registries_analysis/notebooks/02-subjects&geographic.ipynb

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{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import ast\n",
"import csv\n",
"import json\n",
"import reverse_geocoder as rg\n",
"\n",
"import numpy as np\n",
"import pandas as pd\n",
"\n",
"import pycountry_convert\n",
"\n",
"import matplotlib.pyplot as plt\n",
"from matplotlib_venn import venn2, venn2_circles\n",
"\n",
"import plotly\n",
"from plotly.offline import iplot, init_notebook_mode\n",
"import plotly.graph_objs as go\n",
"import plotly.express as px\n",
"\n",
"pd.set_option('display.max_columns', None)"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"def country_to_countrycode(country):\n",
" if pd.isna(country):\n",
" return np.nan\n",
" else:\n",
" try:\n",
" return pycountry_convert.country_name_to_country_alpha3(country)\n",
" except:\n",
" return np.nan\n",
" \n",
"def countrycode_iso2_to_countrycode_iso3(country):\n",
" if pd.isna(country):\n",
" return np.nan\n",
" else:\n",
" try:\n",
" return pycountry_convert.country_name_to_country_alpha3(pycountry_convert.country_alpha2_to_country_name(country))\n",
" except:\n",
" return np.nan\n",
"\n",
"def countrycode_to_continent(country_code):\n",
" if pd.isna(country_code):\n",
" return np.nan\n",
" else:\n",
" try:\n",
" return pycountry_convert.country_alpha2_to_continent_code(pycountry_convert.country_alpha3_to_country_alpha2(country_code))\n",
" except:\n",
" return np.nan"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Loading datasets"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**re3data**"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
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" <td>[{'name': 'Images', 'scheme': 'parse'}, {'name...</td>\n",
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" <td>[dataProvider]</td>\n",
" <td>[US History]</td>\n",
" <td>[{'institutionName': 'The U.S. National Archiv...</td>\n",
" <td>[{\"policyName\": \"Contribution Policy\", \"policy...</td>\n",
" <td>{\"databaseAccessType\": \"open\", \"databaseAcces...</td>\n",
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" <td>[]</td>\n",
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" <td>no</td>\n",
" <td>{\"api\": \"https://www.archives.gov/developer#to...</td>\n",
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" <td>{\"syndication\": \"http://www.archives.gov/socia...</td>\n",
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" <td>2012-07-04</td>\n",
" <td>2021-05-25</td>\n",
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" </tr>\n",
" <tr>\n",
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" <td>r3d100000004</td>\n",
" <td>Datenbank Gesprochenes Deutsch</td>\n",
" <td>deu</td>\n",
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" <td>https://dgd.ids-mannheim.de/</td>\n",
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" <td>The \"Database for Spoken German (DGD)\" is a co...</td>\n",
" <td>eng</td>\n",
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" <td>{\"size\": \"34 corpora\", \"updatedp\": \"2020-02-03\"}</td>\n",
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" <td>[{\"policyName\": \"Erfurter Aufruf zur Sicherung...</td>\n",
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" <td>r3d100000005</td>\n",
" <td>UNC Dataverse</td>\n",
" <td>eng</td>\n",
" <td>[{'additionalName': 'University of North Carol...</td>\n",
" <td>https://dataverse.unc.edu/</td>\n",
" <td>[]</td>\n",
" <td>[\"https://dataverse.unc.edu/\", \"odumarchive@un...</td>\n",
" <td>UNC Dataverse is an open-source repository sof...</td>\n",
" <td>eng</td>\n",
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" <td>[institutional]</td>\n",
" <td>{\"size\": \"186 dataverses; 25.272 studies; 229....</td>\n",
" <td>2011</td>\n",
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" <td>[\"eng\"]</td>\n",
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" <td>[dataProvider, serviceProvider]</td>\n",
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" <td>[]</td>\n",
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" <td>restricted</td>\n",
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" <td>[\"ARK\", \"DOI\", \"PURL\", \"URN\", \"hdl\"]</td>\n",
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" </tr>\n",
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" <td>r3d100000006</td>\n",
" <td>Archaeology Data Service</td>\n",
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" <td>https://archaeologydataservice.ac.uk/</td>\n",
" <td>[FAIRsharing_doi:10.25504/FAIRsharing.hm1mfg]</td>\n",
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" <td>yes</td>\n",
" <td>{\"api\": \"https://archaeologydataservice.ac.uk/...</td>\n",
" <td>[\"DOI\"]</td>\n",
" <td>https://archaeologydataservice.ac.uk/advice/te...</td>\n",
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" </tr>\n",
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],
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2021-07-22 11:03:05 +02:00
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2021-07-22 11:03:05 +02:00
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2021-07-22 11:03:05 +02:00
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"4 [{\"policyName\": \"ADS Guides to good practice\",... \n",
"\n",
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" dataUploadLicense software \\\n",
"0 [] [\"DataVerse\"] \n",
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"4 [{\"dataUploadLicenseName\": \"Guidelines for Dep... [\"other\"] \n",
"\n",
" versioning api \\\n",
"0 NaN {} \n",
"1 no {\"api\": \"https://www.archives.gov/developer#to... \n",
"2 yes {} \n",
"3 yes {\"api\": \"https://guides.dataverse.org/en/lates... \n",
"4 yes {\"api\": \"https://archaeologydataservice.ac.uk/... \n",
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" pidSystem \\\n",
"0 [\"DOI\"] \n",
"1 [\"none\"] \n",
"2 [\"none\"] \n",
"3 [\"ARK\", \"DOI\", \"PURL\", \"URN\", \"hdl\"] \n",
"4 [\"DOI\"] \n",
"\n",
" citationGuidelineURL aidSystem \\\n",
"0 NaN [] \n",
"1 https://aad.archives.gov/aad/help/getting-star... [] \n",
"2 http://agd.ids-mannheim.de/konditionen.shtml [] \n",
"3 https://dataverse.org/best-practices/data-cita... [] \n",
"4 https://archaeologydataservice.ac.uk/advice/te... [] \n",
"\n",
" enhancedPublication qualityManagement certificate \\\n",
"0 unknown yes [\"other\"] \n",
"1 unknown unknown [] \n",
"2 unknown unknown [\"RatSWD\"] \n",
"3 unknown yes [] \n",
"4 unknown yes [\"other\"] \n",
"\n",
" metadataStandard \\\n",
"0 [{\"metadataStandardName\": \"DDI - Data Document... \n",
"1 [] \n",
"2 [] \n",
"3 [{\"metadataStandardName\": \"DDI - Data Document... \n",
"4 [{\"metadataStandardName\": \"DataCite Metadata S... \n",
"\n",
" syndication \\\n",
"0 {} \n",
"1 {\"syndication\": \"http://www.archives.gov/socia... \n",
"2 {} \n",
"3 {} \n",
"4 {\"syndication\": \"https://archaeologydataservic... \n",
"\n",
" remarks entryDate lastUpdate \n",
"0 Odum Dataverse is covered by Thomson Reuters D... 2013-06-10 2021-07-06 \n",
"1 NaN 2012-07-04 2021-05-25 \n",
"2 NaN 2012-07-20 2020-08-27 \n",
"3 UNC Dataverse is covered by Clarivate Data Cit... 2012-07-23 2021-08-11 \n",
"4 ADS is covered by Clarivate Data Citation Inde... 2012-07-23 2021-09-02 "
2021-07-22 11:03:05 +02:00
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"re3data_df = pd.read_csv('../data/raw/re3data.tsv', delimiter='\\t',\n",
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" converters={'subject': ast.literal_eval,\n",
" 'keyword': ast.literal_eval,\n",
" 'additionalName': ast.literal_eval,\n",
" 'repositoryIdentifier': ast.literal_eval,\n",
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" 'type': ast.literal_eval,\n",
" 'contentType': ast.literal_eval,\n",
" 'providerType': ast.literal_eval,\n",
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" 'institution': ast.literal_eval\n",
" })\n",
"\n",
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"re3data_df.head()"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"scrolled": false
},
"outputs": [
{
"data": {
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2021-07-22 11:03:05 +02:00
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" <td>864</td>\n",
" <td>2459</td>\n",
" <td>2737</td>\n",
" <td>6</td>\n",
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" <td>9</td>\n",
" <td>1289</td>\n",
" <td>352</td>\n",
" <td>80</td>\n",
" <td>107</td>\n",
" <td>1389</td>\n",
" <td>2249</td>\n",
" <td>1338</td>\n",
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" <td>2720</td>\n",
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" <td>12</td>\n",
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" <td>145</td>\n",
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" <td>172</td>\n",
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" <td>http://icgem.gfz-potsdam.de/home</td>\n",
" <td>[]</td>\n",
" <td>[]</td>\n",
" <td>The National Archives and Records Administrati...</td>\n",
" <td>eng</td>\n",
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" <td>[disciplinary]</td>\n",
" <td>{\"size\": \"\", \"updatedp\": \"\"}</td>\n",
" <td>2008</td>\n",
" <td>2015</td>\n",
" <td>[\"eng\"]</td>\n",
" <td>[{'name': '1 Humanities and Social Sciences', ...</td>\n",
" <td>https://learn.scholarsportal.info/all-guides/d...</td>\n",
" <td>[{'name': 'Standard office documents', 'scheme...</td>\n",
" <td>[dataProvider]</td>\n",
2021-07-22 11:03:05 +02:00
" <td>[multidisciplinary]</td>\n",
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" <td>[][]</td>\n",
" <td>{\"databaseAccessType\": \"open\", \"databaseAcces...</td>\n",
" <td>[]</td>\n",
" <td>[{\"dataAccessType\": \"open\", \"dataAccessRestric...</td>\n",
" <td>[{\"dataLicenseName\": \"CC\", \"dataLicenseURL\": \"...</td>\n",
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" <td>unknown</td>\n",
" <td>yes</td>\n",
" <td>[]</td>\n",
" <td>[]</td>\n",
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" <td>is covered by Elsevier.</td>\n",
" <td>2016-05-10</td>\n",
" <td>2021-09-03</td>\n",
2021-07-22 11:03:05 +02:00
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" <td>1</td>\n",
2021-07-22 11:03:05 +02:00
" <td>2</td>\n",
" <td>2554</td>\n",
" <td>569</td>\n",
2021-07-22 11:03:05 +02:00
" <td>2</td>\n",
" <td>1876</td>\n",
" <td>202</td>\n",
" <td>2</td>\n",
" <td>2723</td>\n",
" <td>1733</td>\n",
" <td>1450</td>\n",
" <td>92</td>\n",
" <td>11</td>\n",
" <td>2063</td>\n",
" <td>226</td>\n",
" <td>14</td>\n",
" <td>30</td>\n",
" <td>1771</td>\n",
" <td>193</td>\n",
2021-07-22 11:03:05 +02:00
" <td>6</td>\n",
" <td>312</td>\n",
" <td>2571</td>\n",
" <td>2159</td>\n",
" <td>1269</td>\n",
" <td>64</td>\n",
" <td>1793</td>\n",
" <td>2013</td>\n",
" <td>1226</td>\n",
" <td>1108</td>\n",
" <td>1498</td>\n",
" <td>1361</td>\n",
" <td>72</td>\n",
" <td>2155</td>\n",
" <td>1608</td>\n",
" <td>1515</td>\n",
" <td>2509</td>\n",
" <td>1669</td>\n",
" <td>2162</td>\n",
" <td>14</td>\n",
" <td>20</td>\n",
" <td>137</td>\n",
2021-07-22 11:03:05 +02:00
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],
"text/plain": [
" orgIdentifier repositoryName repositoryName.language additionalName \\\n",
"count 2739 2739 2739 2739 \n",
"unique 2739 2736 19 2162 \n",
"top r3d100000001 Språkbanken eng [] \n",
"freq 1 2 2554 569 \n",
"\n",
" repositoryURL repositoryIdentifier \\\n",
"count 2716 2739 \n",
"unique 2713 864 \n",
"top http://icgem.gfz-potsdam.de/home [] \n",
"freq 2 1876 \n",
"\n",
" repositoryContact description \\\n",
"count 2739 2739 \n",
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"top [] The National Archives and Records Administrati... \n",
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"\n",
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"count 2739 \n",
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" missionStatementURL \\\n",
"count 2318 \n",
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"freq 14 \n",
"\n",
" contentType providerType \\\n",
"count 2739 2739 \n",
"unique 1338 5 \n",
"top [{'name': 'Standard office documents', 'scheme... [dataProvider] \n",
"freq 30 1771 \n",
"\n",
" keyword \\\n",
"count 2739 \n",
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"\n",
" institution policy \\\n",
"count 2739 2739 \n",
"unique 2720 2319 \n",
"top [{'institutionName': 'National Center for Biot... [][] \n",
"freq 6 312 \n",
"\n",
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"count 2739 2739 \n",
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"\n",
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"freq 64 1793 \n",
"\n",
" dataUploadLicense software versioning api pidSystem \\\n",
"count 2739 2739 1316 2739 2739 \n",
"unique 681 23 2 1146 29 \n",
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"freq 2013 1226 1108 1498 1361 \n",
"\n",
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"count 1512 2739 \n",
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"freq 72 2155 \n",
"\n",
" enhancedPublication qualityManagement certificate metadataStandard \\\n",
"count 2737 2739 2739 2739 \n",
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"freq 1608 1515 2509 1669 \n",
"\n",
" syndication remarks entryDate lastUpdate \n",
"count 2739 1674 2739 2739 \n",
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"freq 2162 14 20 137 "
2021-07-22 11:03:05 +02:00
]
},
"execution_count": 4,
2021-07-22 11:03:05 +02:00
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"re3data_df.describe(include='all')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**openDOAR**"
]
},
{
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"execution_count": 48,
2021-07-22 11:03:05 +02:00
"metadata": {},
"outputs": [
{
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2021-07-22 11:03:05 +02:00
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2021-07-22 11:03:05 +02:00
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2021-07-22 11:03:05 +02:00
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2021-07-22 11:03:05 +02:00
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2021-07-22 11:03:05 +02:00
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" <td>http://cadmus.eui.eu/</td>\n",
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2021-07-22 11:03:05 +02:00
" <td>institutional</td>\n",
" <td>[\"nl\", \"en\", \"fr\", \"de\", \"it\"]</td>\n",
" <td>2021-09-13 13:35:36</td>\n",
" <td>2006-01-04 12:07:07</td>\n",
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" <td>[{'name': 'european university institute', 'al...</td>\n",
" <td>[{\"policy_url\": \"https://www.eui.eu/research/e...</td>\n",
" <td>{\"name\": \"dspace\", \"version\": \"5.2\"}</td>\n",
" <td>http://cadmus.eui.eu/oai/request</td>\n",
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2021-07-22 11:03:05 +02:00
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" <td>105</td>\n",
" <td>{\"name\": \"document server@uhasselt\", \"language...</td>\n",
" <td>[]</td>\n",
" <td>https://doclib.uhasselt.be/dspace/</td>\n",
" <td>this site is a university repository providing...</td>\n",
2021-07-22 11:03:05 +02:00
" <td>institutional</td>\n",
" <td>[\"nl\", \"en\", \"fr\", \"de\"]</td>\n",
" <td>2021-04-16 15:23:52</td>\n",
" <td>2006-01-24 15:46:44</td>\n",
2021-07-22 11:03:05 +02:00
" <td>[multidisciplinary]</td>\n",
" <td>[journal_articles, conference_and_workshop_pap...</td>\n",
" <td>[{'name': 'uhasselt', 'alternativeName': 'hass...</td>\n",
" <td>[]</td>\n",
" <td>{\"name\": \"dspace\", \"version\": \"1.7.2\"}</td>\n",
" <td>http://doclib.uhasselt.be/dspace-oai/request</td>\n",
" <td>yes</td>\n",
" <td>fully_functional</td>\n",
" <td>0.0</td>\n",
" <td>27376.0</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>101</td>\n",
" <td>{\"name\": \"utrecht university repository\", \"lan...</td>\n",
" <td>[]</td>\n",
" <td>http://dspace.library.uu.nl</td>\n",
" <td>this site is a university repository providing...</td>\n",
" <td>institutional</td>\n",
" <td>[\"nl\", \"en\"]</td>\n",
" <td>2021-04-16 15:22:03</td>\n",
" <td>2006-01-13 12:55:13</td>\n",
" <td>[multidisciplinary]</td>\n",
" <td>[journal_articles, conference_and_workshop_pap...</td>\n",
" <td>[{'name': 'university of utrecht', 'alternativ...</td>\n",
" <td>[]</td>\n",
" <td>{\"name\": \"dspace\", \"version\": \"\"}</td>\n",
" <td>https://dspace.library.uu.nl/oai/request</td>\n",
" <td>yes</td>\n",
" <td>fully_functional</td>\n",
" <td>1686.0</td>\n",
" <td>185637.0</td>\n",
2021-07-22 11:03:05 +02:00
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" system_metadata.id repository_metadata.name \\\n",
"0 175 {\"name\": \"hku theses online\", \"language\": \"en\"} \n",
"1 64 {\"name\": \"research support scheme - central eu... \n",
"2 151 {\"name\": \"cadmus, eui research repository\", \"l... \n",
"3 105 {\"name\": \"document server@uhasselt\", \"language... \n",
"4 101 {\"name\": \"utrecht university repository\", \"lan... \n",
"\n",
" repository_metadata.alternativename repository_metadata.url \\\n",
"0 [] http://hub.hku.hk/handle/10722/1057 \n",
"1 [] http://rss.archives.ceu.hu/ \n",
"2 [] http://cadmus.eui.eu/ \n",
"3 [] https://doclib.uhasselt.be/dspace/ \n",
"4 [] http://dspace.library.uu.nl \n",
"\n",
" repository_metadata.description repository_metadata.type \\\n",
"0 this is an institutional repository providing ... institutional \n",
"1 this is an institutional repository collecting... institutional \n",
"2 cadmus is the name of the eui research reposit... institutional \n",
"3 this site is a university repository providing... institutional \n",
"4 this site is a university repository providing... institutional \n",
"\n",
" repository_metadata.content_languages system_metadata.date_modified \\\n",
"0 [\"zh\", \"en\"] 2021-03-25 10:16:18 \n",
"1 [\"cs\", \"en\", \"hu\", \"ru\"] 2021-03-25 09:48:31 \n",
"2 [\"nl\", \"en\", \"fr\", \"de\", \"it\"] 2021-09-13 13:35:36 \n",
"3 [\"nl\", \"en\", \"fr\", \"de\"] 2021-04-16 15:23:52 \n",
"4 [\"nl\", \"en\"] 2021-04-16 15:22:03 \n",
"\n",
" system_metadata.date_created \\\n",
"0 2005-12-21 12:44:08 \n",
"1 2006-01-04 14:59:30 \n",
"2 2006-01-04 12:07:07 \n",
"3 2006-01-24 15:46:44 \n",
"4 2006-01-13 12:55:13 \n",
"\n",
" repository_metadata.content_subjects \\\n",
"0 [multidisciplinary] \n",
"1 [multidisciplinary] \n",
"2 [history and archaeology, multidisciplinary, s... \n",
"3 [multidisciplinary] \n",
"4 [multidisciplinary] \n",
"\n",
" repository_metadata.content_types \\\n",
"0 [bibliographic_references, theses_and_disserta... \n",
"1 [unpub_reports_and_working_papers] \n",
"2 [journal_articles, theses_and_dissertations, u... \n",
"3 [journal_articles, conference_and_workshop_pap... \n",
"4 [journal_articles, conference_and_workshop_pap... \n",
"\n",
" organization \\\n",
"0 [{'name': 'university of hong kong', 'alternat... \n",
"1 [{'name': 'central european university', 'alte... \n",
"2 [{'name': 'european university institute', 'al... \n",
"3 [{'name': 'uhasselt', 'alternativeName': 'hass... \n",
"4 [{'name': 'university of utrecht', 'alternativ... \n",
"\n",
" policy_urls \\\n",
"0 [] \n",
"1 [] \n",
"2 [{\"policy_url\": \"https://www.eui.eu/research/e... \n",
"3 [] \n",
"4 [] \n",
"\n",
" repository_metadata.software \\\n",
"0 {\"name\": \"dspace\", \"version\": \"cris-5.3.1-snap... \n",
"1 {\"name\": \"eprints\", \"version\": \"2.2.1\"} \n",
"2 {\"name\": \"dspace\", \"version\": \"5.2\"} \n",
"3 {\"name\": \"dspace\", \"version\": \"1.7.2\"} \n",
"4 {\"name\": \"dspace\", \"version\": \"\"} \n",
"\n",
" repository_metadata.oai_url \\\n",
"0 NaN \n",
"1 http://rss.archives.ceu.hu/perl/oai2 \n",
"2 http://cadmus.eui.eu/oai/request \n",
"3 http://doclib.uhasselt.be/dspace-oai/request \n",
"4 https://dspace.library.uu.nl/oai/request \n",
"\n",
" system_metadata.publicly_visible repository_metadata.repository_status \\\n",
"0 yes fully_functional \n",
"1 yes fully_functional \n",
"2 yes fully_functional \n",
"3 yes fully_functional \n",
"4 yes fully_functional \n",
"\n",
" repository_metadata.fulltext_record_count \\\n",
"0 NaN \n",
"1 NaN \n",
"2 3867.0 \n",
"3 0.0 \n",
"4 1686.0 \n",
"\n",
" repository_metadata.metadata_record_count \n",
"0 11850.0 \n",
"1 164.0 \n",
"2 24869.0 \n",
"3 27376.0 \n",
"4 185637.0 "
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]
},
"execution_count": 48,
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"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"opendoar_df = pd.read_csv('../data/raw/openDoar.tsv', delimiter='\\t',\n",
" converters={'repository_metadata.content_subjects': ast.literal_eval,\n",
" 'repository_metadata.alternativename': ast.literal_eval,\n",
" 'repository_metadata.content_types': ast.literal_eval,\n",
" 'organization': ast.literal_eval\n",
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" },\n",
" dtype={'system_metadata.id': str})\n",
"\n",
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"opendoar_df.head()"
]
},
{
"cell_type": "code",
"execution_count": 6,
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"metadata": {},
"outputs": [
{
"data": {
"text/html": [
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"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>system_metadata.id</th>\n",
" <th>repository_metadata.name</th>\n",
" <th>repository_metadata.alternativename</th>\n",
" <th>repository_metadata.url</th>\n",
" <th>repository_metadata.description</th>\n",
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" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>count</th>\n",
" <td>5742</td>\n",
" <td>5742</td>\n",
" <td>5742</td>\n",
" <td>5742</td>\n",
" <td>5421</td>\n",
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" <td>5742</td>\n",
" <td>5742</td>\n",
" <td>5742</td>\n",
" <td>5742</td>\n",
" <td>4402</td>\n",
" <td>5742</td>\n",
" <td>5595</td>\n",
" <td>2.299000e+03</td>\n",
" <td>4.197000e+03</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>unique</th>\n",
" <td>5742</td>\n",
" <td>5713</td>\n",
" <td>2108</td>\n",
" <td>5705</td>\n",
" <td>4619</td>\n",
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" <td>4</td>\n",
" <td>330</td>\n",
" <td>2372</td>\n",
" <td>5573</td>\n",
" <td>821</td>\n",
" <td>478</td>\n",
" <td>5201</td>\n",
" <td>642</td>\n",
" <td>321</td>\n",
" <td>4370</td>\n",
" <td>1</td>\n",
" <td>7</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>top</th>\n",
" <td>175</td>\n",
" <td>{\"name\": \"hiroshima associated repository port...</td>\n",
" <td>[]</td>\n",
" <td>http://harp.lib.hiroshima-u.ac.jp/</td>\n",
" <td>this site provides access to the research outp...</td>\n",
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" <td>institutional</td>\n",
" <td>[\"en\"]</td>\n",
" <td>2020-09-18 12:53:48</td>\n",
" <td>2020-09-18 12:53:48</td>\n",
" <td>[\"multidisciplinary\"]</td>\n",
" <td>[theses_and_dissertations]</td>\n",
" <td>[{'name': 'rijksuniversiteit groningen', 'alte...</td>\n",
" <td>[]</td>\n",
" <td>{\"name\": \"dspace\", \"version\": \"\"}</td>\n",
" <td>https://kidoks.bsz-bw.de/oai</td>\n",
" <td>yes</td>\n",
" <td>fully_functional</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>freq</th>\n",
" <td>1</td>\n",
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" <td>3</td>\n",
" <td>3595</td>\n",
" <td>3</td>\n",
" <td>95</td>\n",
" <td>5096</td>\n",
" <td>1917</td>\n",
" <td>82</td>\n",
" <td>82</td>\n",
" <td>3227</td>\n",
" <td>465</td>\n",
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" <td>26</td>\n",
" <td>5098</td>\n",
" <td>822</td>\n",
" <td>3</td>\n",
" <td>5742</td>\n",
" <td>5276</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>mean</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>5.010186e+03</td>\n",
" <td>1.760546e+05</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>std</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>4.206295e+04</td>\n",
" <td>6.600825e+06</td>\n",
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" </tr>\n",
" <tr>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>0.000000e+00</td>\n",
" <td>0.000000e+00</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>25%</th>\n",
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" <td>NaN</td>\n",
" <td>NaN</td>\n",
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" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>0.000000e+00</td>\n",
" <td>8.950000e+02</td>\n",
2021-07-22 11:03:05 +02:00
" </tr>\n",
" <tr>\n",
" <th>50%</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>4.220000e+02</td>\n",
" <td>4.026000e+03</td>\n",
2021-07-22 11:03:05 +02:00
" </tr>\n",
" <tr>\n",
" <th>75%</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>2.930500e+03</td>\n",
" <td>1.630400e+04</td>\n",
2021-07-22 11:03:05 +02:00
" </tr>\n",
" <tr>\n",
" <th>max</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>1.817531e+06</td>\n",
" <td>4.200000e+08</td>\n",
2021-07-22 11:03:05 +02:00
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" system_metadata.id repository_metadata.name \\\n",
"count 5742 5742 \n",
"unique 5742 5713 \n",
"top 175 {\"name\": \"hiroshima associated repository port... \n",
"freq 1 3 \n",
"mean NaN NaN \n",
"std NaN NaN \n",
"min NaN NaN \n",
"25% NaN NaN \n",
"50% NaN NaN \n",
"75% NaN NaN \n",
"max NaN NaN \n",
"\n",
" repository_metadata.alternativename \\\n",
"count 5742 \n",
"unique 2108 \n",
"top [] \n",
"freq 3595 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN \n",
"\n",
" repository_metadata.url \\\n",
"count 5742 \n",
"unique 5705 \n",
"top http://harp.lib.hiroshima-u.ac.jp/ \n",
"freq 3 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN \n",
"\n",
" repository_metadata.description \\\n",
"count 5421 \n",
"unique 4619 \n",
"top this site provides access to the research outp... \n",
"freq 95 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN \n",
"\n",
" repository_metadata.type repository_metadata.content_languages \\\n",
"count 5742 5742 \n",
"unique 4 330 \n",
"top institutional [\"en\"] \n",
"freq 5096 1917 \n",
"mean NaN NaN \n",
"std NaN NaN \n",
"min NaN NaN \n",
"25% NaN NaN \n",
"50% NaN NaN \n",
"75% NaN NaN \n",
"max NaN NaN \n",
"\n",
" system_metadata.date_modified system_metadata.date_created \\\n",
"count 5742 5742 \n",
"unique 2372 5573 \n",
"top 2020-09-18 12:53:48 2020-09-18 12:53:48 \n",
"freq 82 82 \n",
"mean NaN NaN \n",
"std NaN NaN \n",
"min NaN NaN \n",
"25% NaN NaN \n",
"50% NaN NaN \n",
"75% NaN NaN \n",
"max NaN NaN \n",
"\n",
" repository_metadata.content_subjects repository_metadata.content_types \\\n",
"count 5742 5742 \n",
"unique 821 478 \n",
"top [\"multidisciplinary\"] [theses_and_dissertations] \n",
"freq 3227 465 \n",
"mean NaN NaN \n",
"std NaN NaN \n",
"min NaN NaN \n",
"25% NaN NaN \n",
"50% NaN NaN \n",
"75% NaN NaN \n",
"max NaN NaN \n",
"\n",
" organization policy_urls \\\n",
"count 5742 5742 \n",
"unique 5201 642 \n",
"top [{'name': 'rijksuniversiteit groningen', 'alte... [] \n",
"freq 26 5098 \n",
"mean NaN NaN \n",
"std NaN NaN \n",
"min NaN NaN \n",
"25% NaN NaN \n",
"50% NaN NaN \n",
"75% NaN NaN \n",
"max NaN NaN \n",
"\n",
" repository_metadata.software repository_metadata.oai_url \\\n",
"count 5742 4402 \n",
"unique 321 4370 \n",
"top {\"name\": \"dspace\", \"version\": \"\"} https://kidoks.bsz-bw.de/oai \n",
"freq 822 3 \n",
"mean NaN NaN \n",
"std NaN NaN \n",
"min NaN NaN \n",
"25% NaN NaN \n",
"50% NaN NaN \n",
"75% NaN NaN \n",
"max NaN NaN \n",
"\n",
" system_metadata.publicly_visible repository_metadata.repository_status \\\n",
"count 5742 5595 \n",
"unique 1 7 \n",
"top yes fully_functional \n",
"freq 5742 5276 \n",
"mean NaN NaN \n",
"std NaN NaN \n",
"min NaN NaN \n",
"25% NaN NaN \n",
"50% NaN NaN \n",
"75% NaN NaN \n",
"max NaN NaN \n",
"\n",
" repository_metadata.fulltext_record_count \\\n",
"count 2.299000e+03 \n",
"unique NaN \n",
"top NaN \n",
"freq NaN \n",
"mean 5.010186e+03 \n",
"std 4.206295e+04 \n",
"min 0.000000e+00 \n",
"25% 0.000000e+00 \n",
"50% 4.220000e+02 \n",
"75% 2.930500e+03 \n",
"max 1.817531e+06 \n",
"\n",
" repository_metadata.metadata_record_count \n",
"count 4.197000e+03 \n",
"unique NaN \n",
"top NaN \n",
"freq NaN \n",
"mean 1.760546e+05 \n",
"std 6.600825e+06 \n",
"min 0.000000e+00 \n",
"25% 8.950000e+02 \n",
"50% 4.026000e+03 \n",
"75% 1.630400e+04 \n",
"max 4.200000e+08 "
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]
},
"execution_count": 6,
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"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"opendoar_df.describe(include='all')"
]
},
{
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"metadata": {},
"source": [
"**ROAR**"
]
},
{
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"execution_count": 9,
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"metadata": {},
"outputs": [
{
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" eprintid rev_number eprint_status userid importid source \\\n",
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" oai_pmh sword_endpoint \\\n",
"0 http://archivesic.ccsd.cnrs.fr/oai/oai.php NaN \n",
"1 http://www.diva-portal.org/oai/mdh/OAI NaN \n",
"2 NaN NaN \n",
"3 http://edoc.sub.uni-hamburg.de/klimawandel/oai NaN \n",
"4 http://creativematter.skidmore.edu/do/oai/ NaN \n",
"\n",
" rss_feed twitter_feed \\\n",
"0 NaN NaN \n",
"1 NaN NaN \n",
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"3 NaN NaN \n",
"4 http://creativematter.skidmore.edu/recent.rss NaN \n",
"\n",
" description fulltext open_access \\\n",
"0 NaN NaN NaN \n",
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"\n",
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"4 http://www.skidmore.edu/ us \n",
"\n",
" location_city location_latitude location_longitude software \\\n",
"0 NaN NaN NaN hal \n",
"1 Uppsala 59.8667 17.6333 diva \n",
"2 Bellevue, WA 47.6034 -122.155 dspace \n",
"3 Hamburg 53.5511 9.9937 opus \n",
"4 Saratoga Springs 43.0961 -73.7818 bepress \n",
"\n",
" geoname version subjects date note \\\n",
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"2 geoname_2_PT other NaN 2006-05-04 10:48:14 NaN \n",
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"4 geoname_2_US other NaN 2015-07-06 17:35:50 NaN \n",
"\n",
" suggestions activity_low activity_medium activity_high recordcount \\\n",
"0 NaN 0 0 0 25 \n",
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"\n",
" recordhistory fulltexts_total \\\n",
"0 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,... NaN \n",
"1 0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,8,39,100,100,100... NaN \n",
"2 NaN NaN \n",
"3 NaN NaN \n",
"4 NaN NaN \n",
"\n",
" fulltexts_docs fulltexts_rtotal fulltexts_rdocs registry_name \\\n",
"0 NaN NaN NaN [opendoar, celestial] \n",
"1 NaN NaN NaN [opendoar, celestial] \n",
"2 NaN NaN NaN NaN \n",
"3 NaN NaN NaN [opendoar, celestial] \n",
"4 NaN NaN NaN celestial \n",
"\n",
" registry_id submit_to submitted_to_name submitted_to_done \\\n",
"0 [58, 669] NaN NaN NaN \n",
"1 [258, 526] NaN NaN NaN \n",
"2 NaN NaN NaN NaN \n",
"3 [3408, 5881] NaN NaN NaN \n",
"4 5882 NaN NaN NaN \n",
"\n",
" webometrics_rank webometrics_size webometrics_visibility \\\n",
"0 NaN NaN NaN \n",
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"2 NaN NaN NaN \n",
"3 NaN NaN NaN \n",
"4 NaN NaN NaN \n",
"\n",
" webometrics_rich_files webometrics_scholar monthly_deposits total_deposits \\\n",
"0 NaN NaN NaN NaN \n",
"1 NaN NaN NaN NaN \n",
"2 NaN NaN NaN NaN \n",
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"\n",
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"3 NaN \n",
"4 NaN "
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]
},
"execution_count": 9,
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"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"roar_df = pd.read_csv('../data/raw/export_roar_CSV.csv', dtype='str')\n",
"roar_df = roar_df.groupby('eprintid').aggregate(set)\n",
"\n",
"def value_or_list(cell_set):\n",
" copy = set(cell_set)\n",
" copy.discard(np.nan) \n",
" if len(copy) == 0:\n",
" return np.nan\n",
" if len(copy) == 1:\n",
" return copy.pop()\n",
" return list(copy)\n",
" \n",
"roar_df = roar_df.applymap(value_or_list)\n",
"roar_df.reset_index(inplace=True)\n",
"\n",
"roar_df.head()"
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]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
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" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>std</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>min</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>25%</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>50%</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>75%</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>max</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" eprintid rev_number eprint_status userid importid source \\\n",
"count 5375 5375 5375 5375 0.0 0.0 \n",
"unique 5375 658 1 2135 NaN NaN \n",
"top 1 11 archive 1 NaN NaN \n",
"freq 1 332 5375 1333 NaN NaN \n",
"mean NaN NaN NaN NaN NaN NaN \n",
"std NaN NaN NaN NaN NaN NaN \n",
"min NaN NaN NaN NaN NaN NaN \n",
"25% NaN NaN NaN NaN NaN NaN \n",
"50% NaN NaN NaN NaN NaN NaN \n",
"75% NaN NaN NaN NaN NaN NaN \n",
"max NaN NaN NaN NaN NaN NaN \n",
"\n",
" dir datestamp lastmod \\\n",
"count 5375 5375 5375 \n",
"unique 5375 4127 3966 \n",
"top disk0/00/00/00/01 2010-01-06 13:43:48 2011-07-06 08:24:53 \n",
"freq 1 16 8 \n",
"mean NaN NaN NaN \n",
"std NaN NaN NaN \n",
"min NaN NaN NaN \n",
"25% NaN NaN NaN \n",
"50% NaN NaN NaN \n",
"75% NaN NaN NaN \n",
"max NaN NaN NaN \n",
"\n",
" status_changed type succeeds commentary \\\n",
"count 5375 5375 107 0.0 \n",
"unique 4158 12 107 NaN \n",
"top 2010-01-06 13:43:48 institutional 10164 NaN \n",
"freq 16 3795 1 NaN \n",
"mean NaN NaN NaN NaN \n",
"std NaN NaN NaN NaN \n",
"min NaN NaN NaN NaN \n",
"25% NaN NaN NaN NaN \n",
"50% NaN NaN NaN NaN \n",
"75% NaN NaN NaN NaN \n",
"max NaN NaN NaN NaN \n",
"\n",
" metadata_visibility latitude longitude relation_type relation_uri \\\n",
"count 5375 0.0 0.0 0.0 0.0 \n",
"unique 2 NaN NaN NaN NaN \n",
"top show NaN NaN NaN NaN \n",
"freq 5334 NaN NaN NaN NaN \n",
"mean NaN NaN NaN NaN NaN \n",
"std NaN NaN NaN NaN NaN \n",
"min NaN NaN NaN NaN NaN \n",
"25% NaN NaN NaN NaN NaN \n",
"50% NaN NaN NaN NaN NaN \n",
"75% NaN NaN NaN NaN NaN \n",
"max NaN NaN NaN NaN NaN \n",
"\n",
" item_issues_id item_issues_type \\\n",
"count 63 63 \n",
"unique 48 5 \n",
"top bad_oai_pmh_url_0 duplicate_title \n",
"freq 15 33 \n",
"mean NaN NaN \n",
"std NaN NaN \n",
"min NaN NaN \n",
"25% NaN NaN \n",
"50% NaN NaN \n",
"75% NaN NaN \n",
"max NaN NaN \n",
"\n",
" item_issues_description \\\n",
"count 63 \n",
"unique 62 \n",
"top Duplicate title to <xhtml:table xmlns:xhtml=\"h... \n",
"freq 2 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN \n",
"\n",
" item_issues_timestamp item_issues_status item_issues_reported_by \\\n",
"count 63 63 0.0 \n",
"unique 4 3 NaN \n",
"top 2010-01-13 10:44:49 discovered NaN \n",
"freq 45 38 NaN \n",
"mean NaN NaN NaN \n",
"std NaN NaN NaN \n",
"min NaN NaN NaN \n",
"25% NaN NaN NaN \n",
"50% NaN NaN NaN \n",
"75% NaN NaN NaN \n",
"max NaN NaN NaN \n",
"\n",
" item_issues_resolved_by item_issues_comment item_issues_count \\\n",
"count 0.0 0.0 2245 \n",
"unique NaN NaN 4 \n",
"top NaN NaN 0 \n",
"freq NaN NaN 2204 \n",
"mean NaN NaN NaN \n",
"std NaN NaN NaN \n",
"min NaN NaN NaN \n",
"25% NaN NaN NaN \n",
"50% NaN NaN NaN \n",
"75% NaN NaN NaN \n",
"max NaN NaN NaN \n",
"\n",
" sword_depositor sword_slug exemplar home_page \\\n",
"count 0.0 0.0 265 5368 \n",
"unique NaN NaN 2 5202 \n",
"top NaN NaN FALSE http://eprints.upnjatim.ac.id/ \n",
"freq NaN NaN 258 4 \n",
"mean NaN NaN NaN NaN \n",
"std NaN NaN NaN NaN \n",
"min NaN NaN NaN NaN \n",
"25% NaN NaN NaN NaN \n",
"50% NaN NaN NaN NaN \n",
"75% NaN NaN NaN NaN \n",
"max NaN NaN NaN NaN \n",
"\n",
" title oai_pmh \\\n",
"count 5373 4267 \n",
"unique 5076 3994 \n",
"top Repositorio Institucional http://kce.docressources.info/ws/PMBWs_2 \n",
"freq 7 4 \n",
"mean NaN NaN \n",
"std NaN NaN \n",
"min NaN NaN \n",
"25% NaN NaN \n",
"50% NaN NaN \n",
"75% NaN NaN \n",
"max NaN NaN \n",
"\n",
" sword_endpoint \\\n",
"count 176 \n",
"unique 170 \n",
"top http://producao.usp.br/sword/servicedocument \n",
"freq 2 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN \n",
"\n",
" rss_feed \\\n",
"count 1521 \n",
"unique 1468 \n",
"top http://eprints.upnjatim.ac.id/cgi/latest_tool?... \n",
"freq 5 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN \n",
"\n",
" twitter_feed \\\n",
"count 115 \n",
"unique 111 \n",
"top http://my.indexcopernicus.com/fredemoreno \n",
"freq 2 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN \n",
"\n",
" description fulltext open_access mandate \\\n",
"count 3782 4127 4127 3676 \n",
"unique 3304 2 2 2 \n",
"top info:other:archives.eprints.org:import TRUE TRUE FALSE \n",
"freq 112 2758 2652 2699 \n",
"mean NaN NaN NaN NaN \n",
"std NaN NaN NaN NaN \n",
"min NaN NaN NaN NaN \n",
"25% NaN NaN NaN NaN \n",
"50% NaN NaN NaN NaN \n",
"75% NaN NaN NaN NaN \n",
"max NaN NaN NaN NaN \n",
"\n",
" organisation_title organisation_home_page \\\n",
"count 4396 4226 \n",
"unique 3802 3771 \n",
"top Chinese Academy of Science (中国科学院) http://www.cas.cn/ \n",
"freq 9 9 \n",
"mean NaN NaN \n",
"std NaN NaN \n",
"min NaN NaN \n",
"25% NaN NaN \n",
"50% NaN NaN \n",
"75% NaN NaN \n",
"max NaN NaN \n",
"\n",
" location_country location_city location_latitude location_longitude \\\n",
"count 5080 3655 3681 3664 \n",
"unique 143 1861 2887 2917 \n",
"top us Lima 34.1607 -118.139 \n",
"freq 886 69 25 25 \n",
"mean NaN NaN NaN NaN \n",
"std NaN NaN NaN NaN \n",
"min NaN NaN NaN NaN \n",
"25% NaN NaN NaN NaN \n",
"50% NaN NaN NaN NaN \n",
"75% NaN NaN NaN NaN \n",
"max NaN NaN NaN NaN \n",
"\n",
" software geoname version subjects date \\\n",
"count 4637 4671 5375 1250 5360 \n",
"unique 31 126 53 906 4830 \n",
"top dspace geoname_2_US other K1 2006-05-04 10:48:14 \n",
"freq 2307 840 4771 53 99 \n",
"mean NaN NaN NaN NaN NaN \n",
"std NaN NaN NaN NaN NaN \n",
"min NaN NaN NaN NaN NaN \n",
"25% NaN NaN NaN NaN NaN \n",
"50% NaN NaN NaN NaN NaN \n",
"75% NaN NaN NaN NaN NaN \n",
"max NaN NaN NaN NaN NaN \n",
"\n",
" note \\\n",
"count 215 \n",
"unique 207 \n",
"top DSpace@Işık is a growing collection of Işık Un... \n",
"freq 2 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN \n",
"\n",
" suggestions activity_low \\\n",
"count 187 2291 \n",
"unique 171 72 \n",
"top This repository is hosted by the Texas Digital... 0 \n",
"freq 9 2015 \n",
"mean NaN NaN \n",
"std NaN NaN \n",
"min NaN NaN \n",
"25% NaN NaN \n",
"50% NaN NaN \n",
"75% NaN NaN \n",
"max NaN NaN \n",
"\n",
" activity_medium activity_high recordcount \\\n",
"count 2291 2291 2293 \n",
"unique 54 16 741 \n",
"top 0 0 100 \n",
"freq 2077 2213 733 \n",
"mean NaN NaN NaN \n",
"std NaN NaN NaN \n",
"min NaN NaN NaN \n",
"25% NaN NaN NaN \n",
"50% NaN NaN NaN \n",
"75% NaN NaN NaN \n",
"max NaN NaN NaN \n",
"\n",
" recordhistory fulltexts_total \\\n",
"count 2291 270 \n",
"unique 1704 135 \n",
"top 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,... 0 \n",
"freq 95 113 \n",
"mean NaN NaN \n",
"std NaN NaN \n",
"min NaN NaN \n",
"25% NaN NaN \n",
"50% NaN NaN \n",
"75% NaN NaN \n",
"max NaN NaN \n",
"\n",
" fulltexts_docs fulltexts_rtotal fulltexts_rdocs registry_name \\\n",
"count 258 270 258 4603 \n",
"unique 118 134 117 9 \n",
"top 0 0 0 [opendoar, celestial] \n",
"freq 114 113 114 1775 \n",
"mean NaN NaN NaN NaN \n",
"std NaN NaN NaN NaN \n",
"min NaN NaN NaN NaN \n",
"25% NaN NaN NaN NaN \n",
"50% NaN NaN NaN NaN \n",
"75% NaN NaN NaN NaN \n",
"max NaN NaN NaN NaN \n",
"\n",
" registry_id submit_to submitted_to_name \\\n",
"count 4578 293 205 \n",
"unique 4256 7 1 \n",
"top 2479 [opendoar, celestial, roarmap] opendoar \n",
"freq 4 92 205 \n",
"mean NaN NaN NaN \n",
"std NaN NaN NaN \n",
"min NaN NaN NaN \n",
"25% NaN NaN NaN \n",
"50% NaN NaN NaN \n",
"75% NaN NaN NaN \n",
"max NaN NaN NaN \n",
"\n",
" submitted_to_done webometrics_rank webometrics_size \\\n",
"count 205 148 148 \n",
"unique 1 148 148 \n",
"top 2021-01-25 24 46 \n",
"freq 205 1 1 \n",
"mean NaN NaN NaN \n",
"std NaN NaN NaN \n",
"min NaN NaN NaN \n",
"25% NaN NaN NaN \n",
"50% NaN NaN NaN \n",
"75% NaN NaN NaN \n",
"max NaN NaN NaN \n",
"\n",
" webometrics_visibility webometrics_rich_files webometrics_scholar \\\n",
"count 148 148 148 \n",
"unique 148 146 143 \n",
"top 20 824 806 \n",
"freq 1 3 5 \n",
"mean NaN NaN NaN \n",
"std NaN NaN NaN \n",
"min NaN NaN NaN \n",
"25% NaN NaN NaN \n",
"50% NaN NaN NaN \n",
"75% NaN NaN NaN \n",
"max NaN NaN NaN \n",
"\n",
" monthly_deposits total_deposits \\\n",
"count 756 756 \n",
"unique 346 342 \n",
"top 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,... 0 \n",
"freq 387 387 \n",
"mean NaN NaN \n",
"std NaN NaN \n",
"min NaN NaN \n",
"25% NaN NaN \n",
"50% NaN NaN \n",
"75% NaN NaN \n",
"max NaN NaN \n",
"\n",
" association \n",
"count 217 \n",
"unique 3 \n",
"top russell_group \n",
"freq 127 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN "
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"roar_df.describe(include='all')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**FAIRsharing**"
]
},
{
"cell_type": "code",
"execution_count": 57,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
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" .dataframe thead th {\n",
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"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>id</th>\n",
" <th>type</th>\n",
" <th>attributes.created-at</th>\n",
" <th>attributes.updated-at</th>\n",
" <th>attributes.metadata.doi</th>\n",
" <th>attributes.metadata.name</th>\n",
" <th>attributes.metadata.status</th>\n",
" <th>attributes.metadata.contacts</th>\n",
" <th>attributes.metadata.homepage</th>\n",
" <th>attributes.metadata.identifier</th>\n",
" <th>attributes.metadata.description</th>\n",
" <th>attributes.metadata.support-links</th>\n",
" <th>attributes.metadata.year-creation</th>\n",
" <th>attributes.metadata.data-processes</th>\n",
" <th>attributes.legacy-ids</th>\n",
" <th>attributes.fairsharing-registry</th>\n",
" <th>attributes.record-type</th>\n",
" <th>attributes.subjects</th>\n",
" <th>attributes.domains</th>\n",
" <th>attributes.taxonomies</th>\n",
" <th>attributes.user-defined-tags</th>\n",
" <th>attributes.countries</th>\n",
" <th>attributes.name</th>\n",
" <th>attributes.abbreviation</th>\n",
" <th>attributes.url</th>\n",
" <th>attributes.doi</th>\n",
" <th>attributes.fairsharing-licence</th>\n",
" <th>attributes.description</th>\n",
" <th>attributes.publications</th>\n",
" <th>attributes.licence-links</th>\n",
" <th>attributes.metadata.citations</th>\n",
" <th>attributes.metadata.abbreviation</th>\n",
" <th>attributes.metadata.access-points</th>\n",
" <th>attributes.metadata.associated-tools</th>\n",
" <th>attributes.metadata.deprecation-date</th>\n",
" <th>attributes.metadata.deprecation-reason</th>\n",
" <th>attributes.metadata.tombstone</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>1723</td>\n",
" <td>fairsharing-records</td>\n",
" <td>2014-11-04T15:23:40.000Z</td>\n",
" <td>2021-09-30T11:39:06.829Z</td>\n",
" <td>10.25504/FAIRsharing.8t18te</td>\n",
" <td>Cell Image Library</td>\n",
" <td>ready</td>\n",
" <td>[{'contact-name': 'David Orloff', 'contact-ema...</td>\n",
" <td>http://www.cellimagelibrary.org</td>\n",
" <td>1723</td>\n",
" <td>This library is a public and easily accessible...</td>\n",
" <td>[{'url': 'http://www.cellimagelibrary.org/page...</td>\n",
" <td>2010.0</td>\n",
" <td>[{'name': 'live update', 'type': 'data release...</td>\n",
" <td>[biodbcore-000180, bsg-d000180]</td>\n",
" <td>Database</td>\n",
" <td>repository</td>\n",
" <td>[Cell Biology, Life Science]</td>\n",
" <td>[Cell, Microscopy, Light microscopy, Electron ...</td>\n",
" <td>[All]</td>\n",
" <td>[]</td>\n",
" <td>[United States]</td>\n",
" <td>FAIRsharing record for: Cell Image Library</td>\n",
" <td>None</td>\n",
" <td>https://fairsharing.org/10.25504/FAIRsharing.8...</td>\n",
" <td>10.25504/FAIRsharing.8t18te</td>\n",
" <td>https://creativecommons.org/licenses/by-sa/4.0...</td>\n",
" <td>This FAIRsharing record describes: This librar...</td>\n",
" <td>[{'id': 232, 'pubmed_id': 23203874, 'title': '...</td>\n",
" <td>[{'licence-name': 'Cell Image Library Data Pol...</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>3101</td>\n",
" <td>fairsharing-records</td>\n",
" <td>2020-09-16T08:49:13.000Z</td>\n",
" <td>2021-09-30T11:36:45.452Z</td>\n",
" <td>NaN</td>\n",
" <td>WHOI Ship Data-Grabber System</td>\n",
" <td>ready</td>\n",
" <td>NaN</td>\n",
" <td>http://4dgeo.whoi.edu/shipdata/SDG_shipdata.html</td>\n",
" <td>3101</td>\n",
" <td>The WHOI Ship DataGrabber system provides the ...</td>\n",
" <td>[{'url': 'http://4dgeo.whoi.edu/shipdata/SDG_o...</td>\n",
" <td>2004.0</td>\n",
" <td>[{'url': 'http://4dgeo.whoi.edu/sdg-bin/dv_mai...</td>\n",
" <td>[biodbcore-001609, bsg-d001609]</td>\n",
" <td>Database</td>\n",
" <td>repository</td>\n",
" <td>[Earth Science, Water Research, Oceanography]</td>\n",
" <td>[]</td>\n",
" <td>[Not applicable]</td>\n",
" <td>[subseafloor environments]</td>\n",
" <td>[United States]</td>\n",
" <td>FAIRsharing record for: WHOI Ship Data-Grabber...</td>\n",
" <td>None</td>\n",
" <td>https://fairsharing.org/fairsharing_records/3101</td>\n",
" <td>None</td>\n",
" <td>https://creativecommons.org/licenses/by-sa/4.0...</td>\n",
" <td>This FAIRsharing record describes: The WHOI Sh...</td>\n",
" <td>[]</td>\n",
" <td>[{'licence-name': 'NDSF Data Archive Policy', ...</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>2649</td>\n",
" <td>fairsharing-records</td>\n",
" <td>2018-08-07T20:23:32.000Z</td>\n",
" <td>2021-09-30T11:39:07.898Z</td>\n",
" <td>NaN</td>\n",
" <td>Electron Microscope Public Image Archive</td>\n",
" <td>ready</td>\n",
" <td>[{'contact-name': 'General contact', 'contact-...</td>\n",
" <td>https://www.ebi.ac.uk/pdbe/emdb/empiar/</td>\n",
" <td>2649</td>\n",
" <td>EMPIAR, the Electron Microscopy Public Image A...</td>\n",
" <td>[{'url': 'https://www.ebi.ac.uk/support/EMPIAR...</td>\n",
" <td>2015.0</td>\n",
" <td>[{'url': 'https://www.ebi.ac.uk/pdbe/emdb/empi...</td>\n",
" <td>[biodbcore-001140, bsg-d001140]</td>\n",
" <td>Database</td>\n",
" <td>repository</td>\n",
" <td>[Bioinformatics, Biology]</td>\n",
" <td>[Protein image, Microscopy, Electron microscop...</td>\n",
" <td>[All]</td>\n",
" <td>[]</td>\n",
" <td>[Greece, Czech Republic, United Kingdom, Icela...</td>\n",
" <td>FAIRsharing record for: Electron Microscope Pu...</td>\n",
" <td>EMPIAR</td>\n",
" <td>https://fairsharing.org/fairsharing_records/2649</td>\n",
" <td>None</td>\n",
" <td>https://creativecommons.org/licenses/by-sa/4.0...</td>\n",
" <td>This FAIRsharing record describes: EMPIAR, the...</td>\n",
" <td>[{'id': 2232, 'pubmed_id': 27067018, 'title': ...</td>\n",
" <td>[{'licence-name': 'EMBL-EBI Terms of Use', 'li...</td>\n",
" <td>[{'doi': '10.1038/nmeth.3806', 'pubmed-id': 27...</td>\n",
" <td>EMPIAR</td>\n",
" <td>[{'url': 'https://www.ebi.ac.uk/pdbe/emdb/empi...</td>\n",
" <td>[{'url': 'https://www.ebi.ac.uk/pdbe/emdb/empi...</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>2657</td>\n",
" <td>fairsharing-records</td>\n",
" <td>2018-08-13T15:12:11.000Z</td>\n",
" <td>2021-09-30T11:37:28.736Z</td>\n",
" <td>10.25504/FAIRsharing.tnByoG</td>\n",
" <td>ClinicalStudyDataRequest.com</td>\n",
" <td>ready</td>\n",
" <td>[{'contact-email': 'support@clinicalstudydatar...</td>\n",
" <td>https://clinicalstudydatarequest.com/</td>\n",
" <td>2657</td>\n",
" <td>ClinicalStudyDataRequest.com (CSDR) is a conso...</td>\n",
" <td>[{'url': 'https://clinicalstudydatarequest.com...</td>\n",
" <td>2014.0</td>\n",
" <td>[{'url': 'https://clinicalstudydatarequest.com...</td>\n",
" <td>[biodbcore-001149, bsg-d001149]</td>\n",
" <td>Database</td>\n",
" <td>repository</td>\n",
" <td>[Preclinical Studies, Biomedical Science]</td>\n",
" <td>[]</td>\n",
" <td>[Homo sapiens]</td>\n",
" <td>[]</td>\n",
" <td>[Worldwide]</td>\n",
" <td>FAIRsharing record for: ClinicalStudyDataReque...</td>\n",
" <td>CSDR</td>\n",
" <td>https://fairsharing.org/10.25504/FAIRsharing.t...</td>\n",
" <td>10.25504/FAIRsharing.tnByoG</td>\n",
" <td>https://creativecommons.org/licenses/by-sa/4.0...</td>\n",
" <td>This FAIRsharing record describes: ClinicalStu...</td>\n",
" <td>[]</td>\n",
" <td>[{'licence-name': 'CSDR Data Sharing Agreement...</td>\n",
" <td>NaN</td>\n",
" <td>CSDR</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>2078</td>\n",
" <td>fairsharing-records</td>\n",
" <td>2014-11-04T15:23:40.000Z</td>\n",
" <td>2021-09-30T11:34:43.129Z</td>\n",
" <td>10.25504/FAIRsharing.3axym7</td>\n",
" <td>Germplasm Resources Information Network</td>\n",
" <td>ready</td>\n",
" <td>[{'contact-email': 'dbmu@ars-grin.gov'}]</td>\n",
" <td>https://www.ars-grin.gov/</td>\n",
" <td>2078</td>\n",
" <td>GRIN provides National Genetic Resources Progr...</td>\n",
" <td>[{'url': 'https://www.ars-grin.gov/Pages/Colle...</td>\n",
" <td>2010.0</td>\n",
" <td>[{'url': 'https://www.ars-grin.gov/', 'name': ...</td>\n",
" <td>[biodbcore-000546, bsg-d000546]</td>\n",
" <td>Database</td>\n",
" <td>repository</td>\n",
" <td>[Life Science]</td>\n",
" <td>[Cell, Cell culture, Germplasm]</td>\n",
" <td>[Bacteria, Metazoa, Viridiplantae]</td>\n",
" <td>[]</td>\n",
" <td>[United States]</td>\n",
" <td>FAIRsharing record for: Germplasm Resources In...</td>\n",
" <td>GRIN</td>\n",
" <td>https://fairsharing.org/10.25504/FAIRsharing.3...</td>\n",
" <td>10.25504/FAIRsharing.3axym7</td>\n",
" <td>https://creativecommons.org/licenses/by-sa/4.0...</td>\n",
" <td>This FAIRsharing record describes: GRIN provid...</td>\n",
" <td>[]</td>\n",
" <td>[]</td>\n",
" <td>NaN</td>\n",
" <td>GRIN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" id type attributes.created-at \\\n",
"0 1723 fairsharing-records 2014-11-04T15:23:40.000Z \n",
"1 3101 fairsharing-records 2020-09-16T08:49:13.000Z \n",
"2 2649 fairsharing-records 2018-08-07T20:23:32.000Z \n",
"3 2657 fairsharing-records 2018-08-13T15:12:11.000Z \n",
"4 2078 fairsharing-records 2014-11-04T15:23:40.000Z \n",
"\n",
" attributes.updated-at attributes.metadata.doi \\\n",
"0 2021-09-30T11:39:06.829Z 10.25504/FAIRsharing.8t18te \n",
"1 2021-09-30T11:36:45.452Z NaN \n",
"2 2021-09-30T11:39:07.898Z NaN \n",
"3 2021-09-30T11:37:28.736Z 10.25504/FAIRsharing.tnByoG \n",
"4 2021-09-30T11:34:43.129Z 10.25504/FAIRsharing.3axym7 \n",
"\n",
" attributes.metadata.name attributes.metadata.status \\\n",
"0 Cell Image Library ready \n",
"1 WHOI Ship Data-Grabber System ready \n",
"2 Electron Microscope Public Image Archive ready \n",
"3 ClinicalStudyDataRequest.com ready \n",
"4 Germplasm Resources Information Network ready \n",
"\n",
" attributes.metadata.contacts \\\n",
"0 [{'contact-name': 'David Orloff', 'contact-ema... \n",
"1 NaN \n",
"2 [{'contact-name': 'General contact', 'contact-... \n",
"3 [{'contact-email': 'support@clinicalstudydatar... \n",
"4 [{'contact-email': 'dbmu@ars-grin.gov'}] \n",
"\n",
" attributes.metadata.homepage \\\n",
"0 http://www.cellimagelibrary.org \n",
"1 http://4dgeo.whoi.edu/shipdata/SDG_shipdata.html \n",
"2 https://www.ebi.ac.uk/pdbe/emdb/empiar/ \n",
"3 https://clinicalstudydatarequest.com/ \n",
"4 https://www.ars-grin.gov/ \n",
"\n",
" attributes.metadata.identifier \\\n",
"0 1723 \n",
"1 3101 \n",
"2 2649 \n",
"3 2657 \n",
"4 2078 \n",
"\n",
" attributes.metadata.description \\\n",
"0 This library is a public and easily accessible... \n",
"1 The WHOI Ship DataGrabber system provides the ... \n",
"2 EMPIAR, the Electron Microscopy Public Image A... \n",
"3 ClinicalStudyDataRequest.com (CSDR) is a conso... \n",
"4 GRIN provides National Genetic Resources Progr... \n",
"\n",
" attributes.metadata.support-links \\\n",
"0 [{'url': 'http://www.cellimagelibrary.org/page... \n",
"1 [{'url': 'http://4dgeo.whoi.edu/shipdata/SDG_o... \n",
"2 [{'url': 'https://www.ebi.ac.uk/support/EMPIAR... \n",
"3 [{'url': 'https://clinicalstudydatarequest.com... \n",
"4 [{'url': 'https://www.ars-grin.gov/Pages/Colle... \n",
"\n",
" attributes.metadata.year-creation \\\n",
"0 2010.0 \n",
"1 2004.0 \n",
"2 2015.0 \n",
"3 2014.0 \n",
"4 2010.0 \n",
"\n",
" attributes.metadata.data-processes \\\n",
"0 [{'name': 'live update', 'type': 'data release... \n",
"1 [{'url': 'http://4dgeo.whoi.edu/sdg-bin/dv_mai... \n",
"2 [{'url': 'https://www.ebi.ac.uk/pdbe/emdb/empi... \n",
"3 [{'url': 'https://clinicalstudydatarequest.com... \n",
"4 [{'url': 'https://www.ars-grin.gov/', 'name': ... \n",
"\n",
" attributes.legacy-ids attributes.fairsharing-registry \\\n",
"0 [biodbcore-000180, bsg-d000180] Database \n",
"1 [biodbcore-001609, bsg-d001609] Database \n",
"2 [biodbcore-001140, bsg-d001140] Database \n",
"3 [biodbcore-001149, bsg-d001149] Database \n",
"4 [biodbcore-000546, bsg-d000546] Database \n",
"\n",
" attributes.record-type attributes.subjects \\\n",
"0 repository [Cell Biology, Life Science] \n",
"1 repository [Earth Science, Water Research, Oceanography] \n",
"2 repository [Bioinformatics, Biology] \n",
"3 repository [Preclinical Studies, Biomedical Science] \n",
"4 repository [Life Science] \n",
"\n",
" attributes.domains \\\n",
"0 [Cell, Microscopy, Light microscopy, Electron ... \n",
"1 [] \n",
"2 [Protein image, Microscopy, Electron microscop... \n",
"3 [] \n",
"4 [Cell, Cell culture, Germplasm] \n",
"\n",
" attributes.taxonomies attributes.user-defined-tags \\\n",
"0 [All] [] \n",
"1 [Not applicable] [subseafloor environments] \n",
"2 [All] [] \n",
"3 [Homo sapiens] [] \n",
"4 [Bacteria, Metazoa, Viridiplantae] [] \n",
"\n",
" attributes.countries \\\n",
"0 [United States] \n",
"1 [United States] \n",
"2 [Greece, Czech Republic, United Kingdom, Icela... \n",
"3 [Worldwide] \n",
"4 [United States] \n",
"\n",
" attributes.name attributes.abbreviation \\\n",
"0 FAIRsharing record for: Cell Image Library None \n",
"1 FAIRsharing record for: WHOI Ship Data-Grabber... None \n",
"2 FAIRsharing record for: Electron Microscope Pu... EMPIAR \n",
"3 FAIRsharing record for: ClinicalStudyDataReque... CSDR \n",
"4 FAIRsharing record for: Germplasm Resources In... GRIN \n",
"\n",
" attributes.url \\\n",
"0 https://fairsharing.org/10.25504/FAIRsharing.8... \n",
"1 https://fairsharing.org/fairsharing_records/3101 \n",
"2 https://fairsharing.org/fairsharing_records/2649 \n",
"3 https://fairsharing.org/10.25504/FAIRsharing.t... \n",
"4 https://fairsharing.org/10.25504/FAIRsharing.3... \n",
"\n",
" attributes.doi \\\n",
"0 10.25504/FAIRsharing.8t18te \n",
"1 None \n",
"2 None \n",
"3 10.25504/FAIRsharing.tnByoG \n",
"4 10.25504/FAIRsharing.3axym7 \n",
"\n",
" attributes.fairsharing-licence \\\n",
"0 https://creativecommons.org/licenses/by-sa/4.0... \n",
"1 https://creativecommons.org/licenses/by-sa/4.0... \n",
"2 https://creativecommons.org/licenses/by-sa/4.0... \n",
"3 https://creativecommons.org/licenses/by-sa/4.0... \n",
"4 https://creativecommons.org/licenses/by-sa/4.0... \n",
"\n",
" attributes.description \\\n",
"0 This FAIRsharing record describes: This librar... \n",
"1 This FAIRsharing record describes: The WHOI Sh... \n",
"2 This FAIRsharing record describes: EMPIAR, the... \n",
"3 This FAIRsharing record describes: ClinicalStu... \n",
"4 This FAIRsharing record describes: GRIN provid... \n",
"\n",
" attributes.publications \\\n",
"0 [{'id': 232, 'pubmed_id': 23203874, 'title': '... \n",
"1 [] \n",
"2 [{'id': 2232, 'pubmed_id': 27067018, 'title': ... \n",
"3 [] \n",
"4 [] \n",
"\n",
" attributes.licence-links \\\n",
"0 [{'licence-name': 'Cell Image Library Data Pol... \n",
"1 [{'licence-name': 'NDSF Data Archive Policy', ... \n",
"2 [{'licence-name': 'EMBL-EBI Terms of Use', 'li... \n",
"3 [{'licence-name': 'CSDR Data Sharing Agreement... \n",
"4 [] \n",
"\n",
" attributes.metadata.citations \\\n",
"0 NaN \n",
"1 NaN \n",
"2 [{'doi': '10.1038/nmeth.3806', 'pubmed-id': 27... \n",
"3 NaN \n",
"4 NaN \n",
"\n",
" attributes.metadata.abbreviation \\\n",
"0 NaN \n",
"1 NaN \n",
"2 EMPIAR \n",
"3 CSDR \n",
"4 GRIN \n",
"\n",
" attributes.metadata.access-points \\\n",
"0 NaN \n",
"1 NaN \n",
"2 [{'url': 'https://www.ebi.ac.uk/pdbe/emdb/empi... \n",
"3 NaN \n",
"4 NaN \n",
"\n",
" attributes.metadata.associated-tools \\\n",
"0 NaN \n",
"1 NaN \n",
"2 [{'url': 'https://www.ebi.ac.uk/pdbe/emdb/empi... \n",
"3 NaN \n",
"4 NaN \n",
"\n",
" attributes.metadata.deprecation-date attributes.metadata.deprecation-reason \\\n",
"0 NaN NaN \n",
"1 NaN NaN \n",
"2 NaN NaN \n",
"3 NaN NaN \n",
"4 NaN NaN \n",
"\n",
" attributes.metadata.tombstone \n",
"0 NaN \n",
"1 NaN \n",
"2 NaN \n",
"3 NaN \n",
"4 NaN "
]
},
"execution_count": 57,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"with open('../data/raw/fairsharing_dump_api_09_2021.json') as f:\n",
" lines = f.read().splitlines()\n",
" \n",
"fairsharing_df = pd.DataFrame(lines)\n",
"fairsharing_df.columns = ['json_element']\n",
"fairsharing_df['json_element'].apply(json.loads)\n",
"fairsharing_df = pd.json_normalize(fairsharing_df['json_element'].apply(json.loads))\n",
"\n",
"fairsharing_df.head()"
]
},
{
"cell_type": "code",
"execution_count": 58,
"metadata": {},
"outputs": [
{
"data": {
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" <th></th>\n",
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" <th>attributes.created-at</th>\n",
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" <th>attributes.subjects</th>\n",
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" <th>attributes.user-defined-tags</th>\n",
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" <td>1723</td>\n",
" <td>fairsharing-records</td>\n",
" <td>2014-11-04T15:23:40.000Z</td>\n",
" <td>2021-09-30T11:39:06.829Z</td>\n",
" <td>10.25504/FAIRsharing.8t18te</td>\n",
" <td>OmicsDB</td>\n",
" <td>ready</td>\n",
" <td>[{'contact-name': 'Sam Hokin', 'contact-email'...</td>\n",
" <td>http://www.cellimagelibrary.org</td>\n",
" <td>NaN</td>\n",
" <td>This library is a public and easily accessible...</td>\n",
" <td>[{'url': 'https://github.com/gbif/ipt/wiki/IPT...</td>\n",
" <td>NaN</td>\n",
" <td>[{'url': 'http://qf.iodp.tamu.edu/qfsearch/sea...</td>\n",
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" <td>FAIRsharing record for: OmicsDB</td>\n",
" <td>CGD</td>\n",
" <td>https://fairsharing.org/10.25504/FAIRsharing.8...</td>\n",
" <td>10.25504/FAIRsharing.8t18te</td>\n",
" <td>https://creativecommons.org/licenses/by-sa/4.0...</td>\n",
" <td>This FAIRsharing record describes: This librar...</td>\n",
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" <td>[]</td>\n",
" <td>[{'doi': '10.1093/nar/gkz890', 'pubmed-id': 31...</td>\n",
" <td>CGD</td>\n",
" <td>[{'url': 'https://github.com/Ensembl', 'name':...</td>\n",
" <td>[{'url': 'http://www.h-invitational.jp/hinv/bl...</td>\n",
" <td>2021-9-17</td>\n",
" <td>This resource is no longer available at the st...</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <tr>\n",
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" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>1996.000000</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
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" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>2445.000000</td>\n",
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" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
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" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
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"</table>\n",
"</div>"
],
"text/plain": [
" id type attributes.created-at \\\n",
"count 1797 1797 1797 \n",
"unique 1797 1 1162 \n",
"top 1723 fairsharing-records 2014-11-04T15:23:40.000Z \n",
"freq 1 1797 636 \n",
"mean NaN NaN NaN \n",
"std NaN NaN NaN \n",
"min NaN NaN NaN \n",
"25% NaN NaN NaN \n",
"50% NaN NaN NaN \n",
"75% NaN NaN NaN \n",
"max NaN NaN NaN \n",
"\n",
" attributes.updated-at attributes.metadata.doi \\\n",
"count 1797 1354 \n",
"unique 1797 1354 \n",
"top 2021-09-30T11:39:06.829Z 10.25504/FAIRsharing.8t18te \n",
"freq 1 1 \n",
"mean NaN NaN \n",
"std NaN NaN \n",
"min NaN NaN \n",
"25% NaN NaN \n",
"50% NaN NaN \n",
"75% NaN NaN \n",
"max NaN NaN \n",
"\n",
" attributes.metadata.name attributes.metadata.status \\\n",
"count 1797 1797 \n",
"unique 1796 4 \n",
"top OmicsDB ready \n",
"freq 2 1540 \n",
"mean NaN NaN \n",
"std NaN NaN \n",
"min NaN NaN \n",
"25% NaN NaN \n",
"50% NaN NaN \n",
"75% NaN NaN \n",
"max NaN NaN \n",
"\n",
" attributes.metadata.contacts \\\n",
"count 1678 \n",
"unique 1576 \n",
"top [{'contact-name': 'Sam Hokin', 'contact-email'... \n",
"freq 6 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN \n",
"\n",
" attributes.metadata.homepage attributes.metadata.identifier \\\n",
"count 1797 1797.000000 \n",
"unique 1797 NaN \n",
"top http://www.cellimagelibrary.org NaN \n",
"freq 1 NaN \n",
"mean NaN 2446.100167 \n",
"std NaN 520.058757 \n",
"min NaN 1547.000000 \n",
"25% NaN 1996.000000 \n",
"50% NaN 2445.000000 \n",
"75% NaN 2897.000000 \n",
"max NaN 3346.000000 \n",
"\n",
" attributes.metadata.description \\\n",
"count 1797 \n",
"unique 1797 \n",
"top This library is a public and easily accessible... \n",
"freq 1 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN \n",
"\n",
" attributes.metadata.support-links \\\n",
"count 1608 \n",
"unique 1594 \n",
"top [{'url': 'https://github.com/gbif/ipt/wiki/IPT... \n",
"freq 6 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN \n",
"\n",
" attributes.metadata.year-creation \\\n",
"count 1492.000000 \n",
"unique NaN \n",
"top NaN \n",
"freq NaN \n",
"mean 2007.636059 \n",
"std 10.953269 \n",
"min 1894.000000 \n",
"25% 2004.000000 \n",
"50% 2010.000000 \n",
"75% 2014.000000 \n",
"max 2021.000000 \n",
"\n",
" attributes.metadata.data-processes \\\n",
"count 1565 \n",
"unique 1563 \n",
"top [{'url': 'http://qf.iodp.tamu.edu/qfsearch/sea... \n",
"freq 2 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN \n",
"\n",
" attributes.legacy-ids attributes.fairsharing-registry \\\n",
"count 1797 1797 \n",
"unique 1797 1 \n",
"top [biodbcore-000180, bsg-d000180] Database \n",
"freq 1 1797 \n",
"mean NaN NaN \n",
"std NaN NaN \n",
"min NaN NaN \n",
"25% NaN NaN \n",
"50% NaN NaN \n",
"75% NaN NaN \n",
"max NaN NaN \n",
"\n",
" attributes.record-type attributes.subjects attributes.domains \\\n",
"count 1797 1797 1797 \n",
"unique 3 888 1163 \n",
"top repository [Life Science] [] \n",
"freq 926 350 265 \n",
"mean NaN NaN NaN \n",
"std NaN NaN NaN \n",
"min NaN NaN NaN \n",
"25% NaN NaN NaN \n",
"50% NaN NaN NaN \n",
"75% NaN NaN NaN \n",
"max NaN NaN NaN \n",
"\n",
" attributes.taxonomies attributes.user-defined-tags \\\n",
"count 1797 1797 \n",
"unique 378 384 \n",
"top [All] [] \n",
"freq 502 1193 \n",
"mean NaN NaN \n",
"std NaN NaN \n",
"min NaN NaN \n",
"25% NaN NaN \n",
"50% NaN NaN \n",
"75% NaN NaN \n",
"max NaN NaN \n",
"\n",
" attributes.countries attributes.name \\\n",
"count 1797 1797 \n",
"unique 185 1796 \n",
"top [United States] FAIRsharing record for: OmicsDB \n",
"freq 594 2 \n",
"mean NaN NaN \n",
"std NaN NaN \n",
"min NaN NaN \n",
"25% NaN NaN \n",
"50% NaN NaN \n",
"75% NaN NaN \n",
"max NaN NaN \n",
"\n",
" attributes.abbreviation \\\n",
"count 1638 \n",
"unique 1626 \n",
"top CGD \n",
"freq 3 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN \n",
"\n",
" attributes.url \\\n",
"count 1797 \n",
"unique 1797 \n",
"top https://fairsharing.org/10.25504/FAIRsharing.8... \n",
"freq 1 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN \n",
"\n",
" attributes.doi \\\n",
"count 1354 \n",
"unique 1354 \n",
"top 10.25504/FAIRsharing.8t18te \n",
"freq 1 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN \n",
"\n",
" attributes.fairsharing-licence \\\n",
"count 1797 \n",
"unique 1 \n",
"top https://creativecommons.org/licenses/by-sa/4.0... \n",
"freq 1797 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN \n",
"\n",
" attributes.description \\\n",
"count 1797 \n",
"unique 1797 \n",
"top This FAIRsharing record describes: This librar... \n",
"freq 1 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN \n",
"\n",
" attributes.publications attributes.licence-links \\\n",
"count 1797 1797 \n",
"unique 1109 1082 \n",
"top [] [] \n",
"freq 661 716 \n",
"mean NaN NaN \n",
"std NaN NaN \n",
"min NaN NaN \n",
"25% NaN NaN \n",
"50% NaN NaN \n",
"75% NaN NaN \n",
"max NaN NaN \n",
"\n",
" attributes.metadata.citations \\\n",
"count 326 \n",
"unique 320 \n",
"top [{'doi': '10.1093/nar/gkz890', 'pubmed-id': 31... \n",
"freq 6 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN \n",
"\n",
" attributes.metadata.abbreviation \\\n",
"count 1638 \n",
"unique 1626 \n",
"top CGD \n",
"freq 3 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN \n",
"\n",
" attributes.metadata.access-points \\\n",
"count 449 \n",
"unique 444 \n",
"top [{'url': 'https://github.com/Ensembl', 'name':... \n",
"freq 3 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN \n",
"\n",
" attributes.metadata.associated-tools \\\n",
"count 618 \n",
"unique 615 \n",
"top [{'url': 'http://www.h-invitational.jp/hinv/bl... \n",
"freq 2 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN \n",
"\n",
" attributes.metadata.deprecation-date \\\n",
"count 217 \n",
"unique 55 \n",
"top 2021-9-17 \n",
"freq 84 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN \n",
"\n",
" attributes.metadata.deprecation-reason \\\n",
"count 217 \n",
"unique 86 \n",
"top This resource is no longer available at the st... \n",
"freq 113 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN \n",
"\n",
" attributes.metadata.tombstone \n",
"count 1 \n",
"unique 1 \n",
"top True \n",
"freq 1 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN "
]
},
"execution_count": 58,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"fairsharing_df.describe(include='all')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Subjects analysis"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**re3data**"
]
},
{
"cell_type": "code",
"execution_count": 38,
"metadata": {},
"outputs": [
{
"data": {
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"</div>"
],
"text/plain": [
" orgIdentifier subject\n",
"0 r3d100000001 1 Humanities and Social Sciences\n",
"0 r3d100000001 111 Social Sciences\n",
"0 r3d100000001 11104 Political Science\n",
"0 r3d100000001 112 Economics\n",
"0 r3d100000001 12 Social and Behavioural Sciences\n",
"... ... ...\n",
"2738 r3d100013652 102 History\n",
"2738 r3d100013652 105 Literary Studies\n",
"2738 r3d100013652 108 Philosophy\n",
"2738 r3d100013652 10801 History of Philosophy\n",
"2738 r3d100013652 11 Humanities\n",
"\n",
"[16654 rows x 2 columns]"
]
},
"execution_count": 38,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"re3data_subjects = re3data_df[['orgIdentifier', 'subject']].explode('subject')\n",
"re3data_subjects['subject'] = re3data_subjects['subject'].apply(lambda x: x['name'] if x is not np.nan else np.nan)\n",
"re3data_subjects"
]
},
{
"cell_type": "code",
"execution_count": 42,
"metadata": {},
"outputs": [
{
"data": {
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"/*!\n",
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" * @license MIT\n",
" */function i(t,e){if(t===e)return 0;for(var r=t.length,n=e.length,i=0,a=Math.min(r,n);i<a;++i)if(t[i]!==e[i]){r=t[i],n=e[i];break}return r<n?-1:n<r?1:0}function a(t){return r.Buffer&&\"function\"==typeof r.Buffer.isBuffer?r.Buffer.isBuffer(t):!(null==t||!t._isBuffer)}var o=t(\"util/\"),s=Object.prototype.hasOwnProperty,l=Array.prototype.slice,c=\"foo\"===function(){}.name;function u(t){return Object.prototype.toString.call(t)}function f(t){return!a(t)&&(\"function\"==typeof r.ArrayBuffer&&(\"function\"==typeof ArrayBuffer.isView?ArrayBuffer.isView(t):!!t&&(t instanceof DataView||!!(t.buffer&&t.buffer instanceof ArrayBuffer))))}var h=e.exports=y,p=/\\s*function\\s+([^\\(\\s]*)\\s*/;function d(t){if(o.isFunction(t)){if(c)return t.name;var e=t.toString().match(p);return e&&e[1]}}function g(t,e){return\"string\"==typeof t?t.length<e?t:t.slice(0,e):t}function m(t){if(c||!o.isFunction(t))return o.inspect(t);var e=d(t);return\"[Function\"+(e?\": \"+e:\"\")+\"]\"}function v(t,e,r,n,i){throw new h.AssertionError({message:r,actual:t,expected:e,operator:n,stackStartFunction:i})}function y(t,e){t||v(t,!0,e,\"==\",h.ok)}function x(t,e,r,n){if(t===e)return!0;if(a(t)&&a(e))return 0===i(t,e);if(o.isDate(t)&&o.isDate(e))return t.getTime()===e.getTime();if(o.isRegExp(t)&&o.isRegExp(e))return t.source===e.source&&t.global===e.global&&t.multiline===e.multiline&&t.lastIndex===e.lastIndex&&t.ignoreCase===e.ignoreCase;if(null!==t&&\"object\"==typeof t||null!==e&&\"object\"==typeof e){if(f(t)&&f(e)&&u(t)===u(e)&&!(t instanceof Float32Array||t instanceof Float64Array))return 0===i(new Uint8Array(t.buffer),new Uint8Array(e.buffer));if(a(t)!==a(e))return!1;var s=(n=n||{actual:[],expected:[]}).actual.indexOf(t);return-1!==s&&s===n.expected.indexOf(e)||(n.actual.push(t),n.expected.push(e),function(t,e,r,n){if(null==t||null==e)return!1;if(o.isPrimitive(t)||o.isPrimitive(e))return t===e;if(r&&Object.getPrototypeOf(t)!==Object.getPrototypeOf(e))return!1;var i=b(t),a=b(e);if(i&&!a||!i&&a)return!1;if(i)return t=l.call(t),e=l.call(e),x(t,e,r);var s,c,u=T(t),f=T(e);if(u.length!==f.length)return!1;for(u.sort(),f.sort(),c=u.length-1;c>=0;c--)if(u[c]!==f[c])return!1;for(c=u.length-1;c>=0;c--)if(s=u[c],!x(t[s],e[s],r,n))return!1;return!0}(t,e,r,n))}return r?t===e:t==e}function b(t){return\"[object Arguments]\"==Object.prototype.toString.call(t)}function _(t,e){if(!t||!e)return!1;if(\"[object RegExp]\"==Object.prototype.toString.call(e))return e.test(t);try{if(t instanceof e)return!0}catch(t){}return!Error.isPrototypeOf(e)&&!0===e.call({},t)}function w(t,e,r,n){var i;if(\"function\"!=typeof e)throw new TypeError('\"block\" argument must be a function');\"string\"==typeof r&&(n=r,r=null),i=function(t){var e;try{t()}catch(t){e=t}return e}(e),n=(r&&r.name?\" (\"+r.name+\").\":\".\")+(n?\" \"+n:\".\"),t&&!i&&v(i,r,\"Missing expected exception\"+n);var a=\"string\"==typeof n,s=!t&&i&&!r;if((!t&&o.isError(i)&&a&&_(i,r)||s)&&v(i,r,\"Got unwanted exception\"+n),t&&i&&r&&!_(i,r)||!t&&i)throw i}h.AssertionError=function(t){this.name=\"AssertionError\",this.actual=t.actual,this.expected=t.expected,this.operator=t.operator,t.message?(this.message=t.message,this.generatedMessage=!1):(this.message=function(t){return g(m(t.actual),128)+\" \"+t.operator+\" \"+g(m(t.expected),128)}(this),this.generatedMessage=!0);var e=t.stackStartFunction||v;if(Error.captureStackTrace)Error.captureStackTrace(this,e);else{var r=new Error;if(r.stack){var n=r.stack,i=d(e),a=n.indexOf(\"\\n\"+i);if(a>=0){var o=n.indexOf(\"\\n\",a+1);n=n.substring(o+1)}this.stack=n}}},o.inherits(h.AssertionError,Error),h.fail=v,h.ok=y,h.equal=function(t,e,r){t!=e&&v(t,e,r,\"==\",h.equal)},h.notEqual=function(t,e,r){t==e&&v(t,e,r,\"!=\",h.notEqual)},h.deepEqual=function(t,e,r){x(t,e,!1)||v(t,e,r,\"deepEqual\",h.deepEqual)},h.deepStrictEqual=function(t,e,r){x(t,e,!0)||v(t,e,r,\"deepStrictEqual\",h.deepStrictEqual)},h.notDeepEqual=function(t,e,r){x(t,e,!1)&&v(t,e,r,\"notDeepEqual\",h.notDeepEqual)},h.notDeepStrictEqual=function t(e,r,n){x(e,r,!0)&&v(e,r,n,\"notDeepStrictEqual\",t)},h.strictEqual=function(t,e
"/*!\n",
" * The buffer module from node.js, for the browser.\n",
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" * @author Feross Aboukhadijeh <https://feross.org>\n",
" * @license MIT\n",
" */\n",
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"/*!\n",
" * @overview es6-promise - a tiny implementation of Promises/A+.\n",
" * @copyright Copyright (c) 2014 Yehuda Katz, Tom Dale, Stefan Penner and contributors (Conversion to ES6 API by Jake Archibald)\n",
" * @license Licensed under MIT license\n",
" * See https://raw.githubusercontent.com/stefanpenner/es6-promise/master/LICENSE\n",
" * @version v4.2.8+1e68dce6\n",
" */\n",
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"/*!\n",
" * Determine if an object is a Buffer\n",
" *\n",
" * @author Feross Aboukhadijeh <https://feross.org>\n",
" * @license MIT\n",
" */\n",
"e.exports=function(t){return null!=t&&(n(t)||function(t){return\"function\"==typeof t.readFloatLE&&\"function\"==typeof t.slice&&n(t.slice(0,0))}(t)||!!t._isBuffer)}},{}],466:[function(t,e,r){\"use strict\";e.exports=\"undefined\"!=typeof navigator&&(/MSIE/.test(navigator.userAgent)||/Trident\\//.test(navigator.appVersion))},{}],467:[function(t,e,r){\"use strict\";e.exports=a,e.exports.isMobile=a,e.exports.default=a;var n=/(android|bb\\d+|meego).+mobile|avantgo|bada\\/|blackberry|blazer|compal|elaine|fennec|hiptop|iemobile|ip(hone|od)|iris|kindle|lge |maemo|midp|mmp|mobile.+firefox|netfront|opera m(ob|in)i|palm( os)?|phone|p(ixi|re)\\/|plucker|pocket|psp|series[46]0|symbian|treo|up\\.(browser|link)|vodafone|wap|windows (ce|phone)|xda|xiino/i,i=/(android|bb\\d+|meego).+mobile|avantgo|bada\\/|blackberry|blazer|compal|elaine|fennec|hiptop|iemobile|ip(hone|od)|iris|kindle|lge |maemo|midp|mmp|mobile.+firefox|netfront|opera m(ob|in)i|palm( os)?|phone|p(ixi|re)\\/|plucker|pocket|psp|series[46]0|symbian|treo|up\\.(browser|link)|vodafone|wap|windows (ce|phone)|xda|xiino|android|ipad|playbook|silk/i;function a(t){t||(t={});var e=t.ua;if(e||\"undefined\"==typeof navigator||(e=navigator.userAgent),e&&e.headers&&\"string\"==typeof e.headers[\"user-agent\"]&&(e=e.headers[\"user-agent\"]),\"string\"!=typeof e)return!1;var r=t.tablet?i.test(e):n.test(e);return!r&&t.tablet&&t.featureDetect&&navigator&&navigator.maxTouchPoints>1&&-1!==e.indexOf(\"Macintosh\")&&-1!==e.indexOf(\"Safari\")&&(r=!0),r}},{}],468:[function(t,e,r){\"use strict\";e.exports=function(t){var e=typeof t;return null!==t&&(\"object\"===e||\"function\"===e)}},{}],469:[function(t,e,r){\"use strict\";var n=Object.prototype.toString;e.exports=function(t){var e;return\"[object Object]\"===n.call(t)&&(null===(e=Object.getPrototypeOf(t))||e===Object.getPrototypeOf({}))}},{}],470:[function(t,e,r){\"use strict\";e.exports=function(t){for(var e,r=t.length,n=0;n<r;n++)if(((e=t.charCodeAt(n))<9||e>13)&&32!==e&&133!==e&&160!==e&&5760!==e&&6158!==e&&(e<8192||e>8205)&&8232!==e&&8233!==e&&8239!==e&&8287!==e&&8288!==e&&12288!==e&&65279!==e)return!1;return!0}},{}],471:[function(t,e,r){\"use strict\";e.exports=function(t){return\"string\"==typeof t&&(t=t.trim(),!!(/^[mzlhvcsqta]\\s*[-+.0-9][^mlhvzcsqta]+/i.test(t)&&/[\\dz]$/i.test(t)&&t.length>4))}},{}],472:[function(t,e,r){e.exports=function(t,e,r){return t*(1-r)+e*r}},{}],473:[function(t,e,r){!function(t,n){\"object\"==typeof r&&\"undefined\"!=typeof e?e.exports=n():(t=t||self).mapboxgl=n()}(this,(function(){\"use strict\";var t,e,r;function n(n,i){if(t)if(e){var a=\"var sharedChunk = {}; (\"+t+\")(sharedChunk); (\"+e+\")(sharedChunk);\",o={};t(o),(r=i(o)).workerUrl=window.URL.createObjectURL(new Blob([a],{type:\"text/javascript\"}))}else e=i;else t=i}return n(0,(function(t){function e(t,e){return t(e={exports:{}},e.exports),e.exports}var r=n;function n(t,e,r,n){this.cx=3*t,this.bx=3*(r-t)-this.cx,this.ax=1-this.cx-this.bx,this.cy=3*e,this.by=3*(n-e)-this.cy,this.ay=1-this.cy-this.by,this.p1x=t,this.p1y=n,this.p2x=r,this.p2y=n}n.prototype.sampleCurveX=function(t){return((this.ax*t+this.bx)*t+this.cx)*t},n.prototype.sampleCurveY=function(t){return((this.ay*t+this.by)*t+this.cy)*t},n.prototype.sampleCurveDerivativeX=function(t){return(3*this.ax*t+2*this.bx)*t+this.cx},n.prototype.solveCurveX=function(t,e){var r,n,i,a,o;for(void 0===e&&(e=1e-6),i=t,o=0;o<8;o++){if(a=this.sampleCurveX(i)-t,Math.abs(a)<e)return i;var s=this.sampleCurveDerivativeX(i);if(Math.abs(s)<1e-6)break;i-=a/s}if((i=t)<(r=0))return r;if(i>(n=1))return n;for(;r<n;){if(a=this.sampleCurveX(i),Math.abs(a-t)<e)return i;t>a?r=i:n=i,i=.5*(n-r)+r}return i},n.prototype.solve=function(t,e){return this.sampleCurveY(this.solveCurveX(t,e))};var i=a;function a(t,e){this.x=t,this.y=e}function o(t,e,n,i){var a=new r(t,e,n,i);return function(t){return a.solve(t)}}a.prototype={clone:function(){return new a(this.x,this.y)},add:function(t){return this.clone()._add(t)},sub:function(t){return this.clone()._sub(t)},multByPoint:function(t){return this.clone()._multByPoint(t)},divByPoi
"/*\n",
"object-assign\n",
"(c) Sindre Sorhus\n",
"@license MIT\n",
"*/\n",
"\"use strict\";var n=Object.getOwnPropertySymbols,i=Object.prototype.hasOwnProperty,a=Object.prototype.propertyIsEnumerable;function o(t){if(null==t)throw new TypeError(\"Object.assign cannot be called with null or undefined\");return Object(t)}e.exports=function(){try{if(!Object.assign)return!1;var t=new String(\"abc\");if(t[5]=\"de\",\"5\"===Object.getOwnPropertyNames(t)[0])return!1;for(var e={},r=0;r<10;r++)e[\"_\"+String.fromCharCode(r)]=r;if(\"0123456789\"!==Object.getOwnPropertyNames(e).map((function(t){return e[t]})).join(\"\"))return!1;var n={};return\"abcdefghijklmnopqrst\".split(\"\").forEach((function(t){n[t]=t})),\"abcdefghijklmnopqrst\"===Object.keys(Object.assign({},n)).join(\"\")}catch(t){return!1}}()?Object.assign:function(t,e){for(var r,s,l=o(t),c=1;c<arguments.length;c++){for(var u in r=Object(arguments[c]))i.call(r,u)&&(l[u]=r[u]);if(n){s=n(r);for(var f=0;f<s.length;f++)a.call(r,s[f])&&(l[s[f]]=r[s[f]])}}return l}},{}],500:[function(t,e,r){\"use strict\";e.exports=function(t,e,r,n,i,a,o,s,l,c){var u=e+a+c;if(f>0){var f=Math.sqrt(u+1);t[0]=.5*(o-l)/f,t[1]=.5*(s-n)/f,t[2]=.5*(r-a)/f,t[3]=.5*f}else{var h=Math.max(e,a,c);f=Math.sqrt(2*h-u+1);e>=h?(t[0]=.5*f,t[1]=.5*(i+r)/f,t[2]=.5*(s+n)/f,t[3]=.5*(o-l)/f):a>=h?(t[0]=.5*(r+i)/f,t[1]=.5*f,t[2]=.5*(l+o)/f,t[3]=.5*(s-n)/f):(t[0]=.5*(n+s)/f,t[1]=.5*(o+l)/f,t[2]=.5*f,t[3]=.5*(r-i)/f)}return t}},{}],501:[function(t,e,r){\"use strict\";e.exports=function(t){var e=(t=t||{}).center||[0,0,0],r=t.rotation||[0,0,0,1],n=t.radius||1;e=[].slice.call(e,0,3),u(r=[].slice.call(r,0,4),r);var i=new f(r,e,Math.log(n));i.setDistanceLimits(t.zoomMin,t.zoomMax),(\"eye\"in t||\"up\"in t)&&i.lookAt(0,t.eye,t.center,t.up);return i};var n=t(\"filtered-vector\"),i=t(\"gl-mat4/lookAt\"),a=t(\"gl-mat4/fromQuat\"),o=t(\"gl-mat4/invert\"),s=t(\"./lib/quatFromFrame\");function l(t,e,r){return Math.sqrt(Math.pow(t,2)+Math.pow(e,2)+Math.pow(r,2))}function c(t,e,r,n){return Math.sqrt(Math.pow(t,2)+Math.pow(e,2)+Math.pow(r,2)+Math.pow(n,2))}function u(t,e){var r=e[0],n=e[1],i=e[2],a=e[3],o=c(r,n,i,a);o>1e-6?(t[0]=r/o,t[1]=n/o,t[2]=i/o,t[3]=a/o):(t[0]=t[1]=t[2]=0,t[3]=1)}function f(t,e,r){this.radius=n([r]),this.center=n(e),this.rotation=n(t),this.computedRadius=this.radius.curve(0),this.computedCenter=this.center.curve(0),this.computedRotation=this.rotation.curve(0),this.computedUp=[.1,0,0],this.computedEye=[.1,0,0],this.computedMatrix=[.1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],this.recalcMatrix(0)}var h=f.prototype;h.lastT=function(){return Math.max(this.radius.lastT(),this.center.lastT(),this.rotation.lastT())},h.recalcMatrix=function(t){this.radius.curve(t),this.center.curve(t),this.rotation.curve(t);var e=this.computedRotation;u(e,e);var r=this.computedMatrix;a(r,e);var n=this.computedCenter,i=this.computedEye,o=this.computedUp,s=Math.exp(this.computedRadius[0]);i[0]=n[0]+s*r[2],i[1]=n[1]+s*r[6],i[2]=n[2]+s*r[10],o[0]=r[1],o[1]=r[5],o[2]=r[9];for(var l=0;l<3;++l){for(var c=0,f=0;f<3;++f)c+=r[l+4*f]*i[f];r[12+l]=-c}},h.getMatrix=function(t,e){this.recalcMatrix(t);var r=this.computedMatrix;if(e){for(var n=0;n<16;++n)e[n]=r[n];return e}return r},h.idle=function(t){this.center.idle(t),this.radius.idle(t),this.rotation.idle(t)},h.flush=function(t){this.center.flush(t),this.radius.flush(t),this.rotation.flush(t)},h.pan=function(t,e,r,n){e=e||0,r=r||0,n=n||0,this.recalcMatrix(t);var i=this.computedMatrix,a=i[1],o=i[5],s=i[9],c=l(a,o,s);a/=c,o/=c,s/=c;var u=i[0],f=i[4],h=i[8],p=u*a+f*o+h*s,d=l(u-=a*p,f-=o*p,h-=s*p);u/=d,f/=d,h/=d;var g=i[2],m=i[6],v=i[10],y=g*a+m*o+v*s,x=g*u+m*f+v*h,b=l(g-=y*a+x*u,m-=y*o+x*f,v-=y*s+x*h);g/=b,m/=b,v/=b;var _=u*e+a*r,w=f*e+o*r,T=h*e+s*r;this.center.move(t,_,w,T);var k=Math.exp(this.computedRadius[0]);k=Math.max(1e-4,k+n),this.radius.set(t,Math.log(k))},h.rotate=function(t,e,r,n){this.recalcMatrix(t),e=e||0,r=r||0;var i=this.computedMatrix,a=i[0],o=i[4],s=i[8],u=i[1],f=i[5],h=i[9],p=i[2],d=i[6],g=i[10],m=e*a+r*u,v=e*o+r*f,y=e*s+r*h,x=-(d*y-g*v),b=-(g*m-p*y),_=-(p*v-d*m),w=Math.sqrt(Math.max(0,1-Math.pow(x,2)-Math.pow(b,2)-Math.pow(_,2))),T=c(x,b,_,w);T>1e-6?(x/=T,b/=
"/*!\n",
" * pad-left <https://github.com/jonschlinkert/pad-left>\n",
" *\n",
" * Copyright (c) 2014-2015, Jon Schlinkert.\n",
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],
"source": [
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"data\n",
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},
{
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"metadata": {},
"outputs": [],
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"title": {
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"<div> <div id=\"33aede89-84d1-4e23-ac63-72d4e781518e\" class=\"plotly-graph-div\" style=\"height:525px; width:100%;\"></div> <script type=\"text/javascript\"> require([\"plotly\"], function(Plotly) { window.PLOTLYENV=window.PLOTLYENV || {}; if (document.getElementById(\"33aede89-84d1-4e23-ac63-72d4e781518e\")) { Plotly.newPlot( \"33aede89-84d1-4e23-ac63-72d4e781518e\", [{\"name\": \"FAIRsharing\", \"type\": \"bar\", \"x\": [\"Life Science\", \"Biomedical Science\", \"Earth Science\", \"Genomics\", \"Environmental Science\", \"Oceanography\", \"Epidemiology\", \"Biology\", \"Biodiversity\", \"Atmospheric Science\", \"Genetics\", \"Health Science\", \"Virology\", \"Proteomics\", \"Bioinformatics\", \"Agriculture\", \"Geology\", \"Transcriptomics\", \"Clinical Studies\", \"Humanities and Social Sciences\", \"Preclinical Studies\", \"Chemistry\", \"Comparative Genomics\", \"Botany\", \"Data Management\", \"Medicine\", \"Natural Science\", \"Functional Genomics\", \"Meteorology\", \"Geophysics\", \"Systems Biology\", \"Social Science\", \"Ecology\", \"Engineering Science\", \"Geography\", \"Data Submission, Annotation and Curation\", \"Metabolomics\", \"Marine Biology\", \"Economics\", \"Physics\", \"Biochemistry\", \"Ontology and Terminology\", \"Hydrology\", \"Astrophysics and Astronomy\", \"Molecular biology\", \"Infectious Disease Medicine\", \"Medical Virology\", \"Computational Biology\", \"Neurobiology\", \"Phylogenetics\", \"Structural Biology\", \"Humanities\", \"Developmental Biology\", \"Computer Science\", \"Immunology\", \"Geochemistry\", \"Anatomy\", \"Social and Behavioural Science\", \"Microbiology\", \"Remote Sensing\", \"Epigenetics\", \"Critical Care Medicine\", \"Knowledge and Information Systems\", \"Public Health\", \"Plant Genetics\", \"Data Visualization\", \"Ecosystem Science\", \"Neuroscience\", \"Demographics\", \"Forest Management\", \"Data Integration\", \"Oncology\", \"Cell Biology\", \"Drug Discovery\", \"Materials Science\", \"Metagenomics\", \"Hydrogeology\", \"Soil Science\", \"Glycomics\", \"Population Genetics\", \"Plant Breeding\", \"Paleontology\", \"Water Research\", \"Immunogenetics\", \"Geodesy\", \"Taxonomy\", \"Water Management\", \"Energy Engineering\", \"Human Genetics\", \"Software Engineering\", \"Mineralogy\", \"Pharmacology\", \"Phylogenomics\", \"Computational Neuroscience\", \"Freshwater Science\", \"Global Health\", \"Medical Informatics\", \"Epigenomics\", \"Animal Genetics\", \"Statistics\", \"Evolutionary Biology\", \"Translational Medicine\", \"Psychology\", \"Culture\", \"Political Science\", \"Cheminformatics\", \"Phylogeny\", \"Nutritional Science\", \"Microbial Ecology\", \"Mathematics\", \"Phenomics\", \"Natural History\", \"Physical Geography\", \"Population Dynamics\", \"Nanotechnology\", \"Zoology\", \"Drug Development\", \"Education Science\", \"Enzymology\", \"Analytical Chemistry\", \"Classical Archaeology\", \"Neurophysiology\", \"Informatics\", \"Omics\", \"Data Governance\", \"Organic Chemistry\", \"Pathology\", \"Database Management\", \"Biotechnology\", \"History\", \"Food Security\", \"Maritime Engineering\", \"Plant Anatomy\", \"Bioengineering\", \"Urban Planning\", \"Cartography\", \"Art\", \"Civil Engineering\", \"Architecture\", \"Materials Engineering\", \"Geoinformatics\", \"Anthropology\", \"Animal Husbandry\", \"Molecular Chemistry\", \"Fine Arts\", \"Aerospace Engineering\", \"Business Administration\", \"Tropical Medicine\", \"Communication Science\", \"Cardiology\", \"Molecular Genetics\", \"Endocrinology\", \"Criminology\", \"Chemical Engineering\", \"Transportation Planning\", \"Linguistics\", \"Fisheries Science\", \"Thermodynamics\", \"Computational Chemistry\", \"Agronomy\", \"Toxicology\", \"Economic and Social History\", \"Respiratory Medicine\", \"Physiology\", \"Medicinal Chemistry\", \"Art History\", \"Geriatric Medicine\", \"Primary Health Care\", \"Synth
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"source": [
"data = fairsharing_subjects.groupby('attributes.subjects')[['id']].count().sort_values('id', ascending=False)\n",
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"plot = [\n",
" go.Bar(\n",
" x=data.index,\n",
" y=data['id'],\n",
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" name='FAIRsharing'\n",
" )\n",
"]\n",
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")\n",
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"fig = go.Figure(plot, layout).show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Geographic analysis"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**re3data**"
]
},
{
"cell_type": "code",
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"execution_count": 69,
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"metadata": {},
"outputs": [
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" institutionType institutionURL \\\n",
"0 non-profit https://odum.unc.edu/archive/ \n",
"1 non-profit http://www.archives.gov/ \n",
"2 non-profit http://www.usa.gov/ \n",
"3 non-profit http://agd.ids-mannheim.de/index.shtml \n",
"4 non-profit https://odum.unc.edu/ \n",
"\n",
" institutionIdentifier responsibilityStartDate responsibilityEndDate \\\n",
"0 [] \n",
"1 [] \n",
"2 [] \n",
"3 [] 2004 \n",
"4 [] \n",
"\n",
" institutionContact \n",
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"0 [] \n",
"1 [http://www.archives.gov/contact/] \n",
"2 [http://www.usa.gov/Contact.shtml] \n",
"3 [agd@ids-mannheim.de] \n",
"4 [https://odum.unc.edu/contact/contact-form/, o... "
]
},
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"execution_count": 69,
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"metadata": {},
"output_type": "execute_result"
}
],
"source": [
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"re3data_institutions = re3data_df.explode('institution')[['orgIdentifier', 'institution']]\n",
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"re3data_institutions = re3data_institutions[~re3data_institutions.institution.isna()].reset_index(drop=True)\n",
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"re3data_institutions = re3data_institutions.join(pd.json_normalize(re3data_institutions.institution))\n",
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"re3data_institutions.head()"
]
},
{
"cell_type": "code",
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"execution_count": 70,
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"metadata": {},
"outputs": [],
"source": [
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"re3data_institutions['org_continent'] = re3data_institutions.institutionCountry.map(countrycode_to_continent)"
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]
},
{
"cell_type": "code",
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"execution_count": 71,
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"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"array(['AAA', 'EEC'], dtype=object)"
]
},
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"execution_count": 71,
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"metadata": {},
"output_type": "execute_result"
}
],
"source": [
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"re3data_institutions[re3data_institutions.org_continent.isna()].institutionCountry.unique()"
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]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"AAA is used for international collaborations; we skip this.\n",
"EEC is used for the EU commission; we fix the continent manually."
]
},
{
"cell_type": "code",
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"execution_count": 72,
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"metadata": {},
"outputs": [],
"source": [
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"re3data_institutions.loc[re3data_institutions.institutionCountry == 'EEC', 'org_continent'] = 'EU'"
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]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**OpenDOAR**"
]
},
{
"cell_type": "code",
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"execution_count": 77,
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"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
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" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
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" <th>system_metadata.id</th>\n",
" <th>organization</th>\n",
" <th>name</th>\n",
" <th>alternativeName</th>\n",
" <th>country</th>\n",
" <th>url</th>\n",
" <th>identifier</th>\n",
" <th>location.latitude</th>\n",
" <th>location.longiture</th>\n",
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" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
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" <td>175</td>\n",
" <td>{'name': 'university of hong kong', 'alternati...</td>\n",
" <td>university of hong kong</td>\n",
" <td>hku</td>\n",
" <td>CHN</td>\n",
" <td>http://www.hku.hk</td>\n",
" <td>[{'identifier': 'https://ror.org/02zhqgq86', '...</td>\n",
" <td>22.2824</td>\n",
" <td>114.138</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
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" <td>64</td>\n",
" <td>{'name': 'central european university', 'alter...</td>\n",
" <td>central european university</td>\n",
" <td>ceu</td>\n",
" <td>HUN</td>\n",
" <td>https://www.ceu.edu</td>\n",
" <td>[{'identifier': 'https://ror.org/02zx40v98', '...</td>\n",
" <td>47.5005</td>\n",
" <td>19.0494</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
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" <td>151</td>\n",
" <td>{'name': 'european university institute', 'alt...</td>\n",
" <td>european university institute</td>\n",
" <td>eui</td>\n",
" <td>ITA</td>\n",
" <td>http://www.eui.eu/</td>\n",
" <td>[{'identifier': 'https://ror.org/0031wrj91', '...</td>\n",
" <td>43.8017</td>\n",
" <td>11.286</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
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" <td>105</td>\n",
" <td>{'name': 'uhasselt', 'alternativeName': 'hasse...</td>\n",
" <td>uhasselt</td>\n",
" <td>hasselt university</td>\n",
" <td>BEL</td>\n",
" <td>https://www.uhasselt.be</td>\n",
" <td>[{'identifier': 'https://ror.org/04nbhqj75', '...</td>\n",
" <td>50.9253</td>\n",
" <td>5.39083</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
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" <td>101</td>\n",
" <td>{'name': 'university of utrecht', 'alternative...</td>\n",
" <td>university of utrecht</td>\n",
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" <td></td>\n",
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" <td>NLD</td>\n",
" <td>https://www.uu.nl</td>\n",
" <td>[{'identifier': 'https://ror.org/04pp8hn57', '...</td>\n",
" <td>52.0902</td>\n",
" <td>5.1223</td>\n",
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" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
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" system_metadata.id organization \\\n",
"0 175 {'name': 'university of hong kong', 'alternati... \n",
"1 64 {'name': 'central european university', 'alter... \n",
"2 151 {'name': 'european university institute', 'alt... \n",
"3 105 {'name': 'uhasselt', 'alternativeName': 'hasse... \n",
"4 101 {'name': 'university of utrecht', 'alternative... \n",
"\n",
" name alternativeName country \\\n",
"0 university of hong kong hku CHN \n",
"1 central european university ceu HUN \n",
"2 european university institute eui ITA \n",
"3 uhasselt hasselt university BEL \n",
"4 university of utrecht NLD \n",
"\n",
" url identifier \\\n",
"0 http://www.hku.hk [{'identifier': 'https://ror.org/02zhqgq86', '... \n",
"1 https://www.ceu.edu [{'identifier': 'https://ror.org/02zx40v98', '... \n",
"2 http://www.eui.eu/ [{'identifier': 'https://ror.org/0031wrj91', '... \n",
"3 https://www.uhasselt.be [{'identifier': 'https://ror.org/04nbhqj75', '... \n",
"4 https://www.uu.nl [{'identifier': 'https://ror.org/04pp8hn57', '... \n",
"\n",
" location.latitude location.longiture \n",
"0 22.2824 114.138 \n",
"1 47.5005 19.0494 \n",
"2 43.8017 11.286 \n",
"3 50.9253 5.39083 \n",
"4 52.0902 5.1223 "
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]
},
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"execution_count": 77,
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"metadata": {},
"output_type": "execute_result"
}
],
"source": [
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"opendoar_institutions = opendoar_df.explode('organization')[['system_metadata.id', 'organization']]\n",
"opendoar_institutions = opendoar_institutions[~opendoar_institutions.organization.isna()].reset_index(drop=True)\n",
"opendoar_institutions = opendoar_institutions.join(pd.json_normalize(opendoar_institutions.organization))\n",
"opendoar_institutions['country'] = opendoar_institutions.country.map(str.upper, na_action='ignore')\n",
"opendoar_institutions['country'] = opendoar_institutions.country.map(countrycode_iso2_to_countrycode_iso3, na_action='ignore')\n",
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"opendoar_institutions.head()"
]
},
{
"cell_type": "code",
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"execution_count": 78,
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"metadata": {},
"outputs": [],
"source": [
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"opendoar_institutions['org_continent'] = opendoar_institutions.country.map(countrycode_to_continent)"
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]
},
{
"cell_type": "code",
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"execution_count": 79,
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"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"array([nan, 'UMI'], dtype=object)"
]
},
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"execution_count": 79,
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"metadata": {},
"output_type": "execute_result"
}
],
"source": [
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"opendoar_institutions[opendoar_institutions.org_continent.isna()].country.unique()"
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]
},
{
"cell_type": "code",
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"execution_count": 80,
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"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
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" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
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" <th>system_metadata.id</th>\n",
" <th>organization</th>\n",
" <th>name</th>\n",
" <th>alternativeName</th>\n",
" <th>country</th>\n",
" <th>url</th>\n",
" <th>identifier</th>\n",
" <th>location.latitude</th>\n",
" <th>location.longiture</th>\n",
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" <th>org_continent</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
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" <th>4357</th>\n",
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" <td>5379</td>\n",
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" <td>{'name': 'kettering university', 'alternativeN...</td>\n",
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" <td>kettering university</td>\n",
" <td></td>\n",
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" <td>UMI</td>\n",
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" <td>https://www.kettering.edu</td>\n",
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" <td>[{'identifier': 'https://ror.org/03rcspa57', '...</td>\n",
" <td>43.0125</td>\n",
" <td>83.7125</td>\n",
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" <td>NA</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
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" system_metadata.id organization \\\n",
"4357 5379 {'name': 'kettering university', 'alternativeN... \n",
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"\n",
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" name alternativeName country url \\\n",
"4357 kettering university UMI https://www.kettering.edu \n",
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"\n",
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" identifier location.latitude \\\n",
"4357 [{'identifier': 'https://ror.org/03rcspa57', '... 43.0125 \n",
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"\n",
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" location.longiture org_continent \n",
"4357 83.7125 NA "
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]
},
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"execution_count": 80,
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"metadata": {},
"output_type": "execute_result"
}
],
"source": [
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"opendoar_institutions.loc[opendoar_institutions.country == 'UMI', 'org_continent'] = 'NA'\n",
"opendoar_institutions[opendoar_institutions.country == 'UMI']"
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]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**ROAR**"
]
},
{
"cell_type": "code",
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"execution_count": 93,
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"metadata": {},
"outputs": [],
"source": [
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"roar_institutions = roar_df.explode('location_country')\n",
"roar_institutions['location_country'] = roar_institutions.location_country.map(str.upper, na_action='ignore')\n",
"roar_institutions['location_country'] = roar_institutions.location_country.map(countrycode_iso2_to_countrycode_iso3)\n",
"roar_institutions['continent'] = roar_institutions.location_country.map(countrycode_to_continent)"
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]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**FAIRsharing**"
]
},
{
"cell_type": "code",
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"execution_count": 101,
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"metadata": {},
"outputs": [],
"source": [
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"fairsharing_countries = fairsharing_df.explode('attributes.countries')\n",
"fairsharing_countries['countrycode'] = fairsharing_countries['attributes.countries'].map(country_to_countrycode)\n",
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"fairsharing_countries['continent'] = fairsharing_countries.countrycode.map(countrycode_to_continent)"
]
},
{
"cell_type": "code",
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"execution_count": 103,
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"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
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"array(['Worldwide', 'European Union', nan], dtype=object)"
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]
},
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"execution_count": 103,
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"metadata": {},
"output_type": "execute_result"
}
],
"source": [
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"fairsharing_countries[fairsharing_countries.countrycode.isna()]['attributes.countries'].unique()"
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]
},
{
"cell_type": "code",
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"execution_count": 105,
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"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
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"array(['Worldwide', 'European Union', nan, 'Antarctica'], dtype=object)"
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]
},
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"execution_count": 105,
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"metadata": {},
"output_type": "execute_result"
}
],
"source": [
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"fairsharing_countries[fairsharing_countries.continent.isna()]['attributes.countries'].unique()"
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]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Fix manually some rows"
]
},
{
"cell_type": "code",
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"execution_count": 106,
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"metadata": {},
"outputs": [],
"source": [
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"fairsharing_countries.loc[fairsharing_countries['attributes.countries'] == 'Republic of Ireland', ['attributes.countries', 'countrycode', 'continent']] = ['Ireland', 'IE', 'EU']\n",
"fairsharing_countries.loc[fairsharing_countries['attributes.countries'] == 'European Union', ['countrycode', 'continent']] = ['EU', 'EU']"
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]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Make Antactica disappear (only one repo)"
]
},
{
"cell_type": "code",
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"execution_count": 107,
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"metadata": {},
"outputs": [
{
"data": {
"text/html": [
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" .dataframe thead th {\n",
" text-align: right;\n",
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"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
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" <th>id</th>\n",
" <th>type</th>\n",
" <th>attributes.created-at</th>\n",
" <th>attributes.updated-at</th>\n",
" <th>attributes.metadata.doi</th>\n",
" <th>attributes.metadata.name</th>\n",
" <th>attributes.metadata.status</th>\n",
" <th>attributes.metadata.contacts</th>\n",
" <th>attributes.metadata.homepage</th>\n",
" <th>attributes.metadata.identifier</th>\n",
" <th>attributes.metadata.description</th>\n",
" <th>attributes.metadata.support-links</th>\n",
" <th>attributes.metadata.year-creation</th>\n",
" <th>attributes.metadata.data-processes</th>\n",
" <th>attributes.legacy-ids</th>\n",
" <th>attributes.fairsharing-registry</th>\n",
" <th>attributes.record-type</th>\n",
" <th>attributes.subjects</th>\n",
" <th>attributes.domains</th>\n",
" <th>attributes.taxonomies</th>\n",
" <th>attributes.user-defined-tags</th>\n",
" <th>attributes.countries</th>\n",
" <th>attributes.name</th>\n",
" <th>attributes.abbreviation</th>\n",
" <th>attributes.url</th>\n",
" <th>attributes.doi</th>\n",
" <th>attributes.fairsharing-licence</th>\n",
" <th>attributes.description</th>\n",
" <th>attributes.publications</th>\n",
" <th>attributes.licence-links</th>\n",
" <th>attributes.metadata.citations</th>\n",
" <th>attributes.metadata.abbreviation</th>\n",
" <th>attributes.metadata.access-points</th>\n",
" <th>attributes.metadata.associated-tools</th>\n",
" <th>attributes.metadata.deprecation-date</th>\n",
" <th>attributes.metadata.deprecation-reason</th>\n",
" <th>attributes.metadata.tombstone</th>\n",
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" <th>countrycode</th>\n",
" <th>continent</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
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" <th>782</th>\n",
" <td>2462</td>\n",
" <td>fairsharing-records</td>\n",
" <td>2017-06-27T13:30:19.000Z</td>\n",
" <td>2021-09-30T11:35:28.523Z</td>\n",
" <td>10.25504/FAIRsharing.ewyejx</td>\n",
2021-07-22 11:03:05 +02:00
" <td>Antabif IPT - AntOBIS IPT - GBIF Belgium</td>\n",
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" <td>ready</td>\n",
" <td>[{'contact-name': 'Anton Van de Putte', 'conta...</td>\n",
2021-07-22 11:03:05 +02:00
" <td>http://ipt.biodiversity.aq/</td>\n",
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" <td>2462</td>\n",
" <td>The Belgium Biodiversity Platform hosts this d...</td>\n",
" <td>[{'url': 'a.heughebaert@biodiversity.be', 'nam...</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>[biodbcore-000944, bsg-d000944]</td>\n",
" <td>Database</td>\n",
" <td>repository</td>\n",
2021-07-22 11:03:05 +02:00
" <td>[Biodiversity, Life Science]</td>\n",
2021-10-08 14:28:56 +02:00
" <td>[Taxonomic classification]</td>\n",
" <td>[All]</td>\n",
" <td>[]</td>\n",
" <td>Antarctica</td>\n",
" <td>FAIRsharing record for: Antabif IPT - AntOBIS ...</td>\n",
" <td>None</td>\n",
" <td>https://fairsharing.org/10.25504/FAIRsharing.e...</td>\n",
" <td>10.25504/FAIRsharing.ewyejx</td>\n",
" <td>https://creativecommons.org/licenses/by-sa/4.0...</td>\n",
" <td>This FAIRsharing record describes: The Belgium...</td>\n",
" <td>[]</td>\n",
" <td>[{'licence-name': 'Apache License 2.0', 'licen...</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
2021-07-22 11:03:05 +02:00
" <td>AQ</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
2021-10-08 14:28:56 +02:00
" id type attributes.created-at \\\n",
"782 2462 fairsharing-records 2017-06-27T13:30:19.000Z \n",
"\n",
" attributes.updated-at attributes.metadata.doi \\\n",
"782 2021-09-30T11:35:28.523Z 10.25504/FAIRsharing.ewyejx \n",
"\n",
" attributes.metadata.name attributes.metadata.status \\\n",
"782 Antabif IPT - AntOBIS IPT - GBIF Belgium ready \n",
"\n",
" attributes.metadata.contacts \\\n",
"782 [{'contact-name': 'Anton Van de Putte', 'conta... \n",
"\n",
" attributes.metadata.homepage attributes.metadata.identifier \\\n",
"782 http://ipt.biodiversity.aq/ 2462 \n",
"\n",
" attributes.metadata.description \\\n",
"782 The Belgium Biodiversity Platform hosts this d... \n",
"\n",
" attributes.metadata.support-links \\\n",
"782 [{'url': 'a.heughebaert@biodiversity.be', 'nam... \n",
"\n",
" attributes.metadata.year-creation attributes.metadata.data-processes \\\n",
"782 NaN NaN \n",
"\n",
" attributes.legacy-ids attributes.fairsharing-registry \\\n",
"782 [biodbcore-000944, bsg-d000944] Database \n",
"\n",
" attributes.record-type attributes.subjects \\\n",
"782 repository [Biodiversity, Life Science] \n",
"\n",
" attributes.domains attributes.taxonomies \\\n",
"782 [Taxonomic classification] [All] \n",
"\n",
" attributes.user-defined-tags attributes.countries \\\n",
"782 [] Antarctica \n",
"\n",
" attributes.name \\\n",
"782 FAIRsharing record for: Antabif IPT - AntOBIS ... \n",
"\n",
" attributes.abbreviation \\\n",
"782 None \n",
"\n",
" attributes.url \\\n",
"782 https://fairsharing.org/10.25504/FAIRsharing.e... \n",
2021-07-22 11:03:05 +02:00
"\n",
2021-10-08 14:28:56 +02:00
" attributes.doi \\\n",
"782 10.25504/FAIRsharing.ewyejx \n",
2021-07-22 11:03:05 +02:00
"\n",
2021-10-08 14:28:56 +02:00
" attributes.fairsharing-licence \\\n",
"782 https://creativecommons.org/licenses/by-sa/4.0... \n",
2021-07-22 11:03:05 +02:00
"\n",
2021-10-08 14:28:56 +02:00
" attributes.description \\\n",
"782 This FAIRsharing record describes: The Belgium... \n",
"\n",
" attributes.publications \\\n",
"782 [] \n",
"\n",
" attributes.licence-links \\\n",
"782 [{'licence-name': 'Apache License 2.0', 'licen... \n",
"\n",
" attributes.metadata.citations attributes.metadata.abbreviation \\\n",
"782 NaN NaN \n",
"\n",
" attributes.metadata.access-points attributes.metadata.associated-tools \\\n",
"782 NaN NaN \n",
"\n",
" attributes.metadata.deprecation-date \\\n",
"782 NaN \n",
"\n",
" attributes.metadata.deprecation-reason attributes.metadata.tombstone \\\n",
"782 NaN NaN \n",
2021-07-22 11:03:05 +02:00
"\n",
" countrycode continent \n",
2021-10-08 14:28:56 +02:00
"782 AQ NaN "
2021-07-22 11:03:05 +02:00
]
},
2021-10-08 14:28:56 +02:00
"execution_count": 107,
2021-07-22 11:03:05 +02:00
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
2021-10-08 14:28:56 +02:00
"fairsharing_countries.loc[fairsharing_countries['attributes.countries'] == 'Antarctica', ['countrycode', 'continent']] = ['AQ', np.nan]\n",
2021-07-22 11:03:05 +02:00
"fairsharing_countries[fairsharing_countries.countrycode == 'AQ']"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Country coverage"
]
},
{
"cell_type": "code",
2021-10-08 14:28:56 +02:00
"execution_count": 114,
2021-07-22 11:03:05 +02:00
"metadata": {},
"outputs": [
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"data1 = re3data_institutions.groupby('institutionCountry')[['orgIdentifier']].count().sort_values('orgIdentifier', ascending=False)\n",
"data2 = opendoar_institutions.groupby('country')[['system_metadata.id']].count().sort_values('system_metadata.id', ascending=False)\n",
"data3 = roar_institutions.groupby('location_country')[['eprintid']].count().sort_values('eprintid', ascending=False)\n",
"data4 = fairsharing_countries.groupby('countrycode')[['id']].count().sort_values('id', ascending=False)\n",
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"source": [
"### Continental coverage"
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},
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},
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],
"source": [
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"data1 = re3data_institutions.groupby('org_continent')[['orgIdentifier']].count()\n",
"data2 = opendoar_institutions.groupby('org_continent')[['system_metadata.id']].count()\n",
"data3 = roar_institutions.groupby('continent')[['eprintid']].count()\n",
"data4 = fairsharing_countries.groupby('continent')[['id']].count()\n",
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"\n",
"plot = [\n",
" go.Scatterpolar(\n",
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" r=data1.orgIdentifier,\n",
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" theta=data1.index,\n",
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" r=data2['system_metadata.id'],\n",
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