{ "cells": [ { "cell_type": "code", "execution_count": 13, "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": 14, "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": 15, "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 [58, 669] NaN NaN NaN \n", "1 [526, 258] NaN NaN NaN \n", "2 NaN NaN NaN NaN \n", "3 [5881, 3408] 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": 19, "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": 20, "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.support-linksattributes.metadata.year-creationattributes.metadata.data-processesattributes.legacy-idsattributes.fairsharing-registryattributes.record-typeattributes.subjectsattributes.domainsattributes.taxonomiesattributes.user-defined-tagsattributes.countriesattributes.nameattributes.abbreviationattributes.urlattributes.doiattributes.fairsharing-licenceattributes.descriptionattributes.publicationsattributes.licence-linksattributes.metadata.citationsattributes.metadata.abbreviationattributes.metadata.access-pointsattributes.metadata.associated-toolsattributes.metadata.deprecation-dateattributes.metadata.deprecation-reasonattributes.metadata.tombstone
01723fairsharing-records2014-11-04T15:23:40.000Z2021-09-30T11:39:06.829Z10.25504/FAIRsharing.8t18teCell Image Libraryready[{'contact-name': 'David Orloff', 'contact-ema...http://www.cellimagelibrary.org1723This library is a public and easily accessible...[{'url': 'http://www.cellimagelibrary.org/page...2010.0[{'name': 'live update', 'type': 'data release...[biodbcore-000180, bsg-d000180]Databaserepository[Cell Biology, Life Science][Cell, Microscopy, Light microscopy, Electron ...[All][][United States]FAIRsharing record for: Cell Image LibraryNonehttps://fairsharing.org/10.25504/FAIRsharing.8...10.25504/FAIRsharing.8t18tehttps://creativecommons.org/licenses/by-sa/4.0...This FAIRsharing record describes: This librar...[{'id': 232, 'pubmed_id': 23203874, 'title': '...[{'licence-name': 'Cell Image Library Data Pol...NaNNaNNaNNaNNaNNaNNaN
13101fairsharing-records2020-09-16T08:49:13.000Z2021-09-30T11:36:45.452ZNaNWHOI Ship Data-Grabber SystemreadyNaNhttp://4dgeo.whoi.edu/shipdata/SDG_shipdata.html3101The WHOI Ship DataGrabber system provides the ...[{'url': 'http://4dgeo.whoi.edu/shipdata/SDG_o...2004.0[{'url': 'http://4dgeo.whoi.edu/sdg-bin/dv_mai...[biodbcore-001609, bsg-d001609]Databaserepository[Earth Science, Water Research, Oceanography][][Not applicable][subseafloor environments][United States]FAIRsharing record for: WHOI Ship Data-Grabber...Nonehttps://fairsharing.org/fairsharing_records/3101Nonehttps://creativecommons.org/licenses/by-sa/4.0...This FAIRsharing record describes: The WHOI Sh...[][{'licence-name': 'NDSF Data Archive Policy', ...NaNNaNNaNNaNNaNNaNNaN
22649fairsharing-records2018-08-07T20:23:32.000Z2021-09-30T11:39:07.898ZNaNElectron Microscope Public Image Archiveready[{'contact-name': 'General contact', 'contact-...https://www.ebi.ac.uk/pdbe/emdb/empiar/2649EMPIAR, the Electron Microscopy Public Image A...[{'url': 'https://www.ebi.ac.uk/support/EMPIAR...2015.0[{'url': 'https://www.ebi.ac.uk/pdbe/emdb/empi...[biodbcore-001140, bsg-d001140]Databaserepository[Bioinformatics, Biology][Protein image, Microscopy, Electron microscop...[All][][Greece, Czech Republic, United Kingdom, Icela...FAIRsharing record for: Electron Microscope Pu...EMPIARhttps://fairsharing.org/fairsharing_records/2649Nonehttps://creativecommons.org/licenses/by-sa/4.0...This FAIRsharing record describes: EMPIAR, the...[{'id': 2232, 'pubmed_id': 27067018, 'title': ...[{'licence-name': 'EMBL-EBI Terms of Use', 'li...[{'doi': '10.1038/nmeth.3806', 'pubmed-id': 27...EMPIAR[{'url': 'https://www.ebi.ac.uk/pdbe/emdb/empi...[{'url': 'https://www.ebi.ac.uk/pdbe/emdb/empi...NaNNaNNaN
32657fairsharing-records2018-08-13T15:12:11.000Z2021-09-30T11:37:28.736Z10.25504/FAIRsharing.tnByoGClinicalStudyDataRequest.comready[{'contact-email': 'support@clinicalstudydatar...https://clinicalstudydatarequest.com/2657ClinicalStudyDataRequest.com (CSDR) is a conso...[{'url': 'https://clinicalstudydatarequest.com...2014.0[{'url': 'https://clinicalstudydatarequest.com...[biodbcore-001149, bsg-d001149]Databaserepository[Preclinical Studies, Biomedical Science][][Homo sapiens][][Worldwide]FAIRsharing record for: ClinicalStudyDataReque...CSDRhttps://fairsharing.org/10.25504/FAIRsharing.t...10.25504/FAIRsharing.tnByoGhttps://creativecommons.org/licenses/by-sa/4.0...This FAIRsharing record describes: ClinicalStu...[][{'licence-name': 'CSDR Data Sharing Agreement...NaNCSDRNaNNaNNaNNaNNaN
42078fairsharing-records2014-11-04T15:23:40.000Z2021-09-30T11:34:43.129Z10.25504/FAIRsharing.3axym7Germplasm Resources Information Networkready[{'contact-email': 'dbmu@ars-grin.gov'}]https://www.ars-grin.gov/2078GRIN provides National Genetic Resources Progr...[{'url': 'https://www.ars-grin.gov/Pages/Colle...2010.0[{'url': 'https://www.ars-grin.gov/', 'name': ...[biodbcore-000546, bsg-d000546]Databaserepository[Life Science][Cell, Cell culture, Germplasm][Bacteria, Metazoa, Viridiplantae][][United States]FAIRsharing record for: Germplasm Resources In...GRINhttps://fairsharing.org/10.25504/FAIRsharing.3...10.25504/FAIRsharing.3axym7https://creativecommons.org/licenses/by-sa/4.0...This FAIRsharing record describes: GRIN provid...[][]NaNGRINNaNNaNNaNNaNNaN
\n", "" ], "text/plain": [ " id type attributes.created-at \\\n", "0 1723 fairsharing-records 2014-11-04T15:23:40.000Z \n", "1 3101 fairsharing-records 2020-09-16T08:49:13.000Z \n", "2 2649 fairsharing-records 2018-08-07T20:23:32.000Z \n", "3 2657 fairsharing-records 2018-08-13T15:12:11.000Z \n", "4 2078 fairsharing-records 2014-11-04T15:23:40.000Z \n", "\n", " attributes.updated-at attributes.metadata.doi \\\n", "0 2021-09-30T11:39:06.829Z 10.25504/FAIRsharing.8t18te \n", "1 2021-09-30T11:36:45.452Z NaN \n", "2 2021-09-30T11:39:07.898Z NaN \n", "3 2021-09-30T11:37:28.736Z 10.25504/FAIRsharing.tnByoG \n", "4 2021-09-30T11:34:43.129Z 10.25504/FAIRsharing.3axym7 \n", "\n", " attributes.metadata.name attributes.metadata.status \\\n", "0 Cell Image Library ready \n", "1 WHOI Ship Data-Grabber System ready \n", "2 Electron Microscope Public Image Archive ready \n", "3 ClinicalStudyDataRequest.com ready \n", "4 Germplasm Resources Information Network ready \n", "\n", " attributes.metadata.contacts \\\n", "0 [{'contact-name': 'David Orloff', 'contact-ema... \n", "1 NaN \n", "2 [{'contact-name': 'General contact', 'contact-... \n", "3 [{'contact-email': 'support@clinicalstudydatar... \n", "4 [{'contact-email': 'dbmu@ars-grin.gov'}] \n", "\n", " attributes.metadata.homepage \\\n", "0 http://www.cellimagelibrary.org \n", "1 http://4dgeo.whoi.edu/shipdata/SDG_shipdata.html \n", "2 https://www.ebi.ac.uk/pdbe/emdb/empiar/ \n", "3 https://clinicalstudydatarequest.com/ \n", "4 https://www.ars-grin.gov/ \n", "\n", " attributes.metadata.identifier \\\n", "0 1723 \n", "1 3101 \n", "2 2649 \n", "3 2657 \n", "4 2078 \n", "\n", " attributes.metadata.description \\\n", "0 This library is a public and easily accessible... \n", "1 The WHOI Ship DataGrabber system provides the ... \n", "2 EMPIAR, the Electron Microscopy Public Image A... \n", "3 ClinicalStudyDataRequest.com (CSDR) is a conso... \n", "4 GRIN provides National Genetic Resources Progr... \n", "\n", " attributes.metadata.support-links \\\n", "0 [{'url': 'http://www.cellimagelibrary.org/page... \n", "1 [{'url': 'http://4dgeo.whoi.edu/shipdata/SDG_o... \n", "2 [{'url': 'https://www.ebi.ac.uk/support/EMPIAR... \n", "3 [{'url': 'https://clinicalstudydatarequest.com... \n", "4 [{'url': 'https://www.ars-grin.gov/Pages/Colle... \n", "\n", " attributes.metadata.year-creation \\\n", "0 2010.0 \n", "1 2004.0 \n", "2 2015.0 \n", "3 2014.0 \n", "4 2010.0 \n", "\n", " attributes.metadata.data-processes \\\n", "0 [{'name': 'live update', 'type': 'data release... \n", "1 [{'url': 'http://4dgeo.whoi.edu/sdg-bin/dv_mai... \n", "2 [{'url': 'https://www.ebi.ac.uk/pdbe/emdb/empi... \n", "3 [{'url': 'https://clinicalstudydatarequest.com... \n", "4 [{'url': 'https://www.ars-grin.gov/', 'name': ... \n", "\n", " attributes.legacy-ids attributes.fairsharing-registry \\\n", "0 [biodbcore-000180, bsg-d000180] Database \n", "1 [biodbcore-001609, bsg-d001609] Database \n", "2 [biodbcore-001140, bsg-d001140] Database \n", "3 [biodbcore-001149, bsg-d001149] Database \n", "4 [biodbcore-000546, bsg-d000546] Database \n", "\n", " attributes.record-type attributes.subjects \\\n", "0 repository [Cell Biology, Life Science] \n", "1 repository [Earth Science, Water Research, Oceanography] \n", "2 repository [Bioinformatics, Biology] \n", "3 repository [Preclinical Studies, Biomedical Science] \n", "4 repository [Life Science] \n", "\n", " attributes.domains \\\n", "0 [Cell, Microscopy, Light microscopy, Electron ... \n", "1 [] \n", "2 [Protein image, Microscopy, Electron microscop... \n", "3 [] \n", "4 [Cell, Cell culture, Germplasm] \n", "\n", " attributes.taxonomies attributes.user-defined-tags \\\n", "0 [All] [] \n", "1 [Not applicable] [subseafloor environments] \n", "2 [All] [] \n", "3 [Homo sapiens] [] \n", "4 [Bacteria, Metazoa, Viridiplantae] [] \n", "\n", " attributes.countries \\\n", "0 [United States] \n", "1 [United States] \n", "2 [Greece, Czech Republic, United Kingdom, Icela... \n", "3 [Worldwide] \n", "4 [United States] \n", "\n", " attributes.name attributes.abbreviation \\\n", "0 FAIRsharing record for: Cell Image Library None \n", "1 FAIRsharing record for: WHOI Ship Data-Grabber... None \n", "2 FAIRsharing record for: Electron Microscope Pu... EMPIAR \n", "3 FAIRsharing record for: ClinicalStudyDataReque... CSDR \n", "4 FAIRsharing record for: Germplasm Resources In... GRIN \n", "\n", " attributes.url \\\n", "0 https://fairsharing.org/10.25504/FAIRsharing.8... \n", "1 https://fairsharing.org/fairsharing_records/3101 \n", "2 https://fairsharing.org/fairsharing_records/2649 \n", "3 https://fairsharing.org/10.25504/FAIRsharing.t... \n", "4 https://fairsharing.org/10.25504/FAIRsharing.3... \n", "\n", " attributes.doi \\\n", "0 10.25504/FAIRsharing.8t18te \n", "1 None \n", "2 None \n", "3 10.25504/FAIRsharing.tnByoG \n", "4 10.25504/FAIRsharing.3axym7 \n", "\n", " attributes.fairsharing-licence \\\n", "0 https://creativecommons.org/licenses/by-sa/4.0... \n", "1 https://creativecommons.org/licenses/by-sa/4.0... \n", "2 https://creativecommons.org/licenses/by-sa/4.0... \n", "3 https://creativecommons.org/licenses/by-sa/4.0... \n", "4 https://creativecommons.org/licenses/by-sa/4.0... \n", "\n", " attributes.description \\\n", "0 This FAIRsharing record describes: This librar... \n", "1 This FAIRsharing record describes: The WHOI Sh... \n", "2 This FAIRsharing record describes: EMPIAR, the... \n", "3 This FAIRsharing record describes: ClinicalStu... \n", "4 This FAIRsharing record describes: GRIN provid... \n", "\n", " attributes.publications \\\n", "0 [{'id': 232, 'pubmed_id': 23203874, 'title': '... \n", "1 [] \n", "2 [{'id': 2232, 'pubmed_id': 27067018, 'title': ... \n", "3 [] \n", "4 [] \n", "\n", " attributes.licence-links \\\n", "0 [{'licence-name': 'Cell Image Library Data Pol... \n", "1 [{'licence-name': 'NDSF Data Archive Policy', ... \n", "2 [{'licence-name': 'EMBL-EBI Terms of Use', 'li... \n", "3 [{'licence-name': 'CSDR Data Sharing Agreement... \n", "4 [] \n", "\n", " attributes.metadata.citations \\\n", "0 NaN \n", "1 NaN \n", "2 [{'doi': '10.1038/nmeth.3806', 'pubmed-id': 27... \n", "3 NaN \n", "4 NaN \n", "\n", " attributes.metadata.abbreviation \\\n", "0 NaN \n", "1 NaN \n", "2 EMPIAR \n", "3 CSDR \n", "4 GRIN \n", "\n", " attributes.metadata.access-points \\\n", "0 NaN \n", "1 NaN \n", "2 [{'url': 'https://www.ebi.ac.uk/pdbe/emdb/empi... \n", "3 NaN \n", "4 NaN \n", "\n", " attributes.metadata.associated-tools \\\n", "0 NaN \n", "1 NaN \n", "2 [{'url': 'https://www.ebi.ac.uk/pdbe/emdb/empi... \n", "3 NaN \n", "4 NaN \n", "\n", " attributes.metadata.deprecation-date attributes.metadata.deprecation-reason \\\n", "0 NaN NaN \n", "1 NaN NaN \n", "2 NaN NaN \n", "3 NaN NaN \n", "4 NaN NaN \n", "\n", " attributes.metadata.tombstone \n", "0 NaN \n", "1 NaN \n", "2 NaN \n", "3 NaN \n", "4 NaN " ] }, "execution_count": 21, "metadata": {}, "output_type": "execute_result" } ], "source": [ "with open('../data/raw/fairsharing_dump_api_09_2021.json') as f:\n", " lines = f.read().splitlines()\n", " \n", "fairsharing_df = pd.DataFrame(lines)\n", "fairsharing_df.columns = ['json_element']\n", "fairsharing_df['json_element'].apply(json.loads)\n", "fairsharing_df = pd.json_normalize(fairsharing_df['json_element'].apply(json.loads))\n", "\n", "fairsharing_df.head()" ] }, { "cell_type": "code", "execution_count": 22, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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" ], "text/plain": [ " id type attributes.created-at \\\n", "count 1797 1797 1797 \n", "unique 1797 1 1162 \n", "top 1723 fairsharing-records 2014-11-04T15:23:40.000Z \n", "freq 1 1797 636 \n", "mean NaN NaN NaN \n", "std NaN NaN NaN \n", "min NaN NaN NaN \n", "25% NaN NaN NaN \n", "50% NaN NaN NaN \n", "75% NaN NaN NaN \n", "max NaN NaN NaN \n", "\n", " attributes.updated-at attributes.metadata.doi \\\n", "count 1797 1354 \n", "unique 1797 1354 \n", "top 2021-09-30T11:39:06.829Z 10.25504/FAIRsharing.8t18te \n", "freq 1 1 \n", "mean NaN NaN \n", "std NaN NaN \n", "min NaN NaN \n", "25% NaN NaN \n", "50% NaN NaN \n", "75% NaN NaN \n", "max NaN NaN \n", "\n", " attributes.metadata.name attributes.metadata.status \\\n", "count 1797 1797 \n", "unique 1796 4 \n", "top OmicsDB ready \n", "freq 2 1540 \n", "mean NaN NaN \n", "std NaN NaN \n", "min NaN NaN \n", "25% NaN NaN \n", "50% NaN NaN \n", "75% NaN NaN \n", "max NaN NaN \n", "\n", " attributes.metadata.contacts \\\n", "count 1678 \n", "unique 1576 \n", "top [{'contact-name': 'Sam Hokin', 'contact-email'... \n", "freq 6 \n", "mean NaN \n", "std NaN \n", "min NaN \n", "25% NaN \n", "50% NaN \n", "75% NaN \n", "max NaN \n", "\n", " attributes.metadata.homepage attributes.metadata.identifier \\\n", "count 1797 1797.000000 \n", "unique 1797 NaN \n", "top http://www.cellimagelibrary.org NaN \n", "freq 1 NaN \n", "mean NaN 2446.100167 \n", "std NaN 520.058757 \n", "min NaN 1547.000000 \n", "25% NaN 1996.000000 \n", "50% NaN 2445.000000 \n", "75% NaN 2897.000000 \n", "max NaN 3346.000000 \n", "\n", " attributes.metadata.description \\\n", "count 1797 \n", "unique 1797 \n", "top This library is a public and easily accessible... \n", "freq 1 \n", "mean NaN \n", "std NaN \n", "min NaN \n", "25% NaN \n", "50% NaN \n", "75% NaN \n", "max NaN \n", "\n", " attributes.metadata.support-links \\\n", "count 1608 \n", "unique 1594 \n", "top [{'url': 'https://github.com/gbif/ipt/wiki/IPT... \n", "freq 6 \n", "mean NaN \n", "std NaN \n", "min NaN \n", "25% NaN \n", "50% NaN \n", "75% NaN \n", "max NaN \n", "\n", " attributes.metadata.year-creation \\\n", "count 1492.000000 \n", "unique NaN \n", "top NaN \n", "freq NaN \n", "mean 2007.636059 \n", "std 10.953269 \n", "min 1894.000000 \n", "25% 2004.000000 \n", "50% 2010.000000 \n", "75% 2014.000000 \n", "max 2021.000000 \n", "\n", " attributes.metadata.data-processes \\\n", "count 1565 \n", "unique 1563 \n", "top [{'url': 'http://qf.iodp.tamu.edu/qfsearch/sea... \n", "freq 2 \n", "mean NaN \n", "std NaN \n", "min NaN \n", "25% NaN \n", "50% NaN \n", "75% NaN \n", "max NaN \n", "\n", " attributes.legacy-ids attributes.fairsharing-registry \\\n", "count 1797 1797 \n", "unique 1797 1 \n", "top [biodbcore-000180, bsg-d000180] Database \n", "freq 1 1797 \n", "mean NaN NaN \n", "std NaN NaN \n", "min NaN NaN \n", "25% NaN NaN \n", "50% NaN NaN \n", "75% NaN NaN \n", "max NaN NaN \n", "\n", " attributes.record-type attributes.subjects attributes.domains \\\n", "count 1797 1797 1797 \n", "unique 3 888 1163 \n", "top repository [Life Science] [] \n", "freq 926 350 265 \n", "mean NaN NaN NaN \n", "std NaN NaN NaN \n", "min NaN NaN NaN \n", "25% NaN NaN NaN \n", "50% NaN NaN NaN \n", "75% NaN NaN NaN \n", "max NaN NaN NaN \n", "\n", " attributes.taxonomies attributes.user-defined-tags \\\n", "count 1797 1797 \n", "unique 378 384 \n", "top [All] [] \n", "freq 502 1193 \n", "mean NaN NaN \n", "std NaN NaN \n", "min NaN NaN \n", "25% NaN NaN \n", "50% NaN NaN \n", "75% NaN NaN \n", "max NaN NaN \n", "\n", " attributes.countries attributes.name \\\n", "count 1797 1797 \n", "unique 185 1796 \n", "top [United States] FAIRsharing record for: OmicsDB \n", "freq 594 2 \n", "mean NaN NaN \n", "std NaN NaN \n", "min NaN NaN \n", "25% NaN NaN \n", "50% NaN NaN \n", "75% NaN NaN \n", "max NaN NaN \n", "\n", " attributes.abbreviation \\\n", "count 1638 \n", "unique 1626 \n", "top CGD \n", "freq 3 \n", "mean NaN \n", "std NaN \n", "min NaN \n", "25% NaN \n", "50% NaN \n", "75% NaN \n", "max NaN \n", "\n", " attributes.url \\\n", "count 1797 \n", "unique 1797 \n", "top https://fairsharing.org/10.25504/FAIRsharing.8... \n", "freq 1 \n", "mean NaN \n", "std NaN \n", "min NaN \n", "25% NaN \n", "50% NaN \n", "75% NaN \n", "max NaN \n", "\n", " attributes.doi \\\n", "count 1354 \n", "unique 1354 \n", "top 10.25504/FAIRsharing.8t18te \n", "freq 1 \n", "mean NaN \n", "std NaN \n", "min NaN \n", "25% NaN \n", "50% NaN \n", "75% NaN \n", "max NaN \n", "\n", " attributes.fairsharing-licence \\\n", "count 1797 \n", "unique 1 \n", "top https://creativecommons.org/licenses/by-sa/4.0... \n", "freq 1797 \n", "mean NaN \n", "std NaN \n", "min NaN \n", "25% NaN \n", "50% NaN \n", "75% NaN \n", "max NaN \n", "\n", " attributes.description \\\n", "count 1797 \n", "unique 1797 \n", "top This FAIRsharing record describes: This librar... \n", "freq 1 \n", "mean NaN \n", "std NaN \n", "min NaN \n", "25% NaN \n", "50% NaN \n", "75% NaN \n", "max NaN \n", "\n", " attributes.publications attributes.licence-links \\\n", "count 1797 1797 \n", "unique 1109 1082 \n", "top [] [] \n", "freq 661 716 \n", "mean NaN NaN \n", "std NaN NaN \n", "min NaN NaN \n", "25% NaN NaN \n", "50% NaN NaN \n", "75% NaN NaN \n", "max NaN NaN \n", "\n", " attributes.metadata.citations \\\n", "count 326 \n", "unique 320 \n", "top [{'doi': '10.1093/nar/gkz890', 'pubmed-id': 31... \n", "freq 6 \n", "mean NaN \n", "std NaN \n", "min NaN \n", "25% NaN \n", "50% NaN \n", "75% NaN \n", "max NaN \n", "\n", " attributes.metadata.abbreviation \\\n", "count 1638 \n", "unique 1626 \n", "top CGD \n", "freq 3 \n", "mean NaN \n", "std NaN \n", "min NaN \n", "25% NaN \n", "50% NaN \n", "75% NaN \n", "max NaN \n", "\n", " attributes.metadata.access-points \\\n", "count 449 \n", "unique 444 \n", "top [{'url': 'https://github.com/Ensembl', 'name':... \n", "freq 3 \n", "mean NaN \n", "std NaN \n", "min NaN \n", "25% NaN \n", "50% NaN \n", "75% NaN \n", "max NaN \n", "\n", " attributes.metadata.associated-tools \\\n", "count 618 \n", "unique 615 \n", "top [{'url': 'http://www.h-invitational.jp/hinv/bl... \n", "freq 2 \n", "mean NaN \n", "std NaN \n", "min NaN \n", "25% NaN \n", "50% NaN \n", "75% NaN \n", "max NaN \n", "\n", " attributes.metadata.deprecation-date \\\n", "count 217 \n", "unique 55 \n", "top 2021-9-17 \n", "freq 84 \n", "mean NaN \n", "std NaN \n", "min NaN \n", "25% NaN \n", "50% NaN \n", "75% NaN \n", "max NaN \n", "\n", " attributes.metadata.deprecation-reason \\\n", "count 217 \n", "unique 86 \n", "top This resource is no longer available at the st... \n", "freq 113 \n", "mean NaN \n", "std NaN \n", "min NaN \n", "25% NaN \n", "50% NaN \n", "75% NaN \n", "max NaN \n", "\n", " attributes.metadata.tombstone \n", "count 1 \n", "unique 1 \n", "top True \n", "freq 1 \n", "mean NaN \n", "std NaN \n", "min NaN \n", "25% NaN \n", "50% NaN \n", "75% NaN \n", "max NaN " ] }, "execution_count": 22, "metadata": {}, "output_type": "execute_result" } ], "source": [ "fairsharing_df.describe(include='all')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Subjects analysis" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "**re3data**" ] }, { "cell_type": "code", "execution_count": 23, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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orgIdentifiersubject
0r3d1000000011 Humanities and Social Sciences
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0r3d10000000112 Social and Behavioural Sciences
.........
2791r3d1000137334 Engineering Sciences
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2792r3d100013735204 Microbiology, Virology and Immunology
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17032 rows × 2 columns

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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": 23, "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": 24, "metadata": {}, "outputs": [ { "data": { "text/html": [ " \n", " " ] }, "metadata": {}, 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" ] }, "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": 31, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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orgIdentifierinstitutioninstitutionNameinstitutionAdditionalNameinstitutionCountryresponsabilityTypeinstitutionTypeinstitutionURLinstitutionIdentifierresponsibilityStartDateresponsibilityEndDateinstitutionContact
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...
\n", "
" ], "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": 31, "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": 32, "metadata": {}, "outputs": [], "source": [ "re3data_institutions['org_continent'] = re3data_institutions.institutionCountry.map(countrycode_to_continent)" ] }, { "cell_type": "code", "execution_count": 33, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "array(['AAA', 'EEC'], dtype=object)" ] }, "execution_count": 33, "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": 34, "metadata": {}, "outputs": [], "source": [ "re3data_institutions.loc[re3data_institutions.institutionCountry == 'EEC', 'org_continent'] = 'EU'" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "**OpenDOAR**" ] }, { "cell_type": "code", "execution_count": 35, "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', '...
\n", "
" ], "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": 35, "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": 36, "metadata": {}, "outputs": [], "source": [ "opendoar_institutions['org_continent'] = opendoar_institutions.country.map(countrycode_to_continent)" ] }, { "cell_type": "code", "execution_count": 37, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "array([nan, 'UMI'], dtype=object)" ] }, "execution_count": 37, "metadata": {}, "output_type": "execute_result" } ], "source": [ "opendoar_institutions[opendoar_institutions.org_continent.isna()].country.unique()" ] }, { "cell_type": "code", "execution_count": 38, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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system_metadata.idorganizationnamealternativeNamecountryurlidentifierlocation.latitudelocation.longitureorg_continent
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": 38, "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": 39, "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": 40, "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": 41, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "array(['Worldwide', 'European Union', nan], dtype=object)" ] }, "execution_count": 41, "metadata": {}, "output_type": "execute_result" } ], "source": [ "fairsharing_countries[fairsharing_countries.countrycode.isna()]['attributes.countries'].unique()" ] }, { "cell_type": "code", "execution_count": 42, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "array(['Worldwide', 'European Union', nan, 'Antarctica'], dtype=object)" ] }, "execution_count": 42, "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": 43, "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": 44, "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.support-linksattributes.metadata.year-creationattributes.metadata.data-processesattributes.legacy-idsattributes.fairsharing-registryattributes.record-typeattributes.subjectsattributes.domainsattributes.taxonomiesattributes.user-defined-tagsattributes.countriesattributes.nameattributes.abbreviationattributes.urlattributes.doiattributes.fairsharing-licenceattributes.descriptionattributes.publicationsattributes.licence-linksattributes.metadata.citationsattributes.metadata.abbreviationattributes.metadata.access-pointsattributes.metadata.associated-toolsattributes.metadata.deprecation-dateattributes.metadata.deprecation-reasonattributes.metadata.tombstonecountrycodecontinent
7822462fairsharing-records2017-06-27T13:30:19.000Z2021-09-30T11:35:28.523Z10.25504/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...[{'url': 'a.heughebaert@biodiversity.be', 'nam...NaNNaN[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...NaNNaNNaNNaNNaNNaNNaNAQNaN
\n", "
" ], "text/plain": [ " id type attributes.created-at \\\n", "782 2462 fairsharing-records 2017-06-27T13:30:19.000Z \n", "\n", " attributes.updated-at attributes.metadata.doi \\\n", "782 2021-09-30T11:35:28.523Z 10.25504/FAIRsharing.ewyejx \n", "\n", " attributes.metadata.name attributes.metadata.status \\\n", "782 Antabif IPT - AntOBIS IPT - GBIF Belgium ready \n", "\n", " attributes.metadata.contacts \\\n", "782 [{'contact-name': 'Anton Van de Putte', 'conta... \n", "\n", " attributes.metadata.homepage attributes.metadata.identifier \\\n", "782 http://ipt.biodiversity.aq/ 2462 \n", "\n", " attributes.metadata.description \\\n", "782 The Belgium Biodiversity Platform hosts this d... \n", "\n", " attributes.metadata.support-links \\\n", "782 [{'url': 'a.heughebaert@biodiversity.be', 'nam... \n", "\n", " attributes.metadata.year-creation attributes.metadata.data-processes \\\n", "782 NaN NaN \n", "\n", " attributes.legacy-ids attributes.fairsharing-registry \\\n", "782 [biodbcore-000944, bsg-d000944] Database \n", "\n", " attributes.record-type attributes.subjects \\\n", "782 repository [Biodiversity, Life Science] \n", "\n", " attributes.domains attributes.taxonomies \\\n", "782 [Taxonomic classification] [All] \n", "\n", " attributes.user-defined-tags attributes.countries \\\n", "782 [] Antarctica \n", "\n", " attributes.name \\\n", "782 FAIRsharing record for: Antabif IPT - AntOBIS ... \n", "\n", " attributes.abbreviation \\\n", "782 None \n", "\n", " attributes.url \\\n", "782 https://fairsharing.org/10.25504/FAIRsharing.e... \n", "\n", " attributes.doi \\\n", "782 10.25504/FAIRsharing.ewyejx \n", "\n", " attributes.fairsharing-licence \\\n", "782 https://creativecommons.org/licenses/by-sa/4.0... \n", "\n", " attributes.description \\\n", "782 This FAIRsharing record describes: The Belgium... \n", "\n", " attributes.publications \\\n", "782 [] \n", "\n", " attributes.licence-links \\\n", "782 [{'licence-name': 'Apache License 2.0', 'licen... \n", "\n", " attributes.metadata.citations attributes.metadata.abbreviation \\\n", "782 NaN NaN \n", "\n", " attributes.metadata.access-points attributes.metadata.associated-tools \\\n", "782 NaN NaN \n", "\n", " attributes.metadata.deprecation-date \\\n", "782 NaN \n", "\n", " attributes.metadata.deprecation-reason attributes.metadata.tombstone \\\n", "782 NaN NaN \n", "\n", " countrycode continent \n", "782 AQ NaN " ] }, "execution_count": 44, "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": 45, "metadata": {}, "outputs": [ { "data": { "application/vnd.plotly.v1+json": { "config": { "plotlyServerURL": "https://plot.ly" }, "data": [ { "name": 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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 }