Staying Organized: Hunting for the perfect workflow

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Alright, so let me start by saying that I am not a naturally organized person. In grad school you have to be organized or you die. It's really that simple. So, naturally, I realized I needed a system of organization; I didn't want to die.

I didn't want just any system though, I wanted a robust, efficient system that could archive my knowledge forever, and be accessible from anywhere using any device.

The first decision: making the switch to digital notes.
I made the switch to digital note taking because:
  1. I was tired of holding onto notebooks
  2. I wanted to index my notes forever
  3. I wanted to access my notes anywhere (no more forgetting the notebook you need)
  4. I wanted to record audio of my lectures
  5. I wanted to take notes directly on any PDF or powerpoint and index those forever.
To solve this dilemma, I went with a Samsung Galaxy note 10.1 (2013). I bought it for $150 off craigslist, rooted it so I could update the Android OS and installed LectureNotes. I will do a blog post on this later, but for now just know I use a tablet to record and take digital notes in all my classes.

Creating a workflow

My workflow consists of four main tasks:
  1. Researching
  2. Reading
  3. Note taking and Annotating
  4. Archiving and Indexing
There are numerous workflows that accomplish these tasks, but all of the ones I have seen are filled with inefficiencies; e.g. manually importing files, manually indexing and organizing, etc. Time is money and money is time and I don't have a lot of either, so I wanted the computer to do as much of the work for me as possible. It was also important for my notes and ideas to be accessible from any device on any OS, as I am constantly in an entanglement of OSX, Windows, Android and even Chrome (no Linux yet). So I spent many late nights crafting the perfect workflow. That's not to say my workflow is perfect; it's not, but it's a great start and I bet you'll like it.

The workflow

Evernote is the bread and butter of my workflow. It organizes and indexes all of material, including PDFs, audio recordings and web clippings. It's my second brain. I chose Evernote because of it's cloud syncing abilities and powerful search tools. It can recognize any type of writing, including handwriting and scanned documents.
Zotero is my reference manager. What organization apps like Evernote and One Note lack are robust reference managers. With Zotero, I can simply drag & drop my PDFs and auto-generate citations in any format. Zotero has the ability to create folders and tag articles as well, so you can stay organized.
Zotero and Evernote each have handy Firefox extensions. The Evernote extension allows you to save entire web pages, while the Zotero one I use to auto-generate and index citations of peer-reviewed articles. Also Firefox is awesome because it is open source.
LectureNotes is my note taking app of choice for lectures. I can import PDFs of my lectures and take notes while I record audio of the lecture. It also has one-click exporting to Evernote, which is super handy.
Zotfile is an integral part of my workflow. It's an add-on for Zotero that aids in automation. It auto-imports PDFs into Zotero and allows you to specify a folder for which you can one-click export PDFs. When this is used with a cloud service such as Dropbox, you can access your referenced PDFs anywhere.
Dropbox allows further automation in my workflow. By setting the ZotFile location folder to a Dropbox folder, I can effectively use any device with Dropbox to import PDFs automatically into Evernote, thanks in part to Hazel and a simple AppleScrip (see below)..
Hazel is a niffy little app that allows you to set rules and conditions on specific folders. So for example, if you wanted to automatically index a file to a specific folder based on the name of the file, then Hazel could do that. It can also be set to execute a script anytime a file is imported into a folder, which is what I have done.
I use Preview to annotate and take notes directly on my PDFs. I originally liked the app Skim (OSX), but it's drawback was that in order for my annotations to save, I had to re-export the PDF. With preview I don't have to export, I can simply save, and my annotations will be visible across any PDF reader, including within Evernote.

Getting Zotero to talk to Evernote

The trickiest part of my workflow was getting Zotero to integrate with Evernote. As I hint at above, I use a combination of Zotfile, Dropbox, Hazel and an AppleScript to get the two apps to work together, with one-click.

Here is how I do it:
  1. Install ZotFile, Dropbox, Hazel (or any app that allows you to set a folder action).
  2. Set the ZotFile location setting to a dropbox folder. E.g. I have a folder in Dropbox called "Zotero" that I point to.
  3. Set Hazel to the following settings.
  4. Now edit the AppleScript using the following script. E.g. I have my script set to import any files in my Zotero Dropbox folder to a notebook in Evernote called "Zotero Import" as well as tag the file "^journal". You can edit the script as you see fit.
  5. To get the script to run, you simply right-click on any parent item in Zotero > manage attachments > rename. It looks like this.
The script will then run and Evernote will automatically open to the imported file(s), that you can then move to the correct notebook and add tags as you see fit.

My tagging system in Evernote

Evernote allows you to organize by stacks and notebooks (think folder and sub-folder) as well as by tags. Tags can be really powerful. Early on you will want to come up with an organization system that makes sense to you.

For me, I have a stack called "University of Arizona" that then has a notebook for each of my classes. I also have a pretty organized tagging system:
! denotes the university from which the information pertains
* denotes the class to which the information pertains (e.g. paleoclimate)
. denotes the section of the class for which the information pertains (e.g. "reading" = class reading; ".lecture" = class lecture)
^ denotes the medium of information (e.g. ^journal = source from peer-reviewed journal)
# denotes the subject to which the information pertains (e.g. #oceanacidification = ocean acidification)

Here are what my tags look like.

An example of my workflow

Here is an example of my workflow to give you a better idea of how it functions.

Let's say I am reading this article in the journal Nature Climate Change.
A. I need to get the PDF into Zotero so I can generate a citation for my thesis. I can do this in two ways:
  1. Use the Zotero Firefox extension and simply click the "Save to Zotero" button. This will save the PDF of the article into whatever collection (folder) I have open in Zotero, and automatically generate the citation (see here). At the same time, Zotfile moves the PDF into the dropbox folder, activating the AppleScript, which then imports the PDF into Evernote.
  2. I could manually download the PDF, and then drag the PDF into Zotero. I will then have to right-click on the PDF to generate the citation. To the export using Zotfile, I have to click on the parent item of the PDF > manage attachments > rename, and then the file will export to the Dropbox folder, executing the AppleScript via Hazel, which then imports the PDF into Evernote. Using this method (#2) is more redundant and inifiiceint.
B. Once the PDF is in Evernote, I can then open it and start annotating. As soon as I save, the annotations will be saved in Evernote and synced with the cloud. However, this will eat up your allotted monthly sync limit with Evernote, as every annotation will re-sync. To prevent this you can import into Zotero using option 2, then annotate, then use the right-click > manage attachments > rename to import to Evernote. Whatever floats your boat!

Future Improvements

The biggest inefficiency in my workflow right now is when I import into Evernote from Zotero. I have to manually move the imports into the correct notebook and then add tags myself. However, I have found an app that can potentially solve this. It is called Paperless, and it is essentially a script that can scan any document and match conditions you set, then import and tag that file. Check it out here.

Copying the notelink (from Evernote) to Zotero is the only missing piece of the puzzle that I do not know how to solve. I know the method to do this will be via AppleScript, but I do not know how to call up the most recent document in Zotero and paste to it. If anyone knows, please leave a comment.

In the future I would love to move to an all open source workflow. However, Evernote and its cross-platform apps, as well as the web-clipper and OCR search feature make it the current cream of the crop. But last night I stumbled upon an app by the name of Paperworks that looks promising. It is still relatively early on in its development, but it looks pretty and offers encryption. Read about why it was created on Reddit and checkout the homepage for it too.
Dad
10/30/2015 08:33:45 pm

Wow!!! Incredible son! How you figured that out is amazing!!!

Reply
7/19/2016 04:50:54 am

Hi Chris, I really like your article, thanks for sharing! I used some of your ideas for a workshop on research management, to my PhD colleagues. I'm now planning to write a blog post summarizing the workshop. Can I use some of your images on it - obviously giving the credit? Best of luck!

Reply
2/10/2017 12:01:49 pm

It's been more than a year since you've posted this workflow. How is it working out for you? It's better than anything I've been able to come up, but it's still quite complicated and I'm sure if I implement it I will likely fall back on other habits. I'm interested to hear how useful/easy you've found it and whether you are sticking to it still, or if you've found a better solution.


I love evernote for it's search, gathering and organizing capabilities, but I prefer zotero for my references because of the automatic metadata and Word integration. If only they can be efficiently combined in the way you describe conceptually.

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Daniel
8/9/2017 09:36:11 am

Do you know how he defined "theFile" in AppleScript?

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Przemyslaw Piotr Damski
5/9/2018 01:30:16 am

Fine thing, but how to do it if I work on Windows rather than iOS?

Reply
Doug
11/5/2018 02:45:55 pm

Great write up! I've been using evernote for years, and recently realized the benefits of also having a reference manager. Your workflow helped me to implement a similar workflow on Windows. I want to point out (for windows users - not sure about apple) that Evernote has a feature to automatically import files as notes from an "Import Folder" (Tools->Import Folder). I believe this would help to take the place of Hazel/Apple Script. My workflow is then: Webpage -> Zotero + ZotFile-> Evernote + cloud storage (i.e. my ZotFile "Location of Files" is the same folder as my Evernote "Import Folder").

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4/14/2019 01:16:50 pm

Wow, this is remarkable. I came across this in a circuitous way. But I'm blown away by your creativity.

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