registries_analysis/notebooks/01-Explorative.ipynb

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{
"cells": [
{
"cell_type": "code",
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"execution_count": 40,
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"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",
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"import pycountry_convert\n",
"\n",
"import matplotlib.pyplot as plt\n",
"from matplotlib_venn import venn2, venn2_circles\n",
"\n",
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"import plotly\n",
"from plotly.offline import iplot, init_notebook_mode\n",
"import plotly.graph_objs as go\n",
"import plotly.express as px"
]
},
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{
"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_alpha2(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(country_code)\n",
" except:\n",
" return np.nan"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Loading datasets"
]
},
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{
"cell_type": "markdown",
"metadata": {},
"source": [
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"**FAIRsharing**"
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]
},
{
"cell_type": "code",
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"execution_count": 3,
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"metadata": {},
"outputs": [
{
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" <th></th>\n",
" <th>full_name</th>\n",
" <th>short_name</th>\n",
" <th>fs_url</th>\n",
" <th>url</th>\n",
" <th>countries</th>\n",
" <th>subjects</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>GenBank</td>\n",
" <td>GenBank</td>\n",
" <td>https://fairsharing.org/10.25504/FAIRsharing.9...</td>\n",
" <td>https://www.ncbi.nlm.nih.gov/genbank/</td>\n",
" <td>[European Union, Japan, United States]</td>\n",
" <td>[Bioinformatics, Data Management, Data Submiss...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>GlycoNAVI</td>\n",
" <td>GlycoNAVI</td>\n",
" <td>https://fairsharing.org/10.25504/FAIRsharing.w...</td>\n",
" <td>https://glyconavi.org/</td>\n",
" <td>[Japan]</td>\n",
" <td>[Chemistry, Glycomics, Life Science, Organic C...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>ADHDgene</td>\n",
" <td>ADHDgene</td>\n",
" <td>https://fairsharing.org/10.25504/FAIRsharing.m...</td>\n",
" <td>http://adhd.psych.ac.cn/</td>\n",
" <td>[China]</td>\n",
" <td>[Biomedical Science, Genetics]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>Allele frequency resource for research and tea...</td>\n",
" <td>ALFRED</td>\n",
" <td>https://fairsharing.org/10.25504/FAIRsharing.y...</td>\n",
" <td>http://alfred.med.yale.edu</td>\n",
" <td>[United States]</td>\n",
" <td>[Life Science]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>Animal Transcription Factor Database</td>\n",
" <td>AnimalTFDB</td>\n",
" <td>https://fairsharing.org/10.25504/FAIRsharing.e...</td>\n",
" <td>http://bioinfo.life.hust.edu.cn/AnimalTFDB/</td>\n",
" <td>[China]</td>\n",
" <td>[Life Science]</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
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"text/plain": [
" full_name short_name \\\n",
"0 GenBank GenBank \n",
"1 GlycoNAVI GlycoNAVI \n",
"2 ADHDgene ADHDgene \n",
"3 Allele frequency resource for research and tea... ALFRED \n",
"4 Animal Transcription Factor Database AnimalTFDB \n",
"\n",
" fs_url \\\n",
"0 https://fairsharing.org/10.25504/FAIRsharing.9... \n",
"1 https://fairsharing.org/10.25504/FAIRsharing.w... \n",
"2 https://fairsharing.org/10.25504/FAIRsharing.m... \n",
"3 https://fairsharing.org/10.25504/FAIRsharing.y... \n",
"4 https://fairsharing.org/10.25504/FAIRsharing.e... \n",
"\n",
" url \\\n",
"0 https://www.ncbi.nlm.nih.gov/genbank/ \n",
"1 https://glyconavi.org/ \n",
"2 http://adhd.psych.ac.cn/ \n",
"3 http://alfred.med.yale.edu \n",
"4 http://bioinfo.life.hust.edu.cn/AnimalTFDB/ \n",
"\n",
" countries \\\n",
"0 [European Union, Japan, United States] \n",
"1 [Japan] \n",
"2 [China] \n",
"3 [United States] \n",
"4 [China] \n",
"\n",
" subjects \n",
"0 [Bioinformatics, Data Management, Data Submiss... \n",
"1 [Chemistry, Glycomics, Life Science, Organic C... \n",
"2 [Biomedical Science, Genetics] \n",
"3 [Life Science] \n",
"4 [Life Science] "
]
},
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"execution_count": 3,
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"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"fairsharing_df = pd.read_csv('../data/raw/FAIRsharingDBrec_summary20210304.csv', \n",
" delimiter='|', header=0,\n",
" names=['full_name', 'short_name', 'fs_url', 'url', 'countries', 'subjects'])\n",
"fairsharing_df['subjects'] = fairsharing_df.subjects.str.split(pat=',')\n",
"fairsharing_df['countries'] = fairsharing_df.countries.str.split(pat=',')\n",
"fairsharing_df.head()"
]
},
{
"cell_type": "code",
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"execution_count": 4,
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"metadata": {},
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" <th>count</th>\n",
" <td>1752</td>\n",
" <td>1752</td>\n",
" <td>1752</td>\n",
" <td>1752</td>\n",
" <td>1749</td>\n",
" <td>1690</td>\n",
" </tr>\n",
" <tr>\n",
" <th>unique</th>\n",
" <td>1752</td>\n",
" <td>1741</td>\n",
" <td>1752</td>\n",
" <td>1752</td>\n",
" <td>178</td>\n",
" <td>834</td>\n",
" </tr>\n",
" <tr>\n",
" <th>top</th>\n",
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" <td>FunTree: A Resource For Exploring The Function...</td>\n",
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" <td>CGD</td>\n",
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" <td>https://fairsharing.org/10.25504/FAIRsharing.5...</td>\n",
" <td>https://idn.ceos.org</td>\n",
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" <td>[United States]</td>\n",
" <td>[Life Science]</td>\n",
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" <th>freq</th>\n",
" <td>1</td>\n",
" <td>3</td>\n",
" <td>1</td>\n",
" <td>1</td>\n",
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" <td>367</td>\n",
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" full_name short_name \\\n",
"count 1752 1752 \n",
"unique 1752 1741 \n",
"top FunTree: A Resource For Exploring The Function... CGD \n",
"freq 1 3 \n",
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"\n",
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" fs_url \\\n",
"count 1752 \n",
"unique 1752 \n",
"top https://fairsharing.org/10.25504/FAIRsharing.5... \n",
"freq 1 \n",
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"\n",
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" url countries subjects \n",
"count 1752 1749 1690 \n",
"unique 1752 178 834 \n",
"top https://idn.ceos.org [United States] [Life Science] \n",
"freq 1 588 367 "
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]
},
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"execution_count": 4,
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"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"fairsharing_df.describe()"
]
},
{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
"**re3data**"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"scrolled": true
},
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"outputs": [
{
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" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>4</td>\n",
" <td>10|re3data_____::3f2e20af26ead0432f5470d8b739638d</td>\n",
" <td>http://planttfdb.cbi.pku.edu.cn/</td>\n",
" <td>Plant Transcription Factor Database</td>\n",
" <td>PlantTFDB</td>\n",
" <td>NaN</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>['Life Sciences', 'Basic Biological and Medica...</td>\n",
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" <td>7</td>\n",
" <td>10|re3data_____::e1db3f9d2fa6c8d8067bc471ab50bdfc</td>\n",
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" <td>Space Physics Data Facility</td>\n",
" <td>NASA's Space Physics Data Facility SPDF</td>\n",
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" <tr>\n",
" <th>2</th>\n",
" <td>13</td>\n",
" <td>10|re3data_____::59521daca59ac29b811343cc4cd370cf</td>\n",
" <td>http://card.westgis.ac.cn/</td>\n",
" <td>Cold and Arid Regions Science Data Center at L...</td>\n",
" <td>CARD WDC for Glaciology and Geocryology World ...</td>\n",
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" <td>14</td>\n",
" <td>10|re3data_____::ec1ba1674c852466c266acb64c618d15</td>\n",
" <td>https://www.psycharchives.org/</td>\n",
" <td>Psycharchives</td>\n",
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" <td>NaN</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
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" <td>10|re3data_____::2ada591fb1bc9aee72a6d3e0c1ae8a76</td>\n",
" <td>https://www.ihfc-iugg.org/products/global-heat...</td>\n",
" <td>The Global Heat Flow Database of the Internati...</td>\n",
" <td>International Heat-flow Database</td>\n",
" <td>NaN</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>['Natural Sciences', 'Geology and Palaeontolog...</td>\n",
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"text/plain": [
" index id \\\n",
"0 4 10|re3data_____::3f2e20af26ead0432f5470d8b739638d \n",
"1 7 10|re3data_____::e1db3f9d2fa6c8d8067bc471ab50bdfc \n",
"2 13 10|re3data_____::59521daca59ac29b811343cc4cd370cf \n",
"3 14 10|re3data_____::ec1ba1674c852466c266acb64c618d15 \n",
"4 19 10|re3data_____::2ada591fb1bc9aee72a6d3e0c1ae8a76 \n",
"\n",
" url \\\n",
"0 http://planttfdb.cbi.pku.edu.cn/ \n",
"1 https://spdf.gsfc.nasa.gov/ \n",
"2 http://card.westgis.ac.cn/ \n",
"3 https://www.psycharchives.org/ \n",
"4 https://www.ihfc-iugg.org/products/global-heat... \n",
"\n",
" official_name \\\n",
"0 Plant Transcription Factor Database \n",
"1 Space Physics Data Facility \n",
"2 Cold and Arid Regions Science Data Center at L... \n",
"3 Psycharchives \n",
"4 The Global Heat Flow Database of the Internati... \n",
"\n",
" english_name description latitude \\\n",
"0 PlantTFDB NaN 0.0 \n",
"1 NASA's Space Physics Data Facility SPDF NaN 0.0 \n",
"2 CARD WDC for Glaciology and Geocryology World ... NaN 0.0 \n",
"3 NaN NaN 0.0 \n",
"4 International Heat-flow Database NaN 0.0 \n",
"\n",
" longitude subjects \n",
"0 0.0 ['Life Sciences', 'Basic Biological and Medica... \n",
"1 0.0 ['Natural Sciences', 'Astrophysics and Astrono... \n",
"2 0.0 ['Natural Sciences', 'Geosciences (including G... \n",
"3 0.0 ['Humanities and Social Sciences', 'Psychology... \n",
"4 0.0 ['Natural Sciences', 'Geology and Palaeontolog... "
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]
},
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"execution_count": 5,
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"metadata": {},
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"output_type": "execute_result"
}
],
"source": [
"re3data_df = pd.read_csv('../data/raw/re3data_opendoar.csv')\n",
"re3data_df = re3data_df[re3data_df.id.str.contains('re3data')].reset_index()\n",
"re3data_df.head()"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
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"outputs": [
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" <th>count</th>\n",
" <td>2693.000000</td>\n",
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" <td>2693</td>\n",
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" <td>10|re3data_____::fc8141eebc533cb225498718479f4e66</td>\n",
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" <td>European Climate Assessment &amp; Dataset project</td>\n",
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" <td>The Atmospheric Science Data Center (ASDC) at ...</td>\n",
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" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>0.114497</td>\n",
" <td>0.067998</td>\n",
" <td>NaN</td>\n",
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" <tr>\n",
" <th>std</th>\n",
" <td>2518.294468</td>\n",
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" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>4.585469</td>\n",
" <td>2.447173</td>\n",
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" <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",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
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" <th>75%</th>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
" <td>0.000000</td>\n",
" <td>0.000000</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>max</th>\n",
" <td>8705.000000</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>234.000000</td>\n",
" <td>123.000000</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" index id \\\n",
"count 2693.000000 2693 \n",
"unique NaN 2693 \n",
"top NaN 10|re3data_____::fc8141eebc533cb225498718479f4e66 \n",
"freq NaN 1 \n",
"mean 4443.650947 NaN \n",
"std 2518.294468 NaN \n",
"min 4.000000 NaN \n",
"25% 2266.000000 NaN \n",
"50% 4506.000000 NaN \n",
"75% 6660.000000 NaN \n",
"max 8705.000000 NaN \n",
2021-07-02 17:49:38 +02:00
"\n",
2021-07-06 15:23:24 +02:00
" url official_name \\\n",
"count 2673 2693 \n",
"unique 2661 2668 \n",
"top http://wdcpc.org/ European Climate Assessment & Dataset project \n",
"freq 2 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",
2021-07-02 17:49:38 +02:00
"\n",
2021-07-06 15:23:24 +02:00
" english_name description \\\n",
"count 2034 38 \n",
"unique 2010 38 \n",
"top ECA&D The Atmospheric Science Data Center (ASDC) at ... \n",
"freq 2 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",
2021-07-02 17:49:38 +02:00
"\n",
2021-07-06 15:23:24 +02:00
" latitude longitude \\\n",
"count 2693.000000 2693.000000 \n",
"unique NaN NaN \n",
"top NaN NaN \n",
"freq NaN NaN \n",
"mean 0.114497 0.067998 \n",
"std 4.585469 2.447173 \n",
"min 0.000000 0.000000 \n",
"25% 0.000000 0.000000 \n",
"50% 0.000000 0.000000 \n",
"75% 0.000000 0.000000 \n",
"max 234.000000 123.000000 \n",
"\n",
" subjects \n",
"count 2693 \n",
"unique 1427 \n",
"top ['Humanities and Social Sciences', 'Life Scien... \n",
"freq 209 \n",
"mean NaN \n",
"std NaN \n",
"min NaN \n",
"25% NaN \n",
"50% NaN \n",
"75% NaN \n",
"max NaN "
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]
},
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"execution_count": 6,
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"metadata": {},
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"output_type": "execute_result"
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}
],
"source": [
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"re3data_df.describe(include='all')"
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]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
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"**OpenDOAR**"
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]
},
{
"cell_type": "code",
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"execution_count": 7,
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"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
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" }\n",
"\n",
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" }\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>index</th>\n",
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" <th>id</th>\n",
" <th>url</th>\n",
" <th>official_name</th>\n",
" <th>english_name</th>\n",
" <th>description</th>\n",
" <th>latitude</th>\n",
" <th>longitude</th>\n",
" <th>subjects</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
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" <td>0</td>\n",
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" <td>10|opendoar____::e833e042f509c996b1b25324d56659fb</td>\n",
" <td>http://www.bilbao.net/bld</td>\n",
" <td>BLD - Bilboko Liburutegi Digitala</td>\n",
" <td>BLD - Bilboko Liburutegi Digitala</td>\n",
" <td>BLD is a repository of digital documents, desi...</td>\n",
" <td>43.256699</td>\n",
" <td>-2.924100</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
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" <td>1</td>\n",
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" <td>10|opendoar____::f621585df244e9596dc70a39b579efb1</td>\n",
" <td>https://researchdirect.westernsydney.edu.au/</td>\n",
" <td>Western Sydney ResearchDirect</td>\n",
" <td>Western Sydney ResearchDirect</td>\n",
" <td>NaN</td>\n",
" <td>0.000000</td>\n",
" <td>0.000000</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
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" <td>2</td>\n",
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" <td>10|opendoar____::437d7d1d97917cd627a34a6a0fb41136</td>\n",
" <td>http://redress.lancs.ac.uk/Learning_Space/</td>\n",
" <td>Learning Space Catalogue</td>\n",
" <td>NaN</td>\n",
" <td>This repository is a Social Science e-Science ...</td>\n",
" <td>54.010760</td>\n",
" <td>-2.784990</td>\n",
" <td>['Social Sciences General', 'Science General',...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
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" <td>3</td>\n",
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" <td>10|opendoar____::d840cc5d906c3e9c84374c8919d2074e</td>\n",
" <td>http://digitallibrary.usc.edu/search/controlle...</td>\n",
" <td>USC Digital Library</td>\n",
" <td>USC Digital Library</td>\n",
2021-07-06 15:23:24 +02:00
" <td>This is an institutional repository providing ...</td>\n",
" <td>34.052200</td>\n",
" <td>-118.242996</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>5</td>\n",
" <td>10|opendoar____::4ba3c163cd1efd4c14e3a415fa0a3010</td>\n",
" <td>http://www.ufgd.edu.br:8080/jspui/</td>\n",
" <td>Repositório de Divulgação das Produções Cientí...</td>\n",
" <td>Repositório de Divulgação das Produções Cientí...</td>\n",
" <td>This site provides access to the research outp...</td>\n",
" <td>-22.221800</td>\n",
" <td>-54.806400</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
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"text/plain": [
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" index id \\\n",
"0 0 10|opendoar____::e833e042f509c996b1b25324d56659fb \n",
"1 1 10|opendoar____::f621585df244e9596dc70a39b579efb1 \n",
"2 2 10|opendoar____::437d7d1d97917cd627a34a6a0fb41136 \n",
"3 3 10|opendoar____::d840cc5d906c3e9c84374c8919d2074e \n",
"4 5 10|opendoar____::4ba3c163cd1efd4c14e3a415fa0a3010 \n",
"\n",
" url \\\n",
"0 http://www.bilbao.net/bld \n",
"1 https://researchdirect.westernsydney.edu.au/ \n",
"2 http://redress.lancs.ac.uk/Learning_Space/ \n",
"3 http://digitallibrary.usc.edu/search/controlle... \n",
"4 http://www.ufgd.edu.br:8080/jspui/ \n",
"\n",
" official_name \\\n",
"0 BLD - Bilboko Liburutegi Digitala \n",
"1 Western Sydney ResearchDirect \n",
"2 Learning Space Catalogue \n",
"3 USC Digital Library \n",
"4 Repositório de Divulgação das Produções Cientí... \n",
"\n",
" english_name \\\n",
"0 BLD - Bilboko Liburutegi Digitala \n",
"1 Western Sydney ResearchDirect \n",
"2 NaN \n",
"3 USC Digital Library \n",
"4 Repositório de Divulgação das Produções Cientí... \n",
"\n",
" description latitude longitude \\\n",
"0 BLD is a repository of digital documents, desi... 43.256699 -2.924100 \n",
"1 NaN 0.000000 0.000000 \n",
"2 This repository is a Social Science e-Science ... 54.010760 -2.784990 \n",
"3 This is an institutional repository providing ... 34.052200 -118.242996 \n",
"4 This site provides access to the research outp... -22.221800 -54.806400 \n",
"\n",
" subjects \n",
"0 [] \n",
"1 [] \n",
"2 ['Social Sciences General', 'Science General',... \n",
"3 [] \n",
"4 [] "
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]
},
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"execution_count": 7,
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"metadata": {},
"output_type": "execute_result"
}
],
"source": [
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"opendoar_df = pd.read_csv('../data/raw/re3data_opendoar.csv')\n",
"opendoar_df = opendoar_df[opendoar_df.id.str.contains('opendoar')].reset_index()\n",
"opendoar_df.head()"
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]
},
{
"cell_type": "code",
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"execution_count": 8,
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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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" 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>index</th>\n",
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" <th>id</th>\n",
" <th>url</th>\n",
" <th>official_name</th>\n",
" <th>english_name</th>\n",
" <th>description</th>\n",
" <th>latitude</th>\n",
" <th>longitude</th>\n",
" <th>subjects</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>count</th>\n",
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" <td>6014.000000</td>\n",
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" <td>6014</td>\n",
" <td>6013</td>\n",
" <td>6014</td>\n",
" <td>5500</td>\n",
" <td>5776</td>\n",
" <td>6014.000000</td>\n",
" <td>6014.000000</td>\n",
" <td>6014</td>\n",
" </tr>\n",
" <tr>\n",
" <th>unique</th>\n",
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" <td>NaN</td>\n",
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" <td>6014</td>\n",
" <td>5953</td>\n",
" <td>5946</td>\n",
" <td>5413</td>\n",
" <td>4920</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>201</td>\n",
" </tr>\n",
" <tr>\n",
" <th>top</th>\n",
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" <td>NaN</td>\n",
" <td>10|opendoar____::17256f049f1e3fede17c7a313f7657f4</td>\n",
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" <td>http://harp.lib.hiroshima-u.ac.jp/</td>\n",
" <td>Hiroshima Associated Repository Portal</td>\n",
" <td>AURA</td>\n",
" <td>This site provides access to the research outp...</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>[]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>freq</th>\n",
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" <td>NaN</td>\n",
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" <td>1</td>\n",
" <td>3</td>\n",
" <td>3</td>\n",
" <td>4</td>\n",
" <td>98</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>5273</td>\n",
" </tr>\n",
" <tr>\n",
" <th>mean</th>\n",
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" <td>4312.407549</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>38.649393</td>\n",
" <td>7.810948</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>std</th>\n",
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" <td>2510.699848</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>788.406173</td>\n",
" <td>71.689788</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>min</th>\n",
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" <td>0.000000</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>-79.029999</td>\n",
" <td>-683.103027</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>25%</th>\n",
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" <td>2129.250000</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>4.644632</td>\n",
" <td>-49.273300</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>50%</th>\n",
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" <td>4297.000000</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>37.930449</td>\n",
" <td>4.788870</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>75%</th>\n",
2021-07-06 15:23:24 +02:00
" <td>6476.750000</td>\n",
2021-07-02 17:49:38 +02:00
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>47.294400</td>\n",
" <td>30.685501</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>max</th>\n",
2021-07-06 15:23:24 +02:00
" <td>8706.000000</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>61138.800781</td>\n",
" <td>178.438995</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
2021-07-06 15:23:24 +02:00
" index id \\\n",
"count 6014.000000 6014 \n",
"unique NaN 6014 \n",
"top NaN 10|opendoar____::17256f049f1e3fede17c7a313f7657f4 \n",
"freq NaN 1 \n",
"mean 4312.407549 NaN \n",
"std 2510.699848 NaN \n",
"min 0.000000 NaN \n",
"25% 2129.250000 NaN \n",
"50% 4297.000000 NaN \n",
"75% 6476.750000 NaN \n",
"max 8706.000000 NaN \n",
2021-07-02 17:49:38 +02:00
"\n",
" url \\\n",
"count 6013 \n",
"unique 5953 \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",
" official_name english_name \\\n",
"count 6014 5500 \n",
"unique 5946 5413 \n",
"top Hiroshima Associated Repository Portal AURA \n",
"freq 3 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",
" description latitude \\\n",
"count 5776 6014.000000 \n",
"unique 4920 NaN \n",
"top This site provides access to the research outp... NaN \n",
"freq 98 NaN \n",
"mean NaN 38.649393 \n",
"std NaN 788.406173 \n",
"min NaN -79.029999 \n",
"25% NaN 4.644632 \n",
"50% NaN 37.930449 \n",
"75% NaN 47.294400 \n",
"max NaN 61138.800781 \n",
"\n",
" longitude subjects \n",
"count 6014.000000 6014 \n",
"unique NaN 201 \n",
"top NaN [] \n",
"freq NaN 5273 \n",
"mean 7.810948 NaN \n",
"std 71.689788 NaN \n",
"min -683.103027 NaN \n",
"25% -49.273300 NaN \n",
"50% 4.788870 NaN \n",
"75% 30.685501 NaN \n",
"max 178.438995 NaN "
]
},
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"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"opendoar_df.describe(include='all')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Basic cleaning"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**re3data**"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"re3data_df.loc[(re3data_df.latitude == 0.0) & (re3data_df.longitude == 0.0), ['latitude', 'longitude']] = [np.nan, np.nan]"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"0 ['Life Sciences', 'Basic Biological and Medica...\n",
"1 ['Natural Sciences', 'Astrophysics and Astrono...\n",
"2 ['Natural Sciences', 'Geosciences (including G...\n",
"3 ['Humanities and Social Sciences', 'Psychology...\n",
"4 ['Natural Sciences', 'Geology and Palaeontolog...\n",
" ... \n",
"2688 ['Life Sciences', 'Basic Biological and Medica...\n",
"2689 ['Natural Sciences', 'Atmospheric Science and ...\n",
"2690 ['Natural Sciences', 'Atmospheric Science and ...\n",
"2691 ['Natural Sciences', 'Atmospheric Science and ...\n",
"2692 ['Life Sciences', 'Plant Sciences', 'Plant Gen...\n",
"Name: subjects, Length: 2693, dtype: object"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"re3data_df.subjects"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [],
"source": [
"re3data_df['subjects'] = re3data_df.subjects.apply(lambda x: ast.literal_eval(x))"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [],
"source": [
"def merge_lists(lists):\n",
" res = []\n",
" for l in lists:\n",
" res = res + l\n",
" return res\n",
"\n",
"re3data_cleaned_subjects = re3data_df.explode('subjects').subjects.str.split(',| and ', expand=True)\\\n",
" .apply(lambda row: row.dropna().tolist(), axis=1)\\\n",
" .reset_index()\\\n",
" .groupby('index')[0].apply(lambda x: merge_lists(x))"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"index\n",
"0 [Life Sciences, Basic Biological, Medical Rese...\n",
"1 [Natural Sciences, Astrophysics, Astronomy, Ph...\n",
"2 [Natural Sciences, Geosciences (including Geog...\n",
"3 [Humanities, Social Sciences, Psychology, Soci...\n",
"4 [Natural Sciences, Geology, Palaeontology, Geo...\n",
" ... \n",
"2688 [Life Sciences, Basic Biological, Medical Rese...\n",
"2689 [Natural Sciences, Atmospheric Science, Oceano...\n",
"2690 [Natural Sciences, Atmospheric Science, Oceano...\n",
"2691 [Natural Sciences, Atmospheric Science, Oceano...\n",
"2692 [Life Sciences, Plant Sciences, Plant Genetics...\n",
"Name: 0, Length: 2693, dtype: object"
]
},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"re3data_cleaned_subjects"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [],
"source": [
"re3data_df = re3data_df.join(re3data_cleaned_subjects)"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [],
"source": [
"re3data_df.drop(columns=['subjects'], inplace=True)\n",
"re3data_df.rename(columns={0:'subjects'}, inplace=True)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**OpenDOAR**"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {
"scrolled": true
},
"outputs": [
{
"data": {
"text/plain": [
"0 []\n",
"1 []\n",
"2 ['Social Sciences General', 'Science General',...\n",
"3 []\n",
"4 []\n",
" ... \n",
"6009 ['Multidisciplinary']\n",
"6010 []\n",
"6011 ['Business and Economics']\n",
"6012 ['Earth and Planetary Sciences', 'Ecology and ...\n",
"6013 []\n",
"Name: subjects, Length: 6014, dtype: object"
]
},
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"opendoar_df.subjects"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {},
"outputs": [],
"source": [
"opendoar_df['subjects'] = opendoar_df.subjects.apply(lambda x: ast.literal_eval(x))"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [],
"source": [
"opendoar_cleaned_subjects = opendoar_df.explode('subjects').subjects.str.split(',| and ', expand=True)\\\n",
" .apply(lambda row: row.dropna().tolist(), axis=1)\\\n",
" .reset_index()\\\n",
" .groupby('index')[0].apply(lambda x: merge_lists(x))"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"index\n",
"0 []\n",
"1 []\n",
"2 [Social Sciences General, Science General, Com...\n",
"3 []\n",
"4 []\n",
" ... \n",
"6009 [Multidisciplinary]\n",
"6010 []\n",
"6011 [Business, Economics]\n",
"6012 [Earth, Planetary Sciences, Ecology, Environme...\n",
"6013 []\n",
"Name: 0, Length: 6014, dtype: object"
]
},
"execution_count": 19,
2021-07-02 17:49:38 +02:00
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
2021-07-06 15:23:24 +02:00
"opendoar_cleaned_subjects"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [],
"source": [
"opendoar_df = opendoar_df.join(opendoar_cleaned_subjects)"
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {},
"outputs": [],
"source": [
"opendoar_df.drop(columns=['subjects'], inplace=True)\n",
"opendoar_df.rename(columns={0: 'subjects'}, inplace=True)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Subjects analysis"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {},
"outputs": [],
"source": [
"fairsharing_subjects = fairsharing_df.explode('subjects')\n",
"re3data_subjects = re3data_df.explode('subjects')\n",
"opendoar_subjects = opendoar_df.explode('subjects')"
2021-07-02 17:49:38 +02:00
]
},
{
"cell_type": "code",
2021-07-06 15:23:24 +02:00
"execution_count": 23,
2021-07-02 17:49:38 +02:00
"metadata": {},
"outputs": [
2021-07-06 15:23:24 +02:00
{
"data": {
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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",
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" * @author Feross Aboukhadijeh <https://feross.org>\n",
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" * pad-left <https://github.com/jonschlinkert/pad-left>\n",
" *\n",
" * Copyright (c) 2014-2015, Jon Schlinkert.\n",
" * Licensed under the MIT license.\n",
" */\n",
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"/*\n",
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"title": {
2021-07-06 15:23:24 +02:00
"text": "Subject coverage"
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},
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2021-07-06 15:23:24 +02:00
"<div> <div id=\"0cbc7f56-7708-45d2-a4e7-71161f18ac5f\" 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(\"0cbc7f56-7708-45d2-a4e7-71161f18ac5f\")) { Plotly.newPlot( \"0cbc7f56-7708-45d2-a4e7-71161f18ac5f\", [{\"name\": \"FAIRsharing\", \"type\": \"bar\", \"x\": [\"Life Science\", \"Biomedical Science\", \"Earth Science\", \"Genomics\", \"Environmental Science\", \"Oceanography\", \"Biodiversity\", \"Atmospheric Science\", \"Epidemiology\", \"Genetics\", \"Health Science\", \"Virology\", \"Biology\", \"Proteomics\", \"Bioinformatics\", \"Agriculture\", \"Geology\", \"Preclinical Studies\", \"Transcriptomics\", \"Chemistry\", \"Comparative Genomics\", \"Data Management\", \"Clinical Studies\", \"Botany\", \"Functional Genomics\", \"Medicine\", \"Geophysics\", \"Meteorology\", \"Humanities and Social Sciences\", \"Natural Science\", \"Social Science\", \"Systems Biology\", \"Geography\", \"Ecology\", \"Data Submission\", \" Annotation and Curation\", \"Metabolomics\", \"Engineering Science\", \"Marine Biology\", \"Physics\", \"Economics\", \"Hydrology\", \"Ontology and Terminology\", \"Biochemistry\", \"Astrophysics and Astronomy\", \"Phylogenetics\", \"Molecular biology\", \"Epigenetics\", \"Medical Virology\", \"Remote Sensing\", \"Infectious Disease Medicine\", \"Immunology\", \"Humanities\", \"Anatomy\", \"Computational Biology\", \"Structural Biology\", \"Neurobiology\", \"Plant Genetics\", \"Computer Science\", \"Public Health\", \"Knowledge and Information Systems\", \"Microbiology\", \"Demographics\", \"Social and Behavioural Science\", \"Data Visualization\", \"Oncology\", \"Developmental Biology\", \"Critical Care Medicine\", \"Hydrogeology\", \"Data Integration\", \"Glycomics\", \"Ecosystem Science\", \"Soil Science\", \"Geochemistry\", \"Population Genetics\", \"Drug Discovery\", \"Materials Science\", \"Water Research\", \"Neuroscience\", \"Forest Management\", \"Plant Breeding\", \"Metagenomics\", \"Energy Engineering\", \"Water Management\", \"Paleontology\", \"Software Engineering\", \"Geodesy\", \"Taxonomy\", \"Cell Biology\", \"Phylogenomics\", \"Immunogenetics\", \"Pharmacology\", \"Mineralogy\", \"Freshwater Science\", \"Medical Informatics\", \"Statistics\", \"Epigenomics\", \"Human Genetics\", \"Phylogeny\", \"Global Health\", \"Animal Genetics\", \"Cheminformatics\", \"Evolutionary Biology\", \"Zoology\", \"Mathematics\", \"Microbial Ecology\", \"Population Dynamics\", \"Political Science\", \"Nanotechnology\", \"Psychology\", \"Physical Geography\", \"Education Science\", \"Drug Development\", \"Culture\", \"Translational Medicine\", \"Pathology\", \"Food Security\", \"Informatics\", \"Neurophysiology\", \"Natural History\", \"Phenomics\", \"Nutritional Science\", \"Computational Neuroscience\", \"Biotechnology\", \"Bioengineering\", \"Geoinformatics\", \"Data Governance\", \"Cartography\", \"History\", \"Analytical Chemistry\", \"Organic Chemistry\", \"Urban Planning\", \"Plant Anatomy\", \"Enzymology\", \"Classical Archaeology\", \"Animal Husbandry\", \"Maritime Engineering\", \"Materials Engineering\", \"Database Management\", \"Cardiology\", \"Anthropology\", \"Architecture\", \"Transportation Planning\", \"Criminology\", \"Primary Health Care\", \"Molecular Genetics\", \"Toxicology\", \"Omics\", \"Communication Science\", \"Agronomy\", \"Physiology\", \"Art\", \"Endocrinology\", \"Fisheries Science\", \"Economic and Social History\", \"Drug Metabolism\", \"Thermodynamics\", \"Plant Ecology\", \"Tropical Medicine\", \"Aerospace Engineering\", \"Data Quality\", \"Chemical Engineering\", \"Data Mining\", \"Health Services Research\", \"Linguistics\", \"Medicinal Chemistry\", \"Agricultural Engineering\", \"Geriatric Medicine\", \"Toxicogenomics\", \"Drug Repo
2021-07-02 17:49:38 +02:00
" \n",
2021-07-06 15:23:24 +02:00
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"var x = new MutationObserver(function (mutations, observer) {{\n",
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]
},
"metadata": {},
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"output_type": "display_data"
}
],
"source": [
"data1 = fairsharing_subjects.groupby('subjects')[['url']].count().sort_values('url', ascending=False)\n",
"data2 = re3data_subjects.groupby('subjects')[['url']].count().sort_values('url', ascending=False)\n",
"data3 = opendoar_subjects.groupby('subjects')[['url']].count().sort_values('url', ascending=False)\n",
"\n",
"plot = [\n",
" go.Bar(\n",
" x=data1.index,\n",
" y=data1['url'],\n",
" name='FAIRsharing'\n",
" ),\n",
" go.Bar(\n",
" x=data2.index,\n",
" y=data2['url'],\n",
" name='re3data',\n",
" visible = 'legendonly'\n",
" ),\n",
" go.Bar(\n",
" x=data3.index,\n",
" y=data3['url'],\n",
" name='OpenDOAR',\n",
" visible = 'legendonly'\n",
" )\n",
"]\n",
"\n",
"layout = go.Layout(\n",
" title='Subject coverage',\n",
" xaxis=dict(tickangle=45, tickfont=dict(size=12))\n",
")\n",
"\n",
"fig = go.Figure(plot, layout).show()"
]
},
{
"cell_type": "code",
"execution_count": 24,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"311"
]
},
"execution_count": 24,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"len(fairsharing_subjects.subjects.unique())"
]
},
{
"cell_type": "code",
"execution_count": 25,
"metadata": {
"scrolled": true
},
"outputs": [
{
"data": {
"text/plain": [
"414"
]
},
"execution_count": 25,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"len(re3data_subjects.subjects.unique())"
]
},
{
"cell_type": "code",
"execution_count": 26,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"64"
]
},
"execution_count": 26,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"len(opendoar_subjects.subjects.unique())"
]
},
{
"cell_type": "code",
"execution_count": 27,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"array([nan, 'Social Sciences General', 'Science General', 'Computers',\n",
" 'IT', 'Physics', 'Astronomy', 'Multidisciplinary', 'Arts',\n",
" 'Humanities General', 'Philosophy', 'Religion', 'Business',\n",
" 'Economics', 'Law', 'Politics', 'Psychology', 'Health', 'Medicine',\n",
" 'History', 'Archaeology', 'Education', 'Technology General',\n",
" 'Library', 'Information Science', 'Earth', 'Planetary Sciences',\n",
" 'Geography', 'Regional Studies', 'Architecture', 'Ecology',\n",
" 'Environment', 'Electrical', 'Electronic Engineering', 'Biology',\n",
" 'Biochemistry', 'Mathematics', 'Statistics', 'Civil Engineering',\n",
" 'Agriculture', ' Food', 'Veterinary', 'Language', 'Literature',\n",
" 'Chemistry', 'Chemical Technology', 'Mechanical Engineering',\n",
" 'Materials', 'Fine', 'Performing Arts', 'Management', 'Planning',\n",
" ' Language', ' Health', 'Veterinary ', ' Technology General',\n",
" 'Medicine ', ' History', 'IT ', ' Law', 'Social Sciences General ',\n",
" ' Science General', ' Philosophy', 'Performing Arts '],\n",
" dtype=object)"
]
},
"execution_count": 27,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"opendoar_subjects.subjects.unique()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Geographic analysis"
]
},
{
"cell_type": "code",
"execution_count": 28,
"metadata": {},
"outputs": [],
"source": [
"fairsharing_countries = fairsharing_df.explode('countries')\n",
"fairsharing_countries['countrycode'] = fairsharing_countries.countries.map(lambda c: country_to_countrycode(c))\n",
"fairsharing_countries['continent'] = fairsharing_countries.countrycode.map(lambda cc: countrycode_to_continent(cc))"
]
},
{
"cell_type": "code",
"execution_count": 29,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"array(['European Union', 'Republic of Ireland', 'Worldwide', nan],\n",
" dtype=object)"
]
},
"execution_count": 29,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"fairsharing_countries[fairsharing_countries.countrycode.isna()].countries.unique()"
]
},
{
"cell_type": "code",
"execution_count": 30,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"array(['European Union', 'Republic of Ireland', 'Worldwide', 'Antarctica',\n",
" nan], dtype=object)"
]
},
"execution_count": 30,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"fairsharing_countries[fairsharing_countries.continent.isna()].countries.unique()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Manually fixing exceptions"
]
},
{
"cell_type": "code",
"execution_count": 31,
"metadata": {},
"outputs": [],
"source": [
"fairsharing_countries.loc[fairsharing_countries.countries == 'Republic of Ireland', ['countries', 'countrycode', 'continent']] = ['Ireland', 'IE', 'EU']\n",
"fairsharing_countries.loc[fairsharing_countries.countries == 'Antarctica', ['countrycode', 'continent']] = ['AQ', np.nan]\n",
"fairsharing_countries.loc[fairsharing_countries.countries == 'European Union', ['countrycode', 'continent']] = ['EU', 'EU']"
]
},
{
"cell_type": "code",
"execution_count": 32,
"metadata": {},
"outputs": [
{
"data": {
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"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>full_name</th>\n",
" <th>short_name</th>\n",
" <th>fs_url</th>\n",
" <th>url</th>\n",
" <th>countries</th>\n",
" <th>subjects</th>\n",
" <th>countrycode</th>\n",
" <th>continent</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>915</th>\n",
" <td>Antabif IPT - AntOBIS IPT - GBIF Belgium</td>\n",
" <td>Antabif IPT - AntOBIS IPT - GBIF Belgium</td>\n",
" <td>https://fairsharing.org/10.25504/FAIRsharing.e...</td>\n",
" <td>http://ipt.biodiversity.aq/</td>\n",
" <td>Antarctica</td>\n",
" <td>[Biodiversity, Life Science]</td>\n",
" <td>AQ</td>\n",
" <td>NaN</td>\n",
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],
"text/plain": [
" full_name \\\n",
"915 Antabif IPT - AntOBIS IPT - GBIF Belgium \n",
"\n",
" short_name \\\n",
"915 Antabif IPT - AntOBIS IPT - GBIF Belgium \n",
"\n",
" fs_url \\\n",
"915 https://fairsharing.org/10.25504/FAIRsharing.e... \n",
"\n",
" url countries subjects \\\n",
"915 http://ipt.biodiversity.aq/ Antarctica [Biodiversity, Life Science] \n",
"\n",
" countrycode continent \n",
"915 AQ NaN "
]
},
"execution_count": 32,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"fairsharing_countries[fairsharing_countries.countrycode == 'AQ']"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"For re3data"
]
},
{
"cell_type": "code",
"execution_count": 65,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"index 5\n",
"id 5\n",
"url 5\n",
"official_name 5\n",
"english_name 5\n",
"description 5\n",
"latitude 5\n",
"longitude 5\n",
"subjects 5\n",
"dtype: int64"
]
},
"execution_count": 65,
"metadata": {},
"output_type": "execute_result"
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}
],
"source": [
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"re3data_df[re3data_df.latitude.notna()].count()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Location is basically absent in re3data"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"For OpenDOAR"
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]
},
{
"cell_type": "code",
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"execution_count": 34,
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"metadata": {},
"outputs": [
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{
"name": "stdout",
"output_type": "stream",
"text": [
"Loading formatted geocoded file...\n"
]
},
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{
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" <th>lon</th>\n",
" <th>name</th>\n",
" <th>admin1</th>\n",
" <th>admin2</th>\n",
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" <th>continent</th>\n",
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" </tr>\n",
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" <tr>\n",
" <th>0</th>\n",
" <td>43.26271</td>\n",
" <td>-2.92528</td>\n",
" <td>Bilbao</td>\n",
" <td>Basque Country</td>\n",
" <td>Bizkaia</td>\n",
" <td>ES</td>\n",
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" <td>EU</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>4.88447</td>\n",
" <td>-1.75536</td>\n",
" <td>Takoradi</td>\n",
" <td>Western</td>\n",
" <td></td>\n",
" <td>GH</td>\n",
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" <td>AF</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>53.98333</td>\n",
" <td>-2.78333</td>\n",
" <td>Galgate</td>\n",
" <td>England</td>\n",
" <td>Lancashire</td>\n",
" <td>GB</td>\n",
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" <td>EU</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>34.05223</td>\n",
" <td>-118.24368</td>\n",
" <td>Los Angeles</td>\n",
" <td>California</td>\n",
" <td>Los Angeles County</td>\n",
" <td>US</td>\n",
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" <td>NA</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>-22.22111</td>\n",
" <td>-54.80556</td>\n",
" <td>Dourados</td>\n",
" <td>Mato Grosso do Sul</td>\n",
" <td>Dourados</td>\n",
" <td>BR</td>\n",
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" <td>SA</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
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" <td>...</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>6009</th>\n",
" <td>40.85631</td>\n",
" <td>14.24641</td>\n",
" <td>Napoli</td>\n",
" <td>Campania</td>\n",
" <td>Provincia di Napoli</td>\n",
" <td>IT</td>\n",
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" <td>EU</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>6010</th>\n",
" <td>38.19394</td>\n",
" <td>15.55256</td>\n",
" <td>Messina</td>\n",
" <td>Sicily</td>\n",
" <td>Messina</td>\n",
" <td>IT</td>\n",
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" <td>EU</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>6011</th>\n",
" <td>54.32133</td>\n",
" <td>10.13489</td>\n",
" <td>Kiel</td>\n",
" <td>Schleswig-Holstein</td>\n",
" <td></td>\n",
" <td>DE</td>\n",
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" <td>EU</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>6012</th>\n",
" <td>43.40785</td>\n",
" <td>-73.25955</td>\n",
" <td>Granville</td>\n",
" <td>New York</td>\n",
" <td>Washington County</td>\n",
" <td>US</td>\n",
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" <td>NA</td>\n",
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" </tr>\n",
" <tr>\n",
" <th>6013</th>\n",
" <td>33.96095</td>\n",
" <td>-83.37794</td>\n",
" <td>Athens</td>\n",
" <td>Georgia</td>\n",
" <td>Clarke County</td>\n",
" <td>US</td>\n",
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" <td>NA</td>\n",
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" </tr>\n",
" </tbody>\n",
"</table>\n",
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"<p>6014 rows × 7 columns</p>\n",
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"</div>"
],
"text/plain": [
" lat lon name admin1 \\\n",
"0 43.26271 -2.92528 Bilbao Basque Country \n",
"1 4.88447 -1.75536 Takoradi Western \n",
"2 53.98333 -2.78333 Galgate England \n",
"3 34.05223 -118.24368 Los Angeles California \n",
"4 -22.22111 -54.80556 Dourados Mato Grosso do Sul \n",
"... ... ... ... ... \n",
"6009 40.85631 14.24641 Napoli Campania \n",
"6010 38.19394 15.55256 Messina Sicily \n",
"6011 54.32133 10.13489 Kiel Schleswig-Holstein \n",
"6012 43.40785 -73.25955 Granville New York \n",
"6013 33.96095 -83.37794 Athens Georgia \n",
"\n",
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" admin2 cc continent \n",
"0 Bizkaia ES EU \n",
"1 GH AF \n",
"2 Lancashire GB EU \n",
"3 Los Angeles County US NA \n",
"4 Dourados BR SA \n",
"... ... .. ... \n",
"6009 Provincia di Napoli IT EU \n",
"6010 Messina IT EU \n",
"6011 DE EU \n",
"6012 Washington County US NA \n",
"6013 Clarke County US NA \n",
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"\n",
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"[6014 rows x 7 columns]"
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]
},
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"execution_count": 34,
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"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"reverse_geocoding = pd.DataFrame(rg.search(opendoar_df[['latitude', 'longitude']].apply(tuple, axis=1).tolist()))\n",
"reverse_geocoding['lat'] = reverse_geocoding['lat'].astype('float')\n",
"reverse_geocoding['lon'] = reverse_geocoding['lon'].astype('float')\n",
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"reverse_geocoding['continent'] = reverse_geocoding.cc.map(countrycode_to_continent)\n",
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"reverse_geocoding"
]
},
{
"cell_type": "code",
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"execution_count": 35,
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"metadata": {},
"outputs": [],
"source": [
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"opendoar_df = opendoar_df.join(reverse_geocoding)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Manual fix of null lat/lon"
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]
},
{
"cell_type": "code",
2021-07-06 15:23:24 +02:00
"execution_count": 36,
2021-07-02 17:49:38 +02:00
"metadata": {},
"outputs": [],
"source": [
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"opendoar_df.loc[(opendoar_df.latitude == 0.0) & (opendoar_df.longitude == 0.0), ['latitude', 'longitude', 'cc', 'continent']] = [np.nan, np.nan, np.nan, np.nan]\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**Country intersection**"
]
},
{
"cell_type": "code",
"execution_count": 63,
"metadata": {},
"outputs": [
{
"data": {
"image/png": "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
"text/plain": [
"<Figure size 432x288 with 1 Axes>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"venn2([set(fairsharing_countries.countrycode.dropna()), set(opendoar_df.cc.dropna())], set_labels = ('FAIRsharing', 'OpenDOAR'))\n",
"plt.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**Country coverage**"
2021-07-02 17:49:38 +02:00
]
},
{
"cell_type": "code",
2021-07-06 15:23:24 +02:00
"execution_count": 37,
2021-07-02 17:49:38 +02:00
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.plotly.v1+json": {
"config": {
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"plotlyServerURL": "https://plot.ly"
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"data": [
{
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"name": "FAIRsharing",
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"type": "bar",
"x": [
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"FR",
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"ES",
2021-07-06 15:23:24 +02:00
"JP",
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"CZ",
"NO",
"DK",
"EU",
"AT",
"FI",
"IE",
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"SG",
"KR",
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"BR",
2021-07-06 15:23:24 +02:00
"NZ",
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2021-07-02 17:49:38 +02:00
"TR",
2021-07-06 15:23:24 +02:00
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"y": [
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2021-07-06 15:23:24 +02:00
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2021-07-02 17:49:38 +02:00
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2021-07-06 15:23:24 +02:00
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2021-07-06 15:23:24 +02:00
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2021-07-06 15:23:24 +02:00
"NO",
2021-07-02 17:49:38 +02:00
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2021-07-06 15:23:24 +02:00
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2021-07-02 17:49:38 +02:00
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2021-07-06 15:23:24 +02:00
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2021-07-02 17:49:38 +02:00
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2021-07-06 15:23:24 +02:00
"GR",
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2021-07-02 17:49:38 +02:00
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2021-07-06 15:23:24 +02:00
"HU",
2021-07-02 17:49:38 +02:00
"RU",
2021-07-06 15:23:24 +02:00
"EC",
2021-07-02 17:49:38 +02:00
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2021-07-06 15:23:24 +02:00
"KE",
"RS",
"BY",
2021-07-02 17:49:38 +02:00
"CZ",
2021-07-06 15:23:24 +02:00
"IE",
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"MY",
"FI",
"NZ",
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"IR",
"CL",
2021-07-06 15:23:24 +02:00
"VE",
"TH",
2021-07-02 17:49:38 +02:00
"LT",
"DK",
"SD",
2021-07-06 15:23:24 +02:00
"LK",
"DZ",
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"SI",
2021-07-06 15:23:24 +02:00
"BD",
"EG",
"NI",
"TZ",
2021-07-02 17:49:38 +02:00
"KZ",
"HK",
2021-07-06 15:23:24 +02:00
"CU",
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"UG",
"PH",
"MD",
"BG",
"ZW",
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"SV",
2021-07-06 15:23:24 +02:00
"SA",
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"CY",
"JM",
2021-07-02 17:49:38 +02:00
"UY",
2021-07-06 15:23:24 +02:00
"RO",
2021-07-02 17:49:38 +02:00
"BW",
2021-07-06 15:23:24 +02:00
"PA",
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2021-07-02 17:49:38 +02:00
"PK",
2021-07-06 15:23:24 +02:00
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2021-07-02 17:49:38 +02:00
"DO",
2021-07-06 15:23:24 +02:00
"KG",
2021-07-02 17:49:38 +02:00
"LV",
2021-07-06 15:23:24 +02:00
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"SG",
"GE",
"BO",
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"SK",
2021-07-02 17:49:38 +02:00
"FJ",
2021-07-06 15:23:24 +02:00
"VA",
"LS",
"MV",
"PR",
"MZ",
"MN",
"MA",
"LU",
"PY",
"PW",
"GS",
"MW",
"AL",
"MR",
"MO",
"WF",
"VN",
"RW",
"NC",
"GT",
"SY",
"BJ",
"NP",
"GP",
"CM",
"TT",
"AF",
"LA",
"MT"
],
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"source": [
"data1 = fairsharing_countries.groupby('countrycode')[['url']].count().sort_values('url', ascending=False)\n",
"data2 = opendoar_df.groupby('cc')[['id']].count().sort_values('id', ascending=False)\n",
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2021-07-06 15:23:24 +02:00
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2021-07-02 17:49:38 +02:00
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2021-07-06 15:23:24 +02:00
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2021-07-02 17:49:38 +02:00
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],
"source": [
2021-07-06 15:23:24 +02:00
"data1 = fairsharing_countries.groupby('continent')[['url']].count()\n",
"data2 = opendoar_df.groupby('continent')[['url']].count()\n",
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"\n",
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"plot = [\n",
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},
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