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

WEBVTT

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So the first question,

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have you tried ivy-bibtex or bibtex-completion earlier

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and how it compares to eBib?

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Well, I would say that I use both.

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I don't think there is very much a comparison

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because for me, they're achieving different goals.

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When I want to just very quickly find the paper

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in the entirety of the literature,

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I can just go here and open ivy-bibtex and see it.

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Bibtex now needs to parse my bib files,

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so it may take a second.

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Yeah, so if I want to just search, I'll do this.

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If I want a bigger view, then I can open eBib,

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but I don't use eBib so much as a tool

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to find just one literature. I use it for other purposes.

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So I think they're not really mutually exclusive,

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like you can use both.

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And they don't think that the features that one provides

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are something that the other also provides.

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They're different kind of goals for me.

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Also, for the answers, is it OK

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if I don't write anything down and I can just write them

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After, when I have time, and I'll just talk.

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Yeah, that's OK. We'll transcribe all the answers later.

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So you can just go ahead and talk.

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And do you find showing abstract

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on your navigation panel helpful?

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I always delete the abstract info,

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and my bib files make things more concise.

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So for me, I think it is helpful to see the abstract.

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I think that if you're in a regular screen,

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you have the space to have that.

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And yeah, for example, if I go again here,

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it's kind of indeed a bit more,

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a bit longer than it can be.

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And also you find a bigger abstract somewhere.

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It may be more space,

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but like, for example, this, yeah, this is a big abstract.

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And for example, yeah, this takes a bit more space,

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but I find it easy because the only case

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where I'm actually looking at this panel

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and trying to see things is when I'm going to be either,

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is when I'm going to be trying to find something

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that I don't remember the title to search immediately.

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And if you don't remember the title

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and you're trying to search,

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the abstract will be a way

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that helps you search better maybe.

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and also the other thing they use

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is also the small little descriptions

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I add in the note entries to help me

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but I think that the abstract is nice to be there

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in case you don't remember

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to find something from the title

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or from your notes

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and just need something more general.

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So yes it can be large and not always convenient,

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but I generally like it being there

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in case I need it for anything. Then the next question.

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Also, if any question is not fully answered by what I'm saying,

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feel free to add more to your question

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and we can discuss more. I don't have a problem.

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So for the next one, yeah, I copied this from IRC

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because I prefer to answer it orally

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because it's a bit longer than the others answering in IRC.

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So it seems that there's a meta problem here.

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There's too much information.

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And does this tool reduce the cognitive load?

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Well, for me, it does reduce the cognitive load because

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Indeed, there's a lot of information,

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but that's how managing literature works, essentially.

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It necessarily has to have a lot of cognitive load,

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because you are trying to

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process more information

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than your brain can process to begin with.

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So you really need a tool

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to help you not keep everything in your mind,

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process the information externally.

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They do think that the way I do this, for me at least,

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it does help with reducing cognitive load.

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Because I'm here, for example,

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if I'm looking for something, I do not remember,

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I've read most of these papers not too many months ago,

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so a lot of them are recent.

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If I don't look at what I have written for it,

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I do not remember anything.

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So indeed, you have this kind of cognitive load

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that I cannot remember everything.

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But on the other hand, I think the tool helps

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because my notes are what keeps, what I want to remember.

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So it doesn't stay in my mind, it stays in the text.

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And regarding things like the reading list,

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I think also for me reduces the cognitive load

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because I will mostly remember

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what the papers I have in that list are,

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but just sorting them by priority helps me

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Okay, this was the thing I wanted to do next.

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Oh, sorry. This is the thing I wanted to do next.

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And I didn't have to remember

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that this is what I want to do next.

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I just had it, I saw it there.

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So for me, it reduces cognitive load,

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but the problem of too much information is 100% there

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because there's objectively

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too much information

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when you're working with literature

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that's by nature and yeah essentially that

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that's for me the thing

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that i'm i'm just putting this information elsewhere

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so i don't have to keep it in my mind

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Okay, so when you download a new article,

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how do you integrate the file to the database?

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So, for example, do you remove

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and rename the file manually?

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So, for me, I also briefly showed that in the talk,

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but I did that very quickly,

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so it's understandable that it wasn't there.

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Essentially, And when I download the article,

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then I will open Ivy Bib Tech and find the article.

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For example, this one is the first.

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You can open the menu in Ivy Bib Tech.

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It's with an alt O, and then it will give you this menu.

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And from here, it will say, add PDF to library.

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And then it will ask from where do you want to add it?

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I don't recommend the URL

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because it doesn't download it properly sometimes.

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As I also mentioned that with Zotra,

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the URLs downloading things,

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especially with academic papers

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that are sometimes paywalled, it doesn't want to work well.

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So I will download the paper

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and then you can just press the F here for file.

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And then you find the file.

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and for example for me all my PDFs are in this folder

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it's still named Zotero PDFs

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from when it was Zotero saving them now

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Zotero no longer saves them

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but I'm too bored to change the name

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and then you just find the paper you want

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so you can see there is an endless list of papers here

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and it then will automatically rename it

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to have the title of the author, a small title and a date.

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I believe the naming is also configurable,

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but I have this notation in my config for many years now

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because that's how everything

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expects to find it, essentially. I do not then move it.

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It's stored in that folder.

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I store all my PDFs in that specific folder.

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And then Emacs knows that all PDFs

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should be found in that folder.

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And it then just looks for the name

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that it expects to find.

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And ivy-bibtex has renamed it automatically to that.

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Okay, I'll wait a bit to continue with that

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for moving to the next question.

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Yeah, ivy-bibtex has that functionality.

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And then annotations with e-readers.

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Viewing and taking an Emacs or Reader touchscreen,

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highlighting notes, noter, think would be an alternative,

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e-book annotation alternative.

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So, I do not use an e-reader, personally.

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The only thing that I have is my tablet,

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I can actually show you. It's this little thing here.

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It's a Chromebook.

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And the reason it's a Chromebook is that

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when I bought it a few years ago,

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it was the most viable alternative I could find

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that can run Linux as a tablet with good touchscreen.

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That was also a bit budget

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because there are some Linux tablets,

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but they were a bit too high cost

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for what I was looking back then.

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And this thing runs Linux essentially

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natively from the Chromebook.

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And I've installed Emacs there. It has all my config.

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And so if I want to take touchscreen notes, I do it there.

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But again, that is in Emacs. And it's mostly with PDFs.

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I'm not sure if it answers exactly the question.

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So if it's an e-reader, if it's, for example, a book,

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I know that if you have an EPUB,

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I think it's called the format for books,

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and Org-noter can also read that.

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So you could also open that file inside Emacs

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using Org-noter and take notes.

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But otherwise, If you're not

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reading everything in Emacs,

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then it's hard to pass annotations

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from outside Emacs to inside it,

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because of course you have less interoperability in that case.

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but I think Emacs is featureful enough

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to where you can do all your reading inside it.

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And Org-noter has a surprising amount of different formats

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where you can read things actually.

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I hope it was clear if you want more on that

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because I know it's a bit more a complex question, I guess,

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also with e-readers.

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And if it is in Emacs or not, feel free to add more.

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And how old do you feel

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about making notes on websites, PDF, videos?

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So I will agree with the other question

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that I answered here.

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If you can convert something to PDF,

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I prefer it because then

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you need to only worry about PDFs

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and it works better that way

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than having to annotate websites.

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There is, I believe, I should have it

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in my bookmarks somewhere.

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There is a, the org-roam protocol

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that allows you to take notes directly out of a website

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and it saves all the metadata of the website.

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I did look at it at some point,

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but I haven't really continued using it too much

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because I find that I don't often take notes

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from a website where I want the and more information

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than just either the link of the website

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or if I want the full text converting into a PDF.

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So I haven't really found

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a very big use case for it,

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but I know that Org-Roam protocol is a thing.

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And then for videos is a bit of a longer story

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because if you want to take notes on videos,

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that's a bit more complex.

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And I don't know of a way to do it in Emacs,

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but I also don't know of an effective way

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to take notes on videos using other tools.

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What I typically do if I'm following the video or something

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is that I will take notes of the more important things.

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I'll take notes of the more important things

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that I was listening in the video.

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And while I'm listening, I will take

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some ideal crude notes,

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not because I don't want to lose

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a lot of my attention during the,

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what I'm trying to learn by taking very good notes.

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So most of the time,

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those kinds of notes will be in paper,

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even just very simple, crude notes.

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And then without any timestamps or anything,

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because that's too complex for what I've done.

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And after watching, I will try to

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consolidate all my thoughts that I wrote down

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into some more permanent notes using Org Roam.

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And then like move on with that also look online

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if I noted that I want to look more on on this subject

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that was mentioned the video

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and I didn't fully understand it

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then I will try and look more and things like that

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so for me that's how I do it because I think that

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Annotating a video directly with timestamps

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and everything is a bit too complex.

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I don't know if you have

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any suggestions for working with that,

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but for me, it has been very troublesome.

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And then how do you add a new article from scratch,

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a PDF that you did not have in your bib file?

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How do you generate the bib entry metadata and abstract?

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So yeah, the package is called Zotra.

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I can also show it again. Let's find something.

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and can open up. Let's not do that.

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If I open it, I need to access it through my institution.

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So I will not open the link, but I can show you essentially

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you run Zotra add entry, this function,

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and it copies what you have currently in your, in your,

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what you have already copied right now

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it's the message I copied before for the Q&A

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but if you open a paper and have the URL copied

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it will immediately come here and will save everything

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and also as I mentioned there's the

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you can also download the patches from there

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but with paywalled articles doesn't always work well

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so I just do it manually

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Oh, system is running low on power. Give me just a second.

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So the computer doesn't turn off as we're speaking. Yes.

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So yeah, the, everything is added from scratch.

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Essentially you copy the URL and give it to Soletrend.

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It does everything. uh when you fact check every details

00:18:17.382 --> 00:18:26.261
for a bib entry your open names published journal

00:18:26.262 --> 00:18:29.461
doi stuff uh so i i generally don't do that

00:18:29.462 --> 00:18:30.861
oh yeah thanks for the person

00:18:30.862 --> 00:18:35.101
that added the link to the zocha

00:18:35.102 --> 00:18:38.381
i i wouldn't say that i fact check the details

00:18:38.382 --> 00:18:40.901
i assume that When they're added,

00:18:40.902 --> 00:18:44.541
they're actually correct.

00:18:44.542 --> 00:18:49.741
Have you actually had trouble with a tool

00:18:49.742 --> 00:18:52.021
that automatically adds them to add them wrong?

00:18:52.022 --> 00:18:54.861
I'm curious. I haven't really heard

00:18:54.862 --> 00:18:59.421
that happening too much.

00:18:59.422 --> 00:19:01.861
I've always thought that, yeah, if you do it manually,

00:19:01.862 --> 00:19:04.621
you need to fact check that you did it correctly.

00:19:04.622 --> 00:19:06.461
But I always assume that if you do it

00:19:06.462 --> 00:19:09.301
automatically through a tool,

00:19:09.302 --> 00:19:11.661
It should already be correct.

00:19:11.662 --> 00:19:15.101
And I don't remember ever having any trouble either

00:19:15.102 --> 00:19:20.221
when I was using Zotero before or now

00:19:20.222 --> 00:19:24.101
with the more Emacs based tools.

00:19:24.102 --> 00:19:29.781
I feel like the big entries are copied correctly.

00:19:29.782 --> 00:19:35.101
I haven't noticed this being incorrect.

00:19:35.102 --> 00:19:40.181
But I'm curious, do you have any point

00:19:40.182 --> 00:19:44.661
On that, I will keep in mind.

00:19:44.662 --> 00:19:48.541
Sometimes, DOI records are not exactly correct.

00:19:48.542 --> 00:19:52.861
For example, they can contain some very strange symbols.

00:19:52.862 --> 00:20:01.901
So that can happen sometimes. OK. Yeah. I don't know.

00:20:01.902 --> 00:20:05.741
I guess then if you want to fact check,

00:20:05.742 --> 00:20:12.141
it's probably the best to do it directly as it is added,

00:20:12.142 --> 00:20:14.901
like it's added, for example, here,

00:20:14.902 --> 00:20:17.941
and you can just directly, when you add it,

00:20:17.942 --> 00:20:23.501
find it and say, is everything correct here?

00:20:23.502 --> 00:20:27.661
Because I think that if you leave it for later,

00:20:27.662 --> 00:20:31.381
it will be much more of a mess.

00:20:31.382 --> 00:20:33.181
So for checking, I would just do it directly

00:20:33.182 --> 00:20:47.261
after I add it to the bit file.

00:20:47.262 --> 00:20:50.621
And let me see, is there anything else?

00:20:50.622 --> 00:20:53.501
I think one common way it can fail

00:20:53.502 --> 00:20:56.381
is when the metadata includes

00:20:56.382 --> 00:20:59.581
HTML tags for math, for example.

00:20:59.582 --> 00:21:03.501
And in some papers, for some journals, it can happen.

00:21:03.502 --> 00:21:05.061
So then you can imagine what happens

00:21:05.062 --> 00:21:06.981
when you try to put that citation

00:21:06.982 --> 00:21:08.741
into your references.

00:21:08.742 --> 00:21:12.421
That's going to be a mess.

00:21:12.422 --> 00:21:17.501
Yeah, okay. I didn't know, to be honest, so yeah.

00:21:17.502 --> 00:21:27.101
Thanks for the information.

00:21:27.102 --> 00:21:29.501
I think our graph has automatic cleaning

00:21:29.502 --> 00:21:30.421
of certain things

00:21:30.422 --> 00:21:34.741
for common errors in the metadata.

00:21:34.742 --> 00:21:37.221
How did you call that?

00:21:37.222 --> 00:21:38.381
I can note it down also here for the discussion.

00:21:38.382 --> 00:21:45.861
Oh, our graph. Or graph. Or graph. Yeah.

00:21:45.862 --> 00:22:12.261
Okay. Okay. I will put it down the pad.

00:22:12.262 --> 00:22:14.141
And I think the next talk,

00:22:14.142 --> 00:22:18.461
the live will move in the next minute anyways.

00:22:18.462 --> 00:22:22.141
And I see we're done with all the questions.

00:22:22.142 --> 00:22:26.141
So thank you everyone. I hope this was interesting.

00:22:26.142 --> 00:22:28.501
Thank you for giving me a lot of questions

00:22:28.502 --> 00:22:31.461
so we had to discuss for the whole time

00:22:31.462 --> 00:22:34.541
and we weren't just here sitting.

00:22:34.542 --> 00:22:36.182
And enjoy the rest of EmacsConf.