In this post I will be taking a rather major departure from the normal topics I cover to discuss something very dear to my heart: digital productivity! I will be presenting a system for digitally capturing, organizing and retrieving the key information from academic papers to ensure that you have the information you need exactly when you need it without tiresome searches.
I am in the 3rd year of my PhD now and I have spent far more time than I probably should have in developing digital systems to help my productivity. This has slowly led to a fairly sophisticated digital organization system, a part of which I want to share with you today. The main reason for this is that while I have stolen almost every digital productivity system I use from someone else, I actually developed this portion of it myself, with a lot of trial and error, and I think it finally works very well. Two final things to say are that I use Evernote on Windows but as far as I am aware everything I suggest here should translate over to mac (at least functionally if not button->button). Also I will be assuming you are already a user of Evernote so I won’t be introducing basic concepts – there are so many good guides elsewhere it isn’t even worth giving a link! – if you are new to the software and I suggest you read those first.
So, if you’re ready, let’s get going.
Firstly, you might be tempted to store your paper pdf’s in Evernote – don’t. Mendeley’s auto meta-data population (i.e. bringing in abstract, author, year, journal etc) and intelligent search function make it far more powerful for this.
No, Evernote is for your personal notes on those papers.
The rest of the post will be separated into three broad sections corresponding to the vital steps of any information processing system:
There will also be some bonus material at the end in ‘Extra Tips’.
Step 1: Create New Tag / Notebook
So when you start taking notes on a new paper, make a new tag for that paper. You could also make a new notebook for each paper (I used to do this) but there is a 250 notebook limit which doesn’t take long to hit in some fields (Ps. If you are interested in using a tag-only system in Evernote see the final section ‘Extra Tips’). I recommend naming the tag / notebook by ‘Year: Authors’ e.g. ‘2015: Jim Bob & Frank’ (oh by the way if you use tags you can’t include commas between authors names – Evernote will get very upset if you try). The reason the year needs to come first is so that once you have multiple tags / notebooks for your various papers in a list they will be automatically sorted by year.
Step 2: Go through paper taking screenshots / notes
The next step is just to start transferring the important stuff from the paper you are reading into notes in Evernote. For speed, I highly recommend screenshotting. Especially for the graphs in a paper, you are going to be want to be taking screenshots, but I am not talking about those old-fashioned whole-screen print-screen things. Find out how to take screenshots of only a portion of the screen. On my computer it is shift + win + s but I think I may have set that up in the far distant past so you might need to look up how to do it on yours.
Step 3: Paste them into notes – single ‘idea’
Paste these screenshots into a note in your tag / notebook and give it a meaningful title. Don’t be tempted to put loads in a single note – try to keep each one to a single ‘concept’ or ‘idea’ – it will make it easier to understand what is in each at a glance later, and will ensure you don’t overlook things ‘further down’ the note. Feel free of course to add your own notes above or below summarizing what is going on.
Step 4: Don’t forget the annotation tools!
Don’t forget the awesome attachment ‘Skitch’ which you might have to download separately but which allows you to add really eye-catching annotations to the notes you bring in very easily.
Step 5: Screenshot text in too!
I personally screenshot text in as well as graphics. You can of course copy it in as text, but I find this makes a nice division for me between the notes I have brought in from the paper and the notes I then make on those notes.
Also on a lot of pdf’s when you copy text over some of it becomes corrupted or is formatted weirdly etc.
I tend to highlight important sections within the paper itself before screenshotting so that I have those highlights in Mendeley too if I ever want to flick through the paper there.
Now that we have got our stuff into Evernote it is time to organize it. These leads us to …
Step 6: Create (no ordinary) Table of Contents Note
Step 7: Make it into a personalized summary note
So you make a table of contents note by selecting all your notes on that paper and clicking the ‘Table of Contents’ button that comes up. This creates a new note with green ‘links’ to all your other notes in it. But we won’t just leave it like that – oh no no. This will be our ‘summary’ note and it is where the real magic begins. Firstly title this note with exactly the same title as you gave the notebook / tag you used to group all your notes on this paper i.e. ‘Year: Authors’. Next at the top of the note give a brief description of the paper – like a personalized abstract – a few lines which will work with however your mind works to immediately remind you what paper this was from the dark recesses of your memory when you come across it again half a year down the line. Secondly add a little more detail to your ‘links’ to the other notes so that when you scan this ‘summary’ note it is clear what is in them. Now …
Step 8: Tag it with ‘PaperSummary’ (non-negotiable) and any other tags needed
Next, we tag this note only. Unless you have any particular reason, you don’t need to tag any of your other notes. Firstly this would take ages so you probably wouldn’t keep up the practise in the long run, and secondly all the ‘lesser notes’ are already linked in this note, so there is no need really.
Firstly we add the tag ‘PaperSummary’ or something similar. This is non-negotiable and you will see the benefit shortly. Then add other tags to describe the paper itself. When I first started this I added 10+ tags to each of my paper summaries, and soon found out that I was only actually using 2-3 of them. Think about the most important sub-categories of your academic life. For example, I am interested in the presentation of risk, and I am interested in which papers look at visual presentation vs verbal presentation so I always tag my summaries as ‘visual’ or ‘verbal’ – I am also interested in whether papers are about ‘Frequentist’ or ‘Bayesian’ statistics so I use those tags also. In some ways it is better to over-tag than under-tag, but also, if tagging becomes too much of a pain then there is a tendency to just stop doing it at all, and then your system really will fall apart. If you are really in a rush then you could add a ‘ToSort’ tag which you would need to review regularly to tag them up properly.
Ok so you have all your paper notes in Evernote, with summary notes which are tagged up. What did we do all that for?
Step 9: Filtering
Once you get beyond 10-20 papers organized in the way I have outlined above, you will really start to see the benefit. Now search for the tag ‘PaperSummary’ and all your summaries from all your papers will come up, in order of when they were published (because we put the Year at the start of the name of each one). Now depending on what you are looking for you can begin to sub-divide these by your descriptive tags – for example I might, as I said above be writing a paper about visual presentation, so I only want to look at those during my research – or perhaps I only want to look at those who looked at visual presentation of risk and at Bayesian statistics, or visual presentation and frequentist, or any other combination! Furthermore once you have found the papers you are interested in you have a personalized an organized summary with links to all the important information on that paper. I struggle to imagine an information retrieval system which could bring you what you want more quickly than this with current technology – if you know of one please tell me and I will put off my real work for another couple of weeks to implement it. This system is also helpful if I want to find a paper but can’t remember exactly who it was or the year – I probably know if it was, say visual or verbal risk presentation, and Bayesian or Frequentist statistics, so if I sub-divide by these then I have a much smaller list to scour through than if I were to search through all my papers one by one. You also of course have a powerful search function if you remember any snippets of text that might be in it. Further you don’t have to explore your papers through these summaries. You can just go to all your paper notebooks / tags (whichever one you chose) and search through them by year (or search for author names) to look at all your notes for that paper. If you click on notebooks/tags and search for a particular author’s name only also, it should bring up every paper they were author on, whether first, second, third, etc … lots of options!
Finally, another great thing you can do at this point is, if you are writing a literature review for a paper or an article you could make a new tag called ‘NewLitReview’ and then as you go through all your summary papers, filtering etc, and then tag the ones you think will be important to the write up with this tag so you can refer back to them anytime and have them all in one place. Once you are done with this review, just delete the tag!
If that isn’t enough to wet your appetite, wait until you see ..
Step 10: Areas Overviews!
So say you are writing a paper on visual presentation of risk, and you look at all your notes on this area and there are still loads – 30, say – way too many to get your head around simply by reading through one by one. How can Evernote help here? Summaries of your summaries, that’s how! Select all the papers you are interested in and make another Table of Contents note.
Step 11: Area Overviews continued …
So as you can see in this link I have a bunch of green titles: these are links to the paper summaries of each of those papers – just like the paper summaries above had links to the other notes about that specific paper. I then have a brief summary of each paper in this area written below the link for that paper – I tend to put them in chronological order (which should happen by default if your list of papers was already in year order, which it should be if you followed the steps above) – and this allows me to really easily scan through and get an intuitive feel for the area very quickly – sometimes if possible I just put the main graph from each paper and one sentence like ‘No effect’ ‘Mild Effect’ etc …. This is often the first stage in preparing to write a literature review (or part of one) for me. At the top of this note it might be nice to write a brief summary of the area as a whole also e.g. ‘Mixed findings, some found a difference between the groups, some didn’t’. Now this is as high as I have ever gone in terms of ‘Summaries of summaries’ but in theory, depending on your area it might be helpful to keep going, so I might have another even-higher-level summary note with links to the ‘Visual’ and ‘Non-Visual’ areas of my field, to compare them perhaps, or compare the ‘Frequentist’ and ‘Bayesian’ areas…. In theory you could have one master summary note just called ‘Statistics’ which would define your entire field and then have links to these four areas, which would have links to …. You get the idea.
Ok I hope all of this has been helpful to you. If you’re thinking ‘But what about the actual write up?’ check out my companion post here
If you still aren’t satisfied, read on for some extra tips and tricks.
Some Final Tips
When you don’t have time…
Firstly, if I ever come across a paper but I am in way too much of a rush to go through the whole process above, I just make a tag / notebook for the paper, make a blank summary note immediately (you can copy the note links in later – you don’t have to do it by making a table of contents note), tag it as ‘PaperSummary’ and ‘ToRead’ and then just screenshot the Title and Abstract over. Done. Once you are quick this takes maybe 30 seconds and if you stick religiously to the rule that you will always do at least this for any relevant paper you come across, it ensures no papers get lost or forgotten about. I guess if you are out and about with just your phone you could even just make the summary note with the year, author, PaperSummary and ToRead tags, and that would suffice to remind you in the future to look into the paper – but I don’t really come across many papers when I am out and about to be honest …
Another thing which can be handy is to create a note for every paper and copy over the text from the reference section from that paper. Tag all of these notes ‘References’ or whatever. Then you can search within just these notes for a given paper to easily see who has cited them.
Finally, if you go the full-tag route … [serious nerdiness alert]
So I am one of those nutty Evernote users who only has three notebooks. One for Inbox i.e. if I don’t have time to sort a note right now, it just goes in inbox and I sort it later. I also have one main notebook (Cabinet) where almost everything eventually goes. The entirety of my organization beyond this point is achieved through tags.
Tags are in theory better than notebooks because notes can belong to multiple tags but only one notebook, and everyone knows the anxiety created by grey areas between two hard-categories (e.g. is this bioengineering note really about Biology or Technology? – well both dangit!). Tags are soft categories – no anxiety needed, just tag them as both! Also you can only have 250 notebooks max, which didn’t take me that long to hit when making a new one for every paper I read.
Anyway, if you do want to go the full tag route, I recommend a system broadly like these:
You don’t have to do it exactly the same but the key point to take away is to use punctuation marks to create different ‘types’ of tags. I use the ! sign for tags relating to areas of my life (e.g. !Personal, !PhD, etc.), the @ sign to refer to tags relating to areas of knowledge (e.g. @Psychology, @Biology) and the . (full stop sign) to refer to tags relating to the type of note it is (e.g. .Article, .Paper, .Idea). I also use the $ sign for tags regarding important people (e.g. $JosephThomas). This system is helpful when you are both tagging your notes and also when searching your massive ‘Cabinet’. For instance if you click on Cabinet then click on tags, and type in ! it will bring up a drop down list of all your ‘Areas of Life’ because they are the only tags that begin with ‘!’. Then once you have chosen an area of life, e.g. ‘!PhD’, you could type in the @ sign, and it will bring another drop down list of all the areas of knowledge within PhD (it will only show tags with at least 1 note within your current search area), and so on … So this system stops you feeling like you are just lost in a sea of a hundred tags and allows you to feel like you understand the ‘structure’ of your note system a little better.
A system like this is also far more minimalistic / clean than a full-notebook system as you can have ‘.Idea’ notes about ‘@Biology’ or .Idea notes about your ‘!Writing’ or even about ‘$JosephThomas’. With a notebook system you would have to have a sub-notebook within the Biology notebook for ideas on that, another one within Writing for ideas on that, another one within JosephThomas … once you give in to the full-tag system, this kind of messy organization will send a shiver down your spine.
[06/05/16 Note: I believe the below has now been incorporated natively into Evernote version 6.0 so you shouldn’t have to go through the hassle of changing regedit files yourself – I’ll leave it in place a while just in case it’s helpful for someone]
However, if you do go the full tag route, there is one more really important thing you will have to do. What drove me nuts when I first did this, was that if I clicked on a tag, then made a new note, the new note would not be tagged with the tag that I was ‘in’. This is different to notebooks. If you are currently ‘in’ a notebook and make a new note, it will be stored in that notebook. This lack of function with tags led to waay too many of my notes being lost in the ether due to me forgetting to tag them with the current tag. However, there is a fix. It requires a little fiddling around in the windows systems – but don’t worry it isn’t too hard.
Firstly close Evernote. Now to go to the ‘Run’ application (you should be able to just search for it from the start menu) then type in ‘regedit’ and click ok. When the window pops up go to HKey_CURRENT_USER/Software/Evernote/ Now click on the Evernote folder and scroll down the list of … whatever they are … until you get to the one called ‘SetNewNoteTags’. Double click on this and change the ‘0’ value to ‘1’. Don’t worry, you won’t break Evernote!
NOW, click on a tag, any tag. Make a new note. Fill in the title of the note and press enter. Magically, the current tag will be assigned to the note. AHHHH. No more stressful losses of notes. So when we make a tag for a paper, and click on that tag and start making notes on the paper, they will all automatically be assigned to that tag – goodbye notebooks!