{"id":3586,"date":"2019-07-12T20:43:48","date_gmt":"2019-07-12T20:43:48","guid":{"rendered":"https:\/\/notebooks.dataone.org\/?p=3586"},"modified":"2019-07-12T20:43:48","modified_gmt":"2019-07-12T20:43:48","slug":"week-8-visualization-with-gephi","status":"publish","type":"post","link":"https:\/\/notebooks.dataone.org\/citation-dataone\/week-8-visualization-with-gephi\/","title":{"rendered":"Week 8: Visualization with Gephi"},"content":{"rendered":"\n<p>Hoi! <\/p>\n\n\n\n<p>This week I&#8217;m happy to share with you some visualizations that reflect components of the DataONE publications and the articles that cite those publications. I created the visualizations with Gephi as I have not found a bibliometrics tool that allows you combine the cited and the citing articles in one visual. I am so thankful to have had Audrey (network analysis whiz and DataONE intern working on <a href=\"https:\/\/notebooks.dataone.org\/networked-lod\/\">visualizing data in the Arctic Data Center repository<\/a>) help me along the way.<\/p>\n\n\n\n<p>Network Stats<\/p>\n\n\n\n<ul><li>Number of unique citing articles: 3,218<\/li><li>Number of cited articles: 113<\/li><li>Number of links: 4,199<\/li><\/ul>\n\n\n\n<p><strong>Modularity<\/strong><\/p>\n\n\n\n<p> I ran modularity on the entire network in Gephi. This allows you to see  various communities using the modularity algorithm presented by Vincent D  Blondel, Jean-Loup Guillaume, Renaud Lambiotte, Etienne Lefebvre (<a href=\"https:\/\/iopscience.iop.org\/article\/10.1088\/1742-5468\/2008\/10\/P10008\/meta\">2008<\/a>). In the visualization below, there are approximately 8 main communities and an overall modularity of 0.752. Once I ran the modularity statistic I looked at the articles&#8217; titles in the network to see if they showed any topical cohesiveness and they did! Using this method I labeled 8 main preliminary topic communities: ecology + citizen science, data sharing, data management, data networks\/visualization, citizen science, problems and solutions, data gathering best practices, and big data\/data processing. Unfortunately, I couldn&#8217;t get the modularity to run in any informative way on just the citing articles so this analysis is based on both cited and citing articles. I&#8217;m going to explore more and see if I can get this to work.<\/p>\n\n\n\n<figure class=\"wp-block-image\"><img loading=\"lazy\" decoding=\"async\" width=\"1183\" height=\"739\" src=\"https:\/\/notebooks.dataone.org\/wp-content\/uploads\/2019\/07\/Full-Network-Zoomed-In_Preview.png\" alt=\"\" class=\"wp-image-3587\" \/><\/figure>\n\n\n\n<p><strong>A degree of 2<\/strong>&#8211; The visualization below represents articles that have citing articles that have connections to at least two DataONE articles. As you can see, the network is significantly reduced.<\/p>\n\n\n\n<figure class=\"wp-block-image\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"768\" src=\"https:\/\/notebooks.dataone.org\/wp-content\/uploads\/2019\/07\/screenshot_111941-1.png\" alt=\"\" class=\"wp-image-3589\" \/><\/figure>\n\n\n\n<p><strong>Citing articles color coded by year<\/strong>&#8211; Dates covered are 2019 (9.52% pink), 2018 (19.94%, pink), 2017 (18.29% green), 2016 (17.52%, blue), 2015 (13.36%, dark grey), 2014 (10.14%, orange), 2013 (6.23%, teal), 2012 (3.6%, dusty pink), 2011-2009 (remaining 1.4%, grey). The cited articles in this visual are black and are not color coded by year. I apologize this visual is cut off. The screenshot tool in Gephi is a bit buggy.<\/p>\n\n\n\n<figure class=\"wp-block-image\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"768\" src=\"https:\/\/notebooks.dataone.org\/wp-content\/uploads\/2019\/07\/Citing-Articles-color-coded-by-year.png\" alt=\"\" class=\"wp-image-3591\" \/><\/figure>\n\n\n\n<p><strong>Citing articles sized and colored by number of different DataONE articles they cited<\/strong>&#8211; The biggest nodes in this network represent articles that cited 7 different DataONE articles and the smallest have cited one. <\/p>\n\n\n\n<figure class=\"wp-block-image\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"1024\" src=\"https:\/\/notebooks.dataone.org\/wp-content\/uploads\/2019\/07\/Citing-articles-sized-according-to-how-many-different-dataone-articles-they-have-cited.png\" alt=\"\" class=\"wp-image-3592\" \/><\/figure>\n\n\n\n<p>In the last visual you can see some nodes that surround the periphery of the network. I am going to dig into this more and figure out what these outliers are all about. Also, in next week&#8217;s blog expect some summary reports, network insights, and results from my data mining of DataONE mentions on the web!<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Hoi! This week I&#8217;m happy to share with you some visualizations that reflect components of the DataONE publications and the articles that cite those publications. I created the visualizations with Gephi as I have not found a bibliometrics tool that allows you combine the cited and the citing articles in <a class=\"more-link\" href=\"https:\/\/notebooks.dataone.org\/citation-dataone\/week-8-visualization-with-gephi\/\">Continue reading <span class=\"screen-reader-text\">  Week 8: Visualization with Gephi<\/span><span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":121,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[393],"tags":[],"_links":{"self":[{"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/posts\/3586"}],"collection":[{"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/users\/121"}],"replies":[{"embeddable":true,"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/comments?post=3586"}],"version-history":[{"count":1,"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/posts\/3586\/revisions"}],"predecessor-version":[{"id":3593,"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/posts\/3586\/revisions\/3593"}],"wp:attachment":[{"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/media?parent=3586"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/categories?post=3586"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/notebooks.dataone.org\/wp-json\/wp\/v2\/tags?post=3586"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}