{ "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": [ { "data": { "text/html": [ "
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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 [669, 58] 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", "1 NaN NaN NaN \n", "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", "3 NaN NaN NaN NaN \n", "4 NaN NaN NaN NaN \n", "\n", " association \n", "0 NaN \n", "1 NaN \n", "2 NaN \n", "3 NaN \n", "4 NaN " ] }, "execution_count": 7, "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()" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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03226fairsharing-records2020-12-09T11:53:44.000Z2022-02-08T10:42:36.452Z10.25504/FAIRsharing.d6423bWDC Sunspot Index and Long-term Solar Observat...ready[{'contact-name': 'Frédéric Clette', 'contact-...http://sidc.be/silso/home3226The WDC-SILSO is an activity of the Operationa...WDC-SILSO[{'url': 'http://www.sidc.be/silso/taxonomy/te...2013.0[{'url': 'http://www.sidc.be/silso/datafiles',...[{'url': 'https://www.re3data.org/repository/r...[biodbcore-001740, bsg-d001740]Databaserepository[Electromagnetism, Astrophysics and Astronomy,...[Climate, Observation design][Not applicable][Climate change, earth observation, Electromag...[Belgium]FAIRsharing record for: WDC Sunspot Index and ...WDC-SILSOhttps://fairsharing.org/10.25504/FAIRsharing.d...10.25504/FAIRsharing.d6423bhttps://creativecommons.org/licenses/by-sa/4.0...This FAIRsharing record describes: The WDC-SIL...[][{'licence-name': 'SILSO legal notices', 'lice...NoneNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
12114fairsharing-records2014-11-04T15:23:40.000Z2022-01-21T14:39:02.195Z10.25504/FAIRsharing.p06nmeBiological Magnetic Resonance Data Bankready[{'contact-name': 'Helpdesk', 'contact-email':...https://bmrb.io/2114BMRB collects, annotates, archives, and dissem...BMRB[{'url': 'https://bmrb.io/bmrb/news/', 'name':...1988.0[{'url': 'https://bmrb.io/data_library/rsync.s...[{'url': 'https://www.re3data.org/repository/r...[biodbcore-000584, bsg-d000584]Databaserepository[Structural Biology][Molecular structure, Protein structure, Pepti...[All][][United States]FAIRsharing record for: Biological Magnetic Re...BMRBhttps://fairsharing.org/10.25504/FAIRsharing.p...10.25504/FAIRsharing.p06nmehttps://creativecommons.org/licenses/by-sa/4.0...This FAIRsharing record describes: BMRB collec...[{'id': 552, 'pubmed_id': 18288446, 'title': '...[{'licence-name': 'wwPDB Privacy and Usage Pol...None[{'doi': '10.1093/nar/gkm957', 'pubmed-id': 17...[{'url': 'https://bmrb.io/validate/', 'name': ...openyeshttps://bmrb.io/deposit/openNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
23022fairsharing-records2020-06-17T10:25:30.000Z2022-02-08T10:41:04.073Z10.25504/FAIRsharing.8b7a2fFisheries and Oceans Canada Pacific Region Dat...ready[{'contact-name': 'Peter Chandler', 'contact-e...http://www.pac.dfo-mpo.gc.ca/science/oceans/da...3022The Institute of Ocean Sciences (IOS)/Ocean Sc...None[{'url': 'DFO.PAC.SCI.IOSData-DonneesISO.SCI.P...NaN[{'name': 'Users must contact the Senior Analy...[{'url': 'https://www.re3data.org/repository/r...[biodbcore-001530, bsg-d001530]Databaserepository[Environmental Science, Meteorology, Earth Sci...[Climate][Not applicable][Salinity, Temperature][Canada]FAIRsharing record for: Fisheries and Oceans C...Nonehttps://fairsharing.org/10.25504/FAIRsharing.8...10.25504/FAIRsharing.8b7a2fhttps://creativecommons.org/licenses/by-sa/4.0...This FAIRsharing record describes: The Institu...[][{'licence-name': 'Fisheries and Oceans Canada...NoneNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
32998fairsharing-records2020-05-21T07:42:30.000Z2022-02-08T10:40:19.531Z10.25504/FAIRsharing.e08886Climate Prediction Centerready[{'contact-name': 'Jon Hoopingarner', 'contact...https://www.cpc.ncep.noaa.gov/2998The Climate Prediction Center (CPC) produces o...CPC[{'url': 'https://www.cpc.ncep.noaa.gov/commen...1970.0[{'url': 'https://www.cpc.ncep.noaa.gov/', 'na...[{'url': 'https://www.re3data.org/repository/r...[biodbcore-001504, bsg-d001504]Databaserepository[Hydrogeology, Geography, Meteorology, Geodesy...[Climate][Not applicable][Forecasting, weather][United States]FAIRsharing record for: Climate Prediction CenterCPChttps://fairsharing.org/10.25504/FAIRsharing.e...10.25504/FAIRsharing.e08886https://creativecommons.org/licenses/by-sa/4.0...This FAIRsharing record describes: The Climate...[][{'licence-name': 'National Weather Service Di...NoneNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
42301fairsharing-records2016-06-03T14:54:08.000Z2021-11-24T13:17:51.201Z10.25504/FAIRsharing.meh9wzAcytostelium Gene Databasedeprecated[{'contact-name': 'Acytostelium genome consort...http://cosmos.bot.kyoto-u.ac.jp/acytodb//cgi-b...2301Genome and transcriptome database of Acytostel...NaNNaN2008.0NaNNaN[biodbcore-000775, bsg-d000775]Databaserepository[Genomics, Life Science, Transcriptomics][DNA sequence data, Gene model annotation][Acytostelium subglobosum][][United Kingdom, Japan]FAIRsharing record for: Acytostelium Gene Data...Nonehttps://fairsharing.org/10.25504/FAIRsharing.m...10.25504/FAIRsharing.meh9wzhttps://creativecommons.org/licenses/by-sa/4.0...This FAIRsharing record describes: Genome and ...[{'id': 1139, 'pubmed_id': 25758444, 'title': ...[]NoneNaNNaNThis resource is no longer available at the st...NaNNaNNaNNaN2021-9-17NaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
\n", "" ], "text/plain": [ " id type attributes.created-at \\\n", "0 3226 fairsharing-records 2020-12-09T11:53:44.000Z \n", "1 2114 fairsharing-records 2014-11-04T15:23:40.000Z \n", "2 3022 fairsharing-records 2020-06-17T10:25:30.000Z \n", "3 2998 fairsharing-records 2020-05-21T07:42:30.000Z \n", "4 2301 fairsharing-records 2016-06-03T14:54:08.000Z \n", "\n", " attributes.updated-at attributes.metadata.doi \\\n", "0 2022-02-08T10:42:36.452Z 10.25504/FAIRsharing.d6423b \n", "1 2022-01-21T14:39:02.195Z 10.25504/FAIRsharing.p06nme \n", "2 2022-02-08T10:41:04.073Z 10.25504/FAIRsharing.8b7a2f \n", "3 2022-02-08T10:40:19.531Z 10.25504/FAIRsharing.e08886 \n", "4 2021-11-24T13:17:51.201Z 10.25504/FAIRsharing.meh9wz \n", "\n", " attributes.metadata.name \\\n", "0 WDC Sunspot Index and Long-term Solar Observat... \n", "1 Biological Magnetic Resonance Data Bank \n", "2 Fisheries and Oceans Canada Pacific Region Dat... \n", "3 Climate Prediction Center \n", "4 Acytostelium Gene Database \n", "\n", " attributes.metadata.status \\\n", "0 ready \n", "1 ready \n", "2 ready \n", "3 ready \n", "4 deprecated \n", "\n", " attributes.metadata.contacts \\\n", "0 [{'contact-name': 'Frédéric Clette', 'contact-... \n", "1 [{'contact-name': 'Helpdesk', 'contact-email':... \n", "2 [{'contact-name': 'Peter Chandler', 'contact-e... \n", "3 [{'contact-name': 'Jon Hoopingarner', 'contact... \n", "4 [{'contact-name': 'Acytostelium genome consort... \n", "\n", " attributes.metadata.homepage \\\n", "0 http://sidc.be/silso/home \n", "1 https://bmrb.io/ \n", "2 http://www.pac.dfo-mpo.gc.ca/science/oceans/da... \n", "3 https://www.cpc.ncep.noaa.gov/ \n", "4 http://cosmos.bot.kyoto-u.ac.jp/acytodb//cgi-b... \n", "\n", " attributes.metadata.identifier \\\n", "0 3226 \n", "1 2114 \n", "2 3022 \n", "3 2998 \n", "4 2301 \n", "\n", " attributes.metadata.description \\\n", "0 The WDC-SILSO is an activity of the Operationa... \n", "1 BMRB collects, annotates, archives, and dissem... \n", "2 The Institute of Ocean Sciences (IOS)/Ocean Sc... \n", "3 The Climate Prediction Center (CPC) produces o... \n", "4 Genome and transcriptome database of Acytostel... \n", "\n", " attributes.metadata.abbreviation \\\n", "0 WDC-SILSO \n", "1 BMRB \n", "2 None \n", "3 CPC \n", "4 NaN \n", "\n", " attributes.metadata.support-links \\\n", "0 [{'url': 'http://www.sidc.be/silso/taxonomy/te... \n", "1 [{'url': 'https://bmrb.io/bmrb/news/', 'name':... \n", "2 [{'url': 'DFO.PAC.SCI.IOSData-DonneesISO.SCI.P... \n", "3 [{'url': 'https://www.cpc.ncep.noaa.gov/commen... \n", "4 NaN \n", "\n", " attributes.metadata.year-creation \\\n", "0 2013.0 \n", "1 1988.0 \n", "2 NaN \n", "3 1970.0 \n", "4 2008.0 \n", "\n", " attributes.metadata.data-processes \\\n", "0 [{'url': 'http://www.sidc.be/silso/datafiles',... \n", "1 [{'url': 'https://bmrb.io/data_library/rsync.s... \n", "2 [{'name': 'Users must contact the Senior Analy... \n", "3 [{'url': 'https://www.cpc.ncep.noaa.gov/', 'na... \n", "4 NaN \n", "\n", " attributes.metadata.cross-references \\\n", "0 [{'url': 'https://www.re3data.org/repository/r... \n", "1 [{'url': 'https://www.re3data.org/repository/r... \n", "2 [{'url': 'https://www.re3data.org/repository/r... \n", "3 [{'url': 'https://www.re3data.org/repository/r... \n", "4 NaN \n", "\n", " attributes.legacy-ids attributes.fairsharing-registry \\\n", "0 [biodbcore-001740, bsg-d001740] Database \n", "1 [biodbcore-000584, bsg-d000584] Database \n", "2 [biodbcore-001530, bsg-d001530] Database \n", "3 [biodbcore-001504, bsg-d001504] Database \n", "4 [biodbcore-000775, bsg-d000775] Database \n", "\n", " attributes.record-type attributes.subjects \\\n", "0 repository [Electromagnetism, Astrophysics and Astronomy,... \n", "1 repository [Structural Biology] \n", "2 repository [Environmental Science, Meteorology, Earth Sci... \n", "3 repository [Hydrogeology, Geography, Meteorology, Geodesy... \n", "4 repository [Genomics, Life Science, Transcriptomics] \n", "\n", " attributes.domains \\\n", "0 [Climate, Observation design] \n", "1 [Molecular structure, Protein structure, Pepti... \n", "2 [Climate] \n", "3 [Climate] \n", "4 [DNA sequence data, Gene model annotation] \n", "\n", " attributes.taxonomies \\\n", "0 [Not applicable] \n", "1 [All] \n", "2 [Not applicable] \n", "3 [Not applicable] \n", "4 [Acytostelium subglobosum] \n", "\n", " attributes.user-defined-tags attributes.countries \\\n", "0 [Climate change, earth observation, Electromag... [Belgium] \n", "1 [] [United States] \n", "2 [Salinity, Temperature] [Canada] \n", "3 [Forecasting, weather] [United States] \n", "4 [] [United Kingdom, Japan] \n", "\n", " attributes.name attributes.abbreviation \\\n", "0 FAIRsharing record for: WDC Sunspot Index and ... WDC-SILSO \n", "1 FAIRsharing record for: Biological Magnetic Re... BMRB \n", "2 FAIRsharing record for: Fisheries and Oceans C... None \n", "3 FAIRsharing record for: Climate Prediction Center CPC \n", "4 FAIRsharing record for: Acytostelium Gene Data... None \n", "\n", " attributes.url \\\n", "0 https://fairsharing.org/10.25504/FAIRsharing.d... \n", "1 https://fairsharing.org/10.25504/FAIRsharing.p... \n", "2 https://fairsharing.org/10.25504/FAIRsharing.8... \n", "3 https://fairsharing.org/10.25504/FAIRsharing.e... \n", "4 https://fairsharing.org/10.25504/FAIRsharing.m... \n", "\n", " attributes.doi \\\n", "0 10.25504/FAIRsharing.d6423b \n", "1 10.25504/FAIRsharing.p06nme \n", "2 10.25504/FAIRsharing.8b7a2f \n", "3 10.25504/FAIRsharing.e08886 \n", "4 10.25504/FAIRsharing.meh9wz \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: The WDC-SIL... \n", "1 This FAIRsharing record describes: BMRB collec... \n", "2 This FAIRsharing record describes: The Institu... \n", "3 This FAIRsharing record describes: The Climate... \n", "4 This FAIRsharing record describes: Genome and ... \n", "\n", " attributes.publications \\\n", "0 [] \n", "1 [{'id': 552, 'pubmed_id': 18288446, 'title': '... \n", "2 [] \n", "3 [] \n", "4 [{'id': 1139, 'pubmed_id': 25758444, 'title': ... \n", "\n", " attributes.licence-links attributes.url-for-logo \\\n", "0 [{'licence-name': 'SILSO legal notices', 'lice... None \n", "1 [{'licence-name': 'wwPDB Privacy and Usage Pol... None \n", "2 [{'licence-name': 'Fisheries and Oceans Canada... None \n", "3 [{'licence-name': 'National Weather Service Di... None \n", "4 [] None \n", "\n", " attributes.metadata.citations \\\n", "0 NaN \n", "1 [{'doi': '10.1093/nar/gkm957', 'pubmed-id': 17... \n", "2 NaN \n", "3 NaN \n", "4 NaN \n", "\n", " attributes.metadata.associated-tools \\\n", "0 NaN \n", "1 [{'url': 'https://bmrb.io/validate/', 'name': ... \n", "2 NaN \n", "3 NaN \n", "4 NaN \n", "\n", " attributes.metadata.deprecation-reason \\\n", "0 NaN \n", "1 \n", "2 NaN \n", "3 NaN \n", "4 This resource is no longer available at the st... \n", "\n", " attributes.metadata.data-access-condition.type \\\n", "0 NaN \n", "1 open \n", "2 NaN \n", "3 NaN \n", "4 NaN \n", "\n", " attributes.metadata.data-contact-information \\\n", "0 NaN \n", "1 yes \n", "2 NaN \n", "3 NaN \n", "4 NaN \n", "\n", " attributes.metadata.data-deposition-condition.url \\\n", "0 NaN \n", "1 https://bmrb.io/deposit/ \n", "2 NaN \n", "3 NaN \n", "4 NaN \n", "\n", " attributes.metadata.data-deposition-condition.type \\\n", "0 NaN \n", "1 open \n", "2 NaN \n", "3 NaN \n", "4 NaN \n", "\n", " attributes.metadata.deprecation-date attributes.metadata.access-points \\\n", "0 NaN NaN \n", "1 NaN NaN \n", "2 NaN NaN \n", "3 NaN NaN \n", "4 2021-9-17 NaN \n", "\n", " attributes.metadata.data-access-condition.url \\\n", "0 NaN \n", "1 NaN \n", "2 NaN \n", "3 NaN \n", "4 NaN \n", "\n", " attributes.metadata.resource-sustainability.url \\\n", "0 NaN \n", "1 NaN \n", "2 NaN \n", "3 NaN \n", "4 NaN \n", "\n", " attributes.metadata.resource-sustainability.name \\\n", "0 NaN \n", "1 NaN \n", "2 NaN \n", "3 NaN \n", "4 NaN \n", "\n", " attributes.metadata.data-preservation-policy.url \\\n", "0 NaN \n", "1 NaN \n", "2 NaN \n", "3 NaN \n", "4 NaN \n", "\n", " attributes.metadata.data-preservation-policy.name \\\n", "0 NaN \n", "1 NaN \n", "2 NaN \n", "3 NaN \n", "4 NaN \n", "\n", " attributes.metadata.data-access-for-pre-publication-review \\\n", "0 NaN \n", "1 NaN \n", "2 NaN \n", "3 NaN \n", "4 NaN \n", "\n", " attributes.metadata.data-versioning attributes.metadata.data-curation.type \\\n", "0 NaN NaN \n", "1 NaN NaN \n", "2 NaN NaN \n", "3 NaN NaN \n", "4 NaN NaN \n", "\n", " attributes.metadata.data-curation.url \\\n", "0 NaN \n", "1 NaN \n", "2 NaN \n", "3 NaN \n", "4 NaN \n", "\n", " attributes.metadata.citation-to-related-publications \\\n", "0 NaN \n", "1 NaN \n", "2 NaN \n", "3 NaN \n", "4 NaN \n", "\n", " attributes.metadata.tombstone \n", "0 NaN \n", "1 NaN \n", "2 NaN \n", "3 NaN \n", "4 NaN " ] }, "execution_count": 9, "metadata": {}, "output_type": "execute_result" } ], "source": [ "with open('../data/raw/fairsharing_dump_api_02_2022.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": 10, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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\\\n", "count 1764 1853 \n", "unique 1623 1853 \n", "top [] http://sidc.be/silso/home \n", "freq 40 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.identifier \\\n", "count 1853.000000 \n", "unique NaN \n", "top NaN \n", "freq NaN \n", "mean 2481.862925 \n", "std 554.072492 \n", "min 1120.000000 \n", "25% 2009.000000 \n", "50% 2473.000000 \n", "75% 2938.000000 \n", "max 3827.000000 \n", "\n", " attributes.metadata.description \\\n", "count 1853 \n", "unique 1853 \n", "top The WDC-SILSO is an activity of the Operationa... \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.abbreviation \\\n", "count 1671 \n", "unique 1655 \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.support-links \\\n", "count 1663 \n", "unique 1646 \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 1541.000000 \n", "unique NaN \n", "top NaN \n", "freq NaN \n", "mean 2007.894873 \n", "std 10.933713 \n", "min 1894.000000 \n", "25% 2004.000000 \n", "50% 2010.000000 \n", "75% 2015.000000 \n", "max 2022.000000 \n", "\n", " attributes.metadata.data-processes \\\n", "count 1626 \n", "unique 1625 \n", "top [{'url': 'https://site.uit.no/dataverseno/abou... \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.cross-references \\\n", "count 790 \n", "unique 790 \n", "top [{'url': 'https://www.re3data.org/repository/r... \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.legacy-ids attributes.fairsharing-registry \\\n", "count 1853 1853 \n", "unique 1799 1 \n", "top [] Database \n", "freq 55 1853 \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 1853 1853 1853 \n", "unique 3 935 1205 \n", "top repository [Life Science] [] \n", "freq 954 345 276 \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 1853 1853 \n", "unique 385 395 \n", "top [All] [] \n", "freq 528 1258 \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 1853 1853 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orgIdentifiersubject
0r3d1000000011 Humanities and Social Sciences
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0r3d10000000112 Social and Behavioural Sciences
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2791r3d1000137334 Engineering Sciences
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" ], "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", "2791 r3d100013733 4 Engineering Sciences\n", "2792 r3d100013735 2 Life Sciences\n", "2792 r3d100013735 204 Microbiology, Virology and Immunology\n", "2792 r3d100013735 21 Biology\n", "2792 r3d100013735 22 Medicine\n", "\n", "[17032 rows x 2 columns]" ] }, "execution_count": 11, "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": 12, "metadata": {}, "outputs": [ { "data": { "text/html": [ " \n", " " ] }, "metadata": {}, 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"yaxis": { "backgroundcolor": "#E5ECF6", "gridcolor": "white", "gridwidth": 2, "linecolor": "white", "showbackground": true, "ticks": "", "zerolinecolor": "white" }, "zaxis": { "backgroundcolor": "#E5ECF6", "gridcolor": "white", "gridwidth": 2, "linecolor": "white", "showbackground": true, "ticks": "", "zerolinecolor": "white" } }, "shapedefaults": { "line": { "color": "#2a3f5f" } }, "ternary": { "aaxis": { "gridcolor": "white", "linecolor": "white", "ticks": "" }, "baxis": { "gridcolor": "white", "linecolor": "white", "ticks": "" }, "bgcolor": "#E5ECF6", "caxis": { "gridcolor": "white", "linecolor": "white", "ticks": "" } }, "title": { "x": 0.05 }, "xaxis": { "automargin": true, "gridcolor": "white", "linecolor": "white", "ticks": "", "title": { "standoff": 15 }, "zerolinecolor": "white", "zerolinewidth": 2 }, "yaxis": { "automargin": true, "gridcolor": "white", "linecolor": "white", "ticks": "", "title": { "standoff": 15 }, "zerolinecolor": "white", "zerolinewidth": 2 } } }, "title": { "text": "Subject coverage FAIRsharing" }, "xaxis": { "tickangle": 45, "tickfont": { "size": 12 } } } }, "text/html": [ "
" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "data = fairsharing_subjects.groupby('attributes.subjects')[['id']].count().sort_values('id', ascending=False)\n", "plot = [\n", " go.Bar(\n", " x=data.index,\n", " y=data['id'],\n", " name='FAIRsharing'\n", " )\n", "]\n", "\n", "layout = go.Layout(\n", " title='Subject coverage FAIRsharing',\n", " xaxis=dict(tickangle=45, tickfont=dict(size=12))\n", ")\n", "\n", "fig = go.Figure(plot, layout).show()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Geographic analysis" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "**re3data**" ] }, { "cell_type": "code", "execution_count": 19, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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0r3d100000001{'institutionName': 'Odum Institute for Resear...Odum Institute for Research in Social Science[]USA[general]non-profithttps://odum.unc.edu/archive/[][]
1r3d100000002{'institutionName': 'The U.S. National Archive...The U.S. National Archives and Records Adminis...[NARA, National Archives]USA[general]non-profithttp://www.archives.gov/[][http://www.archives.gov/contact/]
2r3d100000002{'institutionName': 'The USA.gov', 'institutio...The USA.gov[]USA[general]non-profithttp://www.usa.gov/[][http://www.usa.gov/Contact.shtml]
3r3d100000004{'institutionName': 'Institut für Deutsche Spr...Institut für Deutsche Sprache, Archiv für Gesp...[AGD]DEU[funding, general]non-profithttp://agd.ids-mannheim.de/index.shtml[]2004[agd@ids-mannheim.de]
4r3d100000005{'institutionName': 'Odum Institute for Resear...Odum Institute for Research in Social Science[]USA[technical]non-profithttps://odum.unc.edu/[][https://odum.unc.edu/contact/contact-form/, o...
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" ], "text/plain": [ " orgIdentifier institution \\\n", "0 r3d100000001 {'institutionName': 'Odum Institute for Resear... \n", "1 r3d100000002 {'institutionName': 'The U.S. National Archive... \n", "2 r3d100000002 {'institutionName': 'The USA.gov', 'institutio... \n", "3 r3d100000004 {'institutionName': 'Institut für Deutsche Spr... \n", "4 r3d100000005 {'institutionName': 'Odum Institute for Resear... \n", "\n", " institutionName \\\n", "0 Odum Institute for Research in Social Science \n", "1 The U.S. National Archives and Records Adminis... \n", "2 The USA.gov \n", "3 Institut für Deutsche Sprache, Archiv für Gesp... \n", "4 Odum Institute for Research in Social Science \n", "\n", " institutionAdditionalName institutionCountry responsabilityType \\\n", "0 [] USA [general] \n", "1 [NARA, National Archives] USA [general] \n", "2 [] USA [general] \n", "3 [AGD] DEU [funding, general] \n", "4 [] USA [technical] \n", "\n", " 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", "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... " ] }, "execution_count": 19, "metadata": {}, "output_type": "execute_result" } ], "source": [ "re3data_institutions = re3data_df.explode('institution')[['orgIdentifier', 'institution']]\n", "re3data_institutions = re3data_institutions[~re3data_institutions.institution.isna()].reset_index(drop=True)\n", "re3data_institutions = re3data_institutions.join(pd.json_normalize(re3data_institutions.institution))\n", "re3data_institutions.head()" ] }, { "cell_type": "code", "execution_count": 20, "metadata": {}, "outputs": [], "source": [ "re3data_institutions['org_continent'] = re3data_institutions.institutionCountry.map(countrycode_to_continent)" ] }, { "cell_type": "code", "execution_count": 21, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "array(['AAA', 'EEC'], dtype=object)" ] }, "execution_count": 21, "metadata": {}, "output_type": "execute_result" } ], "source": [ "re3data_institutions[re3data_institutions.org_continent.isna()].institutionCountry.unique()" ] }, { "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", "execution_count": 22, "metadata": {}, "outputs": [], "source": [ "re3data_institutions.loc[re3data_institutions.institutionCountry == 'EEC', 'org_continent'] = 'EU'" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "**OpenDOAR**" ] }, { "cell_type": "code", "execution_count": 23, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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system_metadata.idorganizationnamealternativeNamecountryurlidentifierlocation.latitudelocation.longiture
0134{'name': 'technische universität dortmund', 'a...technische universität dortmundtu dortmundDEUhttps://www.tu-dortmund.de[{'identifier': 'https://ror.org/01k97gp34', '...
158{'name': 'centre pour la communication scienti...centre pour la communication scientifique directeccsdFRAhttps://www.ccsd.cnrs.fr[]
293{'name': 'texas medical center', 'alternativeN...texas medical centertmcUSAhttps://www.tmc.edu[{'identifier': 'https://ror.org/00dqsbj20', '...
368{'name': 'university of southampton', 'alterna...university of southamptonGBRhttps://www.southampton.ac.uk/[{'identifier': 'https://ror.org/01ryk1543', '...
484{'name': 'carleton college', 'alternativeName'...carleton collegeUSAhttps://www.carleton.edu[{'identifier': 'https://ror.org/03jep7677', '...
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" ], "text/plain": [ " system_metadata.id organization \\\n", "0 134 {'name': 'technische universität dortmund', 'a... \n", "1 58 {'name': 'centre pour la communication scienti... \n", "2 93 {'name': 'texas medical center', 'alternativeN... \n", "3 68 {'name': 'university of southampton', 'alterna... \n", "4 84 {'name': 'carleton college', 'alternativeName'... \n", "\n", " name alternativeName country \\\n", "0 technische universität dortmund tu dortmund DEU \n", "1 centre pour la communication scientifique directe ccsd FRA \n", "2 texas medical center tmc USA \n", "3 university of southampton GBR \n", "4 carleton college USA \n", "\n", " url \\\n", "0 https://www.tu-dortmund.de \n", "1 https://www.ccsd.cnrs.fr \n", "2 https://www.tmc.edu \n", "3 https://www.southampton.ac.uk/ \n", "4 https://www.carleton.edu \n", "\n", " identifier location.latitude \\\n", "0 [{'identifier': 'https://ror.org/01k97gp34', '... \n", "1 [] \n", "2 [{'identifier': 'https://ror.org/00dqsbj20', '... \n", "3 [{'identifier': 'https://ror.org/01ryk1543', '... \n", "4 [{'identifier': 'https://ror.org/03jep7677', '... \n", "\n", " location.longiture \n", "0 \n", "1 \n", "2 \n", "3 \n", "4 " ] }, "execution_count": 23, "metadata": {}, "output_type": "execute_result" } ], "source": [ "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", "opendoar_institutions.head()" ] }, { "cell_type": "code", "execution_count": 24, "metadata": {}, "outputs": [], "source": [ "opendoar_institutions['org_continent'] = opendoar_institutions.country.map(countrycode_to_continent)" ] }, { "cell_type": "code", "execution_count": 25, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "array([nan, 'UMI'], dtype=object)" ] }, "execution_count": 25, "metadata": {}, "output_type": "execute_result" } ], "source": [ "opendoar_institutions[opendoar_institutions.org_continent.isna()].country.unique()" ] }, { "cell_type": "code", "execution_count": 26, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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42335379{'name': 'kettering university', 'alternativeN...kettering universityUMIhttps://www.kettering.edu[{'identifier': 'https://ror.org/03rcspa57', '...NA
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" ], "text/plain": [ " system_metadata.id organization \\\n", "4233 5379 {'name': 'kettering university', 'alternativeN... \n", "\n", " name alternativeName country url \\\n", "4233 kettering university UMI https://www.kettering.edu \n", "\n", " identifier location.latitude \\\n", "4233 [{'identifier': 'https://ror.org/03rcspa57', '... \n", "\n", " location.longiture org_continent \n", "4233 NA " ] }, "execution_count": 26, "metadata": {}, "output_type": "execute_result" } ], "source": [ "opendoar_institutions.loc[opendoar_institutions.country == 'UMI', 'org_continent'] = 'NA'\n", "opendoar_institutions[opendoar_institutions.country == 'UMI']" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "**ROAR**" ] }, { "cell_type": "code", "execution_count": 27, "metadata": {}, "outputs": [], "source": [ "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)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "**FAIRsharing**" ] }, { "cell_type": "code", "execution_count": 28, "metadata": {}, "outputs": [], "source": [ "fairsharing_countries = fairsharing_df.explode('attributes.countries')\n", "fairsharing_countries['countrycode'] = fairsharing_countries['attributes.countries'].map(country_to_countrycode)\n", "fairsharing_countries['continent'] = fairsharing_countries.countrycode.map(countrycode_to_continent)" ] }, { "cell_type": "code", "execution_count": 29, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "array(['European Union', 'Worldwide', nan], dtype=object)" ] }, "execution_count": 29, "metadata": {}, "output_type": "execute_result" } ], "source": [ "fairsharing_countries[fairsharing_countries.countrycode.isna()]['attributes.countries'].unique()" ] }, { "cell_type": "code", "execution_count": 30, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "array(['European Union', 'Worldwide', nan, 'Antarctica'], dtype=object)" ] }, "execution_count": 30, "metadata": {}, "output_type": "execute_result" } ], "source": [ "fairsharing_countries[fairsharing_countries.continent.isna()]['attributes.countries'].unique()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Fix manually some rows" ] }, { "cell_type": "code", "execution_count": 31, "metadata": {}, "outputs": [], "source": [ "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']" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Make Antactica disappear (only one repo)" ] }, { "cell_type": "code", "execution_count": 32, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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idtypeattributes.created-atattributes.updated-atattributes.metadata.doiattributes.metadata.nameattributes.metadata.statusattributes.metadata.contactsattributes.metadata.homepageattributes.metadata.identifierattributes.metadata.descriptionattributes.metadata.abbreviationattributes.metadata.support-linksattributes.metadata.year-creationattributes.metadata.data-processesattributes.metadata.cross-referencesattributes.legacy-idsattributes.fairsharing-registryattributes.record-typeattributes.subjectsattributes.domainsattributes.taxonomiesattributes.user-defined-tagsattributes.countriesattributes.nameattributes.abbreviationattributes.urlattributes.doiattributes.fairsharing-licenceattributes.descriptionattributes.publicationsattributes.licence-linksattributes.url-for-logoattributes.metadata.citationsattributes.metadata.associated-toolsattributes.metadata.deprecation-reasonattributes.metadata.data-access-condition.typeattributes.metadata.data-contact-informationattributes.metadata.data-deposition-condition.urlattributes.metadata.data-deposition-condition.typeattributes.metadata.deprecation-dateattributes.metadata.access-pointsattributes.metadata.data-access-condition.urlattributes.metadata.resource-sustainability.urlattributes.metadata.resource-sustainability.nameattributes.metadata.data-preservation-policy.urlattributes.metadata.data-preservation-policy.nameattributes.metadata.data-access-for-pre-publication-reviewattributes.metadata.data-versioningattributes.metadata.data-curation.typeattributes.metadata.data-curation.urlattributes.metadata.citation-to-related-publicationsattributes.metadata.tombstonecountrycodecontinent
3252462fairsharing-records2017-06-27T13:30:19.000Z2021-12-02T18:05:26.741Z10.25504/FAIRsharing.ewyejxAntabif IPT - AntOBIS IPT - GBIF Belgiumready[{'contact-name': 'Anton Van de Putte', 'conta...http://ipt.biodiversity.aq/2462The Belgium Biodiversity Platform hosts this d...NaN[{'url': 'a.heughebaert@biodiversity.be', 'nam...NaNNaNNaN[biodbcore-000944, bsg-d000944]Databaserepository[Biodiversity, Life Science][Taxonomic classification][All][]AntarcticaFAIRsharing record for: Antabif IPT - AntOBIS ...Nonehttps://fairsharing.org/10.25504/FAIRsharing.e...10.25504/FAIRsharing.ewyejxhttps://creativecommons.org/licenses/by-sa/4.0...This FAIRsharing record describes: The Belgium...[][{'licence-name': 'Apache License 2.0', 'licen...None[]NaNNoneNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNAQNaN
10943654fairsharing-records2021-12-02T09:58:02.958Z2021-12-07T14:13:56.118ZNaNSCAR Antarctic Biodiversity Portalready[{'contact-name': 'Anton Van de Putte', 'conta...https://www.biodiversity.aq/3654Antarctic marine and terrestrial biodiversity ...None[{'url': 'https://www.biodiversity.aq/how-to/w...2005.0[{'url': 'https://www.biodiversity.aq/find-dat...[{'url': 'https://www.re3data.org/repository/r...[]Databaseknowledgebase[Zoology, Taxonomy, Ecology, Biodiversity, Oce...[][All][]AntarcticaFAIRsharing record for: SCAR Antarctic Biodive...Nonehttps://fairsharing.org/fairsharing_records/3654Nonehttps://creativecommons.org/licenses/by-sa/4.0...This FAIRsharing record describes: Antarctic m...[][{'licence-name': 'SCAR Antarctic Biodiversity...None[][{'url': 'https://www.biodiversity.aq/tools/r-...NaNNaNNaNNaNNaN[{'url': 'https://data.biodiversity.aq/api/v1....NaNNaNNaNNaNNaNNaNNaNNaNNaNNaNNaNAQNaN
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" ], "text/plain": [ " id type attributes.created-at \\\n", "325 2462 fairsharing-records 2017-06-27T13:30:19.000Z \n", "1094 3654 fairsharing-records 2021-12-02T09:58:02.958Z \n", "\n", " attributes.updated-at attributes.metadata.doi \\\n", "325 2021-12-02T18:05:26.741Z 10.25504/FAIRsharing.ewyejx \n", "1094 2021-12-07T14:13:56.118Z NaN \n", "\n", " attributes.metadata.name attributes.metadata.status \\\n", "325 Antabif IPT - AntOBIS IPT - GBIF Belgium ready \n", "1094 SCAR Antarctic Biodiversity Portal ready \n", "\n", " attributes.metadata.contacts \\\n", "325 [{'contact-name': 'Anton Van de Putte', 'conta... \n", "1094 [{'contact-name': 'Anton Van de Putte', 'conta... \n", "\n", " attributes.metadata.homepage attributes.metadata.identifier \\\n", "325 http://ipt.biodiversity.aq/ 2462 \n", "1094 https://www.biodiversity.aq/ 3654 \n", "\n", " attributes.metadata.description \\\n", "325 The Belgium Biodiversity Platform hosts this d... \n", "1094 Antarctic marine and terrestrial biodiversity ... \n", "\n", " attributes.metadata.abbreviation \\\n", "325 NaN \n", "1094 None \n", "\n", " attributes.metadata.support-links \\\n", "325 [{'url': 'a.heughebaert@biodiversity.be', 'nam... \n", "1094 [{'url': 'https://www.biodiversity.aq/how-to/w... \n", "\n", " attributes.metadata.year-creation \\\n", "325 NaN \n", "1094 2005.0 \n", "\n", " attributes.metadata.data-processes \\\n", "325 NaN \n", "1094 [{'url': 'https://www.biodiversity.aq/find-dat... \n", "\n", " attributes.metadata.cross-references \\\n", "325 NaN \n", "1094 [{'url': 'https://www.re3data.org/repository/r... \n", "\n", " attributes.legacy-ids attributes.fairsharing-registry \\\n", "325 [biodbcore-000944, bsg-d000944] Database \n", "1094 [] Database \n", "\n", " attributes.record-type \\\n", "325 repository \n", "1094 knowledgebase \n", "\n", " attributes.subjects \\\n", "325 [Biodiversity, Life Science] \n", "1094 [Zoology, Taxonomy, Ecology, Biodiversity, Oce... \n", "\n", " attributes.domains attributes.taxonomies \\\n", "325 [Taxonomic classification] [All] \n", "1094 [] [All] \n", "\n", " attributes.user-defined-tags attributes.countries \\\n", "325 [] Antarctica \n", "1094 [] Antarctica \n", "\n", " attributes.name \\\n", "325 FAIRsharing record for: Antabif IPT - AntOBIS ... \n", "1094 FAIRsharing record for: SCAR Antarctic Biodive... \n", "\n", " attributes.abbreviation \\\n", "325 None \n", "1094 None \n", "\n", " attributes.url \\\n", "325 https://fairsharing.org/10.25504/FAIRsharing.e... \n", "1094 https://fairsharing.org/fairsharing_records/3654 \n", "\n", " attributes.doi \\\n", "325 10.25504/FAIRsharing.ewyejx \n", "1094 None \n", "\n", " attributes.fairsharing-licence \\\n", "325 https://creativecommons.org/licenses/by-sa/4.0... \n", "1094 https://creativecommons.org/licenses/by-sa/4.0... \n", "\n", " attributes.description \\\n", "325 This FAIRsharing record describes: The Belgium... \n", "1094 This FAIRsharing record describes: Antarctic m... \n", "\n", " attributes.publications \\\n", "325 [] \n", "1094 [] \n", "\n", " attributes.licence-links \\\n", "325 [{'licence-name': 'Apache License 2.0', 'licen... \n", "1094 [{'licence-name': 'SCAR Antarctic Biodiversity... \n", "\n", " attributes.url-for-logo attributes.metadata.citations \\\n", "325 None [] \n", "1094 None [] \n", "\n", " attributes.metadata.associated-tools \\\n", "325 NaN \n", "1094 [{'url': 'https://www.biodiversity.aq/tools/r-... \n", "\n", " attributes.metadata.deprecation-reason \\\n", "325 None \n", "1094 \n", "\n", " attributes.metadata.data-access-condition.type \\\n", "325 NaN \n", "1094 NaN \n", "\n", " attributes.metadata.data-contact-information \\\n", "325 NaN \n", "1094 NaN \n", "\n", " attributes.metadata.data-deposition-condition.url \\\n", "325 NaN \n", "1094 NaN \n", "\n", " attributes.metadata.data-deposition-condition.type \\\n", "325 NaN \n", "1094 NaN \n", "\n", " attributes.metadata.deprecation-date \\\n", "325 NaN \n", "1094 NaN \n", "\n", " attributes.metadata.access-points \\\n", "325 NaN \n", "1094 [{'url': 'https://data.biodiversity.aq/api/v1.... \n", "\n", " attributes.metadata.data-access-condition.url \\\n", "325 NaN \n", "1094 NaN \n", "\n", " attributes.metadata.resource-sustainability.url \\\n", "325 NaN \n", "1094 NaN \n", "\n", " attributes.metadata.resource-sustainability.name \\\n", "325 NaN \n", "1094 NaN \n", "\n", " attributes.metadata.data-preservation-policy.url \\\n", "325 NaN \n", "1094 NaN \n", "\n", " attributes.metadata.data-preservation-policy.name \\\n", "325 NaN \n", "1094 NaN \n", "\n", " attributes.metadata.data-access-for-pre-publication-review \\\n", "325 NaN \n", "1094 NaN \n", "\n", " attributes.metadata.data-versioning \\\n", "325 NaN \n", "1094 NaN \n", "\n", " attributes.metadata.data-curation.type \\\n", "325 NaN \n", "1094 NaN \n", "\n", " attributes.metadata.data-curation.url \\\n", "325 NaN \n", "1094 NaN \n", "\n", " attributes.metadata.citation-to-related-publications \\\n", "325 NaN \n", "1094 NaN \n", "\n", " attributes.metadata.tombstone countrycode continent \n", "325 NaN AQ NaN \n", "1094 NaN AQ NaN " ] }, "execution_count": 32, "metadata": {}, "output_type": "execute_result" } ], "source": [ "fairsharing_countries.loc[fairsharing_countries['attributes.countries'] == 'Antarctica', ['countrycode', 'continent']] = ['AQ', np.nan]\n", "fairsharing_countries[fairsharing_countries.countrycode == 'AQ']" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Country coverage" ] }, { "cell_type": "code", "execution_count": 33, "metadata": {}, "outputs": [ { "data": { "application/vnd.plotly.v1+json": { "config": { "plotlyServerURL": "https://plot.ly" }, "data": [ { "name": "re3data", "type": "bar", "x": [ "USA", "DEU", "CAN", "GBR", "EEC", "AAA", "FRA", "AUS", "CHE", "JPN", "NLD", "ESP", "IND", "CHN", "ITA", "NOR", "AUT", "SWE", "BEL", "DNK", "RUS", "POL", "GRC", "MEX", "IRL", "ZAF", "CZE", "TWN", "NZL", "BRA", "PRT", "FIN", "EST", "KOR", "COL", "SRB", "ISR", "LTU", "SGP", "ARG", "HUN", "TUR", "SVN", "ISL", "KEN", "HKG", "UKR", "ROU", "IDN", "SVK", "LUX", "PAK", "PER", "LVA", "THA", "CYP", "CHL", "HRV", "GRL", "CMR", "SDN", "VNM", "GHA", "LBN", "BFA", "BEN", "PAN", "MKD", "PHL", "BIH", "FJI", "ETH", "KAZ", "CIV", "LAO", "TUN", "MWI", "LKA", "NAM", "NCL", "SEN", "AZE", "SAU", "PYF", "EGY" ], "y": [ 2993, 1154, 601, 577, 404, 349, 279, 240, 134, 133, 131, 100, 87, 76, 66, 62, 61, 60, 46, 40, 36, 34, 31, 24, 22, 22, 22, 19, 19, 19, 18, 18, 14, 14, 13, 13, 13, 11, 11, 10, 9, 7, 7, 6, 6, 6, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 ] }, { "name": "openDOAR", "type": "bar", "visible": "legendonly", "x": [ "USA", "JPN", "GBR", "DEU", "ESP", "PER", "TUR", "IDN", "FRA", "BRA", "HRV", "ITA", "POL", "UKR", "IND", "COL", "CAN", "AUS", "NLD", "ARG", "NOR", "CHN", "PRT", "TWN", "MEX", "RUS", "SWE", "SRB", "ZAF", "AUT", "HUN", "KEN", "GRC", "BLR", "CHE", "ECU", "KOR", "BEL", "NGA", "IRL", "CHL", "CZE", "MYS", "FIN", "DZA", "NZL", "LTU", "IRN", "THA", "VEN", "LKA", "BGD", "DNK", "CUB", "TZA", "SVN", "SDN", "KAZ", "MDA", "SAU", "UGA", "NIC", "ZWE", "BGR", "URY", "HKG", "CRI", "PHL", "SLV", "EGY", "EST", "PSE", "SGP", "JAM", "CYP", "GHA", "PAN", "ROU", "ETH", "MKD", "ARE", "LVA", "HND", "PAK", "SEN", "SVK", "ISL", "DOM", "LUX", "LBN", "GEO", "ZMB", "BOL", "LBY", "IRQ", "MMR", "MAR", "BWA", "FJI", "AZE", "LSO", "NAM", "ARM", "RWA", "PRY", "BIH", "TUN", "MOZ", "CPV", "UMI", "TTO", "TJK", "VNM", "AFG", "SOM", "QAT", "PRI", "NPL", "NCL", "MWI", "MLT", "ALA", "KWT", "KGZ", "GTM", "GLP", "CMR", "AND", "ALB", "LAO" ], "y": [ 919, 681, 317, 281, 178, 173, 172, 163, 161, 154, 148, 140, 128, 106, 102, 100, 99, 89, 74, 73, 67, 64, 62, 60, 51, 50, 50, 48, 48, 47, 45, 44, 39, 38, 38, 38, 37, 33, 30, 30, 27, 27, 25, 23, 20, 19, 19, 18, 17, 16, 16, 15, 15, 14, 14, 13, 12, 12, 12, 12, 12, 11, 11, 11, 10, 10, 10, 9, 9, 9, 9, 8, 7, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 ] }, { "name": "ROAR", "type": "bar", "visible": "legendonly", "x": [ "USA", "DEU", "GBR", "JPN", "ESP", "BRA", "IDN", "TUR", "PER", "IND", "COL", "POL", "UKR", "FRA", "ITA", "CHN", "CAN", "AUS", "TWN", "SWE", "ARG", "RUS", "PRT", "NOR", "MEX", "KOR", "ZAF", "HUN", "NLD", "MYS", "GRC", "SRB", "BEL", "BLR", "ECU", "KEN", "CHE", "IRL", "AUT", "CHL", "VEN", "FIN", "NZL", "MDA", "NGA", "ROU", "DNK", "DZA", "CZE", "IRN", "PHL", "THA", "CUB", "SDN", "SLV", "ZWE", "EGY", "BGD", "BGR", "LTU", "SVN", "KAZ", "HKG", "SAU", "CRI", "TZA", "UGA", "PAK", "PSE", "NIC", "CYP", "URY", "HRV", "SGP", "EST", "GHA", "AZE", "PAN", "LVA", "JAM", "BWA", "KGZ", "DOM", "MAR", "IRQ", "LBN", "ETH", "BOL", "NPL", "BIH", "MKD", "LKA", "LBY", "SVK", "GUF", "TUN", "NAM", "ARM", "SEN", "ARE", "GLP", "MOZ", "FJI", "DMA", "LSO", "LUX", "MTQ", "GEO", "ISL", "UMI", "ATF", "WSM", "ISR", "SYR", "SOM", "CMR", "RWA", "QAT", "PYF", "PRK", "PRI", "NCL", "MWI", "MLT", "HND", "ALB", "AFG" ], "y": [ 896, 263, 262, 244, 202, 186, 181, 167, 161, 133, 131, 128, 120, 102, 99, 97, 97, 84, 83, 76, 72, 68, 62, 59, 54, 53, 52, 46, 46, 42, 42, 41, 37, 35, 32, 30, 30, 27, 27, 27, 24, 23, 22, 19, 17, 17, 17, 16, 16, 16, 15, 15, 14, 13, 13, 12, 12, 11, 11, 11, 10, 10, 10, 10, 9, 9, 8, 7, 7, 7, 7, 7, 7, 6, 6, 6, 5, 5, 5, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 ] }, { "name": "FAIRsharing", "type": "bar", "visible": "legendonly", "x": [ "USA", "GBR", "DEU", "FRA", "CHE", "NLD", "CHN", "ITA", "ESP", "CAN", "BEL", "JPN", "SWE", "NOR", "EU", "CZE", "DNK", "AUT", "AUS", "FIN", "PRT", "IRL", "ISR", "HUN", "GRC", "LUX", "MLT", "HRV", "LTU", "ISL", "SVK", "MNE", "IND", "POL", "SGP", "KOR", "RUS", "TWN", "MEX", "ZAF", "BRA", "NZL", "SAU", "BGR", "TUR", "ARG", "HKG", "EST", "PAK", "ROU", "UGA", "THA", "AQ", 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" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "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", "\n", "plot = [\n", " go.Bar(\n", " x=data1.index,\n", " y=data1['orgIdentifier'],\n", " name='re3data'\n", " ),\n", " go.Bar(\n", " x=data2.index,\n", " y=data2['system_metadata.id'],\n", " name='openDOAR',\n", " visible = 'legendonly'\n", " ),\n", " go.Bar(\n", " x=data3.index,\n", " y=data3['eprintid'],\n", " name='ROAR',\n", " visible = 'legendonly'\n", " ),\n", " go.Bar(\n", " x=data4.index,\n", " y=data4['id'],\n", 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" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "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", "\n", "plot = [\n", " go.Scatterpolar(\n", " r=data1.orgIdentifier,\n", " theta=data1.index,\n", " fill='toself',\n", " name='re3data'),\n", " go.Scatterpolar(\n", " r=data2['system_metadata.id'],\n", " theta=data2.index,\n", " fill='toself',\n", " name='OpenDOAR'),\n", " go.Scatterpolar(\n", " r=data3.eprintid,\n", " theta=data3.index,\n", " fill='toself',\n", " name='ROAR'),\n", " go.Scatterpolar(\n", " r=data4.id,\n", " theta=data4.index,\n", " fill='toself',\n", " name='FAIRsharing')\n", "]\n", "\n", "layout = go.Layout(polar=dict(\n", " radialaxis=dict(\n", " visible=True\n", " ),\n", " )\n", ")\n", "\n", "go.Figure(plot, layout).show()" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.8.3" } }, "nbformat": 4, "nbformat_minor": 4 }