How do you research?
August 10, 2016 1:44 PM   Subscribe

I work in public health and have worked on a number of different qualitative and quantitative research projects. I feel like my method of managing and taking notes on background research is sub-optimal and I could dramatically improve my strategy. What do you do?

I am relatively early in my career (bachelors, no master's degree) and I have developed a hodge-podge method of keeping track of references since I started doing research. In the past I've used Mendeley to manage all of my references, but I don't love it because I don't feel like I can keep good notes.

I'm curious how people organize their thoughts when you're diving into a relatively unknown topic. Often times, I read an article and pull out quotes or jot down ideas in a Word doc with the full citation at the top and then continue article by article. I then go through and copy and paste all of the citations into my reference doc. I feel like there's a better way to do this.

What do you actually do when you're reading through an academic article? Where do you put quotes? How do you manage citations?

Looking for: systematic ways of keeping track of all of my thoughts and references electronically. Explain to me like I'm 5---what's your step by step process?
posted by allymusiqua to Education (8 answers total) 35 users marked this as a favorite
This is where Endnote is your friend. I personally don't do many in-pdf citations but often put the quote I want in the notes field. Although you can annotate PDFs with it .

I use subfolders for each subcategory of research eg policy-> local government-> smoking-> footpaths. My uni did endnote training online, which is useful. Admittedly I had a bumpy start with it and moist of my academic friends don't use it. Many still use word!!! But I think endnote is great. And it has a cloud-like capability which is handy as you travel around.
posted by taff at 1:59 PM on August 10, 2016 [1 favorite]

This is really one of those things where you have to develop your own style. I am glad that I developed my system at a similar career stage to where you are now. Before I used papers, I filed pdfs by undergraduate course as I took the courses. I have adapted the system that I use a bit over the years.

I use Papers which has similar features to Endnote to organise research articles. For citations when I write myself I use LaTeX and Bibtex.

When I read an academic article, I print the PDF and have pens and highlighters to hand. I read research articles in the order: title, abstract, discussion and conclusion, figures and tables together with their captions, then, if I still need to, anything else. Once I am done, eventually I file the paper PDFs and I find that I rarely refer to them again, but the physical read-and-highlight process and even the process of filing the papers grouped together by relevance helps me to keep my ideas together. I do not take notes electronically via Papers, although one can. I do not find reading from a screen particularly effective - I need to interact with what I am reading when I read it hence highlighting and making notes directly on the articles I read.

If you have a goal in mind for the background research that you are currently doing - for example, an exam or a report to write - this could be the driver for developing a system now. If you stay in research you might end up glad that you put a system together early on. My Papers library has more than a thousand references in it, going back to roughly your current career stage.
posted by Erinaceus europaeus at 2:38 PM on August 10, 2016

Download Citavi (free version) and see what you think. It's an example of citation management software. Basically, you load in your PDF journal articles or books or etc. and it automatically grabs authors, bibliography, abstract, etc. Then you go in and write a commentary on what you've read. Can include cross-links, eg "This is the study that Johnson (link) refers to as a "previous simplistic incarnation", but I feel it's still relevant in situations like ours. See especially Figure 4 with the data at high density." That's not using it to its fullest, but I'm in the sciences, we're much more likely to refer to a summery of the results than to quote a block of text, so I am unfamiliar with its quotation management options. Largely I use it just to do the file management; my grad thesis I had adopted a nomenclature for journal articles "Smith2001_Journal.pdf" so that I could find things when the automatic file names are at best semi-meaningful but varying by publisher and at worst a random string of numbers and letters. So Citavi creates a library, which is great.
posted by aimedwander at 2:40 PM on August 10, 2016

Best answer: I am a mixed-methods researcher. Everyone's process is different. Here's mine:

1. I use Zotero to manage all citations. If I am working on a specific project, I create a folder for that project in Zotero titled "Year_ProjectName" and all citations that are imported are sent directly there. I also have a folder on my computer called "Studies" and for each study I have a folder titled "YearStarted_ProjectName." This is where drafts, etc. go. I try to version my files but am not great with this, but I have Dropbox Pro and that has a rudimentary versioning system. I do use consistent filenames, e.g. "Lastname_R21_v6_2016-08-10." If I save the PDFs of articles, I have a folder within the study folder and my filename convention there is "AuthorLastName-etal_Year_First-words-of-title." However, Zotero will automatically save and store PDFs and uses its own filesystem so I often just access the originals through Zotero (and make sure that my backup system is backing up that folder as well).

2. I have a dedicated notebook (I use Rhodia 96-page notebooks in orange) for each project and I write the name of the topic on the front. All my notes go in here. If I do not write it down, I will not remember it. When I'm taking notes for an article/book, I write the full citation out on the top margin. When I'm just taking notes about whatever (meetings with collaborators, outlines for papers, etc.), I try to put a title on top but don't always. I number my pages manually and save two or three pages at the front of the notebook and write the page number and the author name/date there so I have a table of contents for later reference. When I take notes, I use lots of different color Paper Mate Flair felt tip pens; the different colors are chosen for different things (my own ideas in one color, ideas that relate to other articles in another color, etc.) I will write out full quotes when needed. I also do not read from my screen and print out every article.

3. When I'm ready to start synthesizing things, I make an Excel spreadsheet. Using Zotero, I paste the citations into Column A. In the top row, I put the different topics or ideas or concepts from the articles that I need to synthesize, as well as some basic stuff like method used, number of subjects, location of study, etc. Sometimes I will also use the Tag feature in Zotero to tag articles in the folder with different concepts, but this depends on the size of the project on which I'm working.

I developed this system as a master's student and although my notebook brand has upgraded considerably to accommodate the felt-tip pens that I prefer, this has been how I've consistently done things for almost ten years. It works for me but would not work for everyone. The important thing is to find a system that works well for you and to stick with it once you find it, and not get tempted by shiny new tools unless what you are doing is really is no longer working.
posted by sockermom at 2:50 PM on August 10, 2016 [11 favorites]

I use mendeley for managing PDFs and making a bibliography - I tag with the project, then search in the tag, select all, and copy as citation. I also like that mendeley backs my papers up to the cloud and renames the files using a customizable convention and it's highly searchable. I use a watched folder to add stuff and it works great. But the note taking function sucks, you're right.

I take notes into a lab notebook, basically. Author, year, summary of title before notes, margins get code for the project associated with the notes on each page, mark papers from citations to go back and look up. Then I make a general outline and go through and plug notes into the outline with cites. This makes it easy to see where I need more references.
posted by momus_window at 2:50 PM on August 10, 2016

Over the years (four years in a PhD), I've tried a lot of different things, and have developed this system for organizing my research.

All papers are saved as PDFs to the same folder, with a standard filename format to make finding them easier, e.g.: "Kastenholz 2006 On distributed predicate syntax.pdf"

All papers are entered into BibDesk as soon as I finish reading them.

All papers that are relevant to a project I'm currently working on -- even if I'm just building my understanding and not necessarily citing them yet -- get added to an "annotated bibliography" in Scrivener, which works like this:

Each paper gets its own document, which is tagged by keywords so I can later view all papers related to "tonal alignment" for example. This document contains either the abstract or my own summary. I make sure to state, in my own words, (a) what contribution this paper made, (b) how it is useful to me, and (c) how it relates to other papers I have read.

I also have separate documents for important theories/concepts that I add to as I read. So for example, if I'm exploring autosegmental-metrical theory, I have a document that is basically the outline of an introduction to the theory:

(a) What are the foundational papers?
(b) What is the basic outline of theory?
(c) What are important disagreements about the theory?

Then I add more specific stuff as needed, depending on how in-detail I need to go for my own research. This is a little redundant with the annotated bibliography, but it helps me keep track of all of the different threads.

I also have a document where I copy and paste citations that I intend to follow up on. I usually copy a little bit of the context it appears in as well.
posted by Kutsuwamushi at 3:47 PM on August 10, 2016 [1 favorite]

For my first pass, I keep all my notes in a giant word doc. I put every source into my citation list in ReferencePoint (which I don't recommend, but I'm in the habit of using).

When I find something useful, I often dictate a few sentences or paragraphs for a lit review using Dragon/Nuance (these are always garbage that gets completely rewritten at some point). I usually capture the theoretical framework, research method/sample, findings, and contribution. If there is something funky about the article that I just need to capture in my notes I add DUMP: blahblahblah. I also keep a giant pile of printed articles that I don't use, but they are some sort of safety net for me.

As my research starts to accumulate, I start creating my structure maybe grouping chronologically or by framework or something. At this point I'm writing in my head - I do a ton of writing and outlining in my head, and my first draft is usually pretty close.

I know that there is a better way to do this and will be following this thread closely.
posted by 26.2 at 11:03 PM on August 10, 2016

I did a half a PhD in physics. I use zotero to keep track of all documents, divided into folders by project I'm working on, I generally also save the most important papers to a local folder as pdfs, and then keep notes about how I want to use sources, etc in a paper notebook (same one where I write everything else. I use one at a time and number them chronologically).
I'm a bit of a disorganized researcher though. I rely a lot on my memory. That said, I think your citation manager is your friend. Find one you like.
posted by switchbladenaif at 11:53 PM on August 10, 2016

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