How to read a scientific paper

Introduction

 

Whether you are getting started on a research project or are handed a first scientific paper to read for a class or lab meeting, sitting down to read some primary literature can feel daunting. But never fear, you have lots of support to succeed.

In this post, I will discuss:

  1. What is a scientific paper?

  2. What are the parts of a scientific paper?

  3. How do a read a paper?

  4. How do I find new papers?

Also, check out my YouTube video on this topic here.

Our lab's research was recently featured on the cover of the journal, Nature.

Our lab's research was recently featured on the cover of the journal, Nature.

What is a scientific paper?

You might be wondering how a scientific paper differs from an article you might read in a newspaper or a book. Scientific papers are usually written by teams of scientists (rarely a single scientist) are are meant to either (1) present new data (known as a research paper) or (2) summarize existing literature (known as a review paper). These papers are usually written up by scientists as a manuscript, then submitted to editors of a scientific journal for review. Editors at a journal will send your draft manuscript to (hopefully) experts in your field, who will read your draft and give you comments. This process is known as peer review. After your paper has been reviewed, the editor will decide whether the manuscript will be accepted without modifications (this happens extremely rarely), whether the paper will be accepted if the authors make changes based on the reviewers’ comments (revisions), or if the paper is rejected from the journal. After often several rounds of reviews and revisions, a paper will eventually be accepted and then published in a journal.

What are the parts of a research paper?

Most research papers have the following (although not always in the same order):

  1. Title: The title of a paper generally summarizes what the paper is about and sometimes even states the key conclusion of a paper

  2. Abstract: A paper's abstract is a brief summary of the paper, including the purpose/motivation, a brief description of the methods, results, and conclusions. You can read the abstract to decide whether a paper is relevant to your interest or use is as an overview of the paper before you read it.

  3. Introduction: The introduction summarizes the relevant background information for the paper and sets up the authors’ hypotheses. Ideally, the introduction will explain why the research is novel and/or relevant.

  4. Methods: This is where the authors describe what they did and how they did it. This may include experimental methods, analytical methods (mathematical equations), or statistical methods.

  5. Results: This section describes the conclusions made from the data. Usually, this is accompanied by several figures with figure legends that describe the figure.

  6. Conclusions/Discussion: This section interprets the results section and connects the results to the hypotheses in the introduction. Oftentimes, this section will contextualize the results into the broader literature and propose future directions or shortcomings of the presented research.

  7. Acknowledgements: This is where the authors acknowledge individuals, organizations, or other sources of help for their work as well as any funding sources.

  8. References/literature cited: This is where the sources cited throughout the paper are listed. The citation style used in the paper is set by the journal. If you have to make a references list, use a reference editor like Zotero, Mendeley, EndNote, or Pages (more information on this at the end of this post)

Not all papers are research papers: reviews and meta-analyses

Not all scientific papers present original research, which I what I described above. Some papers (review papers) summarize a swath of research, while others (meta-analyses) also summarize a swath of research, but do it by combining data from a bunch of original research papers and do some new analyses to gain additional insights. These papers generally have different structures, so I won't discuss them there. However, these are also very useful papers to read and review papers especially are good places to start for beginners.

Reading the research paper:

Where do I start?

  1. Read the Abstract First, read the abstract. You may not understand everything, but it will give you a mental "roadmap" for where the paper is going overall.

  2. Read the Introduction Second, read the introduction. This is where the "big picture" and relevance of the work in a broader context will be introduced. There will definitely be lots of terms and new ideas you haven't heard of before. No worries, if you want to learn more, check out the citations and try to read or skim those papers too. It's not a big deal if you don't understand every sentence. I think a good test is, after reading the introduction (maybe a few times), could you summarize the main point in 1-2 sentences?

  3. Read the conclusion Third, skip to the end of the paper and read the key conclusions. After having read the paper, what did the authors want you to take away from? Write down 1-3 main points the authors stress in the conclusion. Be on the look-out for those points earlier in the paper when you read the methods and results.

  4. Read the methods Fourth, skip back up to the methods and see what they did. Oftentimes, you will be presented with a new method you are unfamiliar with. It's a good idea to try to google it and learn more! It's okay if you don't understand all of the details, as long as you have a sense of what the authors did generally and why.

  5. Look at the figures Fifth, now that you have read the conclusions and the methods, look at the figures and try to write the main conclusion from each of the figures. Oftentimes, you can highlight a line in the results section and often also the figure legend that states this as well. Ask yourself, does this figure support the statements they made in the results section?

  6. Read the results section. For each result presented in this section, try to connect/draw a line from the sentence to the figure (or part of the figure) that supports that sentence.

  7. Re-read the conclusions section Now that you have read the entire paper, re-read the conclusions section and see whether the points you wrote down initially are still supported/you think the same. Oftentimes, I find myself making different conclusions or emphasizing different points than I did initially.

  8. Re-read the abstract Now that you have read the entire paper, re-read the abstract. Does each sentence make sense, given what you have read? Have you taken away the same major points from the paper as what was emphasized in the abstract?

Wow, that took me a really long time.

It takes me 30 minutes to an hour to read a paper when I want to understand it in-depth. And I have been reading papers for a long time. When you are just beginning, don't be discouraged if it takes 1-3 hours to read through a paper. I'd try to read it yourself the first time, googling things as needed, and then discussing it with a friend. After discussing with a friend (discussion points below), then go back and read the paper again on your own with fresh eyes.

This is for reading papers in-depth. Not every paper needs to be read this in-depth. Sometimes, you only care about a small portion of a paper or a general idea. Then, it's totally normal to scan it or just read the abstract. This will come once you have more experience reading papers. Don't worry!

Right now, just focus on reading a single paper at a time and understanding it really well. Practice makes perfect!

Discussion points:

Now that you've (tried) to read a paper, how do I know whether I understood what was going on? Here are some questions you might want to ask yourself (or a friend) to evaluate your understanding.

Introduction

  1. What are the big picture questions that this paper aims to address?

  2. What prior research has been done on the topic?

  3. What makes this research question new, novel, interesting, or important?

Methods

  1. How did the researchers conduct their study?

  2. Why did they conduct their study the way they did?

  3. If the researchers had made a mistake in X, how might that change the results/conclusions?

Results/Figures

  1. What is the main conclusion from each figure?

  2. What does the figure axes mean?

  3. What does each point on the figure represent?

  4. Are the data-points represented on the figure from the raw data, or have they been modified in some way (averages/means, log-transformed, a calculated metric from other data, etc.)

  5. If there are multiple figures, how do they work together to allow the reader to draw a broader conclusion?

  6. Write the key conclusion from each plot

Conclusions

  1. Are the conclusions supported by the figures? Write down which figure supports each statement in the conclusion.

  2. What is a logical next experiment for the researchers, based off this paper?

  3. What is the relevance or broader interest of this research?

Finding more papers for a literature review

Now that you're comfortable reading one paper, it's probably a good idea to read several papers as part of a literature review. This is where you read many papers in a single subject area to get a birds-eye-view about the topic.

For example, I did a literature review of all papers written about nectar microbes a few years ago and published it in a review paper: http://web.stanford.edu/~fukamit/chappell-fukami-2018

But how do you find all of the papers on a given topic? Here are some helpful hints:

  1. Find a review paper on the topic of interest. Read the review paper and all relevant papers that it cites AND cites it.

  2. Read the citations for research papers you've found on the topic of interest, especially those cited in the introduction

  3. Read books or book chapters published on your topic of interest

  4. Talk to experts around you (grad students, postdocs, faculty, undergrads) that may have suggestions for you

Where can I look for these papers?

Great question!

  1. I generally start with a paper that I like and then branch out, reading that paper's citations, and those citations, and so on.

Search Engine: There are special search engines for scientific papers. The best is Web of Science which most institutions have access to. This is a site where you can search for high-quality research papers and filter by discipline. Another option, which is definitely not as good, is Google Scholar. Scholar has many more papers than Web of Science, but is so broad, it makes it hard to find what you're looking for.

Very useful operators:

"anything within quotes is searched like a word" (exact match) adding an * after a word will search for any word that starts with the thing before for . For example, communit will return community and communities.

  • Pro tip #2: Finding good keywords is important to getting the papers you're looking for. When you're reading papers, look for important words or phrases in the text, especially the introduction. Most papers will also highlight "key words" in the journal they are published that you can use to search. Search for lists of keywords or phrases, not full sentences.

  1. Google updates You can set up Google Scholar alerts, so that Google sends you an email when new papers come out that have a key word/search term of interest.

Additional Resources:

I made a video summarizing these topics here:

How-tos:

Notebook for reading papers

Citation Manager:

aka, how do I save these papers?

Once you've read several papers, you may want to store them in an organized way and refer back to them. There are citation managers, which are programs where you can save papers inside of them and they will automatically make in-text citations for you (in Google Docs or Word) and bibliographies. I'd suggest using Zotero: https://www.zotero.org/

Callie ChappellComment