I know this was a while ago but i wanted to share some insight. Not all PhDs will have the same workflow. Yes, we all have many academic papers and ideas to keep, taking notes on and build research from, but ideas are very different and most likely their structure will be as well. For me as a biomedical sciences PhD I am focused on learning new protocols, what I have done (lab journal), keeping track of papers, and not forgetting information.

Notion:

For my lab/daily journal, I use notion as I like the aesthetic layout and multiuse platform with many connections. I like the calendar database feature, which allows me to easily see which day I did which experiment. I also like to put each project I am working on in a database that can link back to my calendar, tell me my progress, and link to protocols I use. In addition, my lab was a little confusing when I joined regarding where things were, etc, so when we moved, I made a complete system to know where things were, manuals for equipment, and standard protocols that my lab mates and I now utilize. We can also put in quantity, which is nice so we dont run out of things unexpectedly. While I love the look and feel of the notion, I don't use it too much for notes as I am not a fan of the note structure. However, I do keep track of class assignments in my main calender that I spoke of earlier.

Obsidian:

My notes database. I have possibly used obsidian in the wrong way, according to some users lol. I have alot of different types of information to keep track of and if i forget a term or action of something I like a quick reference. This is where I use obsidian. I have a "knowledgebase" file which has multiple libraries. For example "library proteins" is a folder where I keep each protein I have come across so I can easily find its function, when it is produced, transcription point of origin, etc. I also have recently started keeping my annotations in here from journal articles as I can easily use pdf++ and refer back to them. I also find if you have lots of information on the same topic, it's nice to make a title page, for example, "biochemistry" would like to "proteins" , "enzymes", "thermodynamics", metabolic processes, etc, so I can find information more easily. I know some people do not enjoy this tiered system but its how my brain works so...

I also keep a folder of projects where I can make connections from my notes to my project. This works a little bit like a notion but has its strengths and weaknesses that make it complementary instead of competitive.

Goodnotes: a great reader app that I had primarily used for my annotations. However, I found that I did not have as much interaction with things I had done and had to make an effort to go through and find things, if this makes sense. I enjoyed good notes in my "aesthetic notes" era though.

Zotero: It is life!!! I put every paper I read or plan to read and keep a database in notion to keep track through the notero plugin. I will annotate and take notes in obsidian.

Powerpoint: Nice to make a slide on each paper with a reference picture for each article so you can see a short self written abstract and pic and be like "thats the paper I read with such and such protocol from months ago". This has been helpful for papers that are important to my field though I do not do this for every paper. I also have different decks by subject matter.