articles for Abducens Nerve\n",
"27884 articles for Cervical Vertebrae\n",
"14794 articles for Plasma\n",
"668 articles for Lingual Nerve\n",
"1131 articles for Endolymphatic Sac\n",
"1554 articles for Tarsal Joints\n",
"14505 articles for Forearm\n",
"17741 articles for Diaphragm\n",
"2628 articles for Turbinates\n",
"3614 articles for Venae Cavae\n",
"2118 articles for Ductus Arteriosus\n",
"834 articles for Accessory Nerve\n",
"39129 articles for Central Nervous System\n",
"9824 articles for Aqueous Humor\n",
"28249 articles for Heart Conduction System\n",
"8090 articles for Trigeminal Nerve\n",
"3325 articles for Sebaceous Glands\n",
"1443 articles for Lateral Ventricles\n",
"1667 articles for Bronchial Arteries\n",
"1664 articles for Cranial Sutures\n",
"589 articles for Mushroom Bodies\n",
"2534 articles for Solitary Nucleus\n",
"2974 articles for Cerebellopontine Angle\n",
"311 articles for Oval Window, Ear\n",
"2392 articles for Ophthalmic Artery\n",
"45 articles for Metencephalon\n",
"5837 articles for Paranasal Sinuses\n",
"23514 articles for Spine\n",
"9999 articles for Genitalia, Female\n",
"4778 articles for Heart Valves\n",
"10128 articles for Shoulder\n",
"2952 articles for Peripheral Nervous System\n",
"10927 articles for Ankle Joint\n",
"233195 articles for Kidney\n",
"169 articles for Vernix Caseosa\n",
"8514 articles for Maxillary Sinus\n",
"72190 articles for Bone and Bones\n",
"1653 articles for Nasolacrimal Duct\n",
"1372 articles for Nictitating Membrane\n",
"22727 articles for Mouth Mucosa\n",
"967 articles for Foramen Magnum\n",
"4917 articles for Neck Muscles\n",
"4917 articles for Neck Muscles\n",
"4200 articles for Pulmonary Valve\n",
"435 articles for Broad Ligament\n",
"7822 articles for Sternum\n",
"8288 articles for Parasympathetic Nervous System\n",
"10758 articles for Ear, External\n",
"47891 articles for Coronary Vessels\n",
"3936 articles for Subarachnoid Space\n",
"218 articles for Tensor Tympani\n",
"2145 articles for Hoof and Claw\n",
"9920 articles for Tunica Intima\n",
"107 articles for Perianal Glands\n",
"20836 articles for Autonomic Nervous System\n",
"11922 articles for Retinal Vessels\n",
"11922 articles for Retinal Vessels\n",
"7301 articles for Masticatory Muscles\n",
"909 articles for Salivary Ducts\n",
"3820 articles for Kidney Tubules, Collecting\n",
"1368 articles for Pharyngeal Muscles\n",
"2445 articles for Zygoma\n",
"2319 articles for Petrous Bone\n",
"1122 articles for Stifle\n",
"6609 articles for Pyramidal Tracts\n",
"25500 articles for Fingers\n",
"33091 articles for Heart Atria\n",
"4482 articles for Hair Follicle\n",
"5589 articles for Biliary Tract\n",
"10109 articles for Corpus Luteum\n",
"1594 articles for Hallux\n",
"1660 articles for Popliteal Vein\n",
"3033 articles for Electric Organ\n",
"814 articles for Pterygoid Muscles\n",
"15703 articles for Renal Artery\n",
"398 articles for Bulbourethral Glands\n",
"7019 articles for Sacrum\n",
"16250 articles for Thoracic Vertebrae\n",
"28938 articles for Vagina\n",
"4550 articles for Clavicle\n",
"380364 articles for Liver\n",
"691 articles for Trigeminal Nucleus, Spinal\n",
"3796 articles for Myenteric Plexus\n",
"480 articles for Antlers\n",
"2862 articles for Oculomotor Nerve\n",
"37065 articles for Bronchi\n",
"62498 articles for Retina\n",
"432 articles for Blood-Air Barrier\n",
"11671 articles for Microvilli\n",
"741 articles for Haversian System\n",
"4556 articles for Carotid Sinus\n",
"819 articles for Stria Vascularis\n",
"14679 articles for Orbit\n",
"2948 articles for Cauda Equina\n",
"2831 articles for Septum Pellucidum\n",
"1357 articles for Odontoid Process\n",
"684 articles for Maxillary Nerve\n",
"518 articles for Palatal Muscles\n",
"474 articles for Stomach, Ruminant\n",
"11449 articles for Hepatic Artery\n",
"14622 articles for Shoulder Joint\n",
"939 articles for Seminiferous Epithelium\n",
"29249 articles for Blood Vessels\n",
"1194 articles for Zygapophyseal Joint\n",
"12524 articles for Ear, Middle\n",
"38133 articles for Mandible\n",
"38133 articles for Mandible\n",
"5158 articles for Endocardium\n",
"4368 articles for Mesenteric Veins\n",
"3503 articles for Iliac Vein\n",
"6137 articles for Achilles Tendon\n",
"0 articles for Body Regions\n",
"271 articles for Endolymphatic Duct\n",
"7045 articles for Tears\n",
"10165 articles for Rumen\n",
"3527 articles for Vestibular Nerve\n",
"2468 articles for Arachnoid\n",
"801 articles for Autonomic Pathways\n",
"2013 articles for Animal Structures\n",
"1877 articles for Axis\n",
"9927 articles for Hip\n",
"2086 articles for Subcutaneous Tissue\n",
"38875 articles for Cerebellum\n",
"1549 articles for Saccule and Utricle\n",
"567 articles for Cranial Fossa, Middle\n",
"12864 articles for Adrenal Cortex\n",
"1708 articles for Rectus Abdominis\n",
"157684 articles for Skin\n",
"157684 articles for Skin\n",
"5252 articles for Portal System\n",
"2771 articles for Intestinal Secretions\n",
"1014 articles for Diaphyses\n",
"5584 articles for Epiphyses\n",
"515 articles for Reticulum\n",
"28742 articles for Aorta, Thoracic\n",
"253 articles for Ultimobranchial Body\n",
"17286 articles for Mucous Membrane\n",
"415 articles for Zona Fasciculata\n",
"1970 articles for Loop of Henle\n",
"19445 articles for Nervous System\n",
"22757 articles for Pulmonary Alveoli\n",
"1229 articles for Skeleton\n",
"39457 articles for Pulmonary Artery\n",
"997 articles for Hypogastric Plexus\n",
"58319 articles for Bone Marrow\n",
"32508 articles for Face\n",
"16651 articles for Semen\n",
"12999 articles for Fundus Oculi\n",
"4634 articles for Cochlear Nerve\n",
"2398 articles for Metatarsus\n",
"774 articles for Trochlear Nerve\n",
"7911 articles for Pupil\n",
"472 articles for Internal Capsule\n",
"2963 articles for Olfactory Mucosa\n",
"16244 articles for Medulla Oblongata\n",
"2929 articles for Retinal Artery\n",
"243 articles for Vestibular Nucleus, Lateral\n",
"17700 articles for Membranes\n",
"2844 articles for Radial Nerve\n",
"713 articles for Spinothalamic Tracts\n",
"8041 articles for Mucus\n",
"2456 articles for Rhombencephalon\n",
"52930 articles for Aorta\n",
"121227 articles for Heart\n",
"1178 articles for Psoas Muscles\n",
"24596 articles for Kidney Glomerulus\n",
"1234 articles for Tibial Arteries\n",
"66368 articles for Epithelium\n",
"14496 articles for Vena Cava, Inferior\n",
"7440 articles for Brachial Plexus\n",
"3689 articles for Middle Cerebral Artery\n",
"15658 articles for Penis\n",
"8851 articles for Bile Ducts, Intrahepatic\n",
"55954 articles for Ovary\n",
"2371 articles for Brachiocephalic Trunk\n",
"854 articles for Zona Glomerulosa\n",
"548 articles for Bruch Membrane\n",
"3675 articles for Hematopoietic System\n",
"21597 articles for Hip Joint\n",
"28122 articles for Breast\n",
"387 articles for Neurilemma\n",
"24138 articles for Mitral Valve\n",
"8386 articles for Lower Extremity\n",
"15696 articles for Visual Pathways\n",
"823 articles for Tissues\n",
"1484 articles for Temporomandibular Joint Disc\n",
"28646 articles for Carotid Arteries\n",
"3272 articles for Bundle of His\n",
"13678 articles for Saphenous Vein\n",
"595 articles for Bartholin's Glands\n",
"9188 articles for Abdominal Muscles\n",
"9260 articles for Temporomandibular Joint\n",
"1048 articles for Cervical Plexus\n",
"3224 articles for Skull Base\n",
"5047 articles for Scapula\n",
"5284 articles for Hemolymph\n",
"1338 articles for Third Ventricle\n",
"5289 articles for Colostrum\n",
"3614 articles for Urothelium\n",
"3614 articles for Urothelium\n",
"3244 articles for Zona Pellucida\n",
"3181 articles for Optic Chiasm\n",
"1478 articles for Bile Ducts, Extrahepatic\n",
"990 articles for Medial Forebrain Bundle\n",
"9436 articles for Common Bile Duct\n",
"581 articles for Hymen\n",
"3386 articles for Semicircular Canals\n",
"4909 articles for Decidua\n",
"2272 articles for Axillary Artery\n",
"9983 articles for Jugular Veins\n",
"33182 articles for Saliva\n",
"3906 articles for Nipples\n",
"393 articles for Proventriculus\n",
"5721 articles for Nails\n",
"50679 articles for Thyroid Gland\n",
"1587 articles for Gizzard\n",
"2451 articles for Lumbosacral Plexus\n",
"70373 articles for Lymph Nodes\n",
"4733 articles for Buttocks\n",
"3465 articles for Splenic Artery\n",
"66828 articles for Heart Ventricles\n",
"15152 articles for Tongue\n",
"18641 articles for Basement Membrane\n",
"35262 articles for Sympathetic Nervous System\n",
"10586 articles for Scalp\n",
"640 articles for Foot Joints\n",
"1174 articles for Eccrine Glands\n",
"1815 articles for Olfactory Nerve\n",
"12423 articles for Iliac Artery\n",
"3972 articles for Sella Turcica\n",
"7563 articles for Arterioles\n",
"2196 articles for Carotid Artery, External\n",
"18418 articles for Aorta, Abdominal\n",
"29094 articles for Prostate\n",
"1182 articles for Sebum\n",
"3194 articles for Cranial Nerves\n",
"1232 articles for Toe Joint\n",
"5342 articles for Hepatic Veins\n",
"3263 articles for Vestibular Nuclei\n",
"42737 articles for Embryo, Mammalian\n",
"3458 articles for Seminiferous Tubules\n",
"2099 articles for Stellate Ganglion\n",
"13862 articles for Wrist\n",
"18382 articles for Gastric Juice\n",
"3301 articles for Sacroiliac Joint\n",
"17530 articles for Sputum\n",
"20375 articles for Vagus Nerve\n",
"39231 articles for Cornea\n",
"1590 articles for Tooth Socket\n",
"289 articles for Scent Glands\n",
"16151 articles for Mesencephalon\n",
"3487 articles for Sphenoid Bone\n",
"28659 articles for Skull\n",
"202 articles for Embryonic Structures\n",
"9291 articles for Elbow Joint\n",
"1748 articles for Wool\n",
"377 articles for Rete Testis\n",
"222 articles for Acoustic Maculae\n",
"1371 articles for Clitoris\n",
"2372 articles for Femoral Nerve\n",
"3226 articles for Frontal Bone\n",
"9974 articles for Submandibular Gland\n",
"7307 articles for Jaw\n",
"2780 articles for Mesenteric Artery, Superior\n",
"70663 articles for Spinal Cord\n",
"4713 articles for Glottis\n",
"847 articles for Bile Canaliculi\n",
"21183 articles for Tendons\n",
"647 articles for Fourth Ventricle\n",
"41408 articles for Pituitary Gland\n",
"80 articles for Spinocerebellar Tracts\n",
"4541 articles for Radial Artery\n",
"16069 articles for Optic Nerve\n",
"7352 articles for Vocal Cords\n",
"1469 articles for Limbus Corneae\n",
"68881 articles for Fetus\n",
"4190 articles for Epithelium, Corneal\n",
"3510 articles for Endocrine System\n",
"4346 articles for Viscera\n",
"28981 articles for Eye\n",
"3307 articles for Palate, Soft\n",
"9231 articles for Nasal Cavity\n",
"11184 articles for Pulmonary Veins\n",
"14731 articles for Cerebral Arteries\n",
"9338 articles for Spinal Nerve Roots\n",
"14866 articles for Myelin Sheath\n",
"1583 articles for Acromioclavicular Joint\n",
"18369 articles for Body Fluids\n",
"2572 articles for Cerebellar Nuclei\n",
"5133 articles for Carotid Artery, Common\n",
"6064 articles for Urinary Tract\n",
"18524 articles for Nose\n",
"998 articles for Intercostal Nerves\n",
"23301 articles for Neck\n",
"139139 articles for Myocardium\n",
"7711 articles for Scrotum\n",
"11512 articles for Bile Ducts\n",
"554 articles for Perforant Pathway\n",
"10798 articles for Parathyroid Glands\n",
"12594 articles for Oculomotor Muscles\n",
"8876 articles for Sclera\n",
"1165 articles for Axillary Vein\n",
"6694 articles for Renal Veins\n",
"97 articles for Smegma\n",
"5275 articles for Ganglia, Autonomic\n",
"436 articles for Vestibular Aqueduct\n",
"10345 articles for Kidney Cortex\n",
"743 articles for Endothelium, Lymphatic\n",
"414 articles for Malleus\n",
"6406 articles for Vena Cava, Superior\n",
"865 articles for Malpighian Tubules\n",
"1063 articles for Air Sacs\n",
"1843 articles for Laryngeal Muscles\n",
"1843 articles for Laryngeal Muscles\n",
"1602 articles for Trigeminal Nuclei\n",
"5841 articles for Wing\n",
"494 articles for Musculocutaneous Nerve\n",
"2796 articles for Exocrine Glands\n",
"12080 articles for Umbilical Veins\n",
"4247 articles for Corneal Stroma\n",
"4772 articles for Pancreatic Juice\n",
"176 articles for Bones of Upper Extremity\n",
"1538 articles for Palate, Hard\n",
"7944 articles for Vas Deferens\n",
"17188 articles for Sciatic Nerve\n",
"3779 articles for Oviducts\n",
"17275 articles for Amniotic Fluid\n",
"1028 articles for Round Window, Ear\n",
"24862 articles for Femoral Artery\n",
"6791 articles for Respiratory Mucosa\n",
"1026 articles for Nodose Ganglion\n",
"3787 articles for Epidural Space\n",
"5252 articles for Rotator Cuff\n",
"2051 articles for Sense Organs\n",
"105830 articles for Muscle, Skeletal\n",
"1669 articles for Patellar Ligament\n",
"25856 articles for Fetal Blood\n",
"626 articles for Vasa Vasorum\n",
"5714 articles for Sinoatrial Node\n",
"13702 articles for Immune System\n",
"1373 articles for Eyebrows\n",
"5255 articles for Umbilical Arteries\n",
"3279 articles for Sweat\n",
"8346 articles for Median Nerve\n",
"14662 articles for Respiratory System\n",
"1749 articles for Uvea\n",
"5964 articles for Mononuclear Phagocyte System\n",
"10376 articles for Lymphatic System\n",
"6026 articles for Phrenic Nerve\n",
"852 articles for Bursa, Synovial\n",
"18241 articles for Portal Vein\n",
"26622 articles for Arm\n",
"2545 articles for Bursa of Fabricius\n",
"10455 articles for Fallopian Tubes\n",
"10563 articles for Vestibule, Labyrinth\n",
"12318 articles for Ascitic Fluid\n",
"161 articles for Para-Aortic Bodies\n",
"1739 articles for Salivary Glands, Minor\n",
"34355 articles for Urine\n",
"3219 articles for Chin\n",
"8931 articles for Dura Mater\n",
"9383 articles for Choroid\n",
"1906 articles for Parietal Bone\n",
"53193 articles for Uterus\n",
"2443 articles for Mouth Floor\n",
"12902 articles for Carotid Artery, Internal\n",
"4563 articles for Genitalia\n",
"117 articles for Diagonal Band of Broca\n",
"2209 articles for Follicular Fluid\n",
"7198 articles for Papillary Muscles\n",
"345 articles for Cranial Fossa, Anterior\n",
"2795 articles for Purkinje Fibers\n",
"363 articles for Corpora Allata\n",
"3737 articles for Masseter Muscle\n",
"9742 articles for Thigh\n",
"2448 articles for Musculoskeletal System\n",
"2253 articles for Germinal Center\n",
"3102 articles for Pectoralis Muscles\n",
"859 articles for Neuropil\n",
"13270 articles for Gallbladder\n",
"21944 articles for Digestive System\n",
"28052 articles for Hindlimb\n",
"22087 articles for Cartilage\n",
"428 articles for Scala Tympani\n",
"7357 articles for Seminal Vesicles\n",
"17791 articles for Cardiovascular System\n",
"1529 articles for Uvula\n",
"10135 articles for Pons\n",
"47800 articles for Arteries\n",
"2587 articles for Kidney Tubules, Distal\n",
"4233 articles for Nephrons\n",
"6391 articles for Genitalia, Male\n",
"2762 articles for Forehead\n",
"34 articles for Spiral Ligament of Cochlea\n",
"28880 articles for Brain Stem\n",
"19210 articles for Neuromuscular Junction\n",
"7728 articles for Fascia\n",
"5679 articles for Cloaca\n",
"8664 articles for Endocrine Glands\n",
"9771 articles for Temporal Bone\n",
"4376 articles for Granulation Tissue\n",
"4396 articles for Locus Coeruleus\n",
"20658 articles for Foot\n",
"2961 articles for Ethmoid Sinus\n",
"563 articles for Horns\n",
"34205 articles for Hand\n",
"387999 articles for Brain\n",
"3140 articles for Trigeminal Ganglion\n",
"11795 articles for Iris\n",
"20615 articles for Hair\n",
"62834 articles for Adipose Tissue\n",
"18051 articles for Endothelium\n",
"4025 articles for Cranial Fossa, Posterior\n",
"8664 articles for Lip\n",
"10142 articles for Anterior Cruciate Ligament\n",
"21004 articles for Ureter\n",
"10210 articles for Alveolar Process\n",
"493 articles for Ligamentum Flavum\n",
"212 articles for Zona Reticularis\n",
"13420 articles for Salivary Glands\n",
"14456 articles for Elbow\n",
"20773 articles for Peripheral Nerves\n",
"11241 articles for Ear, Inner\n",
"3260 articles for Sweat Glands\n",
"1919 articles for Spermatic Cord\n",
"587 articles for Anterior Cerebral Artery\n",
"2887 articles for Sphenoid Sinus\n",
"1073 articles for Stapes\n",
"8136 articles for Anterior Chamber\n",
"486 articles for Ejaculatory Ducts\n",
"1024 articles for Subtalar Joint\n",
"1222 articles for Kidney Calices\n",
"7724 articles for Thumb\n",
"1692 articles for Egg Shell\n",
"463 articles for Stapedius\n",
"3191 articles for Cerebral Veins\n",
"23080 articles for Endometrium\n",
"400 articles for Animal Fins\n",
"2838 articles for Cervix Mucus\n",
"2551 articles for Heel\n",
"2892 articles for Hypoglossal Nerve\n",
"7731 articles for Optic Disk\n",
"8219 articles for Popliteal Artery\n",
"17228 articles for Mouth\n",
"11603 articles for Parotid Gland\n",
"80115 articles for Endothelium, Vascular\n",
"6036 articles for Basilar Artery\n",
"2562 articles for Hepatic Duct, Common\n",
"4915 articles for Endothelium, Corneal\n",
"6302 articles for Myometrium\n",
"2124 articles for Abomasum\n",
"1179 articles for Fat Body\n",
"24268 articles for Cervix Uteri\n",
"4278 articles for Ear Canal\n",
"2004 articles for Metatarsophalangeal Joint\n",
"1824 articles for Ethmoid Bone\n",
"6291 articles for Ulnar Nerve\n",
"2884 articles for Occipital Bone\n",
"137988 articles for Muscles\n",
"4101 articles for Subclavian Vein\n",
"1189 articles for Serous Membrane\n",
"7250 articles for Prosencephalon\n",
"6635 articles for Subclavian Artery\n",
"520 articles for Posterior Cerebral Artery\n",
"885 articles for Meibomian Glands\n",
"14977 articles for Synovial Membrane\n",
"16667 articles for Cerebral Ventricles\n",
"33043 articles for Islets of Langerhans\n",
"267 articles for Integumentary System\n",
"890 articles for Coccyx\n",
"13884 articles for Larynx\n",
"20551 articles for Urethra\n",
"748 articles for Ulnar Artery\n",
"501 articles for Trigeminal Caudal Nucleus\n",
"39906 articles for Lumbar Vertebrae\n",
"6506 articles for Cheek\n",
"8329 articles for Facial Nerve\n",
"20971 articles for Kidney Tubules\n",
"7825 articles for Forelimb\n",
"1568 articles for Intercostal Muscles\n",
"462 articles for Obturator Nerve\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": 6,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"\n",
"
\n",
" \n",
" \n",
" | \n",
" uberon_id | \n",
" uberon_name | \n",
" mesh_tree_number | \n",
" mesh_id | \n",
" mesh_name | \n",
" term_query | \n",
" n_articles | \n",
" pubmed_ids | \n",
"
\n",
" \n",
" \n",
" \n",
" 0 | \n",
" UBERON:0001577 | \n",
" facial muscle | \n",
" A02.633.567.400 | \n",
" D005152 | \n",
" Facial Muscles | \n",
" facial muscles[MeSH Terms:noexp] | \n",
" 6400 | \n",
" 25876340|25785922|25675766|25626821|25626793|2... | \n",
"
\n",
" \n",
" 1 | \n",
" UBERON:0001681 | \n",
" nasal bone | \n",
" A02.835.232.781.324.665 | \n",
" D009295 | \n",
" Nasal Bone | \n",
" nasal bone[MeSH Terms:noexp] | \n",
" 2401 | \n",
" 25881382|25636552|25626787|25544298|25533074|2... | \n",
"
\n",
" \n",
" 2 | \n",
" UBERON:0001264 | \n",
" pancreas | \n",
" A03.734 | \n",
" D010179 | \n",
" Pancreas | \n",
" pancreas[MeSH Terms:noexp] | \n",
" 60200 | \n",
" 25876615|25864351|25842673|25796751|25775893|2... | \n",
"
\n",
" \n",
" 3 | \n",
" UBERON:0002356 | \n",
" perineum | \n",
" A01.719 | \n",
" D010502 | \n",
" Perineum | \n",
" perineum[MeSH Terms:noexp] | \n",
" 7214 | \n",
" 25898473|25807837|25767947|25751805|25730811|2... | \n",
"
\n",
" \n",
" 4 | \n",
" UBERON:0001688 | \n",
" incus bone | \n",
" A09.246.397.247.362 | \n",
" D007188 | \n",
" Incus | \n",
" incus[MeSH Terms:noexp] | \n",
" 527 | \n",
" 25182449|25085697|25045723|24969066|24834457|2... | \n",
"
\n",
" \n",
"
\n",
"
"
],
"text/plain": [
" uberon_id uberon_name mesh_tree_number mesh_id \\\n",
"0 UBERON:0001577 facial muscle A02.633.567.400 D005152 \n",
"1 UBERON:0001681 nasal bone A02.835.232.781.324.665 D009295 \n",
"2 UBERON:0001264 pancreas A03.734 D010179 \n",
"3 UBERON:0002356 perineum A01.719 D010502 \n",
"4 UBERON:0001688 incus bone A09.246.397.247.362 D007188 \n",
"\n",
" mesh_name term_query n_articles \\\n",
"0 Facial Muscles facial muscles[MeSH Terms:noexp] 6400 \n",
"1 Nasal Bone nasal bone[MeSH Terms:noexp] 2401 \n",
"2 Pancreas pancreas[MeSH Terms:noexp] 60200 \n",
"3 Perineum perineum[MeSH Terms:noexp] 7214 \n",
"4 Incus incus[MeSH Terms:noexp] 527 \n",
"\n",
" pubmed_ids \n",
"0 25876340|25785922|25675766|25626821|25626793|2... \n",
"1 25881382|25636552|25626787|25544298|25533074|2... \n",
"2 25876615|25864351|25842673|25796751|25775893|2... \n",
"3 25898473|25807837|25767947|25751805|25730811|2... \n",
"4 25182449|25085697|25045723|24969066|24834457|2... "
]
},
"execution_count": 6,
"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": 2,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"uberon_df, uberon_to_pmids = cooccurrence.read_pmids_tsv('data/uberon-pmids.tsv.gz', key='mesh_id')\n",
"disease_df, disease_to_pmids = cooccurrence.read_pmids_tsv('data/disease-pmids.tsv.gz', key='doid_code')"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Total articles containing a doid_code: 3686312\n",
"Total articles containing a mesh_id: 5387135\n",
"Total articles containing both a doid_code and mesh_id: 820072\n",
"\n",
"After removing terms without any cooccurences:\n",
"+ 133 doid_codes remain\n",
"+ 629 mesh_ids remain\n",
"\n",
"Cooccurrence scores calculated for 83657 doid_code -- mesh_id pairs\n"
]
}
],
"source": [
"cooc_df = cooccurrence.score_pmid_cooccurrence(disease_to_pmids, uberon_to_pmids, 'doid_code', 'mesh_id')"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"\n",
"
\n",
" \n",
" \n",
" | \n",
" doid_code | \n",
" doid_name | \n",
" mesh_id | \n",
" mesh_name | \n",
" cooccurrence | \n",
" expected | \n",
" enrichment | \n",
" odds_ratio | \n",
" p_fisher | \n",
"
\n",
" \n",
" \n",
" \n",
" 45214 | \n",
" DOID:10652 | \n",
" Alzheimer's disease | \n",
" D001921 | \n",
" Brain | \n",
" 11209 | \n",
" 1037.397404 | \n",
" 10.804924 | \n",
" 71.792880 | \n",
" 0.000000e+00 | \n",
"
\n",
" \n",
" 45269 | \n",
" DOID:10652 | \n",
" Alzheimer's disease | \n",
" D016548 | \n",
" Prosencephalon | \n",
" 114 | \n",
" 6.426617 | \n",
" 17.738725 | \n",
" 24.829124 | \n",
" 3.728344e-105 | \n",
"
\n",
" \n",
" 44934 | \n",
" DOID:10652 | \n",
" Alzheimer's disease | \n",
" D002531 | \n",
" Cerebellum | \n",
" 303 | \n",
" 75.919555 | \n",
" 3.991067 | \n",
" 4.274664 | \n",
" 4.204287e-89 | \n",
"
\n",
" \n",
" 45209 | \n",
" DOID:10652 | \n",
" Alzheimer's disease | \n",
" D008125 | \n",
" Locus Coeruleus | \n",
" 97 | \n",
" 7.412799 | \n",
" 13.085475 | \n",
" 16.508638 | \n",
" 8.148977e-76 | \n",
"
\n",
" \n",
" 44861 | \n",
" DOID:10652 | \n",
" Alzheimer's disease | \n",
" D010275 | \n",
" Parasympathetic Nervous System | \n",
" 103 | \n",
" 12.918980 | \n",
" 7.972765 | \n",
" 9.086085 | \n",
" 2.664472e-58 | \n",
"
\n",
" \n",
"
\n",
"
"
],
"text/plain": [
" doid_code doid_name mesh_id \\\n",
"45214 DOID:10652 Alzheimer's disease D001921 \n",
"45269 DOID:10652 Alzheimer's disease D016548 \n",
"44934 DOID:10652 Alzheimer's disease D002531 \n",
"45209 DOID:10652 Alzheimer's disease D008125 \n",
"44861 DOID:10652 Alzheimer's disease D010275 \n",
"\n",
" mesh_name cooccurrence expected enrichment \\\n",
"45214 Brain 11209 1037.397404 10.804924 \n",
"45269 Prosencephalon 114 6.426617 17.738725 \n",
"44934 Cerebellum 303 75.919555 3.991067 \n",
"45209 Locus Coeruleus 97 7.412799 13.085475 \n",
"44861 Parasympathetic Nervous System 103 12.918980 7.972765 \n",
"\n",
" odds_ratio p_fisher \n",
"45214 71.792880 0.000000e+00 \n",
"45269 24.829124 3.728344e-105 \n",
"44934 4.274664 4.204287e-89 \n",
"45209 16.508638 8.148977e-76 \n",
"44861 9.086085 2.664472e-58 "
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"cooc_df = uberon_df[['mesh_id', 'mesh_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(['doid_name', 'p_fisher'])\n",
"cooc_df.to_csv('data/disease-uberon-cooccurrence.tsv', index=False, sep='\\t')\n",
"cooc_df.head()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.4.0"
}
},
"nbformat": 4,
"nbformat_minor": 0
}