DOI_from_Crossref.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import urllib.request\n",
    "import json"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "base_url = 'https://api.crossref.org/works/'\n",
    "doi = '10.1371/journal.pcbi.1004668'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "full_url = base_url + doi"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "https://api.crossref.org/works/10.1371/journal.pcbi.1004668\n"
     ]
    }
   ],
   "source": [
    "print(full_url)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "doi_json_data = urllib.request.urlopen(full_url).read()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "b'{\"status\":\"ok\",\"message-type\":\"work\",\"message-version\":\"1.0.0\",\"message\":{\"indexed\":{\"date-parts\":[[2019,9,16]],\"date-time\":\"2019-09-16T23:23:14Z\",\"timestamp\":1568676194886},\"reference-count\":6,\"publisher\":\"Public Library of Science (PLoS)\",\"issue\":\"1\",\"license\":[{\"URL\":\"http:\\\\/\\\\/creativecommons.org\\\\/licenses\\\\/by\\\\/4.0\\\\/\",\"start\":{\"date-parts\":[[2016,1,19]],\"date-time\":\"2016-01-19T00:00:00Z\",\"timestamp\":1453161600000},\"delay-in-days\":0,\"content-version\":\"vor\"}],\"content-domain\":{\"domain\":[\"www.ploscompbiol.org\"],\"crossmark-restriction\":false},\"short-container-title\":[\"PLoS Comput Biol\"],\"DOI\":\"10.1371\\\\/journal.pcbi.1004668\",\"type\":\"journal-article\",\"created\":{\"date-parts\":[[2016,1,19]],\"date-time\":\"2016-01-19T21:35:29Z\",\"timestamp\":1453239329000},\"page\":\"e1004668\",\"update-policy\":\"http:\\\\/\\\\/dx.doi.org\\\\/10.1371\\\\/journal.pcbi.corrections_policy\",\"source\":\"Crossref\",\"is-referenced-by-count\":38,\"title\":[\"A Quick Introduction to Version Control with Git and GitHub\"],\"prefix\":\"10.1371\",\"volume\":\"12\",\"author\":[{\"given\":\"John D.\",\"family\":\"Blischak\",\"sequence\":\"first\",\"affiliation\":[]},{\"given\":\"Emily R.\",\"family\":\"Davenport\",\"sequence\":\"additional\",\"affiliation\":[]},{\"given\":\"Greg\",\"family\":\"Wilson\",\"sequence\":\"additional\",\"affiliation\":[]}],\"member\":\"340\",\"published-online\":{\"date-parts\":[[2016,1,19]]},\"reference\":[{\"key\":\"ref1\",\"doi-asserted-by\":\"crossref\",\"first-page\":\"7\",\"DOI\":\"10.1186\\\\/1751-0473-8-7\",\"article-title\":\"Git can facilitate greater reproducibility and increased transparency in science\",\"volume\":\"8\",\"author\":\"K Ram\",\"year\":\"2013\",\"journal-title\":\"Source Code Biol Med\"},{\"key\":\"ref2\",\"doi-asserted-by\":\"crossref\",\"first-page\":\"e1001745\",\"DOI\":\"10.1371\\\\/journal.pbio.1001745\",\"article-title\":\"Best practices for scientific computing\",\"volume\":\"12\",\"author\":\"G Wilson\",\"year\":\"2014\",\"journal-title\":\"PLoS Biol\"},{\"key\":\"ref3\",\"doi-asserted-by\":\"crossref\",\"first-page\":\"57\",\"DOI\":\"10.1038\\\\/nature11247\",\"article-title\":\"An integrated encyclopedia of DNA elements in the human genome\",\"volume\":\"489\",\"author\":\"B Bernstein\",\"year\":\"2012\",\"journal-title\":\"Nature\"},{\"key\":\"ref4\",\"doi-asserted-by\":\"crossref\",\"first-page\":\"e1003326\",\"DOI\":\"10.1371\\\\/journal.pcbi.1003326\",\"article-title\":\"Practical guidelines for the comprehensive analysis of ChIP-seq data\",\"volume\":\"9\",\"author\":\"T Bailey\",\"year\":\"2013\",\"journal-title\":\"PLoS Comput Biol\"},{\"key\":\"ref5\",\"doi-asserted-by\":\"crossref\",\"first-page\":\"e1000424\",\"DOI\":\"10.1371\\\\/journal.pcbi.1000424\",\"article-title\":\"A quick guide to organizing computational biology projects\",\"volume\":\"5\",\"author\":\"W Noble\",\"year\":\"2009\",\"journal-title\":\"PLoS Comput Biol\"},{\"key\":\"ref6\",\"doi-asserted-by\":\"crossref\",\"first-page\":\"e1002598\",\"DOI\":\"10.1371\\\\/journal.pcbi.1002598\",\"article-title\":\"A quick guide to software licensing for the scientist-programmer\",\"volume\":\"8\",\"author\":\"A Morin\",\"year\":\"2012\",\"journal-title\":\"PLoS Comput Biol\"}],\"container-title\":[\"PLOS Computational Biology\"],\"original-title\":[],\"language\":\"en\",\"link\":[{\"URL\":\"http:\\\\/\\\\/dx.plos.org\\\\/10.1371\\\\/journal.pcbi.1004668\",\"content-type\":\"unspecified\",\"content-version\":\"vor\",\"intended-application\":\"similarity-checking\"}],\"deposited\":{\"date-parts\":[[2017,6,24]],\"date-time\":\"2017-06-24T04:04:33Z\",\"timestamp\":1498277073000},\"score\":1.0,\"subtitle\":[],\"editor\":[{\"given\":\"Francis\",\"family\":\"Ouellette\",\"sequence\":\"first\",\"affiliation\":[]}],\"short-title\":[],\"issued\":{\"date-parts\":[[2016,1,19]]},\"references-count\":6,\"journal-issue\":{\"published-online\":{\"date-parts\":[[2016,1,19]]},\"issue\":\"1\"},\"URL\":\"http:\\\\/\\\\/dx.doi.org\\\\/10.1371\\\\/journal.pcbi.1004668\",\"relation\":{\"cites\":[]},\"ISSN\":[\"1553-7358\"],\"issn-type\":[{\"value\":\"1553-7358\",\"type\":\"electronic\"}]}}'\n"
     ]
    }
   ],
   "source": [
    "print(doi_json_data)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "doi_data = json.loads(doi_json_data)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'status': 'ok', 'message-type': 'work', 'message-version': '1.0.0', 'message': {'indexed': {'date-parts': [[2019, 9, 16]], 'date-time': '2019-09-16T23:23:14Z', 'timestamp': 1568676194886}, 'reference-count': 6, 'publisher': 'Public Library of Science (PLoS)', 'issue': '1', 'license': [{'URL': 'http://creativecommons.org/licenses/by/4.0/', 'start': {'date-parts': [[2016, 1, 19]], 'date-time': '2016-01-19T00:00:00Z', 'timestamp': 1453161600000}, 'delay-in-days': 0, 'content-version': 'vor'}], 'content-domain': {'domain': ['www.ploscompbiol.org'], 'crossmark-restriction': False}, 'short-container-title': ['PLoS Comput Biol'], 'DOI': '10.1371/journal.pcbi.1004668', 'type': 'journal-article', 'created': {'date-parts': [[2016, 1, 19]], 'date-time': '2016-01-19T21:35:29Z', 'timestamp': 1453239329000}, 'page': 'e1004668', 'update-policy': 'http://dx.doi.org/10.1371/journal.pcbi.corrections_policy', 'source': 'Crossref', 'is-referenced-by-count': 38, 'title': ['A Quick Introduction to Version Control with Git and GitHub'], 'prefix': '10.1371', 'volume': '12', 'author': [{'given': 'John D.', 'family': 'Blischak', 'sequence': 'first', 'affiliation': []}, {'given': 'Emily R.', 'family': 'Davenport', 'sequence': 'additional', 'affiliation': []}, {'given': 'Greg', 'family': 'Wilson', 'sequence': 'additional', 'affiliation': []}], 'member': '340', 'published-online': {'date-parts': [[2016, 1, 19]]}, 'reference': [{'key': 'ref1', 'doi-asserted-by': 'crossref', 'first-page': '7', 'DOI': '10.1186/1751-0473-8-7', 'article-title': 'Git can facilitate greater reproducibility and increased transparency in science', 'volume': '8', 'author': 'K Ram', 'year': '2013', 'journal-title': 'Source Code Biol Med'}, {'key': 'ref2', 'doi-asserted-by': 'crossref', 'first-page': 'e1001745', 'DOI': '10.1371/journal.pbio.1001745', 'article-title': 'Best practices for scientific computing', 'volume': '12', 'author': 'G Wilson', 'year': '2014', 'journal-title': 'PLoS Biol'}, {'key': 'ref3', 'doi-asserted-by': 'crossref', 'first-page': '57', 'DOI': '10.1038/nature11247', 'article-title': 'An integrated encyclopedia of DNA elements in the human genome', 'volume': '489', 'author': 'B Bernstein', 'year': '2012', 'journal-title': 'Nature'}, {'key': 'ref4', 'doi-asserted-by': 'crossref', 'first-page': 'e1003326', 'DOI': '10.1371/journal.pcbi.1003326', 'article-title': 'Practical guidelines for the comprehensive analysis of ChIP-seq data', 'volume': '9', 'author': 'T Bailey', 'year': '2013', 'journal-title': 'PLoS Comput Biol'}, {'key': 'ref5', 'doi-asserted-by': 'crossref', 'first-page': 'e1000424', 'DOI': '10.1371/journal.pcbi.1000424', 'article-title': 'A quick guide to organizing computational biology projects', 'volume': '5', 'author': 'W Noble', 'year': '2009', 'journal-title': 'PLoS Comput Biol'}, {'key': 'ref6', 'doi-asserted-by': 'crossref', 'first-page': 'e1002598', 'DOI': '10.1371/journal.pcbi.1002598', 'article-title': 'A quick guide to software licensing for the scientist-programmer', 'volume': '8', 'author': 'A Morin', 'year': '2012', 'journal-title': 'PLoS Comput Biol'}], 'container-title': ['PLOS Computational Biology'], 'original-title': [], 'language': 'en', 'link': [{'URL': 'http://dx.plos.org/10.1371/journal.pcbi.1004668', 'content-type': 'unspecified', 'content-version': 'vor', 'intended-application': 'similarity-checking'}], 'deposited': {'date-parts': [[2017, 6, 24]], 'date-time': '2017-06-24T04:04:33Z', 'timestamp': 1498277073000}, 'score': 1.0, 'subtitle': [], 'editor': [{'given': 'Francis', 'family': 'Ouellette', 'sequence': 'first', 'affiliation': []}], 'short-title': [], 'issued': {'date-parts': [[2016, 1, 19]]}, 'references-count': 6, 'journal-issue': {'published-online': {'date-parts': [[2016, 1, 19]]}, 'issue': '1'}, 'URL': 'http://dx.doi.org/10.1371/journal.pcbi.1004668', 'relation': {'cites': []}, 'ISSN': ['1553-7358'], 'issn-type': [{'value': '1553-7358', 'type': 'electronic'}]}}\n"
     ]
    }
   ],
   "source": [
    "print(doi_data)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "dict"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "type(doi_data)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "dict_keys(['status', 'message-type', 'message-version', 'message'])"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "doi_data.keys()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\n",
      "  \"status\": \"ok\",\n",
      "  \"message-type\": \"work\",\n",
      "  \"message-version\": \"1.0.0\",\n",
      "  \"message\": {\n",
      "    \"indexed\": {\n",
      "      \"date-parts\": [\n",
      "        [\n",
      "          2019,\n",
      "          9,\n",
      "          16\n",
      "        ]\n",
      "      ],\n",
      "      \"date-time\": \"2019-09-16T23:23:14Z\",\n",
      "      \"timestamp\": 1568676194886\n",
      "    },\n",
      "    \"reference-count\": 6,\n",
      "    \"publisher\": \"Public Library of Science (PLoS)\",\n",
      "    \"issue\": \"1\",\n",
      "    \"license\": [\n",
      "      {\n",
      "        \"URL\": \"http://creativecommons.org/licenses/by/4.0/\",\n",
      "        \"start\": {\n",
      "          \"date-parts\": [\n",
      "            [\n",
      "              2016,\n",
      "              1,\n",
      "              19\n",
      "            ]\n",
      "          ],\n",
      "          \"date-time\": \"2016-01-19T00:00:00Z\",\n",
      "          \"timestamp\": 1453161600000\n",
      "        },\n",
      "        \"delay-in-days\": 0,\n",
      "        \"content-version\": \"vor\"\n",
      "      }\n",
      "    ],\n",
      "    \"content-domain\": {\n",
      "      \"domain\": [\n",
      "        \"www.ploscompbiol.org\"\n",
      "      ],\n",
      "      \"crossmark-restriction\": false\n",
      "    },\n",
      "    \"short-container-title\": [\n",
      "      \"PLoS Comput Biol\"\n",
      "    ],\n",
      "    \"DOI\": \"10.1371/journal.pcbi.1004668\",\n",
      "    \"type\": \"journal-article\",\n",
      "    \"created\": {\n",
      "      \"date-parts\": [\n",
      "        [\n",
      "          2016,\n",
      "          1,\n",
      "          19\n",
      "        ]\n",
      "      ],\n",
      "      \"date-time\": \"2016-01-19T21:35:29Z\",\n",
      "      \"timestamp\": 1453239329000\n",
      "    },\n",
      "    \"page\": \"e1004668\",\n",
      "    \"update-policy\": \"http://dx.doi.org/10.1371/journal.pcbi.corrections_policy\",\n",
      "    \"source\": \"Crossref\",\n",
      "    \"is-referenced-by-count\": 38,\n",
      "    \"title\": [\n",
      "      \"A Quick Introduction to Version Control with Git and GitHub\"\n",
      "    ],\n",
      "    \"prefix\": \"10.1371\",\n",
      "    \"volume\": \"12\",\n",
      "    \"author\": [\n",
      "      {\n",
      "        \"given\": \"John D.\",\n",
      "        \"family\": \"Blischak\",\n",
      "        \"sequence\": \"first\",\n",
      "        \"affiliation\": []\n",
      "      },\n",
      "      {\n",
      "        \"given\": \"Emily R.\",\n",
      "        \"family\": \"Davenport\",\n",
      "        \"sequence\": \"additional\",\n",
      "        \"affiliation\": []\n",
      "      },\n",
      "      {\n",
      "        \"given\": \"Greg\",\n",
      "        \"family\": \"Wilson\",\n",
      "        \"sequence\": \"additional\",\n",
      "        \"affiliation\": []\n",
      "      }\n",
      "    ],\n",
      "    \"member\": \"340\",\n",
      "    \"published-online\": {\n",
      "      \"date-parts\": [\n",
      "        [\n",
      "          2016,\n",
      "          1,\n",
      "          19\n",
      "        ]\n",
      "      ]\n",
      "    },\n",
      "    \"reference\": [\n",
      "      {\n",
      "        \"key\": \"ref1\",\n",
      "        \"doi-asserted-by\": \"crossref\",\n",
      "        \"first-page\": \"7\",\n",
      "        \"DOI\": \"10.1186/1751-0473-8-7\",\n",
      "        \"article-title\": \"Git can facilitate greater reproducibility and increased transparency in science\",\n",
      "        \"volume\": \"8\",\n",
      "        \"author\": \"K Ram\",\n",
      "        \"year\": \"2013\",\n",
      "        \"journal-title\": \"Source Code Biol Med\"\n",
      "      },\n",
      "      {\n",
      "        \"key\": \"ref2\",\n",
      "        \"doi-asserted-by\": \"crossref\",\n",
      "        \"first-page\": \"e1001745\",\n",
      "        \"DOI\": \"10.1371/journal.pbio.1001745\",\n",
      "        \"article-title\": \"Best practices for scientific computing\",\n",
      "        \"volume\": \"12\",\n",
      "        \"author\": \"G Wilson\",\n",
      "        \"year\": \"2014\",\n",
      "        \"journal-title\": \"PLoS Biol\"\n",
      "      },\n",
      "      {\n",
      "        \"key\": \"ref3\",\n",
      "        \"doi-asserted-by\": \"crossref\",\n",
      "        \"first-page\": \"57\",\n",
      "        \"DOI\": \"10.1038/nature11247\",\n",
      "        \"article-title\": \"An integrated encyclopedia of DNA elements in the human genome\",\n",
      "        \"volume\": \"489\",\n",
      "        \"author\": \"B Bernstein\",\n",
      "        \"year\": \"2012\",\n",
      "        \"journal-title\": \"Nature\"\n",
      "      },\n",
      "      {\n",
      "        \"key\": \"ref4\",\n",
      "        \"doi-asserted-by\": \"crossref\",\n",
      "        \"first-page\": \"e1003326\",\n",
      "        \"DOI\": \"10.1371/journal.pcbi.1003326\",\n",
      "        \"article-title\": \"Practical guidelines for the comprehensive analysis of ChIP-seq data\",\n",
      "        \"volume\": \"9\",\n",
      "        \"author\": \"T Bailey\",\n",
      "        \"year\": \"2013\",\n",
      "        \"journal-title\": \"PLoS Comput Biol\"\n",
      "      },\n",
      "      {\n",
      "        \"key\": \"ref5\",\n",
      "        \"doi-asserted-by\": \"crossref\",\n",
      "        \"first-page\": \"e1000424\",\n",
      "        \"DOI\": \"10.1371/journal.pcbi.1000424\",\n",
      "        \"article-title\": \"A quick guide to organizing computational biology projects\",\n",
      "        \"volume\": \"5\",\n",
      "        \"author\": \"W Noble\",\n",
      "        \"year\": \"2009\",\n",
      "        \"journal-title\": \"PLoS Comput Biol\"\n",
      "      },\n",
      "      {\n",
      "        \"key\": \"ref6\",\n",
      "        \"doi-asserted-by\": \"crossref\",\n",
      "        \"first-page\": \"e1002598\",\n",
      "        \"DOI\": \"10.1371/journal.pcbi.1002598\",\n",
      "        \"article-title\": \"A quick guide to software licensing for the scientist-programmer\",\n",
      "        \"volume\": \"8\",\n",
      "        \"author\": \"A Morin\",\n",
      "        \"year\": \"2012\",\n",
      "        \"journal-title\": \"PLoS Comput Biol\"\n",
      "      }\n",
      "    ],\n",
      "    \"container-title\": [\n",
      "      \"PLOS Computational Biology\"\n",
      "    ],\n",
      "    \"original-title\": [],\n",
      "    \"language\": \"en\",\n",
      "    \"link\": [\n",
      "      {\n",
      "        \"URL\": \"http://dx.plos.org/10.1371/journal.pcbi.1004668\",\n",
      "        \"content-type\": \"unspecified\",\n",
      "        \"content-version\": \"vor\",\n",
      "        \"intended-application\": \"similarity-checking\"\n",
      "      }\n",
      "    ],\n",
      "    \"deposited\": {\n",
      "      \"date-parts\": [\n",
      "        [\n",
      "          2017,\n",
      "          6,\n",
      "          24\n",
      "        ]\n",
      "      ],\n",
      "      \"date-time\": \"2017-06-24T04:04:33Z\",\n",
      "      \"timestamp\": 1498277073000\n",
      "    },\n",
      "    \"score\": 1.0,\n",
      "    \"subtitle\": [],\n",
      "    \"editor\": [\n",
      "      {\n",
      "        \"given\": \"Francis\",\n",
      "        \"family\": \"Ouellette\",\n",
      "        \"sequence\": \"first\",\n",
      "        \"affiliation\": []\n",
      "      }\n",
      "    ],\n",
      "    \"short-title\": [],\n",
      "    \"issued\": {\n",
      "      \"date-parts\": [\n",
      "        [\n",
      "          2016,\n",
      "          1,\n",
      "          19\n",
      "        ]\n",
      "      ]\n",
      "    },\n",
      "    \"references-count\": 6,\n",
      "    \"journal-issue\": {\n",
      "      \"published-online\": {\n",
      "        \"date-parts\": [\n",
      "          [\n",
      "            2016,\n",
      "            1,\n",
      "            19\n",
      "          ]\n",
      "        ]\n",
      "      },\n",
      "      \"issue\": \"1\"\n",
      "    },\n",
      "    \"URL\": \"http://dx.doi.org/10.1371/journal.pcbi.1004668\",\n",
      "    \"relation\": {\n",
      "      \"cites\": []\n",
      "    },\n",
      "    \"ISSN\": [\n",
      "      \"1553-7358\"\n",
      "    ],\n",
      "    \"issn-type\": [\n",
      "      {\n",
      "        \"value\": \"1553-7358\",\n",
      "        \"type\": \"electronic\"\n",
      "      }\n",
      "    ]\n",
      "  }\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "print(json.dumps(doi_data, indent = 2))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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