# using Zotero & notes for research

This isn't a request for technical help but for other researchers & students to share advice & work practices.

I have recently begin using Zotero to manage citations for my PhD and I'm really happy with it. I was recommended the notes function by a fellow student but I can't get my head around it, so I'd like to hear how others use it.

My current system is to use textedit on Mac to take notes on everything I read, one file per item, named systematically and stored with the pdf of the original item (if there is one) in thematic folders (I don't tend to annotate pdfs themselves, as it's not really how I think). I've had this system going since undergrad so there's a lot in there and I keep it very tidy.

What I was really hoping I could do with Zotero is create annotated bibliographies, which I have to do quite a lot. But having read all the relevant threads I see that can only be done with the extra & abstract fields, which doesn't help me (it's hardly comfortable typing in that box, so if I wanted to use it I'd have to use some other text editor then paste it in).

In the absence of an annotated bibliography function, I'm struggling to see the utility of notes. Yes, they link automatically to the item, which saves me the time of making a text file & typing out a filename, and I presume they can be synced, but I only ever use my own laptop anyway so that doesn't matter much to me.

Am I missing something in my understanding of how notes work? Is there some cool function people are using notes for? Is there a better workaround for creating an annotated bibliography that hasn't been mentioned in the discussions so far?

Many thanks for advice & thanks for Zotero itself.

• The Create Report function in the right click menu can create a report with all of the item reference information and any notes or tags. This is what most people use in your case for an “annotated bibliography”.

If you do want to keep using external text files, you can attach those to the items in Zotero so they are easily accessible. If you don’t want to do that, another thing you can do is install the Zutlio plugin. Among other things, this plugin adds a Create Zotero Select Link option to the right click menu. This creates a link that will automatically take you to the Zotero item when you click it. You can place this at the top of the text files to link to the article they describe. In more advanced text editors, like VS Code or Atom, you can click these links directly in the text editor.
• Thank you bwiernik! The Report function doesn't, as far as I can tell, offer the option to format the information as a citation, which is what I'd need in order to be able to use it for the purposes of academic work.
• @dstillman Would it be possible to add a reference formatted with the default format to the report output?
• Sure, but I think we'd want to make that an option at report generation time to choose between a citation style and a metadata table, along with various other options. That was the original plan for reports — to offer various ways of customizing them — but we've never actually implemented that. I've created a ticket to track that.
• edited May 30, 2019
I have much the same issue for my PhD.

Editing in Extra box is horrible (could we have a pop-up window, I do all work in desktop app)) so I create my notes in Zotero as separate tagged notes but then cut and paste into Extra. I can then create annotated bibliographies.

However create bibliography strips new-lines so if the bnotes are more rthan a couple of lines the result is too dense to be useful. There seems to be no way to format it (from the forums).

So I am adding tags at end of each line then I can do a search and replace in Word to to create the line breaks. All these workrounds are a pain, I cannot understand why Zotero is stripping new-line/white space out of the Extra field (I have not checked Abstract). Fixing this would make Zotero MUCH better.

The forum strips my html new-line tags that I tried to mention between 'adding' and 'tags' but it does not process them.
• This PhD student has a similar issue. I think this topic is converging with how to make my notes showing in bibliography or citations.
I tried to figure out how to do it with the CSSs and whatnot, but it's not my cup of tea, alas. Solution to this problem hugely appreciated!
• If https://github.com/zotero/zotero/issues/1693 is longer-term work I could probably update the RC to do bibliography rather than metadata table to tide things over.
• Hopefully that might be our answer.
• Thanks Emilia, dstilllman, if this could be solved, I'd be really grateful! Even if only something provisionary, that would help me out enormously right now.
• I've seen a lot of misspellings of my name but Emilia is new.
• Sorry about that! I'm lysdectic, and after the first bit everything becomes a blur :)). Obviously - coming from me - it's a compliment if I mistake you for a girl, Emiliano :D
• edited May 30, 2019
I am at the stage where my literature search is a key document for supervisions etc so anything that can make it easier to produce an annotated bibliography would be a godsend. It is a working document so if it has some rough edges that will not be a problem for me as wellas long as the process otherwise is smooyh.

Martin
• I've looked and it can't be done (safely) in the report customizer, sorry.
• # I am willing to pay for someone to make this for me.

Well, I am a grad on a stipend, but yeah.
• I might have found a way to do it in the report customizer after all. Open an issue on https://github.com/retorquere/zotero-report-customizer/issues and I may be able to help.
• That would be so totally and utterly AWESOME!!!
Opening issue :D
Thanks, Emiliano!
• Having something in notes that allows to write a mixture of markup and latex would be ideal.
• @kirk86 that's unlikely to land in the RC, but I can take a look over the weekend whether the BBT "Collected Notes" translator can do this sensibly. But if you want a voice in the process, open an issue at https://github.com/retorquere/zotero-better-bibtex/issues. I don't yet have a clear picture of what you want a markup - latex mix to do, unless you mean using BBT's <pre> support, in which case it wouldn't be in principle infeasible for "Collected Notes".

No promises though.
• @emilianoheyns thanks for the response. The mix of markup latex is for the notes tab in zotero. As it is to me it seems that is very restricted, you can't do anything beyond the basic formatting that it offers. For instance, you can't write math formulas (unless my understanding is wrong). You would have to resort into an external editor to do the work, save the file and link it back via zotero on the correct item.
• I don't want to get (too) lost in a semantic discussion, but in the notes you can indeed not write rendered math formulas -- technically, there's nothing stopping you from entering latex there, it will just not be rendered.

What would be *in principle* possible with BBT is that stuff in latex-protected sections (which is a BBT-specific facility) could be left alone in the same way BBT currently does for other parts. This will look janky in Zotero, but could (again, in principle) be used to generate valid latex which *would* render well.

To be clear, I'm absolutely not going to add mathjax rendering to Zotero. I don't do GUI work unless absolutely inescapably required. And since the notes in Zotero are WYSIWYG, parsing out protected sections is going to be pretty tricky, and I don't know whether it can be done with a reasonable effort. But I'm curious enough to give it a go if you open an issue on the github tracker for better bibtex.

Another option would be to try to find the mathjax sections and inject the mathjax libraries. This might be possible to do in the report customizer. For that you would have to open an issue on the report customizer githhub project. But in any case, you will have to hand-edit latex-like math, and that will remain visible everywhere that's not produced by BBT/report customizer.
• Actually... injecting mathjax into the report may Just Work (TM)... open an issue on the github tracker and we'll find out.
• RC 5.0.22 includes mathjax support.
• @emilianoeheyns Awesome, thanks a bunch ;)
• @emilianoeheyns Thank you for your work,Can I have the date when we will have the version support the mathjax?
• June 6th, 2019
• @emilianoeheyns Thank you for your reply, but I cannot find this version, Could you give a link for this version?
• I am so massively helped with this feature, Emiliano!
The only thing is... (of course there's always one more thing) that I can't figure out how to make each item to start on a new page.
I tried to fiddle with css files, but the report customizer seems to use a different one from the standard report, and I can't figure it out. I'd love to do something about the different fonts and font sizes too, but that's of lesser concern. Editing in Word is no option, because Word messes up the emojis in my tags (it's not up to date with the newest set, can't figure out how to fix that, either).
I even looked into some javascript to run a report, separately, for each item selected, but I can't figure that out, either. My strengths lie elsewhere =)

Can you offer some advice?
• The CSS is baked into the report customizer, but if you open an issue on github I can make a change that allows you to inject css.