When reading scientific articles, it may be hard to focus on the message in each one. As a result, it may be challenging to remember the overall message or essential details later. Or you may recall an interesting fact but do not remember where you read it.  This happens especially when you read the articles from start to finish without taking notes. Here is some advice on reading and interpreting the articles and making notes to easily find (back) essential data.

While reading, you should ask specific questions about each article and write down the answers so you can find them back. Store these notes in a logical place, such as along with the reference in your reference management software or in a note management program. The questions will help you focus your reading, and storing the notes will make it easy to find everything back.


Reading scientific articles

Do not try to read the article in one go, from title to references, but instead start at the introduction to get the ´big picture´ first.  Then, scan the rest of the article by focusing on the headings and subheadings and looking at the Figures and Tables. What do you think they found? Look up terms and methods you are unfamiliar with so you are sure you will be able to understand the message.

Now reread the article asking the following questions:

  • Source: Are the authors at a reputable research institute or work for a company or institute with a specific agenda? Do the researchers disclose any conflict of interest (this section is usually below the discussion)? Is the research published in a reputable peer-reviewed journal or a journal without peer review? (see my blog on predatory journals)

  • Problem: Read the Introduction. What problem is the entire field trying to solve? And what is the purpose of this specific study?

  • Methods:  Study the Methods. What was done? Which techniques were used? What was measured?

  • Results:  Look at the figures and tables in the results section. What are the main results?  Do you agree with their description and interpretation of the results?

  • Conclusions:  Read the Discussion and Conclusions. What are their main conclusions? Do their data support the conclusions? Did they answer their original research question?

  • Limitations:  What limitations to their study do they mention in the discussion? What limitations and pitfalls did you notice?

  • Notes: Write down any other noteworthy insight you come across. What is actually new?

  • Abstract:  Read the abstract. Does it represent the data and conclusions correctly?

  • Comments:  Did anyone write a letter to the editor commenting on the research? If so, read all comments and replies. What is their point? If you get the feeling something about the article is not right, you may want to check on PubPeer whether any issues were reported about this article. And check the journal’s website for corrections or a retraction of the article.

  • Relevance: How is this research relevant to your research?

  • Keywords: What are keywords that are relevant to you? This can be a molecule, pathway, method, population analyzed, location, etc.

    In addition, you can leave notes on the PDF and highlight the most important passages to easily find them back. You may need to look up some of the references to understand the background; the references can also be a good source for further reading


Using AI to summarize articles and answer your questions

One of the most popular AI tools at the moment is ChatGPT. However, ChatGPT cannot access internet links, so you cannot use it to summarize an article by providing a link. You can instead upload any PDF to ChatPDF. After you upload the PDF, the program will give you a minimal summary and three suggestions for follow-up questions. It may be better to pose your own questions, which will provide more useful results. Try it out to see if it works for you; it may be helpful to have ChatPDF explain the concepts, especially for complicated articles.

If you keep the prompts you used in ChatPDF in a file, you can easily cut and paste them for the next PDF you want to analyze, and you are less likely to forget important questions.

Potential prompts:

   What is the problem they tried to solve?

   Which methods did they use?

   What were the main results?

   What were the conclusions?

   What were the limitations of the study?

   What is actually new?

Note that ChatPDF is a language tool that cannot analyze figures. It will also be unable to look for replies to the article (like a letter to the editor), corrections to, or retraction of, the article, and comments on PubPeer. Furthermore, always remember that you need to check the results of AI chat programs to ensure they are correct.

ChatPDF lets you upload two PDFs (of a maximum of 120 pages each) per day for free. If you pay a monthly fee (currently $15 per month), you can upload an unlimited number of PDFs (of a maximum of 2000 pages each).

Storing your notes

If you take notes in your reference manager program (see my blog on the importance of using reference management software), you first import the reference (and PDF) into your database. Then, enter your notes in the appropriate field (for example: ´Research notes´ in Endnote).

If you take your notes in a note management program (such as Evernote or Trello), you may want to create a simple template containing the questions you need to answer. In that case, also include the name of the first author, the year, and the label the reference has in your reference management program (I label PDFs with the first author and year).


reading scientific articles and taking notes
Just highlighting text when reading scientific articles will not make it easy to find important information back: make and store notes as well!  (Image by Hebi B. via Pixabay)