Searching, reading and organizing your literature

Having recently finished my PhD, I understand what it’s like when I see graduate students in my lab struggle with scientific articles. Whether it's finding them, reading them or keeping track of them - I hear ya.

For this reason we decided to bring it up as a topic in our weekly Journal Club discussion group. What is the best approach to tackling scientific literature? How do you hunt down the right articles? How do you read them efficiently to retain the most information? And how do you manage all the open tabs, PDFs and stacks of papers that flood the lab.

It all starts with reference managers. If you’re not currently using one, this is me telling you to download one and start using it immediately.

The most popular ones in our lab are:

Mendeley: This is the only one I’ve ever used, which is why I’m biased when I mention it. However, I do find it has some bugs, particularly when using the Word plug-in. But that could just be my institutions’ admin settings.
Zotero: this gets the most raved reviews from certain enthusiastic lab members. I hear it's the best for plug in applications, including building bibliographies in R.
Research Rabbit: this is the newest one I’ve heard and is great for finding articles. Especially when you find that one seminal paper, you’ve struck a gold mind. It also has a plug in to Zotero for easy referencing.(...does this mean I have to make the switch to Zotero?)
Notion: this discussion was the first time I’ve heard of this one, but it deserves a mention. Let me know if you’ve worked with this one before.

Which reference manager do you use?

Mendeley
Zotero
Research Rabbit
Notion

Now let’s get into the thick of it. We can basically break it down into 3 steps:

Step 1: SEARCHING | Step 2: READING | Step 3: ORGANIZING

Step 1: SEARCHING - You have to actually search for those articles.

Searching starts with a good database and the right keywords. Here are our labs’ top databases when hunting for a decent scientific article:

Web of Science
Research Rabbit
Bibliometrix
Google Scholar (be sure to use specific dates to find recent articles or look up experts in your field and browse their publications)

But alas, a good database is only as good as the keywords used to search it. Never underestimate the power of Boolean operators (AND, OR, NOT).

Here’s an example: imagine you’re searching Zotero and you want to search for remote sensing papers related to forestry or silviculture, you can search using the following:

Remote sensing AND (fore* OR silvi*)

Here’s the breakdown:

Remote sensing: your main keywords

AND: include the main keywords and the other terms (indicated in brackets)

OR: either of the keywords may be present

The * indicates where the search can stop the word. I.e. fore* can include forestry, forests, etc .

There are a lot of variations but these are the basics. Note the same rules do not apply for Google Scholar.

Other resources to find articles can include social media sources such as:

Twitter - following people and labs in your field that tweet recent publications can be a great tool.
Research Gate provides access to a lot of grey literature, reports that are not necessarily published in peer review, Q&A forums and PDFs of articles that are not necessarily open access but are uploaded by the authors.

Some other resources to mention include your university’s online library where you can use keywords similar to the format mentioned above or to gain access to articles from journals that your university subscribes to.

Lastly, emails and alerts from your favourite reference manager or journals can be helpful to keep you updated with recent publications. However, make sure you’re not being bombarded otherwise it will reduce the likelihood that you’ll read any articles. I recommend limiting these notifications to once a week.

Helpful tip: as soon as you see an article that is interesting, download it to your reference manager even if you don’t have time to read it right away. At least this way it will be included in your database when you use the “Ctrl F” when you’re searching for keyword

Step 2: READING - Now you’ve found some articles, but now you have to actually read them.

Let us start off by saying how people read scientific articles varies from person to person and different people may have their own methods or techniques. But i also feel it varies a lot by where you are in your graduate studies. For this reason, I have broken down some suggestions on how to read papers depending on where you are in your academic journey and some key tips.

Scenario 1: You’re at the beginning of graduate school and still learning about your project (your advisor either gives you a reading list or tells you to “read as much as possible” - like that isn’t overwhelming enough)...

Focus on the abstract, the introduction, discussion and conclusion
Use the introduction to learn the background about the topic, the main ideas and the mechanisms that are at play.
Highlight key terminology and references to look up later.
The last paragraph of the introduction is key, as this will tell you what is the objective of the paper.

Bonus tip: use the reference list within the article to look for other papers to read. Highlight the ones with relevant titles and look them up later.

Scenario 2: You’re past ‘Scenario 1’ but haven’t started any experiments or field work and are still learning about the methodology.

To learn specifically about the methods, it may be useful to look at textbooks.
Focus on the methods section for techniques and see if they’re consistent across the most recent publications you’ve read.
In the results section, read the first few lines of every paragraph to get an idea of the results that can be produced using your methods and the variety of ways they can be presented.
Scan the discussion section looking for mentions of limitations to the methods or the data they produced.

Scenario 3: You’ve conducted the experiments/field work and now you’re writing the results or the discussion section of your papers:

You should be able to skip over the introduction section as you are now comfortable with your topic. You may want to read only the last paragraph of the introduction to know the paper’s objective, hypothesis, etc. and see if it aligns with your research.
Maybe skim the methods to make sure they were using methods similar to ones you would use.
Then go right to the results and discussion sections - this is where the good stuff is.
Focus on the figures. This will tell you the most important information and will help train your mind in interpreting data from figures. What do you take away to be the most important points? What do they tell you about the topic, mechanisms or interactions at play? Do they agree or differ from any results you’ve gathered from your own research?
Then read the discussion section. Do the papers’ results align with the ones you concluded? What do the authors’ suggest as the implications of these findings? Is the take home message you gathered from the paper similar to the authors’? What did the authors bring up that you hadn’t thought about or vice versa.

Scenario 4: You just need ONE citation to support a sentence in your discussion (we’ve all been there)

Use as many specific keywords as possible in your search.
Make sure you’re citing studies that actually performed the experiments that prove your statement is true.
Browse the abstract first to make sure the same conditions apply to the statement you’re trying to support.

Secondly, when you read your scientific articles also varies from person to person. After our discussion, we felt that the most important thing is to have a dedicated reading time. This means setting a time throughout the day when you’re most productive. If it’s at the end of the day, make sure it's something you would consider ‘light reading’ and it's ok if you do not retain as much information. If it’s an important paper, make sure your reading time is during your most productive hours.

Helpful tip: Be sure to limit distractions; this can include setting your phone to silent or airplane mode, or using productivity hacks like The Pomodoro Method. If you’re a fan of the Pomodoro Method, here’s an online Pomodoro timer.

A note about taking notes: taking notes is something that can help certain people retain information better. If you’re on these people, here are a few tips that may help:

If you prefer to take notes digitally: Use reference managers like Mendeley and Zotero for highlighting, adding notes and comments.
If you prefer to take notes on hardcopy: Print hardcopies so you can physically highlight and you can read them anywhere. Add important key words or take bullet points in the margins.
My personal trick - one-page bullet journal summaries: I print the first page of the article (saves on paper!) with the abstract and write key notes on the back. An executive summary shouldn’t be longer than one page anyway. I keep a column on the side for references to look up later and always include what I believe to be the take home message. Here’s an example of one that I did digitally (the bonus with this was that I could use hyperlinks to link the references I wanted to look up later).

Step 3: ORGANIZING - Now that you’ve found your articles and you’ve mastered your topic (or not) - how do you keep everything organized?

If we haven’t said it enough, this is where your reference managers will save your life. Forget having folders and folders of PDFs on your hard drive taking up space and making it impossible to locate the one article you’re searching for. Here are some tricks to organizing your PDFs in your reference manager of choice:

Have specific folders within for projects, topics, authors or specific publications you’ve authored.
Star important articles so they’re easy to find and reference back to.
Make sure every imported article has complete reference information. Do this as soon as you import it, otherwise you’ll forget later. Trust me, this will save you so much hassle later on when it comes to citing using a word plug in.
“Control F” is your friend! Use it to search for authors, keywords or methods that you’re looking for.

This may all seem very overwhelming, especially if you’re a new grad student. But this is why it’s important to start your reference manager as early as possible and develop a solid workflow and reading habit for new literature.

Helpful tip: Taking time to read new and interesting articles is not only important to stay up to date with the recent research and methodology but also for the opportunity to think about new ideas and interactions and improve your writing style.

If you have any questions, don’t hesitate to leave a comment or reach out at amy.wotherspoon@ubc.ca

Searching, reading and organizing your literature

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