Workshop: Scientific Work — General Tips when Dealing with Literature

So, I have written a few postings about Finding & Selecting Literature, Managing Literature, and Reading & Using Literature, as well as a Possible Academic Literature Workflow and Topic Notebooks.

The following tips might be helpful as well:

  • Keep your goals in mind — Remember that regarding literature, having is not reading, reading is not understanding, understanding is not citing, and citing is not publishing. You need to understand the domain and enter the community and contribute with your own works.
  • Browse — Sometimes you find interesting journals when you browse publisher sites. E.g., you can browse APA’s journals by subject and subscribe to interesting journals via RSS feeds.
  • Hang in there — Learning to deal with literature takes time, and it gets easier with time. The better you know the domain, the easier you can integrate new literature and make connections. You will need to write down less and remember more.
  • Find a workable solution (and improve over time) — The way you deal with your literature will change over time. Set the right tracks in the beginning, then optimize when you notice that you can save time. E.g., look for scripts that automate some processes (e.g., extracting and reformatting notes from a file) and adapt them to your needs. The way you start organizing your literature will not be the way your literature is organized later. This also means that you should ensure that you can transfer your literature/notes with little effort to another solution.
  • Get high quality PDFs with OCR (PDF + Text) — Problems with the OCR (optical character recognition, allowing you to highlight and copy&paste text) do not go away. You will have recognition errors in your notes and have to correct them manually. This is tedious and drags down the motivation. Even worse, sometimes recognition errors are not simple “spelling errors”, but they distort the text. It can make sense to buy a book and do a good scan yourself even if the text is available as bad copy.
  • Name the files correctly immediately — Once the file has the right name (authorname_(authorname_)year) you can work with it. It stays tied to the source information. You get into trouble if you start making notes with the wrong or incomplete source information.
  • If you have an edited book, split the book into the chapters — You cite the authors of the chapter, not the editors, and having the files available separately makes it easier to work with the text. But keep the original file of the whole book as well.
  • In reading literature focus on the text — Ask questions, highlight, make notes, jot down ideas. It’s stimulation and canvas. Only when you are finished with the text and it cannot tell you more, then transfer it to your notes (e.g., topic notebooks).
  • Make usable notes — You might only want to jot down a few lines but ensure that you can understand your notes later. If you are interrupted (and an interruption can take days) it might take you a while until you transfer it to your notes. So be conscientious about your notes. It’s like capturing and collecting ideas.
  • Get figures in the best quality — If you extract graphics from the text you read and the file is in PDF format, think about getting the figure as PDF as well. You can extract the respective page in Acrobat, then crop the page to the figure. It keeps the same quality level and you can still select the text in the figure. This requires a program to store your notes that can deal with one-page PDF files.
  • Keep the different parts of your literature workflow connected but independent of each other — You should always be able to easily move digital information. Avoid closed systems like the pest. If you cannot get your information out of it easily (e.g., a literature manager without an export function) don’t use it. You’ll be working with literature for 40+ years, times change and companies and products fold. It should not matter, e.g., that you stop using Endnotes and switch to Sente or that you store your notes now in another software. Personally, I am happy that Circus Ponies Notebook offers an .nbml export. The file can be opened with a text editor and while it looks complicated, for example, an outliner cell looks like:
      <cell cd=”2013-03-24 5:06 nachm. +0100″ md=”2013-03-24 5:20 nachm. +0100″>
          <keyword n=”authorname_year”/>
          <text><p style=”p0″><f style=”f1″>Testentry</f></p></text>
    I think it should be possible to write a script that extracts the text while preserving the source information in the keywords. I hope it never comes to that, but it is comforting that it looks manageable (although possibly a pain in the ass).
  • Tag the Literature you have read — Tags can help you to quickly find the literature you look for. You should at least tag the literature you have read.
  • Monitor the literature you have read — Make sure that you not only read the literature critically, e.g., identify conflicts of interest, bad methodology, biases in interpretation, but that you also notice when papers are corrected or even retracted. Recently, some PDFs have CrossMark, which allows you to check for updates, but you might also want to closely monitor the authors you cite frequently. When you have all information tagged in your notes (e.g., topic notebooks) you can quickly check which building blocks of your work just crumbled to dust if an important paper got retracted. In Circus Ponies Notebook for example, you can see all used keywords in the Multindex and jump to the places in the notebook where you have used something from this article. In other programs, simply use the search function. Besides being necessary for citation, a clear source identifier (e.g., authorname_(authorname_)year) is invaluable to weed out bad research.
  • Build your research identity — What you read and work with shapes your identity as a researcher. It determines the kind of arguments you make — or can make, the questions you ask, the methods you use to answer them (of course you can deviate from the literature with new ideas, but when you have new ideas, make sure they are really new, i.e., hit the literature). Keep track of what you read (e.g., tag what you have read) and make sure others know about your areas of expertise: Share you knowledge and build on it with your own works.

So, this wraps up the series about dealing with scientific literature, next up (in a few days): ideas & data …

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