How best to organize large amounts of academic papers, books, etc.

June 29, 2018 4:55 AM

I am entering a PhD program this year and expect to be reading many, many academic papers in .pdf form as well as physical books. I usually print out papers that I expect to be closely working with, so I'm also interested in hearing thoughts about organizing physical copies of papers and books. But mainly I'm interested in software solutions for managing my collection. I know of Endnote, Mendeley, and Zotero. What works best for you, and how do you utilize that software most effectively?

There are a good amount previouslies on Ask, but some are quite old, and while basic software functions might not have changed that much, I imagine support and documentation have. Other previouslies have focused on specific technical information about individual software or have focused on materials that I won't be working with.

Some additional details and questions:

+I know Zotero and Mendeley are basically free, except for additional storage. I am able to buy Endnote at the university price through my library.

+I work mainly in the social sciences, primarily within the disciplines of sociolinguistics and anthropology. So this wouldn't be for medical papers or primary sources like historical documents. Pretty much just .pdfs of modern work, including book reviews, chapters, dissertations, journal publications, etc. What might be the best tagging practices for this kind of collection?

+How easy would it be to access my collection across different devices?

+How best to coordinate and cross-reference my paper collection with my digital collection?

+I'm a little finicky when it comes to highlighting and taking notes. As in, I do it quite a lot, but I like it to be as simple as possible. Highlighting helps with my reading comprehension, and I find it very useful later, during the writing process. Which software has the best highlighting and note-taking functionality?

+Are there good resources out there for learning the intricacies of these programs?

Mainly I'm just interested in hearing what has worked for you and what hasn't. Thanks so much in advance!

posted by lilies.lilies to Technology (16 answers total)

When I was doing my PhD I used Evernote after attending a really helpful training session at my university's library I'm sure your library would offer similar training sessions - maybe follow that up?
posted by nerdfish at 5:50 AM on June 29, 2018

I used Zotero while writing my PhD and stil use it for academic work; I can only recommend it. Zotero contained the references to every source relevant to my dissertation topic. I made use of the tag function and also kept all notes and digital source materials (mainly pdf's of articles) within the program itself. Importing references is a breeze, whether you do it manually, through ISBN or DOI codes, or the browser extension. It also works well with MS Word when it comes to adding references and bibliographies to your texts.

As for tagging, I kept it to a minimum: 'read', 'to read', the chapter number(s) the source was relevant for, whether I had the text in my collection or in the university library - nothing to do with the actual content of the source, actually. I did make sure that the abstract and keywords were included in the reference information, which made searching for specific themes easier.

I prefer to read on paper and have the habit of printing every article I read. So I underlined and took notes by hand, which I imported to Zotero afterwards to make use of the search function. I just kept all these articles in file boxes, attached a post-it to the top with the author's last name and the year of publication, and kept them in alphabetical order. This worked very well; I could easily browse through the collection and retrieve any article in a few seconds (it does, however, restrict your work to the location where you physical sources are stored).

The Zotero support pages and the Zotero forums are invaluable resources.

I did not use Zotero across different devices, and almost never read digital files, so can't say anything about that.

Finally, I used Scrivener to outline and write my dissertation, and heartily recommend it.

Best of luck with your PhD!
posted by Desertshore at 5:53 AM on June 29, 2018

I use Mendeley; I has good note-taking and highlighting functions. You can also add tags to papers.
posted by phoenix_rising at 7:02 AM on June 29, 2018

Zotero is good; my personal favorite is RefWorks (supported by my University and has direct export of records through the library from both catalog and databases). I appreciate the ability to both tag and assign folders, upload pdfs, alter metadata, and share folders. It lets you create citation lists from any tag or folder combination and switch citation styles with a drop-down. I don't highlight, but I do use a custom field for notes and create annotated bibliographies. And the plug-in for MS Word, "Write-n-cite," is excellent--it actually just uses a merge field for the record ID in your paper for in-text citations, allowing you to change metadata in the record and auto-update in your paper.
posted by epanalepsis at 7:16 AM on June 29, 2018

I made a video of my process. Memailing the link to you. Others can ask via memail.
posted by k8t at 7:45 AM on June 29, 2018

I'm a mendeley user. A word of caution... If you collaborate a lot, be on the same system as others.
posted by k8t at 7:47 AM on June 29, 2018

I'll also say - if you're going to use a system, commit to it early and stick with it. I used Zotero a bit, I used endnote a bit, and now I just have a folder with pdfs (named First Author Year Title Keyword, for search purposes) and an excel file I use for annotating new things as I read them because it would take more time than I am willing to devote to it now to go through and properly categorize everything in one of the official PDF management systems.
posted by ChuraChura at 8:10 AM on June 29, 2018

In the hard sciences, I liked readcube because of the integration with citation databases, so I could easily see which papers cited those I was reading. I also found its recommendation engine useful. But it fills a little bit of a different niche than Zotero.
posted by pombe at 8:21 AM on June 29, 2018

Overall, you absolutely want to decide on this once, and it's great that you're thinking about this now. I've used Endnote (which I don't recommend, and I don't know anyone of my scientific generation who uses it), but since I started grad school in 2010, I've used Papers, which I quite like. It'll sync with cloud storage (my library lives in my Google Drive account, and is about 2k papers). It's also got good integration against the major databases for matching PDFs, which saves me a lot of pain, and the in-line citation system works pretty well.
posted by Making You Bored For Science at 9:12 AM on June 29, 2018

Mendeley (now owned by Elsevier) recently started encrypting the database they keep on your computer, which will keep you locked into their system forever. I would avoid them for that reason alone.
posted by grouse at 9:14 AM on June 29, 2018

I was totally oldschool and used a very similar system as ChuraChura, but I added the lastauthor/PI so I could get a feel for which lab felt a certain way about something or if that particular lab had some peculiar system/ technique that was different than other labs.

I don't know about your department, but my committee really liked that I could reference papers by first author, lab, and year to back up my reasoning/ argument.

Papers on a particular topic goes into a folder named for that topic, and if it spans multiple topics, there'd be duplicated spread across different folders.
posted by porpoise at 10:49 AM on June 29, 2018

I don't have a foolproof system for this at all, so I have a lot to learn from the responses here! I just wanted to add to these great suggestions that it can be really helpful to think about how your memory works and use insights about that to guide your organizational system. For my dissertation, for instance, I can often remember something like, "I read something useful for this chapter when I was in Kerry's class 4 years ago," so I organize PDFs both by semester I read them and by topic/relevance to a particular chapter (my system is very old-school, so I just create shortcuts on my hard drive for this). There might be particular triggers that you can incorporate into your organizational scheme in addition to the typical citation/topic information.
posted by dapati at 12:04 PM on June 29, 2018

I use Endnote - I like the fact it syncs with my university ejournal subscriptions, so I can run a search in pubmed and endnote will download and index all the pdfs for me. Takes all the pain out of systematic reviews.

My endnote library is subdivided by topic so it’s easy to browse, or obviously you can search by author or keyword to find specific papers. Cite as you write is a major plus - whatever solution you go with don’t use anything that doesn’t automatically update bibliographies. Endnote Web means I can use it across different devices, and I think there’s an iPad app.

I use Evernote for actual notes, but for me my notes are project-specific while my endnote library encompasses my whole research activity.
posted by tinkletown at 3:11 PM on June 29, 2018

Clinical research: I use Zotero. I like the ease of importing with the Chrome extension, so I create enormous ref lists while trawling PubMed and then cite in-line as I'm writing. If I go back and insert another citation above, it will automatically renumber the citations; ditto changing the reference format if submitting to a different journal than originally planned.

Note that this is different from my "managing multiple PDFs" system. I throw papers into a to-read folder in Dropbox and then read them on the iPad using Documents (ease of highlighting/annotation). When I was taking classes, I had the PDFs organized by semester and professor, but now that it's just me, it's an (ever-growing) pile of things.
posted by basalganglia at 4:29 PM on June 29, 2018

One needs to think about systems for:
Finding
Collecting
Annotating
Bringing together (most important!)
posted by k8t at 9:34 AM on June 30, 2018

I find with RSS feeds and Google Scholar alerts. (This is after I did the initial review and just need to keep up on changes).
I collect with Mendeley.
I have word docs for every concept and update my notes on them.
posted by k8t at 9:35 AM on June 30, 2018