path: root/2025/captions/emacsconf-2025-reference--emacs-as-a-fullyfledged-reference-manager--vidianos-giannitsis--main.vtt

WEBVTT captioned by vidianos

NOTE Introduction

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So, hello everyone, welcome to EmacsConf.

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My name is Vidianos, and I'm a PhD student in KU Leuven,

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and today I'm going to be showing you

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how I managed to use Emacs as a reference manager,

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replacing what was for me Zotero,

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to a fully fledged approach inside Emacs.

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So, what is my typical reference workflow?

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First I need to find literature,

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then I need to collect and organize it,

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which I originally did with Zotero,

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but now with Emacs centered tools

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such as zotra and ebib.

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Then I create a reading list.

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This is a new addition to my workflow

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I started doing after moving this approach to Emacs

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because now everything is well integrated.

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I have made a very nice reading list implementation

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inside org-roam which I am going to be showing today.

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Then obviously I need to read the literature, take notes,

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organize the notes, and ensure I am actually learning

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from what I am reading. This is then done through packages

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such as org-noter and org-roam

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and is not going to be the focus of this talk.

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I already gave a talk about this part of my workflow,

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which I've been doing for many years now.

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You can find that

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or you can find many other people's approaches

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to reading literature and taking notes

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as it is quite a popular topic in the Emacs community.

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Lastly, I will have a short section

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about how I ensure that I can recall the knowledge

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from this literature very easily

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through this reference management system.

NOTE Capture

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So, how can we capture an article in Emacs?

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One of the most commonly known packages is doi-utils

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where doi-utils has a lot of useful things to do

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and one of them is to capture a paper,

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but you need a DOI, and for me, that is a bit inconvenient,

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because what I want to do is that

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I have a URL here of a paper,

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I want to just copy this URL, not copy the DOI,

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and be able to save it immediately to my bib file.

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And that can now be done

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through this function zotra-add-entry.

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And as you can see here,

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there is also a zotra-download-attachment

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that sometimes works, but not always.

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I don't personally recommend it.

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But the problem is that due to articles being

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locked behind paywalls in many cases,

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downloading attachments doesn't work

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through Emacs. Sometimes it doesn't work

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through Zotero. Sometimes you just need to go to the browser,

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say download PDF, and that's the only solution

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that will properly work.

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So how do I then add this to the paper?

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I need to find this paper that is here

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through ivy-bibtex.

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This is the bib file manager I use.

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There is also others like citar.

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I think citar has much better coding and integration

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with other packages, but I haven't really bothered

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to move from ivy-bibtex

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because it does basically everything I want perfectly.

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So I go here, say add pdf to library.

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I find where I saved it,

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and it will suggest to automatically name it something

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which is in full integration

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with the rest of my Emacs packages,

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and all the literature management stuff

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knows to find it with this exact name.

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So it iss saved and now

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when I try to create a file from this,

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which I will show later,

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you will see that the file will already appear there.

NOTE Organizing

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So now let's go to organizing.

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Organizing in Zotero is typically done through a

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hierarchical folder structure.

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This is very familiar to most people and generally works,

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but being someone that takes notes using the Zettelkasten method,

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which has a fully flat hierarchy, nothing goes in folders,

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everything is in the same folder,

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and you find everything because it's connected to other things.

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We have some basic indexes,

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from where you can jump to different points.

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I love this structure, so I also wanted to include it

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in my bibliography management,

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because with folders you have problems like,

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this article can go in that folder, can go in that folder,

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can go in that folder. Where do I actually put it?

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Do I put copies of it in different folders?

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It's just confusing and not really practical in my opinion.

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So I tried to do this approach inside Emacs.

NOTE Ebib

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And how? With Ebib.

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Ebib is an amazing software built inside Emacs.

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It's a reference manager and it works absolutely amazing

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if you configure it to your liking.

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So let's open ebib first.

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This is the interface you will see when opening.

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Actually, by default you will not see anything,

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but I have open three bib files.

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These are opened by default on boot of ebib for me.

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These are my three main master bib files.

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This is the Zotero master bib file,

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which only Zotero can touch. If I change it,

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it will be overwritten. This is my new master bib,

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where I save all the files that I have now started using

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after switching to this approach.

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And then this is the master bib file

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for literature related to my PhD

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and things that I have already read.

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It's a very convenient interface.

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There is also search. There is one searching tool,

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the jump to entry, ebib-jump-to-entry,

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which searches through all open bib files for the title.

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So for example, I can search for membrane fabrication,

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because that's something I am currently doing,

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and go to this. There is another searching tool,

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the ebib-search, which searches through the database

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that you're on right now

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and it does a full text search,

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not only in the titles, but everywhere.

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So, for example, I see that in this paper

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if I go to the abstract and search for the word FTIR,

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which is a chemical analysis,

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it will tell me that it's here.

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Can it find it anywhere else? It cannot. That's okay.

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Let's search for something

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that we'll be able to find more easily,

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like, for example, membrane crystallization

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which is a main focus of my PhD.

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Then it will be able to find it many times,

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many, many times.

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I can also search on the next database

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or on this database and see where is everything that I want.

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So this is different searching tools which are very useful.

NOTE Filters

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Then there's also another tool, that is, filters.

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So I can filter on any field.

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Like, for example, let's say on any field,

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and let's say I'm looking now again

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for membrane crystallization.

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This will now filter to all entries.

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You can see right now there's 18 entries here

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that mention these two words together in any field.

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Sometimes this is easier, because this is permanent.

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It's not like the search that we find one

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and then if you move, you've lost it,

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and you need to find it again.

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This is permanent until I say,

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okay, cancel the filter.

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I mostly work with filters,

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I think they're the most convenient.

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Then there's also the ebib-list-recent

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which is another very useful command.

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It asks you for a number of days

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and it will show you the files that were added

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in the most recent.

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So for example, show me the literature files

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that were added to this bib file in the last month.

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I will see five files in this case,

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because in this bib file, I have mostly entries

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that I have read, these are the files

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I have most recently read and added here.

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While if I go for example here and say that,

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these are files that maybe I haven't read yet,

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but I was planning to read. So this is something useful.

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Although for things I'm planning to read,

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I mostly use the reading list

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that I'm going to show next.

NOTE Dependent databases

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But before that,

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a few more neat things that you can do in Ebib.

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So I have a list of dependent databases.

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For ease, I have already opened them here.

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These, as you can see, have two brackets here,

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indicating that they're dependent on phd_literature_1.bib,

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and these, in my case, act as the sort of index file,

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where I am tagging things based on the structure

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that I wanted to have for the organization.

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So all the organization is flat,

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all the literature is in phd_literature_1,

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however, I have this file

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that has 14 entries.

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I have another file here that has 20 entries.

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And these are smaller indexes

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where I can find things easier,

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but things are not limited to one of these.

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Things can be in all of these, or probably not all of these,

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but can be in three or four of these very easily.

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And how you add things is that I go here,

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and I say not r, it's... M for the dependent databases,

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and I add entry, and it will tell me

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"Where do you want to add this?"

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So when I read a new paper,

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I can say okay, this is related to these three tags,

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and this is sort of like, again,

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it's tagging it and it's putting it

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there, there, and there.

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And then this creates a flat structure

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that however has a great organization,

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similar to how Zettelkasten works

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and I really like working with something like this,

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with dependent databases.

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Another feature that I really like,

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another feature that exists by default... But if I tag,

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this tagging is done through "m",

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and then I can tag different files here,

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and this is to do different actions with these together,

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such as, for example,

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copy them to a different file,

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with "x" I can export the entries somewhere else,

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there are many things that you can do

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when you mark them.

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By the way, one of them is this function,

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which sees everything that I have marked

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and shows me an org-roam-node-find entry

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that is filtered to just these files.

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I can select one and it will take me

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to my notes on this specific paper.

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I find this very useful,

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because I can be looking for something

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and I can say, okay I remember,

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or I did some filtering,

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and I know it's in one of these files

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and now I want to see my in-depth notes on each one

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to remember where exactly I found it.

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So I find this kind of filtering,

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this org-roam related filtering, to be also very effective.

NOTE Reading lists

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So now let's finally move to reading list.

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The reading list in ebib

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reminds me a lot of the philosophy that Emacs uses.

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By default, it is extremely bare bones, not very usable,

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but it is so customizable, to where you can do

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anything that you can imagine through it

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because the limit truly is your imagination.

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It's how much you can code into this

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that actually makes sense

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and you can actually imagine it working.

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Besides that, you can do anything really.

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So we can open ebib and try to find this paper

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that I just added here.

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Then we can create a reading list entry from it.

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Here, my reading list prompts me

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for a priority for this.

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How urgent it is for me to read this.

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It adds a TO-READ, which is a todo entry,

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which helps with organizing my reading list,

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because as you may also be able to see, this has an ID,

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because this is an org-roam node,

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so the TO-READ allows me to organize it inside org-roam.

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It saves the citekey, the link to the paper,

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and also tags it with the parent file node

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because I don't like having orphan nodes in my Zettelkasten.

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I like everything to be linked to at least one thing.

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So everything in the reading list

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is linked to the parent file.

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And now I can find this in the org-roam-node-find menu,

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here. However, that's not very interesting.

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In practice, my typical org-roam-node-find

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does not even include these reading list files

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because I don't really care to have them there.

NOTE Special org-roam-node-find

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I have a special org-roam-node-find

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that is designed to find these in particular.

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And here these have 22. These are the amount of files

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that are currently in my reading list.

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So for example, let's try and press here.

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And magically, this prompts me to select a capture template,

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because what it's doing is that I selected this,

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and because of the citekey, it knows

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that it wants to create a new node for that.

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So I select the capture template.

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It knows that it wants to create this new node for this.

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And now, if I for a second close the reading list,

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now I can already go ahead and take notes on this.

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This is org-noter, in particular,

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and it makes it all very easy

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because it's all integrated in one place.

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If I then close this and open a new Emacs,

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we have this, and the reading list allows me to very quickly

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go from this being reading this item to initializing it.

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Another thing that is very useful is that

00:16:35.040 --> 00:16:38.739
everything is sorted by priority.

00:16:38.740 --> 00:16:41.359
So I need to increase the font size again

00:16:41.360 --> 00:16:48.899
because I closed the previous Emacs.

00:16:48.900 --> 00:16:52.319
So here, I can select what is high priority,

00:16:52.320 --> 00:16:56.399
what is low priority. I can also change the priority

00:16:56.400 --> 00:16:58.799
without needing to be in this file.

00:16:58.800 --> 00:17:05.479
Let's leave this file. I can say, okay, I decided

00:17:05.480 --> 00:17:08.639
that this file is priority B. It needs to be A,

00:17:08.640 --> 00:17:11.899
which is more urgent.

00:17:11.900 --> 00:17:16.079
In my system, there's five different priority levels.

00:17:16.080 --> 00:17:17.999
You can get away with less

00:17:18.000 --> 00:17:20.959
but I like to have the very much low ones

00:17:20.960 --> 00:17:22.999
as this is not urgent at all

00:17:23.000 --> 00:17:27.159
but I want to keep it somewhere. A is very urgent

00:17:27.160 --> 00:17:31.779
and B is urgent but just below A.

00:17:31.780 --> 00:17:34.619
And then the C in the middle is just

00:17:34.620 --> 00:17:35.999
I will eventually read this

00:17:36.000 --> 00:17:41.919
but not something I want to focus my attention on right now.

00:17:41.920 --> 00:17:45.439
So this is mostly about reading list.

00:17:45.440 --> 00:17:46.639
I can also show, for example,

00:17:46.640 --> 00:17:50.679
I have this if I finalize something,

00:17:50.680 --> 00:17:56.799
if I read it. For example, I created a note for this new thing.

00:17:56.800 --> 00:17:59.079
Let's say I finished reading it.

00:17:59.080 --> 00:18:02.179
I want to remove from my reading list.

00:18:02.180 --> 00:18:05.639
It's also just one command and it's done.

NOTE Annotations

00:18:05.640 --> 00:18:08.739
If we now return to the presentation,

00:18:08.740 --> 00:18:11.699
the last thing I want to show is annotations.

00:18:11.700 --> 00:18:17.119
So for annotations, it's the idea that sometimes

00:18:17.120 --> 00:18:23.139
you just need to find something in Ebib quickly.

00:18:23.140 --> 00:18:26.679
So I'm here and I'm looking for something.

00:18:26.680 --> 00:18:30.999
I said I'm here and I'm looking for something.

00:18:31.000 --> 00:18:35.199
And as you can see, there's the annote file everywhere,

00:18:35.200 --> 00:18:40.839
the annote entry, which is a very very small description

00:18:40.840 --> 00:18:43.799
of things that I want to remember for this paper.

00:18:43.800 --> 00:18:48.039
So I can be scrolling here or scrolling

00:18:48.040 --> 00:18:51.811
in one of the smaller files

00:18:51.812 --> 00:18:56.859
and saying this was in this subsection,

00:18:56.860 --> 00:18:59.519
and which paper was it, and I can scroll,

00:18:59.520 --> 00:19:01.711
read all these annotes.

00:19:01.712 --> 00:19:04.919
Each annote takes like 15 seconds to read,

00:19:04.920 --> 00:19:07.359
and really decide, okay,

00:19:07.360 --> 00:19:09.799
it was this paper that I wanted, good.

00:19:09.800 --> 00:19:21.819
Now I can open the note for it, go there, and it's very easy.

NOTE Wrapping up

00:19:21.820 --> 00:19:25.719
So I think that's all. I would like to thank you for your time.

00:19:25.720 --> 00:19:29.319
I would love to see your questions either in IRC,

00:19:29.320 --> 00:19:32.199
I will be, maybe I've already answered

00:19:32.200 --> 00:19:35.039
some of your questions there in the Etherpad,

00:19:35.040 --> 00:19:37.599
or right now, we're going to the live Q&A

00:19:37.600 --> 00:19:42.159
where I'd love to interact with everyone and have a discussion.

00:19:42.160 --> 00:19:44.479
However, if you don't have any questions right now,

00:19:44.480 --> 00:19:48.559
but you have a question later on, feel free to send me an email.

00:19:48.560 --> 00:19:51.739
My mail is also on the site.

00:19:51.740 --> 00:19:54.599
And if you're curious how all this "magic" worked,

00:19:54.600 --> 00:20:00.839
feel free to go to my Github and see the ebib section

00:20:00.840 --> 00:20:04.039
here that will also be linked in the doc page,

00:20:04.040 --> 00:20:06.279
where you can see all the configuration

00:20:06.280 --> 00:20:10.919
that I have done in Ebib for everything to work.

00:20:10.920 --> 00:20:14.000
Thank you again and have a wonderful EmacsConf!