Someone asked me to explain my note taking techniques a few weeks ago. I have been putting it off because it seems like a time-consuming task but I feel I need to do it!
Taking notes from reading literature papers has always been a struggle. I used to use Endnote to store and manage all my references and have my notes in MS Word documents. Depending on the paper or the task, I would store the notes in separate files or in a working document, such as a literature review. I would read the papers a few times, making notes along the way in a Word document . Sometimes I would copy text as a direct quote or I would try to reword text as much as I could, often in dot points. When working on a literature review I would throw things under relevant headings and then try to stitch it together. This did me fairly well when doing my Honours Degree and through to doing my PhD.
However, thanks to a YouTuber, Danny Hatcher, I was introduced to two new applications that changed and enhanced my note taking and literature management. Best of all, they are both are available to use for free!!! The first was Obsidian which is a note management system. It is better that MS OneNote and most of the other note management software. At first, Obsidian may seem overwhelming to get your head around. There are many YouTube videos on how to set it up and and use. Danny Hatcher is a good teacher so look at his channel.
The same YouTuber, Danny, also introduced me to a literature reference management software Zotero. It is much better than Endnote, I must say. One of the main features I like in Zotero is the magic wand. You give it the DOI number of the paper you want to add to the library and it will get the details for you and, in most cases, also the PDF file. Love it. The other important feature is the PDF reader. It allow you to highlight text and insert annotations as you are reading. These highlighted direct quotes along with your annotations are then available outside the PDF. If you set things up right, these can be exported to Obsidian.
The community add-on for Obsidian I currently use is "Citations" using a BibLaTex library format. See YouTube videos for guidance on how to install the add-on.
In Zotero, the add-ons "Better BibTex for Zotero", "Zotero Word for Windows Integration" and "ZotFile". Again, check on YouTube for the latest requirements.
My main work flow
1. Import paper to Zotero, manually or using the magic wand, including the PDF file.
2. Read the paper and on the way highlight any text I may need. I nearly always add annotations to each highlighted text unless it's going to be a direct quote I want to use. My annotations are very rough most times but they are summaries of the content in my own words.
3. Once I have finished reading and making notes, I right click and select "Add note from Annotations".
4. Right click again to Export item.
5. Export annotations to the Zotero directory (always overwriting the previous annotation file).
6. Within Obsidian, I open the annotations file
7. Select all (ctrl-A) and copy.
8. Hit ctrl-P, select "Citations: Open literature note" and select the name of the paper.
9. Paste the annotations at the end of the note.
10. Now, you can copy and paste your notes to your literature review or whatever document for future editing.
11. If you paste to MS Word then delete the Obsidian Citations and add them in using the Zotero plugin so it automatically creates a reference list in whatever format you have chosen (I use APA7).
This is a rough guide. Please check for updates on the relevant websites.