pubmedExtract.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Pubmed Extract\n",
    "Libraries:\n",
    "**Bio:** Biopython to use *NCBI's Entrez* utilities and get PubMed information\n",
    "**OS** use python miscellaneous operating system interfaces, use here to get the working directory\n",
    "**Randinit** generate random number\n",
    "**time** sleep functions - when you want to pause between requests (random number for the time)\n",
    "**Collections** defaultdict for dealing with missing keys"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "# re module to write regular expressions - used to pull out doi's from string\n",
    "import re\n",
    "# import random number generator\n",
    "from random import randint\n",
    "# import to setup sleep and pauses\n",
    "import time\n",
    "# importing \"collections\" for defaultdict\n",
    "# deal with missing keys in data dictionary of fetched records\n",
    "import collections\n",
    "from collections import defaultdict\n",
    "# Biopython for NCBI's Entrez utilities\n",
    "from Bio import Entrez\n",
    "from Bio import SeqIO\n",
    "from Bio import Medline\n",
    "#from Bio import Medline\n",
    "# use return type of MEDLINE\n",
    "from Bio.Alphabet import IUPAC\n",
    "Entrez.email = 'jamison@library.ucla.edu'\n",
    "# crossref api\n",
    "#  How does it work? Simple. You can do one of two things to get directed to the \"polite pool\":\n",
    "# Include a \"mailto\" parameter in your query. For example:\n",
    "#  https://api.crossref.org/works?filter=has-full-text:true&mailto=GroovyBib@example.org\n",
    "# Include a \"mailto:\" in your User-Agent header. For example:\n",
    "# GroovyBib/1.1 (https://example.org/GroovyBib/; mailto:GroovyBib@example.org) BasedOnFunkyLib/1.4.\n",
    "# Note that this only works if you query the API using HTTPS. You really should be doing that anyway (wags finger).\n",
    "from crossref.restful import Works"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### use python os module to see where your files are being saved"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'/home/jmjamison/work/pubmedExtracts'"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# uses python os module\n",
    "# tells you where your default working directory is - ie. where files will be written\n",
    "os.getcwd()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "db=Entrez.einfo(db=\"pubmed\")\n",
    "# print(Entrez.read(Entrez.einfo()))\n",
    "handle = Entrez.einfo(db = \"pubmed\")\n",
    "record = Entrez.read(handle)\n",
    "# print(record)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### query string"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "query='(\"University of California, Los Angeles\"[Affiliation] OR \"University of California, Los Angeles\"[Affiliation] OR \"University of California Los Angeles\"[Affiliation] OR \"University of California at Los Angeles\"[Affiliation] OR \"University of California of Los Angeles\"[Affiliation] OR \"University of California in Los Angeles\"[Affiliation] OR UCLA[Affiliation] OR 90095[Affiliation]) AND (\"2014/01/01\"[PDAT] : \"2018/01/31\"[PDAT])'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['29707650', '29707101', '29702676', '29695168', '29692895', '29686938', '29686739', '29686725', '29682398', '29682382', '29681647', '29676225', '29673526', '29672601', '29671273', '29671268', '29671267', '29671266', '29671265', '29671264']\n"
     ]
    }
   ],
   "source": [
    "handle = Entrez.esearch(db=\"pubmed\", term=query)\n",
    "record=Entrez.read(handle)\n",
    "idList = record[\"IdList\"]\n",
    "print(idList)\n",
    "record[\"Count\"]\n",
    "handle = Entrez.efetch(db=\"pubmed\", id=idList, rettype=\"medline\", retmode=\"json\")\n",
    "records = Medline.parse(handle)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Entrez esearch, read the results\n",
    "#### get count of how many records the query retreives"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['29707650', '29707101', '29702676', '29695168', '29692895', '29686938', '29686739', '29686725', '29682398', '29682382', '29681647', '29676225', '29673526', '29672601', '29671273', '29671268', '29671267', '29671266', '29671265', '29671264']\n",
      "Records retrieved: 21642\n",
      "21642\n"
     ]
    }
   ],
   "source": [
    "handle = Entrez.esearch(db=\"pubmed\", term=query)\n",
    "record=Entrez.read(handle)\n",
    "print(record[\"IdList\"])\n",
    "print(\"Records retrieved: \" + record[\"Count\"])\n",
    "recordCount = record[\"Count\"]\n",
    "print(recordCount)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### same but specify the maximum records, but  get same total number of records\n",
    "####    using retmax"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "21642\n"
     ]
    }
   ],
   "source": [
    "handle=Entrez.esearch(db=\"pubmed\", term=query, retmax=recordCount)\n",
    "result=Entrez.read(handle)\n",
    "record[\"Count\"]\n",
    "recordCount = record[\"Count\"]\n",
    "print(recordCount)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "####  use real expressions to search the AID field for 10.* [doi ]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "10.1021/acscatal.7b03688 \n",
      "\n",
      "\n",
      "{'indexed': {'date-parts': [[2018, 4, 20]], 'date-time': '2018-04-20T18:02:27Z', 'timestamp': 1524247347542}, 'reference-count': 88, 'publisher': 'American Chemical Society (ACS)', 'issue': '2', 'funder': [{'DOI': '10.13039/100007185', 'name': 'University of California, Los Angeles', 'doi-asserted-by': 'publisher', 'award': []}, {'DOI': '10.13039/100000082', 'name': 'Division of Graduate Education', 'doi-asserted-by': 'publisher', 'award': ['DGE-1144087']}, {'DOI': '10.13039/100000057', 'name': 'National Institute of General Medical Sciences', 'doi-asserted-by': 'publisher', 'award': ['R01 GM117016']}], 'content-domain': {'domain': [], 'crossmark-restriction': False}, 'short-container-title': ['ACS Catal.'], 'published-print': {'date-parts': [[2018, 2, 2]]}, 'DOI': '10.1021/acscatal.7b03688', 'type': 'journal-article', 'created': {'date-parts': [[2017, 12, 20]], 'date-time': '2017-12-20T21:26:00Z', 'timestamp': 1513805160000}, 'page': '1003-1008', 'source': 'Crossref', 'is-referenced-by-count': 2, 'title': ['Nickel-Catalyzed Suzuki–Miyaura Coupling of Aliphatic Amides'], 'prefix': '10.1021', 'volume': '8', 'author': [{'given': 'Timothy B.', 'family': 'Boit', 'affiliation': [{'name': 'Department of Chemistry and\\rBiochemistry, University of California, Los Angeles, California 90095, United States'}]}, {'given': 'Nicholas A.', 'family': 'Weires', 'affiliation': [{'name': 'Department of Chemistry and\\rBiochemistry, University of California, Los Angeles, California 90095, United States'}]}, {'given': 'Junyong', 'family': 'Kim', 'affiliation': [{'name': 'Department of Chemistry and\\rBiochemistry, University of California, Los Angeles, California 90095, United States'}]}, {'ORCID': 'http://orcid.org/0000-0002-7793-2629', 'authenticated-orcid': True, 'given': 'Neil K.', 'family': 'Garg', 'affiliation': [{'name': 'Department of Chemistry and\\rBiochemistry, University of California, Los Angeles, California 90095, United States'}]}], 'member': '316', 'published-online': {'date-parts': [[2018, 1, 5]]}, 'container-title': ['ACS Catalysis'], 'original-title': [], 'link': [{'URL': 'http://pubs.acs.org/doi/pdf/10.1021/acscatal.7b03688', 'content-type': 'unspecified', 'content-version': 'vor', 'intended-application': 'similarity-checking'}], 'deposited': {'date-parts': [[2018, 2, 2]], 'date-time': '2018-02-02T09:20:54Z', 'timestamp': 1517563254000}, 'score': 1.0, 'subtitle': [], 'short-title': [], 'issued': {'date-parts': [[2018, 1, 5]]}, 'references-count': 88, 'alternative-id': ['10.1021/acscatal.7b03688'], 'URL': 'http://dx.doi.org/10.1021/acscatal.7b03688', 'relation': {}, 'ISSN': ['2155-5435', '2155-5435'], 'issn-type': [{'value': '2155-5435', 'type': 'print'}, {'value': '2155-5435', 'type': 'electronic'}]}\n",
      "\n",
      "\n",
      "10.1155/2018/4791379 \n",
      "\n",
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      "\n",
      "\n",
      "10.1016/j.anbehav.2017.08.010 \n",
      "\n",
      "\n",
      "{'indexed': {'date-parts': [[2017, 10, 27]], 'date-time': '2017-10-27T23:52:10Z', 'timestamp': 1509148330890}, 'reference-count': 51, 'publisher': 'Elsevier BV', 'license': [{'URL': 'http://www.elsevier.com/tdm/userlicense/1.0/', 'start': {'date-parts': [[2017, 10, 1]], 'date-time': '2017-10-01T00:00:00Z', 'timestamp': 1506816000000}, 'delay-in-days': 0, 'content-version': 'tdm'}], 'content-domain': {'domain': ['elsevier.com', 'sciencedirect.com'], 'crossmark-restriction': True}, 'short-container-title': ['Animal Behaviour'], 'published-print': {'date-parts': [[2017, 10]]}, 'DOI': '10.1016/j.anbehav.2017.08.010', 'type': 'journal-article', 'created': {'date-parts': [[2017, 9, 5]], 'date-time': '2017-09-05T12:17:43Z', 'timestamp': 1504613863000}, 'page': '129-136', 'update-policy': 'http://dx.doi.org/10.1016/elsevier_cm_policy', 'source': 'Crossref', 'is-referenced-by-count': 0, 'title': ['The multidimensional behavioural hypervolumes of two interacting species predict their space use and survival'], 'prefix': '10.1016', 'volume': '132', 'author': [{'ORCID': 'http://orcid.org/0000-0002-8252-1517', 'authenticated-orcid': False, 'given': 'James L.L.', 'family': 'Lichtenstein', 'affiliation': []}, {'given': 'Colin M.', 'family': 'Wright', 'affiliation': []}, {'given': 'Brendan', 'family': 'McEwen', 'affiliation': []}, {'given': 'Noa', 'family': 'Pinter-Wollman', 'affiliation': []}, {'given': 'Jonathan N.', 'family': 'Pruitt', 'affiliation': []}], 'member': '78', 'container-title': ['Animal Behaviour'], 'original-title': [], 'link': [{'URL': 'http://api.elsevier.com/content/article/PII:S0003347217302592?httpAccept=text/xml', 'content-type': 'text/xml', 'content-version': 'vor', 'intended-application': 'text-mining'}, {'URL': 'http://api.elsevier.com/content/article/PII:S0003347217302592?httpAccept=text/plain', 'content-type': 'text/plain', 'content-version': 'vor', 'intended-application': 'text-mining'}], 'deposited': {'date-parts': [[2017, 10, 12]], 'date-time': '2017-10-12T16:18:19Z', 'timestamp': 1507825099000}, 'score': 1.0, 'subtitle': [], 'short-title': [], 'issued': {'date-parts': [[2017, 10]]}, 'references-count': 51, 'alternative-id': ['S0003347217302592'], 'URL': 'http://dx.doi.org/10.1016/j.anbehav.2017.08.010', 'relation': {}, 'ISSN': ['0003-3472'], 'issn-type': [{'value': '0003-3472', 'type': 'print'}], 'subject': ['Animal Science and Zoology', 'Ecology, Evolution, Behavior and Systematics'], 'assertion': [{'value': 'Elsevier', 'name': 'publisher', 'label': 'This article is maintained by'}, {'value': 'The multidimensional behavioural hypervolumes of two interacting species predict their space use and survival', 'name': 'articletitle', 'label': 'Article Title'}, {'value': 'Animal Behaviour', 'name': 'journaltitle', 'label': 'Journal Title'}, {'value': 'http://dx.doi.org/10.1016/j.anbehav.2017.08.010', 'name': 'articlelink', 'label': 'CrossRef DOI link to publisher maintained version'}, {'value': 'article', 'name': 'content_type', 'label': 'Content Type'}, {'value': '© 2017 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.', 'name': 'copyright', 'label': 'Copyright'}]}\n",
      "\n",
      "\n",
      "10.1177/1747493018772788 \n",
      "\n",
      "\n"
     ]
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      "{'indexed': {'date-parts': [[2018, 4, 20]], 'date-time': '2018-04-20T12:40:14Z', 'timestamp': 1524228014184}, 'reference-count': 39, 'publisher': 'SAGE Publications', 'license': [{'URL': 'http://journals.sagepub.com/page/policies/text-and-data-mining-license', 'start': {'date-parts': [[2018, 4, 20]], 'date-time': '2018-04-20T00:00:00Z', 'timestamp': 1524182400000}, 'delay-in-days': 0, 'content-version': 'tdm'}], 'funder': [{'DOI': '10.13039/100007301', 'name': 'Harvard University Center for AIDS Research', 'doi-asserted-by': 'publisher', 'award': ['P30 AI060354']}], 'content-domain': {'domain': ['journals.sagepub.com'], 'crossmark-restriction': True}, 'short-container-title': ['International Journal of Stroke'], 'DOI': '10.1177/1747493018772788', 'type': 'journal-article', 'created': {'date-parts': [[2018, 4, 20]], 'date-time': '2018-04-20T12:20:15Z', 'timestamp': 1524226815000}, 'page': '174749301877278', 'update-policy': 'http://dx.doi.org/10.1177/sage-journals-update-policy', 'source': 'Crossref', 'is-referenced-by-count': 0, 'title': ['Post-stroke social networks, depressive symptoms, and disability in Tanzania: A prospective study'], 'prefix': '10.1177', 'author': [{'given': 'Altaf', 'family': 'Saadi', 'affiliation': [{'name': 'National Clinical Scholars Program, University of California Los Angeles, Los Angeles, CA, USA'}]}, {'given': 'Kigocha', 'family': 'Okeng’o', 'affiliation': [{'name': 'Muhimbili National Hospital, Dar es Salaam, Tanzania'}]}, {'given': 'Maijo R', 'family': 'Biseko', 'affiliation': [{'name': 'Muhimbili National Hospital, Dar es Salaam, Tanzania'}]}, {'given': 'Agness F', 'family': 'Shayo', 'affiliation': [{'name': 'Muhimbili National Hospital, Dar es Salaam, Tanzania'}]}, {'given': 'Theoflo N', 'family': 'Mmbando', 'affiliation': [{'name': 'Muhimbili National Hospital, Dar es Salaam, Tanzania'}]}, {'given': 'Sara J', 'family': 'Grundy', 'affiliation': [{'name': 'Department of Neurology, Massachusetts General Hospital, Boston, MA, USA'}]}, {'given': 'Ai', 'family': 'Xu', 'affiliation': [{'name': 'Biostatistics Center, Massachusetts General Hospital, Boston, MA, USA'}]}, {'given': 'Robert A', 'family': 'Parker', 'affiliation': [{'name': 'Biostatistics Center, Massachusetts General Hospital, Boston, MA, USA'}, {'name': 'Harvard Medical School, Boston, USA'}]}, {'given': 'Leah', 'family': 'Wibecan', 'affiliation': [{'name': 'Massachusetts General Hospital, Boston, MA, USA'}]}, {'given': 'Geetha', 'family': 'Iyer', 'affiliation': [{'name': 'Harvard T.H. 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      "\n",
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      "\n",
      "\n"
     ]
    }
   ],
   "source": [
    "# regular expressions \n",
    "import re\n",
    "from crossref.restful import Works\n",
    "works = Works()\n",
    "\n",
    "\n",
    "# if re.match(\"^169.232.181.10.|127.0.0.1|169.232.10.164.67.152.153|164.67.152.15.\",line): \n",
    "#   '..\\.* \\[doi\\]'\n",
    "f = open('OutputReportTest.txt')\n",
    "\n",
    "while True:\n",
    "    line = f.readline()\n",
    "    m = re.search(r\"\\[\\'.*\\s\\[doi\\]\", line)\n",
    "    if m:\n",
    "        doiLine = m.group(0)\n",
    "        doiLine = re.sub(\"\\[\\'\", \"\", doiLine)\n",
    "        doiLine = re.sub(\"\\[doi\\]\", \"\", doiLine)   \n",
    "        #  https://doi.org/10.1021/acscatal.7b03688 \n",
    "        #print(\"https://doi.org/\" + doiLine)\n",
    "        print(doiLine)\n",
    "        print(\"\\n\")\n",
    "        print(works.doi(doiLine))\n",
    "        print(\"\\n\")\n",
    "        \n",
    "    if not line: break\n",
    "f.close()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Crossref rest api\n",
    "\"singletons\" - Singletons are single results. Retrieving metadata for a specific identifier (e.g. DOI, ISSN, funder_identifier) typically returns in a singleton result."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['29702676', '29695168', '29692895', '29686938', '29686739', '29686725', '29682398', '29682382', '29681647', '29676225', '29673526', '29672601', '29671273', '29671268', '29671267', '29671266', '29671265', '29671264', '29670931', '29670925']\n",
      "29702676\n",
      "\n",
      "Pubmed Record ID (PMID): 29702676\n",
      "Title: Predictors for patients understanding reason for hospitalization.\n",
      "Author Identifier (AUID): ['ORCID: http://orcid.org/0000-0001-9614-345X']\n",
      "Author(s)(AU): ['Weerahandi H', 'Ziaeian B', 'Fogerty RL', 'Jenq GY', 'Horwitz LI']\n",
      "Author affiliation (AD): Department of Medicine, NYU School of Medicine, New York, NY, United States of America. Department of Population Health, NYU School of Medicine, New York, New York, United States of America. Division of Cardiology, UCLA Medical Center, Los Angeles, CA, United States of America. Division of Cardiology, Veteran Affairs Greater Los Angeles Healthcare System, Los Angeles, CA, United States of America. Division of General Internal Medicine, Yale School of Medicine, New Haven, CT, United States of America. Division of Geriatrics and Palliative Medicine, University of Michigan, Ann Arbor, MI, United States of America. Department of Medicine, NYU School of Medicine, New York, NY, United States of America. Department of Population Health, NYU School of Medicine, New York, New York, United States of America. Center for Healthcare Innovation and Delivery Science, NYU Langone Medical Center, New York, New York, United States of America.\n",
      "Article Identifier/DOI (AID): ['10.1371/journal.pone.0196479 [doi]', 'PONE-D-17-14884 [pii]']\n",
      "https://doi.org/10.1371/journal.pone.0196479 \n",
      "\n",
      "DOI: ['10.1371/journal.pone.0196479 [doi]\n",
      "\n",
      "\n",
      "\n",
      "29695168\n",
      "\n",
      "Pubmed Record ID (PMID): 29695168\n",
      "Title: Cortical spreading depression as a site of origin for migraine: Role of CGRP.\n",
      "Author Identifier (AUID): ['ORCID: http://orcid.org/0000-0002-7955-1627']\n",
      "Author(s)(AU): ['Close LN', 'Eftekhari S', 'Wang M', 'Charles AC', 'Russo AF']\n",
      "Author affiliation (AD): 1 Department of Neurosurgery, University of Iowa, Iowa City, IA, USA. 2 UCLA Goldberg Migraine Program, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA. 3 Centre for Neuroscience, Department of Biological Sciences, Xi'an Jiaotong-Liverpool University (XJTLU), SIP, Suzhou, China. 2 UCLA Goldberg Migraine Program, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA. 4 Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA. 5 Department of Neurology, University of Iowa, Iowa City, IA, USA. 6 Veterans Affairs Medical Center, Iowa City, IA, USA.\n",
      "Article Identifier/DOI (AID): ['10.1177/0333102418774299 [doi]']\n",
      "https://doi.org/10.1177/0333102418774299 \n",
      "\n",
      "DOI: ['10.1177/0333102418774299 [doi]\n",
      "\n",
      "\n",
      "\n",
      "29692895\n",
      "PMC5905129\n",
      "Pubmed Record ID (PMID): 29692895\n",
      "Title: Metabolic characterization of isocitrate dehydrogenase (IDH) mutant and IDH wildtype gliomaspheres uncovers cell type-specific vulnerabilities.\n",
      "Author Identifier (AUID): \n",
      "Author(s)(AU): ['Garrett M', 'Sperry J', 'Braas D', 'Yan W', 'Le TM', 'Mottahedeh J', 'Ludwig K', 'Eskin A', 'Qin Y', 'Levy R', 'Breunig JJ', 'Pajonk F', 'Graeber TG', 'Radu CG', 'Christofk H', 'Prins RM', 'Lai A', 'Liau LM', 'Coppola G', 'Kornblum HI']\n",
      "Author affiliation (AD): 1Department of Neurosurgery, and the Interdepartmental Program in the Neurosciences, University of California, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e 2Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e 2Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e 3UCLA Metabolomics Center, UCLA, Los Angeles, USA.0000 0000 9632 6718grid.19006.3e 4Department of Chemistry and Biochemistry, UCLA, Los Angeles, USA.0000 0000 9632 6718grid.19006.3e 2Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e 5Ahmanson Translational Imaging Division, UCLA, Los Angeles, USA.0000 0000 9632 6718grid.19006.3e 6Department of Psychiatry and Biobehavioral Sciences and Semel Institute for Neuroscience & Human Behavior, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e 6Department of Psychiatry and Biobehavioral Sciences and Semel Institute for Neuroscience & Human Behavior, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e 7Department of Human Genetics, UCLA, Los Angeles, USA.0000 0000 9632 6718grid.19006.3e 6Department of Psychiatry and Biobehavioral Sciences and Semel Institute for Neuroscience & Human Behavior, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e 8Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA USA.0000 0001 2152 9905grid.50956.3f 8Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA USA.0000 0001 2152 9905grid.50956.3f 9Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA USA.0000 0001 2152 9905grid.50956.3f 10Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA USA.0000 0001 2152 9905grid.50956.3f 11Department of Radiation Oncology, David Geffen School of Medicine at UCLA, Los Angeles, USA.0000 0000 9632 6718grid.19006.3e 12Jonsson Comprehensive Cancer Center, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e 2Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e 3UCLA Metabolomics Center, UCLA, Los Angeles, USA.0000 0000 9632 6718grid.19006.3e 12Jonsson Comprehensive Cancer Center, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e 2Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e 5Ahmanson Translational Imaging Division, UCLA, Los Angeles, USA.0000 0000 9632 6718grid.19006.3e 12Jonsson Comprehensive Cancer Center, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e 2Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e 3UCLA Metabolomics Center, UCLA, Los Angeles, USA.0000 0000 9632 6718grid.19006.3e 12Jonsson Comprehensive Cancer Center, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e 14Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e 1Department of Neurosurgery, and the Interdepartmental Program in the Neurosciences, University of California, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e 2Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e 12Jonsson Comprehensive Cancer Center, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e 12Jonsson Comprehensive Cancer Center, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e 13Department of Neurology, UCLA, Los Angeles, USA.0000 0000 9632 6718grid.19006.3e 1Department of Neurosurgery, and the Interdepartmental Program in the Neurosciences, University of California, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e 12Jonsson Comprehensive Cancer Center, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e 6Department of Psychiatry and Biobehavioral Sciences and Semel Institute for Neuroscience & Human Behavior, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e 13Department of Neurology, UCLA, Los Angeles, USA.0000 0000 9632 6718grid.19006.3e 2Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e 6Department of Psychiatry and Biobehavioral Sciences and Semel Institute for Neuroscience & Human Behavior, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e 12Jonsson Comprehensive Cancer Center, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e 14Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.0000 0000 9632 6718grid.19006.3e\n",
      "Article Identifier/DOI (AID): ['10.1186/s40170-018-0177-4 [doi]', '177 [pii]']\n",
      "https://doi.org/10.1186/s40170-018-0177-4 \n",
      "\n",
      "DOI: ['10.1186/s40170-018-0177-4 [doi]\n",
      "['R56 NS052563/NS/NINDS NIH HHS/United States', 'R33 CA202900/CA/NCI NIH HHS/United States', 'R01 NS052563/NS/NINDS NIH HHS/United States', 'P30 NS062691/NS/NINDS NIH HHS/United States', 'P50 CA211015/CA/NCI NIH HHS/United States']\n",
      "\n",
      "\n",
      "29686938\n",
      "PMC5909715\n",
      "Pubmed Record ID (PMID): 29686938\n",
      "Title: Adapting and Implementing a School-Based Resilience-Building Curriculum Among Low-Income Racial and Ethnic Minority Students.\n",
      "Author Identifier (AUID): \n",
      "Author(s)(AU): ['Ijadi-Maghsoodi R', 'Marlotte L', 'Garcia E', 'Aralis H', 'Lester P', 'Escudero P', 'Kataoka S']\n",
      "Author affiliation (AD): Investigator, VA Health Service Research & Development (HSR&D) Center for the Study of Healthcare Innovation, Implementation & Policy (CSHIIP), VA Greater Los Angeles Healthcare System, 11301 Wilshire Boulevard, Bldg. 206, Room 246, Los Angeles, CA, 90073, Assistant Professor in Residence, UCLA Nathanson Family Resilience Center, Semel Institute for Neuroscience & Human Behavior, 760 Westwood Plaza, Rm A8-148, Los Angeles, CA 90095. Assistant Director of Training, UCLA Nathanson Family Resilience Center, 760 Westwood Plaza, A8-153, Los Angeles, CA 90095. Assistant Professor, Texas A&M International University, CNS 312F, Laredo, TX 78041. Statistician, UCLA Nathanson Family Resilience Center, Semel Institute for Neuroscience & Human Behavior, 760 Westwood Plaza, A8-236, Los Angeles, CA 90024. Professor in Residence, UCLA Semel Institute for Neuroscience and Human Behavior, Los Angeles, CA 90095. Director of Los Angeles Unified School District School Mental Health, 333 South Beaudry Avenue, Los Angeles, CA 90017. Professor in Residence, UCLA Semel Institute for Neuroscience and Human Behavior, Los Angeles, CA 90095.\n",
      "Article Identifier/DOI (AID): \n",
      "\n",
      "No DOI ?!?!?\n",
      "['K12 DA000357/DA/NIDA NIH HHS/United States']\n",
      "\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "29686739\n",
      "PMC5852854\n",
      "Pubmed Record ID (PMID): 29686739\n",
      "Title: Screening for Emotional Expression in Frontotemporal Dementia: A Pilot Study.\n",
      "Author Identifier (AUID): ['ORCID: 0000-0001-6441-7989']\n",
      "Author(s)(AU): ['Carr AR', 'Ashla MM', 'Jimenez EE', 'Mendez MF']\n",
      "Author affiliation (AD): VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA. Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA. Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA. VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA. Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA. VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA. Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA. Department of Psychiatry & Biobehavioral Sciences, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA.\n",
      "Article Identifier/DOI (AID): ['10.1155/2018/8187457 [doi]']\n",
      "https://doi.org/10.1155/2018/8187457 \n",
      "\n",
      "DOI: ['10.1155/2018/8187457 [doi]\n",
      "\n",
      "\n",
      "\n",
      "29686725\n",
      "PMC5902943\n",
      "Pubmed Record ID (PMID): 29686725\n",
      "Title: Prospective Observational Study on acute Appendicitis Worldwide (POSAW).\n",
      "Author Identifier (AUID): \n",
      "Author(s)(AU): ['Sartelli M', 'Baiocchi GL', 'Di Saverio S', 'Ferrara F', 'Labricciosa FM', 'Ansaloni L', 'Coccolini F', 'Vijayan D', 'Abbas A', 'Abongwa HK', 'Agboola J', 'Ahmed A', 'Akhmeteli L', 'Akkapulu N', 'Akkucuk S', 'Altintoprak F', 'Andreiev AL', 'Anyfantakis D', 'Atanasov B', 'Bala M', 'Balalis D', 'Baraket O', 'Bellanova G', 'Beltran M', 'Melo RB', 'Bini R', 'Bouliaris K', 'Brunelli D', 'Castillo A', 'Catani M', 'Che Jusoh A', 'Chichom-Mefire A', 'Cocorullo G', 'Coimbra R', 'Colak E', 'Costa S', 'Das K', 'Delibegovic S', 'Demetrashvili Z', 'Di Carlo I', 'Kiseleva N', 'El Zalabany T', 'Faro M', 'Ferreira M', 'Fraga GP', 'Gachabayov M', 'Ghnnam WM', 'Gimenez Maurel T', 'Gkiokas G', 'Gomes CA', 'Griffiths E', 'Guner A', 'Gupta S', 'Hecker A', 'Hirano ES', 'Hodonou A', 'Hutan M', 'Ioannidis O', 'Isik A', 'Ivakhov G', 'Jain S', 'Jokubauskas M', 'Karamarkovic A', 'Kauhanen S', 'Kaushik R', 'Kavalakat A', 'Kenig J', 'Khokha V', 'Khor D', 'Kim D', 'Kim JI', 'Kong V', 'Lasithiotakis K', 'Leao P', 'Leon M', 'Litvin A', 'Lohsiriwat V', 'Lopez-Tomassetti Fernandez E', 'Lostoridis E', 'Maciel J', 'Major P', 'Dimova A', 'Manatakis D', 'Marinis A', 'Martinez-Perez A', 'Marwah S', 'McFarlane M', 'Mesina C', 'Pedziwiatr M', 'Michalopoulos N', 'Misiakos E', 'Mohamedahmed A', 'Moldovanu R', 'Montori G', 'Mysore Narayana R', 'Negoi I', 'Nikolopoulos I', 'Novelli G', 'Novikovs V', 'Olaoye I', 'Omari A', 'Ordonez CA', 'Ouadii M', 'Ozkan Z', 'Pal A', 'Palini GM', 'Partecke LI', 'Pata F', 'Pedziwiatr M', 'Pereira Junior GA', 'Pintar T', 'Pisarska M', 'Ploneda-Valencia CF', 'Pouggouras K', 'Prabhu V', 'Ramakrishnapillai P', 'Regimbeau JM', 'Reitz M', 'Rios-Cruz D', 'Saar S', 'Sakakushev B', 'Seretis C', 'Sazhin A', 'Shelat V', 'Skrovina M', 'Smirnov D', 'Spyropoulos C', 'Strzalka M', 'Talving P', 'Teixeira Gonsaga RA', 'Theobald G', 'Tomadze G', 'Torba M', 'Trana C', 'Ulrych J', 'Uzunoglu MY', 'Vasilescu A', 'Occhionorelli S', 'Venara A', 'Vereczkei A', 'Vettoretto N', 'Vlad N', 'Waledziak M', 'Yilmaz TU', 'Yuan KC', 'Yunfeng C', 'Zilinskas J', 'Grelpois G', 'Catena F']\n",
      "Author affiliation (AD): Department of Surgery, Macerata Hospital, Macerata, Italy. 2Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy. 3Emergency Surgery, Maggiore Hospital, Bologna, Italy. 4General Surgery and Polytrauma, San Carlo Borromeo Hospital, Milan, Italy. Department of Biomedical Sciences and Public Health, Unit of Hygiene, Preventive Medicine and Public Health, UNIVPM, Ancona, Italy. 6Department of Surgery, Bufalini Hospital, Cesena, Italy. 6Department of Surgery, Bufalini Hospital, Cesena, Italy. 7General Surgery, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK. 8Emergency Surgery, Mansoura University Hospital, Mansoura, Egypt. 9Emergency Surgery Unit, Maggiore University Hospital, Parma, Italy. Surgery, Kwara State General Hospital, Ilorin, Kwara Nigeria. 11Surgery, Ahmadu Bello University Teaching Hospital Zaria, Zaria, Nigeria. Surgery, First University Clinic, Tbilisi, Georgia. 13General Surgery, Baskent Universitesi Adana Egitim ve Uygulama Hastanesi, Adana, Turkey. 14General Surgery, Training and Research Hospital of Mustafa Kemal University, Hatay, Turkey. 15General Surgery, Sakarya University School of Medicine, Sakarya, Turkey. 7General Surgery, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK. Primary Care, Primary Health Care Centre of Kissamos, Chania, Greece. 17Department of General Surgery, Medical University of Plovdiv, UMHAT Eurohospital, Plovdiv, Bulgaria. 18General Surgery, Hadassah Medical Center, Jerusalem, Israel. Surgical Department, Agios Savvas Anticaner Hospital, Athens, Greece. General Surgery, Hospital Habib Bouguefa de Bizerte, Bizerte, Tunisia. General Surgery, S.S. Annunziata Hospital, Taranto, Italy. Surgery, Hospital San Juan de Dios de La Serena, La Serena, Chile. 23General Surgery, Centro Hospitalar Sao Joao, Porto, Portugal. 24General and Emergency Surgery, San Giovanni Bosco Hospital, Turin, Italy. Surgical Department, General Hospital of Larissa, Larissa, Greece. Chirurgia, Citta di Castello Hospital, Citta di Castello, Italy. 27Department of Surgery, Harbor-UCLA Medical Center, Torrance, USA. 28DEA, La Sapienza Universita di Roma, Policlinico Umberto I, Rome, Italy. General Surgery, Kuala Krai Hospital, Kuala Krai, Kelantan Malaysia. Surgery and Obstetrics/Gynaecology, Regional Hospital, Limbe, Cameroon. 31Emergency Surgery, Azienda Ospedaliera Universitaria Policlinico Paolo Giaccone, Palermo, Italy. 32Trauma/Acute Care Surgery, University of California San Diego, San Diego, USA. General Surgery, Samsun Training and Research Hospital, Samsun, Turkey. 34Surgery, CHVNG/E, EPE, Vila Nova de Gaia, Portugal. 35General Surgery, Numune Training and Research Hospital, Adana, Turkey. 36Colorectal Surgery, Clinic for Surgery, University Clinical Center Tuzla, Tuzla, Bosnia and Herzegovina. Surgery, Kipshidze Central University Hospital, Tbilisi, Georgia. 38Surgery, Hamad General Hospital, Doha, Qatar. 39General and Emergency Surgery, Riga East University Hospital \"Gailezers\", Riga, Latvia. General Surgery, Bahrain Defence Force Hospital, Manama, Bahrain. 41Department of General Surgery, Trauma and Emergency Surgery Division, ABC Medical School, Santo Andrei, SP Brazil. 42General Surgery, Hospital Garcia de Orta, Lisbon, Portugal. 43Division of Trauma Surgery, Hospital de Clinicas, University of Campinas (Unicamp), Campinas, Brazil. Department of Abdominal Surgery, Vladimir City Clinical Hospital of Emergency Medicine, Vladimir, Russia. 45General Surgery Department, Mansoura Faculty of Medicine, Mansoura University, Mansoura, Egypt. 46Cirugia General y del Aparato Digestivo, Hospital Universitario Miguel Servet, Zaragoza, Spain. 47Second Department of Surgery, Aretaieion University Hospital, National and Kapodistrian University of Athens, Athens, Greece. Surgery, Therezinha de Jesus University Hospital, Juiz de Fora, Brazil. 49Upper GI/General Surgery, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK. 50Department of General Surgery, Karadeniz Technical University, Farabi Hospital, Trabzon, Turkey. 51Surgery, Government Medical College and Hospital, Chandigarh, India. 52Department of General and Thoracic Surgery, University Hospital, Giessen, Germany. 43Division of Trauma Surgery, Hospital de Clinicas, University of Campinas (Unicamp), Campinas, Brazil. Chirurgie, Chud-Borgou/Alibori, Parakou, Benin. Surgical Department, Landesklinikum Hainburg, Hainburg An Der Donau, Austria. 554th Surgical Department, Aristotle University of Thessaloniki, Thessaloniki, Greece. 56General Hospital \"George Papanikoalou\", Thessaloniki, Greece. 57General Surgery, Erzincan University Mengucek Gazi Training and Research Hospital, Erzincan, Turkey. General Surgery, City Hospital #1, Moscow, Russia. 59Surgery, S M S Medical college, Jaipur, India. 60Department of Surgery, Hospital of Lithuanian University of Health Sciences Kaunas Clinics, Kaunas, Lithuania. 61Clinic for Emergency Surgery, Faculty of Medicine University of Belgrade, Belgrade, Serbia. 62Division of Digestive Surgery and Urology, Turku University Hospital, Turku, Finland. 51Surgery, Government Medical College and Hospital, Chandigarh, India. 63General Surgery, Jubilee Mission Medical College & Research Institute, Thrissur, India. 643rd Department of General Surgery, Jagiellonian University Medical College, Krakow, Poland. Emergency surgery, City Hospital, Mozyr, Belarus. 66Acute Care Surgery, LAC+USC Medical Center, California, USA. 27Department of Surgery, Harbor-UCLA Medical Center, Torrance, USA. 67Department of Surgery, Inje University Ilsan Paik Hospital, Goyang, Republic of Korea. 68Department of Surgery, Edendale Hospital, Pietermaritzburg, South Africa. General Surgery, Scarborough, York Teaching Hospital, Scarborough, UK. General Surgery, Colorectal Unit, Hospital de Braga, Braga, Portugal. 71General and Digestive Surgery, Hospital Fundacion Jimenez Diaz, Madrid, Spain. Surgical Disciplines, Regional Clinical Hospital, Kaliningrad, Russia. 73Faculty of Medicine, Department of Surgery, Siriraj Hospital, Mahidol University, Bangkok, Thailand. Department of Gastrointestinal Surgery, Insular University Hospital of Gran Canaria, Las Palmas, Spain. 1st Department of Surgery, Kavala General Hospital, Kavala, Greece. 27Department of Surgery, Harbor-UCLA Medical Center, Torrance, USA. 762nd Department of Surgery, Jagiellonian University Medical College, Krakow, Poland. 77Clinic of surgery, Department of Gastrointestinal Surgery, University Hospital Centre Zagreb, Zagreb, Croatia. 78Surgical Department, Konstantopouleio General Hospital, Athens, Greece. 79First Department of Surgery, Tzaneio, Piraeus, Greece. 80Department of General and Digestive Surgery, Hospital Universitario Doctor Peset, Valencia, Spain. 81Department of General Surgery, Post-Graduate Institute of Medical Sciences, Rohtak, India. 82Department of Surgery, Radiology, Anaesthetics and Intensive Care, University of the West Indies, Kingston, Jamaica. 83University Hospital of the West Indies, Kingston, Jamaica. Department of Surgery Second Surgical Clinic, Emergency Hospital of Craiova, Craiova, Romania. 85Department of General Surgery and Emergency Medicine, University Hospital, Krakow, Poland. 863rd Department of Surgery, Ahepa University Hospital, Thessaloniki, Greece. 873rd Department of Surgery, Attikon University Hospital, National and Kapodistrian University of Athens, Medical School, Athens, Greece. General Surgery, Khartoum Teaching Hospital, Khartoum, Sudan. Department of Visceral, Digestive and Oncologic Surgery, Clinique Sainte Marie, Cambrai, France. 6Department of Surgery, Bufalini Hospital, Cesena, Italy. General Surgery, K R Hospital, Mysore, India. General Surgery, Emergency Hospital of Bucharest, Bucharest, Romania. 92General Surgery, Lewisham and Greenwich NHS Trust, London, UK. 93General, Emergency Surgery, Infermi Hospital, Rimini, Italy. 39General and Emergency Surgery, Riga East University Hospital \"Gailezers\", Riga, Latvia. 94Surgery, University of Ilorin Teaching Hospital, Ilorin, Nigeria. 95General Surgery, King Abdullah University Hospital, Irbid, Jordan. 96Division of Trauma and Acute Care Surgery, Department of Surgery, Fundacion Valle del Lili and Universidad del Valle, Cali, Colombia. Surgery Departement, Medical School of Fezm, Sidi Mohamed Benabdellah University, Fez, Morocco. General Surgery, Elazig Training and Research Hospital, Elazig, Turkey. 99General Surgery, King George's Medical University, Lucknow, India. 93General, Emergency Surgery, Infermi Hospital, Rimini, Italy. Surgery, University Hospital, Greifswald, Germany. Department of General Surgery, Sant'Antonio Abate Hospital, Gallarate, Italy. 102Department of Emergency Surgery and Trauma Centre, University Hospital, Krakow, Poland. 103Surgery and Anatomy, Clinics Hospital, Ribeirao Preto, Brazil. 104Abdominal surgery, UMC Ljubljana, Ljubljana, Slovenia. 105Department of Endoscopic, Metabolic and Soft Tissue Tumors Surgery, The University Hospital in Krakow, Krakow, Poland. 106General Surgery, Hospital Civil de Guadalajara \"Dr. Juan I. Menchaca\", Guadalajara, Mexico. 1st Department of Surgery, Kavala General Hospital, Kavala, Greece. 107Surgery, Bharati Vidyapeeth Deemed University Medical College & Hospital, Sangli, Maharashtra India. Laparoscopic and Metabolic Surgery, KIMS Hospital, Cochin, India. 109Digestive Surgery, CHU Amiens-Picardie, Amiens, France. General Surgery, Hospital Municipal Dr. Jose de Carvalho Florence, Sao Jose Dos Campos, Brazil. General Surgery, Hospital General Regional # 1 I.M.S.S, Cuernavaca, Mexico. Acute Care Surgery, North Estonia Medical Center, Tallinn, Estonia. General Surgery, University Hospital St George, Plovdiv, Bulgaria. 114General Surgery, Russells Hall Hospital, Birmingham, UK. General Surgery, City Hospital #1, Moscow, Russia. 115General Surgery, Tan Tock Seng Hospital, Singapore, Singapore. Surgery, Hospital & Oncological Centre Novy Jicin, Novy Jicin, Czech Republic. General Surgery, Clinical Hospital at Chelyabinsk Station OJSC \"Russian Railways\", Chelyabinsk, Russian Federation. 1183rd Department of Surgery, IASO General Hospital, Athens, Greece. 119General Surgery and Polytrauma, University Hospital, Medical College, Jagiellonian University, Krakow, Poland. Acute Care Surgery, North Estonia Medical Center, Tallinn, Estonia. Cirurgia do Trauma, Hospital Escola Padre Albino, Catanduva, Brazil. 7General Surgery, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK. 121Surgery Department #2, Tbilisi State Medical University, Tbilisi, Georgia. General Surgery, Trauma University Hospital, Tirana, Albania. Department of Surgery, Macerata Hospital, Macerata, Italy. 1231st Department of Surgery-Department of Abdominal Thoracic Surgery and Traumatology, General University Hospital, Prague, Czech Republic. 14General Surgery, Training and Research Hospital of Mustafa Kemal University, Hatay, Turkey. First Surgical Clinic, St. Spiridon University Hospital, Iasi, Romania. Emergency Surgery, S. Anna Teaching Hospital, Ferrara, Italy. 126Digestive and Endocrinal Surgery, University Hospital, Angers, France. 127Department of Surgery, Medical School University of Pecs, Pecs, Hungary. Surgery, ASTS Spedali Civili Brescia, Montichiari, Italy. First Surgical Clinic, St. Spiridon University Hospital, Iasi, Romania. 129Department of General, Oncological, Metabolic and Thoracic Surgery, Military Institute of Medicine in Warsaw, Warsaw, Poland. 130Department of General Surgery, Kocaeli University, Kocaeli, Turkey. Trauma and Emergency Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan. 132Department of Surgery, Tianjin Nankai Hospital, Tianjin, China. 60Department of Surgery, Hospital of Lithuanian University of Health Sciences Kaunas Clinics, Kaunas, Lithuania. 109Digestive Surgery, CHU Amiens-Picardie, Amiens, France. 8Emergency Surgery, Mansoura University Hospital, Mansoura, Egypt.\n",
      "Article Identifier/DOI (AID): ['10.1186/s13017-018-0179-0 [doi]', '179 [pii]']\n",
      "https://doi.org/10.1186/s13017-018-0179-0 \n",
      "\n",
      "DOI: ['10.1186/s13017-018-0179-0 [doi]\n",
      "\n",
      "\n",
      "\n",
      "29682398\n",
      "PMC5906067\n",
      "Pubmed Record ID (PMID): 29682398\n",
      "Title: Nickel-Catalyzed Suzuki-Miyaura Coupling of Aliphatic Amides.\n",
      "Author Identifier (AUID): \n",
      "Author(s)(AU): ['Boit TB', 'Weires NA', 'Kim J', 'Garg NK']\n",
      "Author affiliation (AD): Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States. Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States. Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States. Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States.\n",
      "Article Identifier/DOI (AID): ['10.1021/acscatal.7b03688 [doi]']\n",
      "https://doi.org/10.1021/acscatal.7b03688 \n",
      "\n",
      "DOI: ['10.1021/acscatal.7b03688 [doi]\n",
      "['R01 GM117016/GM/NIGMS NIH HHS/United States', 'S10 RR025631/RR/NCRR NIH HHS/United States']\n",
      "\n",
      "\n",
      "29682382\n",
      "PMC5851333\n",
      "Pubmed Record ID (PMID): 29682382\n",
      "Title: Paroxysmal Nocturnal Dyspnea Secondary to Right Ventricular Myxoma: A Novel Presentation of an Unusual Tumor.\n",
      "Author Identifier (AUID): ['ORCID: 0000-0002-7828-1522']\n",
      "Author(s)(AU): ['Knight TE', 'Shiramizu B', 'Ly P', 'Thompson KS', 'Reddy V']\n",
      "Author affiliation (AD): Division of Pediatric Hematology and Oncology, Department of Pediatrics, Children's Hospital of Michigan, Detroit, MI, USA. Division of Pediatric Hematology and Oncology, Department of Pediatrics, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA. Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA. Department of Pathology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA. Clinical Laboratories of Hawaii, Honolulu, HI, USA. Division of Pediatric Cardiology, Department of Pediatrics, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA.\n",
      "Article Identifier/DOI (AID): ['10.1155/2018/4791379 [doi]']\n",
      "https://doi.org/10.1155/2018/4791379 \n",
      "\n",
      "DOI: ['10.1155/2018/4791379 [doi]\n",
      "\n",
      "\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "29681647\n",
      "PMC5909842\n",
      "Pubmed Record ID (PMID): 29681647\n",
      "Title: The multidimensional behavioural hypervolumes of two interacting species predict their space use and survival.\n",
      "Author Identifier (AUID): \n",
      "Author(s)(AU): ['Lichtenstein JLL', 'Wright CM', 'McEwen B', 'Pinter-Wollman N', 'Pruitt JN']\n",
      "Author affiliation (AD): Department of Ecology, Evolution & Marine Biology, University of California Santa Barbara, Santa Barbara, CA, U.S.A. Department of Ecology, Evolution & Marine Biology, University of California Santa Barbara, Santa Barbara, CA, U.S.A. Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, U.S.A. Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, U.S.A. Department of Ecology, Evolution & Marine Biology, University of California Santa Barbara, Santa Barbara, CA, U.S.A.\n",
      "Article Identifier/DOI (AID): ['10.1016/j.anbehav.2017.08.010 [doi]']\n",
      "https://doi.org/10.1016/j.anbehav.2017.08.010 \n",
      "\n",
      "DOI: ['10.1016/j.anbehav.2017.08.010 [doi]\n",
      "['R01 GM115509/GM/NIGMS NIH HHS/United States']\n",
      "\n",
      "\n",
      "29676225\n",
      "\n",
      "Pubmed Record ID (PMID): 29676225\n",
      "Title: Post-stroke social networks, depressive symptoms, and disability in Tanzania: A prospective study.\n",
      "Author Identifier (AUID): \n",
      "Author(s)(AU): ['Saadi A', \"Okeng'o K\", 'Biseko MR', 'Shayo AF', 'Mmbando TN', 'Grundy SJ', 'Xu A', 'Parker RA', 'Wibecan L', 'Iyer G', 'Onesmo PM', 'Kapina BN', 'Regenhardt RW', 'Mateen FJ']\n",
      "Author affiliation (AD): 1 National Clinical Scholars Program, University of California Los Angeles, Los Angeles, CA, USA. 2 108089 Muhimbili National Hospital , Dar es Salaam, Tanzania. 2 108089 Muhimbili National Hospital , Dar es Salaam, Tanzania. 2 108089 Muhimbili National Hospital , Dar es Salaam, Tanzania. 2 108089 Muhimbili National Hospital , Dar es Salaam, Tanzania. 3 Department of Neurology, Massachusetts General Hospital, Boston, MA, USA. 4 Biostatistics Center, Massachusetts General Hospital, Boston, MA, USA. 4 Biostatistics Center, Massachusetts General Hospital, Boston, MA, USA. 5 Harvard Medical School, Boston, USA. 6 Massachusetts General Hospital, Boston, MA, USA. 7 Harvard T.H. Chan School of Public Health, Boston, MA, USA. 2 108089 Muhimbili National Hospital , Dar es Salaam, Tanzania. 2 108089 Muhimbili National Hospital , Dar es Salaam, Tanzania. 8 Partners Neurology Residency, Massachusetts General Hospital and Brigham and Women's Hospital, Boston, MA, USA. 5 Harvard Medical School, Boston, USA. 6 Massachusetts General Hospital, Boston, MA, USA.\n",
      "Article Identifier/DOI (AID): ['10.1177/1747493018772788 [doi]']\n",
      "https://doi.org/10.1177/1747493018772788 \n",
      "\n",
      "DOI: ['10.1177/1747493018772788 [doi]\n",
      "\n",
      "\n",
      "\n",
      "29673526\n",
      "\n",
      "Pubmed Record ID (PMID): 29673526\n",
      "Title: Genetic Reporters of Neuronal Activity: c-Fos and G-CaMP6.\n",
      "Author Identifier (AUID): \n",
      "Author(s)(AU): ['Hudson AE']\n",
      "Author affiliation (AD): UCLA, Los Angeles, CA, United States. Electronic address: ahudson@mednet.ucla.edu.\n",
      "Article Identifier/DOI (AID): ['S0076-6879(18)30036-3 [pii]', '10.1016/bs.mie.2018.01.023 [doi]']\n",
      "\n",
      "No DOI ?!?!?\n",
      "\n",
      "\n",
      "\n",
      "29672601\n",
      "\n",
      "Pubmed Record ID (PMID): 29672601\n",
      "Title: Expression of immune checkpoint regulators, cytotoxic T lymphocyte antigen 4 (CTLA-4) and programmed death-ligand 1 (PD-L1), in female breast carcinomas.\n",
      "Author Identifier (AUID): ['ORCID: http://orcid.org/0000-0002-9986-8058']\n",
      "Author(s)(AU): ['Kassardjian A', 'Shintaku PI', 'Moatamed NA']\n",
      "Author affiliation (AD): Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America. Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America. Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America.\n",
      "Article Identifier/DOI (AID): ['10.1371/journal.pone.0195958 [doi]', 'PONE-D-18-05387 [pii]']\n",
      "https://doi.org/10.1371/journal.pone.0195958 \n",
      "\n",
      "DOI: ['10.1371/journal.pone.0195958 [doi]\n",
      "\n",
      "\n",
      "\n",
      "29671273\n",
      "\n",
      "Pubmed Record ID (PMID): 29671273\n",
      "Title: Intravital Imaging of Human Melanoma Cells in the Mouse Ear Skin by Two-Photon Excitation Microscopy.\n",
      "Author Identifier (AUID): \n",
      "Author(s)(AU): ['Bentolila NY', 'Barnhill RL', 'Lugassy C', 'Bentolila LA']\n",
      "Author affiliation (AD): Genesis Innovation Lab, YULA School, Los Angeles, CA, USA. Department of Pathology, Institut Curie, University of Paris Rene Descartes, Paris, France. Department of Translational Research, Institut Curie, Paris, France. California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA, USA. lbento@chem.ucla.edu. Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA. lbento@chem.ucla.edu.\n",
      "Article Identifier/DOI (AID): ['10.1007/978-1-4939-7724-6_15 [doi]']\n",
      "https://doi.org/10.1007/978-1-4939-7724-6_15 \n",
      "\n",
      "DOI: ['10.1007/978-1-4939-7724-6_15 [doi]\n",
      "\n",
      "\n",
      "\n",
      "29671268\n",
      "\n",
      "Pubmed Record ID (PMID): 29671268\n",
      "Title: Using YFP as a Reporter of Gene Expression in the Green Alga Chlamydomonas reinhardtii.\n",
      "Author Identifier (AUID): \n",
      "Author(s)(AU): ['Blaby-Haas CE', 'Page MD', 'Merchant SS']\n",
      "Author affiliation (AD): Department of Biology, Brookhaven National Laboratory, Upton, NY, USA. cblaby@bnl.gov. Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA. Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA. Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA, USA.\n",
      "Article Identifier/DOI (AID): ['10.1007/978-1-4939-7724-6_10 [doi]']\n",
      "https://doi.org/10.1007/978-1-4939-7724-6_10 \n",
      "\n",
      "DOI: ['10.1007/978-1-4939-7724-6_10 [doi]\n",
      "\n",
      "\n",
      "\n",
      "29671267\n",
      "\n",
      "Pubmed Record ID (PMID): 29671267\n",
      "Title: Reporter Gene Assays Using Viral Functional Genomics Libraries.\n",
      "Author Identifier (AUID): \n",
      "Author(s)(AU): ['Welch G', 'Damoiseaux R', 'Miraglia L']\n",
      "Author affiliation (AD): Department of Genomics, The Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA. Functional Genomics Screening Team, The Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA. Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA. California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA, USA. Johnsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA. Department of Genomics, The Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA. miraglia@gnf.org. Functional Genomics Screening Team, The Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA. miraglia@gnf.org.\n",
      "Article Identifier/DOI (AID): ['10.1007/978-1-4939-7724-6_9 [doi]']\n",
      "https://doi.org/10.1007/978-1-4939-7724-6_9 \n",
      "\n",
      "DOI: ['10.1007/978-1-4939-7724-6_9 [doi]\n",
      "\n",
      "\n",
      "\n",
      "29671266\n",
      "\n",
      "Pubmed Record ID (PMID): 29671266\n",
      "Title: Reporter Gene Assays Using Transfectable Functional Genomics Libraries.\n",
      "Author Identifier (AUID): \n",
      "Author(s)(AU): ['Welch G', 'Damoiseaux R', 'Miraglia L']\n",
      "Author affiliation (AD): Department of Genomics, The Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA. Functional Genomics Screening Team, The Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA. Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA. California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA, USA. Johnsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA. Department of Genomics, The Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA. miraglia@gnf.org. Functional Genomics Screening Team, The Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA. miraglia@gnf.org.\n",
      "Article Identifier/DOI (AID): ['10.1007/978-1-4939-7724-6_8 [doi]']\n",
      "https://doi.org/10.1007/978-1-4939-7724-6_8 \n",
      "\n",
      "DOI: ['10.1007/978-1-4939-7724-6_8 [doi]\n",
      "\n",
      "\n",
      "\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "29671265\n",
      "\n",
      "Pubmed Record ID (PMID): 29671265\n",
      "Title: Making It All Work: Functional Genomics and Reporter Gene Assays.\n",
      "Author Identifier (AUID): \n",
      "Author(s)(AU): ['Welch G', 'Damoiseaux R', 'Miraglia L']\n",
      "Author affiliation (AD): Department of Genomics, The Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA. Functional Genomics Screening Team, The Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA. Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA. California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA, USA. Johnsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA. Department of Genomics, The Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA. miraglia@gnf.org. Functional Genomics Screening Team, The Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA. miraglia@gnf.org.\n",
      "Article Identifier/DOI (AID): ['10.1007/978-1-4939-7724-6_7 [doi]']\n",
      "https://doi.org/10.1007/978-1-4939-7724-6_7 \n",
      "\n",
      "DOI: ['10.1007/978-1-4939-7724-6_7 [doi]\n",
      "\n",
      "\n",
      "\n",
      "29671264\n",
      "\n",
      "Pubmed Record ID (PMID): 29671264\n",
      "Title: High-Throughput Screening of a Luciferase Reporter of Gene Silencing on the Inactive X Chromosome.\n",
      "Author Identifier (AUID): \n",
      "Author(s)(AU): ['Keegan A', 'Plath K', 'Damoiseaux R']\n",
      "Author affiliation (AD): Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA. Johnsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA. Molecular Biology Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA. Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA. Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA. Johnsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA. Molecular Biology Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA. Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA. Johnsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA. rdamoiseaux@mednet.ucla.edu. Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA. rdamoiseaux@mednet.ucla.edu. California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA, USA. rdamoiseaux@mednet.ucla.edu.\n",
      "Article Identifier/DOI (AID): ['10.1007/978-1-4939-7724-6_6 [doi]']\n",
      "https://doi.org/10.1007/978-1-4939-7724-6_6 \n",
      "\n",
      "DOI: ['10.1007/978-1-4939-7724-6_6 [doi]\n",
      "\n",
      "\n",
      "\n",
      "29670931\n",
      "PMC5903406\n",
      "Pubmed Record ID (PMID): 29670931\n",
      "Title: EMERGEncy ID NET: Review of a 20-Year Multisite Emergency Department Emerging Infections Research Network.\n",
      "Author Identifier (AUID): \n",
      "Author(s)(AU): ['Santibanez S', 'Fischer LS', 'Krishnadasan A', 'Sederdahl B', 'Merlin T', 'Moran GJ', 'Talan DA']\n",
      "Author affiliation (AD): Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia. Rollins School of Public Health, Emory University, Atlanta, Georgia. Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia. Department of Emergency Medicine, Olive View-UCLA Medical Center, Los Angeles, California. Rollins School of Public Health, Emory University, Atlanta, Georgia. Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia. Department of Emergency Medicine, Olive View-UCLA Medical Center, Los Angeles, California. Department of Emergency Medicine, Olive View-UCLA Medical Center, Los Angeles, California.\n",
      "Article Identifier/DOI (AID): ['10.1093/ofid/ofx218 [doi]', 'ofx218 [pii]']\n",
      "https://doi.org/10.1093/ofid/ofx218 \n",
      "\n",
      "DOI: ['10.1093/ofid/ofx218 [doi]\n",
      "\n",
      "\n",
      "\n",
      "29670925\n",
      "PMC5895463\n",
      "Pubmed Record ID (PMID): 29670925\n",
      "Title: Pseudocirrhosis in a Patient with New-Onset Dysphagia and History of Ovarian Carcinoma.\n",
      "Author Identifier (AUID): \n",
      "Author(s)(AU): ['Zanazanian A', 'Kalani A', 'Tabibian JH']\n",
      "Author affiliation (AD): Division of Gastroenterology, Olive View-UCLA Medical Center, Sylmar, CA. Division of Digestive Diseases, University of California-Los Angeles, Los Angeles, CA. Division of Gastroenterology, Olive View-UCLA Medical Center, Sylmar, CA. Division of Gastroenterology, University of Pennsylvania, Philadelphia, PA.\n",
      "Article Identifier/DOI (AID): ['10.14309/crj.2018.29 [doi]', 'crj.2018.29 [pii]']\n",
      "https://doi.org/10.14309/crj.2018.29 \n",
      "\n",
      "DOI: ['10.14309/crj.2018.29 [doi]\n",
      "\n",
      "\n",
      "\n"
     ]
    }
   ],
   "source": [
    "handle = Entrez.esearch(db=\"pubmed\", term=query)\n",
    "record=Entrez.read(handle)\n",
    "idList = record[\"IdList\"]\n",
    "print(idList)\n",
    "record[\"Count\"]\n",
    "handle = Entrez.efetch(db=\"pubmed\", id=idList, rettype=\"medline\", retmode=\"json\")\n",
    "records = Medline.parse(handle)\n",
    "Entrez.email = 'jamison@library.ucla.edu'\n",
    "# declaring defaultdict\n",
    "# sets default value 'Key Not found' to absent keys\n",
    "#records = collections.defaultdict(lambda : 'Key Not found')\n",
    "# How does it work? Simple. You can do one of two things to get directed to the \"polite pool\":\n",
    "# Include a \"mailto\" parameter in your query. For example:\n",
    "\n",
    "#  function to extract the doi from the line of text it's in\n",
    "\n",
    "#  regular expressions library\n",
    "import re\n",
    "def getDOI(textLine):\n",
    "    m = re.search(r\"\\[\\'10.*\\s\\[doi\\]\", textLine)\n",
    "    if m:\n",
    "        doiLine = m.group(0)\n",
    "        doiLine = re.sub(\"\\[\\'\", \"\", doiLine)\n",
    "        doiLine = re.sub(\"\\[doi\\]\", \"\", doiLine)   \n",
    "        #  https://doi.org/10.1021/acscatal.7b03688 \n",
    "        print(\"https://doi.org/\" + doiLine)\n",
    "        print(\"\\nDOI: \" + m.group(0))\n",
    "    else:\n",
    "        print(\"\\nNo DOI ?!?!?\")\n",
    "    return;\n",
    "    \n",
    "    \n",
    "works=Works()\n",
    "for record in records:\n",
    "    # print(record[\"PMID\"])\n",
    "    PMID = record[\"PMID\"]\n",
    "    print(PMID) \n",
    "    PMC = record.get('PMC', \"\")\n",
    "    print(PMC) \n",
    "    # print(\"DOI: ID Converter API\")\n",
    "    # getDOI = converterBase + \"?tool=my_tool&email=jamison@library.ucla.edu&ids=\" + PMID\n",
    "    # print(getDOI)\n",
    "    print(\"Pubmed Record ID (PMID): \" + record.get('PMID', \"\"))\n",
    "    # print(record[\"TI\"])\n",
    "    print(\"Title: \" + record.get('TI', \"\"))\n",
    "    # print(record[\"AUID\"])\n",
    "    print(\"Author Identifier (AUID): \" + str(record.get('AUID', \"\")))\n",
    "    # print(record[\"AU\"])\n",
    "    print(\"Author(s)(AU): \" + str(record.get('AU', \"\")) )   \n",
    "    # print(record[\"AID\"])\n",
    "    print(\"Author affiliation (AD): \" + str(record.get('AD', \"\")))  \n",
    "    # print(record[\"AD\"])\n",
    "    # affiliation\n",
    "    doiLine = (\"Article Identifier/DOI (AID): \" + str(record.get('AID', \"\")))\n",
    "    print(doiLine)\n",
    "    getDOI(doiLine)\n",
    "    # print(\"Article Identifier/DOI (AID): \" + str(record.get('AID', \"\")))\n",
    "    # print(record[\"GR\"])\n",
    "    # grant number\n",
    "    print(record.get('GR', \"\"))      \n",
    "    print(\"\\n\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['29702676', '29695168', '29692895', '29686938', '29686739', '29686725', '29682398', '29682382', '29681647', '29676225', '29673526', '29672601', '29671273', '29671268', '29671267', '29671266', '29671265', '29671264', '29670931', '29670925']\n",
      "29702676,29695168,29692895,29686938,29686739,29686725,29682398,29682382,29681647,29676225,29673526,29672601,29671273,29671268,29671267,29671266,29671265,29671264,29670931,29670925\n"
     ]
    }
   ],
   "source": [
    "# f = open('/home/jmjamison/work/pubmedExtracts/outputIdListFull.txt', \"w\")\n",
    "# comment out so this will default to the default working directory# \n",
    "# write out the id list - result\n",
    "f = open('outputIdListFull.txt', \"w\")\n",
    "# first esearch and then efetch\n",
    "handle=Entrez.esearch(db=\"pubmed\", term=query)\n",
    "# read - sould now be a Python dictionary/list\n",
    "searchResult=Entrez.read(handle)\n",
    "handle.close()\n",
    "idList=searchResult[\"IdList\"]\n",
    "ids= ','.join(idList)\n",
    "listCount=searchResult[\"Count\"]# now have a list of record ids\n",
    "#print(idList)\n",
    "#print(ids)\n",
    "#print(searchResult)\n",
    "f.write(str(searchResult[\"IdList\"]))\n",
    "# now have a list of record ids\n",
    "print(idList)\n",
    "print(ids)\n",
    "#print(searchResult)\n",
    "f.close()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### function to extract the doi from the line of text it's in\n",
    "#### regular expressions library"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "#  function to extract the doi from the line of text it's in\n",
    "#  regular expressions library\n",
    "import re\n",
    "\n",
    "def getDOI(textLine):\n",
    "    # extract the doi from the AID author id line\n",
    "    m = re.search(r\"\\[\\'10.*\\s\\[doi\\]\", textLine)\n",
    "    if m:\n",
    "        doiLine = m.group(0)\n",
    "        doiLine = re.sub(\"\\[\\'\", \"\", doiLine)\n",
    "        doiLine = re.sub(\"\\[doi\\]*\", \"\", doiLine)   \n",
    "        #  https://doi.org/10.1021/acscatal.7b03688 \n",
    "        f.write(\"https://doi.org/\" + doiLine)\n",
    "    else:\n",
    "        f.write(\"--No DOI ?!?!?--\")\n",
    "    return;"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### save output as csv"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "21639\n",
      "Total records: 21639\n",
      "Total records processed: 21\n"
     ]
    }
   ],
   "source": [
    "from random import randint\n",
    "import time\n",
    "\n",
    "f = open('outputPubMed.csv', \"w\")\n",
    "\n",
    "# first esearch and then efetch\n",
    "searchHandle=Entrez.esearch(db=\"pubmed\", term=query)\n",
    "\n",
    "# read - sould now be a Python dictionary/list\n",
    "idList=searchResult[\"IdList\"]\n",
    "ids= ','.join(idList)\n",
    "\n",
    "searchResult=Entrez.read(searchHandle)\n",
    "fetchHandle = Entrez.efetch(db=\"pubmed\", id=ids, rettype=\"medline\", retmode=\"text\")\n",
    "handle.close()\n",
    "\n",
    "listCount=searchResult[\"Count\"]\n",
    "print(listCount)\n",
    "# now have a list of record ids\n",
    "\n",
    "records = Medline.parse(fetchHandle)\n",
    "print(\"Total records: \" + listCount)\n",
    "\n",
    "# write out the column headers \n",
    "f.write(\"Pubmed Record*AID-Article Id-DOI*RF-Number of References*Title*AUID-Author Id*AU-Author*GR-Grant Number*AD-Affiliation\\n\")\n",
    "i = 1\n",
    "for record in records:\n",
    "    f.write(record.get('PMID', \"\"))\n",
    "    f.write(\"*\")\n",
    "    #   getDOI(line) will pull out the doi portion of the line and add the https doi org at beginning\n",
    "    doiLine = (str(record.get('AID', \"\")))\n",
    "    getDOI(doiLine)\n",
    "    f.write(\"*\")\n",
    "    f.write(record.get('TI', \"\"))\n",
    "    f.write(\"*\")\n",
    "    f.write(str(record.get('AUID', \"\")))\n",
    "    f.write(\"*\")\n",
    "    f.write(str(record.get('AU', \"\")))\n",
    "    f.write(\"*\")     \n",
    "    f.write(str(record.get('GR', \"\")))\n",
    "    f.write(\"*\")    \n",
    "    f.write(str(record.get('AD', \"\")))\n",
    "    f.write(\"\\n\")\n",
    "    \n",
    "    i = i+1\n",
    "\n",
    "f.close()\n",
    "\n",
    "print(\"Total records processed: \" + str(i))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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