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Best way to read/organize/notate articles on the computer?

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A question for all of you grad students out there. As an undergrad, I read a ton of articles, and always printed them out, highlighted, took notes in the margins, etc. Having the actual paper in front of me made it easier to absorb the information, but was hard to keep organized and led to stacks and stacks of articles in my room by the end of the semester.....

Now, I'd like to switch things over to the digital world, for the sake of saving space and making things easier to organize. So, my question: is there any sort of program/software/whatever that would allow me to read, underline, highlight, annotate, and organize academic articles digitally? For those of you who do a lot of academic reading online, what have you found helpful? I would love to find some sort of program that I could save articles to and then access from any computer (like Google Documents).


I would greatly appreciate any helpful tips you can offer!

Edited by MsCastorp
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Oh man, I'm super curious to hear everyone's responses too. This is something I'm still trying to grapple with as my libraries go increasingly digital and I can't take all my papers with me when I move every year or so. 


I've heard good things about Evernote, particularly in regards to its tagging features and searchablity. As for references, I am still in love with Zoterro (open source politics 4 life) and that's preventing me from making the switch.


I use a free program called PDF Xchange Viewer for reading my pdfs when I have to keep digital. It's got a good assortment of drawing, highlighting, and typing tools that work for me in terms of mark up, but isn't in anyways newly searchable. I'm basically recreating the scribbles I'd write on the page, without any efficiency gains. 


Beyond that, I'm at a loss. Academic e-book software like e-brary (which exists mostly as an IP protection measure for the book's copyright) are pretty terrible. Things load slowly, search is sluggish, and there's way too many authentication steps to make it useful for my casual/regular browsing. There's also a poverty in terms of visual access to information when doing things digitally, and it being more difficult to spatially arrange. For all the foibles of paper, I still find its pedagogically more useful to start there, in terms of mark up and also for more general note taking/writing sketches. My resolution this term is to type up all my written notes at the end of term so that I'll be able to toss the paper copies guilt free and still have the ideas and page numbers at hand for reference.

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There are programs that allow you to annotate readings, like Adobe IX, but you mostly have to pay for them. Some universities offer them free in computer labs. Many software manufacturers offer a student discount. The big key, I've found, comes down to three things: (1) making sure you back up all electronic copies of anything--multiple backups for papers!, (2) having an effective electronic filing system that you can not only find things at will, but can also clean up without spending hours sorting through folders on the various hard drives/cloud storage places you keep things on, and (3) making sure long term file storage is in a file format that doesn't go obsolete when the software manufacturer comes out with new product, like using .pdf and .rtf. Try opening an MS Word 3.1 .doc these days! Argh!


The thing here is study habits. You like paper and working with paper. Can you transition to a screen just as effectively? Can you do the same quality of work, or feel similar satisfaction with your work, when you use a laptop screen or a tablet?


I print stuff that I want to annotate extensively, and then I scan my work and save it as a new .pdf, even when I do keep the paper copies. For everything else, I currently use a personal cloud (home network storage device) for current work and store old work on an external hard drive when it's no longer strictly useful. Instead of annotating the document, I take notes on paper or in a word document. Sometimes, even OneNote. Though, these days, I'm not happy with MicroSoft and will be shifting to something else when I get unlazy enough to go looking for something. I don't do well in a class/discussion setting with a computer or tablet in front of me. I'm one of those people that must constantly look things up, even when it's not as relevant. Example, the exact date a particular WWII battle began, when the year and season were not only all that was needed for the discussion, but information we already possessed. My family will torture me on trips when I have no data signal on my phone by asking questions I don't have the answers to. For me, bringing stuff into the class on a tablet does happen, but not when we will do a deep discussion of that stuff. For that, I print it and leave the electronics stored away. One of these days, I'll start scanning my paper notes & syllabi from old classes into .pdf files and store them, too.


I think that the answer is the one best suited to your learning style and your needs, but also one that involves clear organization. Organizing = stress reduction!

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I use Papers by Mekentosj for exactly what you're describing, something about which I've posted here a number of times. 


If only Papers3 for Windows had... any features at all. To whit:


Missing features


Search screen: missing features

  • pinned search results
  • importing a publication to a collection
  • importing PDF, media or reference files
  • importing a Mendeley or Zotero library
  • sharing search results
  • exporting search results
  • customising search engine access settings
  • it is not possible to click on a search result to view the web page of the publication
  • importing a PDF automatically

Currently supported search engines:

arXiv, ACM, ADS, CERN DS, Crossref, IEEExplore, Highwire, Inspire, Google Books, Google Patents, Google Scholar, Gutenberg, JSTOR, Pubmed, Scopus, ScienceDirect, Springer Link and Web of Science.


Library screen: missing features

  • merging duplicate publications
  • patch editing publication metadata
  • activity tab in the Inspector
  • exporting publications in PDF or other reference formats
  • grid view doesn’t support all column options
  • creating a new publication from reference
  • columns cannot be resized or reordered

Reader screen

  • viewing page thumbnails

Preferences/settings: missing features

  • General setting configurations
Edited by telkanuru
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I use Mendeley for exactly what is requested here. I've used it on Windows, Mac and Linux with no issues at all (same features everywhere). This is how I usually use it (there are other great ways too):


1. Find the PDF for the paper I want to read/add to my library

2. Download it into a special Mendeley-watched folder and Mendeley automatically imports into my Mendeley library.

   (alternatively: I just download it elsewhere and import the PDF from the Mendeley menu separately)
   (alternatively #2: I sometimes use the Mendeley web importer tool to do this directly from the website with the journal article)

3. If you are importing a new-ish paper with meta-data, the author names, titles, other bibliographical information are loaded automatically; otherwise, I copy and paste the DOI or PMID or arxiv ID into the sidebar in Mendeley and hit a search button to automatically import this info.

4. I manually add a few more items if necessary (sometimes I copy/paste the abstract, add my own search keywords/tags [think Gmail labels], add a URL for the article if one isn't automatically imported and I want to access things like online datasets attached to the paper, add a citation key for BiBTeX)

5. I can now read the article and use Mendeley's highlight and sticky note tools to annotate the paper. The sticky notes are searchable and you can view a list of all notes for a certain paper (clicking on notes jumps you to the location of the note)

6. I can also write a summary of the paper in my own words


Other cool things I use Mendeley for:

7. It works like iTunes in terms of file organization -- I can tell it to organize my PDF by author / year / journal etc. whatever. This means once I import the file into Mendeley, I can delete the original and Mendeley takes care of the rest of the organization. I generally used the "Watched Folder" feature and once the file is imported, I clean out the Watched Folders once in awhile. I love this because I never have to think about where to store things or how to name PDFs in a logical way.


8. I have never written a Works Cited / Bibliography by hand since I started using Mendeley. I use BiBTeX so all I have to do is export my library as a BiBTeX file (there's a hotkey for it) and then I compile it in my papers. I know there are also Word plugins if you don't use LaTeX but I have not used that myself. 

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I also use Mendeley... the comment that it is a lot like iTunes is one of the best descriptions I have heard. I've always said it is what would happen if endnote and adobe reader made babies.


I use the plugin for Word for my works cited on both Mac and PC. Sometimes it is a tiny bit slow if you have a ton of citations in your document (in my case, over 200), but it works well.


One problem with the sticky notes being searchable is that on occasion, I'll be looking for a keyword in a paper only to have it tag a note I had written. So one day when I was looking for use of MEF in papers, the results I got were a lot of notes where I'd commented on papers, "Try this in MEF." So be careful how you do your notes!

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One problem with the sticky notes being searchable is that on occasion, I'll be looking for a keyword in a paper only to have it tag a note I had written. So one day when I was looking for use of MEF in papers, the results I got were a lot of notes where I'd commented on papers, "Try this in MEF." So be careful how you do your notes!


This happens to me too! I write notes like "not good for X" and then when I search for "X" and get them!


I think we are supposed to be using labels/tags for this but I'm not very good at doing it properly either.

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Another Mendeley user. I use it as a virtual (pimped) bookshelf. It's great not to cart readings around to class, and to be able to search PDFs when a specific point of discussion comes up. I can honestly say it has made transitioning to grad school so much easier, by eliminating pretty much all the organisational stuff - I just download stuff from Jstor, or the university online blackboard, or wherever, import, and go. I also keep records of books which I don't have in PDF format, so I have a complete list of my readings, tagged by keyword and ordered by date. 


And no, I don't work for them!

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