Elsevier’s the Worst, but I’ve been using Mendeley. Privacy & Ethics vs. Ease of Use, or the Journey Back to Zotero
As a professor in this digital age, I have to keep track of a lot of documents for research, teaching, and administration. Overall, I use a mix of the following tools:
- Evernote: my electronic filing cabinet for student notes, administration tasks. This is my dumping ground for any information I might find useful in the future;
- Calibre: Organizer for eBooks I’ve purchased, both ones that came free of DRM and the ones that I’ve purchased and stripped of DRM; and
- Mendeley: Use this to organize and cite articles, book selections, PDFs of webpages, et cetera for myself and my students.
*Record scratch* Hold up, you use Mendeley? Isn’t Elsevier Satan’s Scribe?
I’ve been a Mendeley user since 2010. Was out of the game when Elsevier bought Mendeley back in 2013 for a cool 65 million dollars.
Before then, I’d been a heavy Zotero user in grad school (nothing was more satisfying then clicking “Refresh” and having 300+ citations and pages and pages of cited works automatically refresh perfectly — ibids and all). But with the rise of Chrome and me largely exiting the academic game when my wife got sick, I abandoned Zotero and Mendeley both.
In 2014 I snuck back into the game when I started a MEd in Educational Technology to try and forge a career in instructional technology. Now that I was knee-deep in research, I needed to pickup one of the tools I’d dropped several years prior. Mendeley was the more polished choice, offering more functionality on a wider array of platforms than the aging Zotero.
Mendeley, oh how I loved thee before I knew thee!
The killer features of Mendeley for me were:
- the ability to annotate PDFs in-app
- the auto-renaming feature — add citation data and 348727.pdf becomes Smith 2010 Fire and the AI Religion.pdf.
- the auto-organization feature — attach a file to a citation entry and *poof!*, the file is automatically placed in the \Smith\Journal of Religion and Technology\ folder on my computer.
I can’t tell you how invaluable the automation of those things were. Mix the above with a cloud-syncing service like Box.com and not only is everything organized, it is also perpetually backed up and accessible everywhere. This is so much better than manually renaming, organizing, and hunting down files on the computer and flash drives.
So, I loaded everything I could into Mendeley and blissfully used it for 4 years through grad school and the move back into academia at a small Midwestern teaching college.
The Elsevier Explication
Then came the reply from Lee Skallerup Bessette that shattered thine ignorance:
Well shit. As Lupe Fiasco tells us:
Now we can say it ain’t our fault if we never heard it
But if we know better, then we probably deserve it.
Restated: with knowledge comes complicity.
Espial Elsevier
You might say, “Is Elsevier that bad?”. Let’s check in with Paul Growder:
Elsevier is the most notorious of the giant for-profit academic publishing firms. They charge truly astonishing subscription costs for academic journals, even though they aren’t obliged to pay authors, referees, etc. For example, one of the more egregious of their yearly subscription rates is the Journal of Nuclear Materials, which will cost libraries $7,442.14 for an electronic subscription, or $11,164.00 for a print subscription. (Full disclosure: I cherry-picked that one for impact.) No, those numbers are not typos. If your institution doesn’t have a subscription, a single article download will cost you $40.
Of course, as an author, you can always choose to make your paper open access. The fee for doing so? $3,500. Apparently some authors actually pay these fees (or, more to the point, have them paid by grant agencies), because the professional validation of peer review is so important for academic careers that it’s worth it to get the stamp of a professional journal on one’s work even if it means that money gets flushed down the toilet for the privilege of getting to post one’s own work on the internet.
Stephen Bainbridge points out that almost 17,000 academics have called for a boycott of Elsevier.
You can also check out a list of their fuckery just in 2013: Elsevier vs. Academia.edu vs. Researcher.
Your Data, Their Profits
“Yeah, yeah, yeah, but that’s Elsevier the parent company. I’m only here what Mendeley brings to the table,” you might reply.
Check out the list of your data Elsevier vacuums up via Mendeley:
- Personal information: first name, last name, email address, password, field of study and academic status
- Articles and papers. “publications and papers you catalog, access, read and manage using the software will be uploaded to your account.”
- Comments and feedback left in groups and other discussions
- Log files and device data: “including, but not limited to, traffic data and other communication data”
- Third party account data.(Facebook data, if you link the accounts)
- Usage Data. “pages you visit and the time you spend on them, the articles you read, access and download and how long you read them, and the articles you upload and information extracted from them, such as abstract, keywords, full-text and cited references.”
That is just a snippet. You can review the rest over at Mendeley’s Privacy Policy.
I dunno about you, but I’m just not comfortable with sharing all of that data with ’em.
So it seems like I need to abandon ship. Otherwise, I’d be trading privacy & ethics for ease of use.
So… Let’s go… Back to Zotero…
As Lee reminded Matt and I, Zotero had graduated to a standalone program with its move to 5.0. Remember, it is created and maintained by a non-profit organization and is free and open-source. Zotero’s privacy policy is much better and gives its users dramatically more control over what is shared.
But, let’s not forget the 3 features that lead me to Mendeley in the first place:
- the ability to annotate in-app
- the auto-renaming feature
- the auto-organization feature
Zotero 5.0, with all of its updates, does not have those features. So what’s a me gonna do?
Go a googling.
Turns out that one is able to get the same functionality with a minimal amount of hoops.
Step 1: Moving your Mendeley Data to Zotero
Wanna sniff out a dead rat? Check out a service’s user data export process. If it is difficult, they are using a dark pattern as a way of keeping you in the service. You’ll find that while you can export a RIS file of your whole library, you’ll have a much harder time moving your annotations and other metadata over without some advanced work.
Zotero forum user AdamSmith listed out the basic steps here: Migrating from Mendeley to Zotero. Here are his key steps:
1. Export library as RIS from Mendeley (go to “all documents”, select all (ctrl+a) and the click “Export” from the File Menu. Select .ris as the filetype.
2. Import that file to Zotero (click on import in the gears menu and select the file exported from Mendeley.
3. The most important thing is WHERE one saves the RIS file. I saved it in my Mendeley organised folder, where my renamed pdfs are outputted by Mendeley.
Step 2: Install ZotFile
ZotFile is a PDF management program for Zotero. Once you install ZotFile, it will auto-rename your PDFs, auto-organize your PDFs and enable a messy, but workable annotation process.
Step 3: Select where you want your files stored
Once you’ve installed ZotFile, in Zotero, go to “Tools -> ZotFile Preferences”. On the General Settings tab, you’ll see the following:
You’ll want to click the radio button for “Custom Location”. You can then choose your local folder of choice. And if you have cloud storage, you can select that folder in order to have a cloud-synced backup of your data!
You’ll also likely want select the checkbox “Use subfolder defined by” in order to sort your PDFs by various wildcards. I use “\%a\”, which will place them in folders by author, though other options are possible.
Step 4: Renaming your files
Now you’ll want to hit up the “Renaming Rules” tab.
You can simply use Zotero to rename or you can customize the options as you see fit. Above is what I use. What’s nice is that you can click the “Update” button to see a preview of your naming scheme.
At this point, you can stop. But if you want to add in some additional functionality, move on to Step 5.
Step 5: Setting up tablet annotations
Now, hit up the “Tablet Settings” tab. Hit the checkbox “Use ZotFile to send and get files from tablet”. Doing so will popup a dialog box asking you to allow it to create the searches necessary for this to work (you can look at these added searches under the “Advanced Settings” tab.
Now you’ll need to fill in the options.
You will need to have some sort of cloud syncing service. All faculty, students, and staff at my college have access to Office 365, so they would be able to use OneDrive with 1TB of storage at no direct cost to them.
Now, you’ll need to find some PDF annotation software on your tablet that supports cloud sync. Here are best I’ve found for iOS and Android:
- iOS: GoodReader: the one app that makes me pine for iOS
- Android: Xodo: The best Android PDF annotation and reading app I’ve found in 5+ years of looking.
After you’ve installed the app on your tablet and signed into the same service that you’ve used to store tablet files earlier in this step, we are ready to try out the annotation feature.
Step 6: Sending the File to the Tablet and Back
First, select the entry you want to send to your tablet.
Then, right click on the entry, click on “Manage Attachments”, and then “Send to Tablet” as shown below.
Now, when you look at the “Tablet Files” search, you’ll see that entry added there:
Now, it is time to get out your tablet and open up that PDF annotation app (Xodo in this case) and open that cloud location. You should see the PDF listed there.
Annotate all you want! Save the annotations on the tablet and come back to your computer.
Then, right click on the entry, click on “Manage Attachments”, and then “Get from Tablet” as shown below.
Now, ZotFile will pull the file back into Zotero and add in the annotations as notes in the entry itself.
The annotations are extracted and added as notes in the reference in Zotero. This is one of the best features of ZotFile.
I did a bit of testing on this and you can see the results of this process.
Everything we highlighted, added as a comment, or underlined shows up in a “Extracted Annotations” note in the reference along with a copy of the PDF that is annotated.
Wrap-Up
After all of the above, we have a holistic method of archiving, recalling, organizing, annotating, and reading PDFs of bibliographic entries.
We’ve left Mendeley and can now request our account be deleted. We’ve moved to a much more ethical, open, and privacy-conscious platform that give us control over our work.
Now that feels good, yo.
