{"id":28846,"date":"2016-05-16T12:25:01","date_gmt":"2016-05-16T17:25:01","guid":{"rendered":"http:\/\/blogs.ams.org\/mathgradblog\/?p=28846"},"modified":"2016-05-16T11:11:31","modified_gmt":"2016-05-16T16:11:31","slug":"summers-here-time-organize-papers","status":"publish","type":"post","link":"https:\/\/blogs.ams.org\/mathgradblog\/2016\/05\/16\/summers-here-time-organize-papers\/","title":{"rendered":"Summer&#8217;s Here: Time to Organize All Those Papers!"},"content":{"rendered":"<div id=\"attachment_28952\" style=\"width: 311px\" class=\"wp-caption alignright\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-28952\" class=\"wp-image-28952 size-full\" src=\"http:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Zotero_logo.png\" alt=\"Zotero_logo\" width=\"301\" height=\"67\" srcset=\"https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Zotero_logo.png 301w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Zotero_logo-300x67.png 300w\" sizes=\"auto, (max-width: 301px) 100vw, 301px\" \/><p id=\"caption-attachment-28952\" class=\"wp-caption-text\">Zotero is free open-source software to help you organize your research references across multiple platforms and devices. Image is in the public domain.<\/p><\/div>\n<p>The start of summer is a great time to get organized: perhaps you finally have time to focus on something other than the next problem set, or perhaps you\u2019re too burned out from finals to do anything else productive.\u00a0 Back in the good old days of undergrad, mathematics was a mysterious substance that emanated from textbooks, whiteboards, the mouths of my classmates, and occasionally, Wikipedia. Now that I\u2019m in graduate school, more and more of what I learn comes from journal articles, which can prove difficult to organize. When I wrote my undergraduate thesis, my papers were all printed\u00a0copies stored in an accordion folder, but as a graduate student reading hundreds of articles, this system is hardly practical.\u00a0 Luckily, there are several\u00a0<strong>reference management programs\u00a0<\/strong>that keep track of papers you\u2019ve read and generate bibliographies for you.\u00a0 After\u00a0searching through many options last winter, I finally settled on <a href=\"https:\/\/www.zotero.org\/\">Zotero<\/a>, which I highly recommend (and no, I am not being paid to write this).<\/p>\n<p>I chose Zotero [zoh-TAIR-oh] because of the following features:<!--more--><\/p>\n<ul>\n<li>It\u2019s free<\/li>\n<li>It only takes one click in Chrome, Firefox, Safari etc. to download a new paper to your collection<\/li>\n<li>You can store the actual PDFs of the papers themselves, not just the bibliographic information<\/li>\n<li>You can write notes about each item or tag them with keywords<\/li>\n<li>You can highlight or annotate the PDFs using another program (e.g. \u201cPreview\u201d on a Mac) and import these highlights\/annotations into Zotero<\/li>\n<li>If you search for a term, Zotero will look through the titles, tags, notes, and even the highlighted passages and annotations you\u2019ve imported for all the documents in your library<\/li>\n<li>Zotero\u00a0will generate bibliographies and in-line citations in both BibTex and MS Word<\/li>\n<\/ul>\n<p>In addition, Zotero lets you share your collections with others, import collections you may have already started in other software packages, and access your collections (well, the citations at least) from multiple computers. \u00a0The PDFs themselves are stored on your original machine (by default, in your &#8220;Downloads&#8221; folder), unless you choose to put them in Dropbox, OneNote, Google Drive, or some other cloud storage. \u00a0You should probably do this anyway to back them up.<\/p>\n<p>My workflow so far looks like this:<\/p>\n<ol>\n<li>Search for a paper or author on Google Scholar<img loading=\"lazy\" decoding=\"async\" class=\"size-large wp-image-28871 aligncenter\" src=\"http:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.11.48-1024x420.png\" alt=\"Screenshot 2016-05-11 19.11.48\" width=\"640\" height=\"263\" srcset=\"https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.11.48-1024x420.png 1024w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.11.48-300x123.png 300w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.11.48-768x315.png 768w\" sizes=\"auto, (max-width: 640px) 100vw, 640px\" \/><\/li>\n<li>Follow the link to the website of the journal article and click the Zotero button to download both the citation and, if your university\u00a0can get\u00a0you access to it, the\u00a0PDF. \u00a0The Zotero download button circled in this picture is available\u00a0for all webpages\u00a0once\u00a0you install the Chrome extension, which I found to be quick and painless. \u00a0Other browsers are also supported.<a href=\"http:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.14.04-1.png\" rel=\"attachment wp-att-28872\"><img loading=\"lazy\" decoding=\"async\" class=\"wp-image-28872 aligncenter\" src=\"http:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.14.04-1-1024x556.png\" alt=\"Screenshot 2016-05-11 19.14.04\" width=\"640\" height=\"348\" srcset=\"https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.14.04-1-1024x556.png 1024w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.14.04-1-300x163.png 300w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.14.04-1-768x417.png 768w\" sizes=\"auto, (max-width: 640px) 100vw, 640px\" \/><\/a><\/li>\n<li>The article is happily stored in Zotero. \u00a0On the left, you have the option of organizing your library into folders. \u00a0On the right, the article metadata is listed. \u00a0The menu above the metadata allows you to add notes or tags, which are then searchable.<img loading=\"lazy\" decoding=\"async\" class=\"size-large wp-image-28861 aligncenter\" src=\"http:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.15.40-1024x509.png\" alt=\"Screenshot 2016-05-11 19.15.40\" width=\"640\" height=\"318\" srcset=\"https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.15.40-1024x509.png 1024w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.15.40-300x149.png 300w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.15.40-768x382.png 768w\" sizes=\"auto, (max-width: 640px) 100vw, 640px\" \/><\/li>\n<li>Using the Mac &#8220;Preview&#8221; program, I highlight and annotate the PDF.<img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-large wp-image-28858\" src=\"http:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.16.53-1024x566.png\" alt=\"Screenshot 2016-05-11 19.16.53\" width=\"640\" height=\"354\" srcset=\"https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.16.53-1024x566.png 1024w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.16.53-300x166.png 300w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.16.53-768x424.png 768w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.16.53.png 1984w\" sizes=\"auto, (max-width: 640px) 100vw, 640px\" \/><\/li>\n<li>When I&#8217;m done, back in Zotero I extract the highlights and annotations. \u00a0I might do this once a month or so, since I can do it for many documents simultaneously.\u00a0<img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-large wp-image-28857\" src=\"http:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.17.57-1024x499.png\" alt=\"Screenshot 2016-05-11 19.17.57\" width=\"640\" height=\"312\" srcset=\"https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.17.57-1024x499.png 1024w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.17.57-300x146.png 300w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.17.57-768x374.png 768w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.17.57.png 1868w\" sizes=\"auto, (max-width: 640px) 100vw, 640px\" \/><\/li>\n<li>Extracted annotations and highlights now appear in the righthand panel.<img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-large wp-image-28856\" src=\"http:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.18.23-1024x248.png\" alt=\"Screenshot 2016-05-11 19.18.23\" width=\"640\" height=\"155\" srcset=\"https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.18.23-1024x248.png 1024w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.18.23-300x73.png 300w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.18.23-768x186.png 768w\" sizes=\"auto, (max-width: 640px) 100vw, 640px\" \/><\/li>\n<li>I can search my entire library for the word &#8220;heck,&#8221; and Zotero will find the annotations where I wrote &#8220;what the heck?&#8221;<img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-large wp-image-28855\" src=\"http:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.19.03-1024x216.png\" alt=\"Screenshot 2016-05-11 19.19.03\" width=\"640\" height=\"135\" srcset=\"https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.19.03-1024x216.png 1024w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.19.03-300x63.png 300w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.19.03-768x162.png 768w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.19.03-940x198.png 940w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.19.03.png 1568w\" sizes=\"auto, (max-width: 640px) 100vw, 640px\" \/><\/li>\n<li>If you use LaTex, simply export everything to BibTex and do your bibliography and citations\u00a0from there. If you need to\u00a0write something in MS\u00a0Word, install the Zotero extension in Word, which will allow you to add citations in just a couple clicks:<img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-large wp-image-28851\" src=\"http:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.27.00-1024x446.png\" alt=\"Screenshot 2016-05-11 19.27.00\" width=\"640\" height=\"279\" srcset=\"https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.27.00-1024x446.png 1024w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.27.00-300x131.png 300w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.27.00-768x335.png 768w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.27.00.png 1996w\" sizes=\"auto, (max-width: 640px) 100vw, 640px\" \/><\/li>\n<li>Upon clicking Word&#8217;s &#8220;Zotero Insert Citation&#8221; button, you&#8217;ll be taken to Zotero where you easily search for the paper you want, and it will be added in whatever citation format you prefer.<img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-large wp-image-28849\" src=\"http:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.27.48-1024x552.png\" alt=\"Screenshot 2016-05-11 19.27.48\" width=\"640\" height=\"345\" srcset=\"https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.27.48-1024x552.png 1024w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.27.48-300x162.png 300w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-19.27.48-768x414.png 768w\" sizes=\"auto, (max-width: 640px) 100vw, 640px\" \/><\/li>\n<li>And with one more click, you can\u00a0generate a\u00a0bibliography.<\/li>\n<\/ol>\n<p><a href=\"http:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-20.17.10.png\" rel=\"attachment wp-att-28875\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-large wp-image-28875\" src=\"http:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-20.17.10-1024x626.png\" alt=\"Screenshot 2016-05-11 20.17.10\" width=\"640\" height=\"391\" srcset=\"https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-20.17.10-1024x626.png 1024w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-20.17.10-300x183.png 300w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-20.17.10-768x470.png 768w, https:\/\/blogs.ams.org\/mathgradblog\/files\/2016\/05\/Screenshot-2016-05-11-20.17.10.png 1956w\" sizes=\"auto, (max-width: 640px) 100vw, 640px\" \/><\/a><\/p>\n<p>I&#8217;ve found this system extremely helpful this semester, and if you don&#8217;t have a system of your own that you like, I suggest you give it a try. \u00a0Zotero is quick to learn, and I have yet to\u00a0run into any bugs. \u00a0Granted, things don&#8217;t always go as smoothly as the example above, so here&#8217;s what to do in some other situations:<\/p>\n<ul>\n<li>If you just have the PDF (say, it was emailed you to) you can have Zotero extract the citation information\u00a0(e.g. author, title, year) from the PDF metadata to allow you to make citations.<\/li>\n<li>If the PDF\u00a0doesn&#8217;t have\u00a0any metadata\u00a0encoded (perhaps you have a scanned book chapter, for instance), you can\u00a0download\u00a0the citation information from the internet\u00a0and then attach your PDF to it.<\/li>\n<li>As a last resort, if you can&#8217;t get the complete citation information online in a downloadable format (as is sometimes the case with books or websites), you can enter the missing\u00a0information by hand.<\/li>\n<li>Conversely, if you find the citation online but not the PDF (or if you don&#8217;t have free access to it), you can still download the citation into Zotero. \u00a0You can always add the PDF later if you get access to it.<\/li>\n<li>The most annoying situation is when I can&#8217;t highlight or annotate the PDF (this often happens if it&#8217;s a scanned copy that was laid slightly\u00a0diagonally in the scanner). \u00a0This isn&#8217;t a Zotero issue of course, but Zotero will still allow you to type notes about the document as a whole in Zotero&#8217;s own\u00a0notes section, even if you don&#8217;t have a way to annotate specific passages.<\/li>\n<\/ul>\n<p>Lastly, if you&#8217;re still not convinced and want to try out other reference management software, here&#8217;s a good place to begin:\u00a0<a href=\"https:\/\/en.wikipedia.org\/wiki\/Comparison_of_reference_management_software\">https:\/\/en.wikipedia.org\/wiki\/Comparison_of_reference_management_software<\/a><\/p>\n<p>Do you have a reference manager that you particularly like? Let us know in the comments below which one is your favorite and why!<\/p>\n<div style=\"margin-top: 0px; margin-bottom: 0px;\" class=\"sharethis-inline-share-buttons\" ><\/div>","protected":false},"excerpt":{"rendered":"<p>The start of summer is a great time to get organized: perhaps you finally have time to focus on something other than the next problem set, or perhaps you\u2019re too burned out from finals to do anything else productive.\u00a0 Back &hellip; <a href=\"https:\/\/blogs.ams.org\/mathgradblog\/2016\/05\/16\/summers-here-time-organize-papers\/\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n<div style=\"margin-top: 0px; margin-bottom: 0px;\" class=\"sharethis-inline-share-buttons\" data-url=https:\/\/blogs.ams.org\/mathgradblog\/2016\/05\/16\/summers-here-time-organize-papers\/><\/div>\n","protected":false},"author":93,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[2,223,224,1],"tags":[226,225,227,228],"class_list":["post-28846","post","type-post","status-publish","format-standard","hentry","category-advice","category-grad-student-life","category-staying-organized","category-uncategorized","tag-citations","tag-reference-management","tag-software","tag-work-flow"],"jetpack_featured_media_url":"","jetpack_shortlink":"https:\/\/wp.me\/p3gbww-7vg","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/blogs.ams.org\/mathgradblog\/wp-json\/wp\/v2\/posts\/28846","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.ams.org\/mathgradblog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.ams.org\/mathgradblog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.ams.org\/mathgradblog\/wp-json\/wp\/v2\/users\/93"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.ams.org\/mathgradblog\/wp-json\/wp\/v2\/comments?post=28846"}],"version-history":[{"count":11,"href":"https:\/\/blogs.ams.org\/mathgradblog\/wp-json\/wp\/v2\/posts\/28846\/revisions"}],"predecessor-version":[{"id":28962,"href":"https:\/\/blogs.ams.org\/mathgradblog\/wp-json\/wp\/v2\/posts\/28846\/revisions\/28962"}],"wp:attachment":[{"href":"https:\/\/blogs.ams.org\/mathgradblog\/wp-json\/wp\/v2\/media?parent=28846"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.ams.org\/mathgradblog\/wp-json\/wp\/v2\/categories?post=28846"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.ams.org\/mathgradblog\/wp-json\/wp\/v2\/tags?post=28846"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}