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Keeping a Bibliography (rieck.me)
52 points by Topolomancer 13 days ago | hide | past | web | favorite | 32 comments





Why not using Zotero or similar? Isn't it much more convenient?

The one thing I wish Zotero would have is the ability to export (and then version control) the collections layout. I don't really trust Zotero to not at some point mess this up, especially if I'm trying to sync multiple accounts after an internet outage, and having the collections layout backed up would really make me trust the platform a lot more.

Yeah, Zotero w/ Better BibTeX is what I use for all of my papers/bibliography. It also keeps .bib files updated as you add stuff to the bib database. This lets you write your paper and add references to the database without worrying about exporting the file over and over again.

It's so good that I don't even think about my bibliography anymore, except when correcting non-standard author name silliness (weird and wrong punctuation and other stuff that happens when pulling nonstandard DOI entries).


Jep Zotero is where it is at! The bibtex support is also very good. So you can do your papers in word an still have a nice latex thesis later.

If you use org mode I highly suggest org-ref (https://github.com/jkitchin/org-ref) that leverages and adds a lot to Bibtex. It makes creating/managing/citing/searching a bibliography a breeze.

Another reference to Zettelkasten! I've only recently become aware of it, though it's pretty clear to see how that concept and the bibliography concerns here complement each other. Anyone have any experience combining the Z method with good reference management for the long-term?

I think most implementations of a Zettelkasten _does_ include a reference system, but it is not explicitly a _part_ of the Zettelkasten, but simply a complementary tool.

I can’t comment on “long-term”, but I have been working on a paper this past week and have used my Zettelkasten notes and references extensively. Writing the draft has mostly consisted of copying snippets and titles from the ZK. Sine all my notes have references in place, the draft already have references ready to be converted to something LaTeX will handle.

I’ve also used the reverse: finding which notes reference a particular paper.


What's the best way to keep track of notes on the documents and books that one reads? I use a combination of Evernote, text files, directories of scanned pages, and so forth, and it's not optimal.

I prefer to keep it simple. I add references in my .bib database via Zotero, then I version control the .bib file (exported from Zotero). And then I add .md files with notes, and the .md files are named according to the citation key in the .bib file. Then I version control those .md files. Advantage is that notes are all in the same format and place, regardless of what reference type (e.g. pdf, webpage, could even cite a video), and they are all very easily searchable, including through time (via version control).

EDIT: I keep a separate folder on my Dropbox (so not version controlled) of the actual resources, such as .pdf files. Again named according to the citation key in the .bib file.


you might wanna have a look at pubs [0]. It is a command line bibliography manager.

The folder structure looks like this:

  ~/.pubs/
      bib/
      doc/
      meta/
      notes/
The bibkey is the filename for the different files in those folders, and for notes you can use markdown. You can then keep your pubs folder under version control (or symlink the (sub)folder(s) to wherever).

[0] https://github.com/pubs/pubs


Thanks, that looks really interesting!

On Mac OS X, I like 'Highlights' because it permits exporting PDF notes into a Markdown file. I then keep all the notes in one large file---which I admit is far from optimal but still easy to search, index, and query. Would be interested what other people think about this.

I searched for this but it says it is coming soon: https://highlightsapp.net/

Did you mean something else?


No, that's the one---but they just updated to a subscription model, which I was unaware of. I have the 'boring' normal version of the app still.

It has a bit of a learning curve but I use a combination of the emacs packages org-mode, org-ref, interleave-mode, and pdf-tools that is heavily influenced by this reddit post (https://www.reddit.com/r/emacs/comments/4gudyw/help_me_with_...).

org-ref is powered by bibtex to manage the bibliography and PDFs

interleave-mode lets me take org-mode notes on each page of a PDF


The article doesn't mention it but entries can include an "annotate" field. I use it to add short summaries and notes. It is not used by the standard bibliography styles, but it can be used to produce an annotated bibliography.

Never used it myself, though, except for detecting my name in a bibliography and highlighting it (for publication lists and some such).

If you prefer to automate most of this --> https://citationsy.com

Has anyone compared JabRef to Zotero? I chose JabRef a while back (its database is nothing more than your bib file, it helps organize your pdfs well enough, it can import bib entries from MathSciNet and the ArXiv, it runs fast enough), but every once in a while I wonder whether the programs I'm not using are the ones that deliver true bibliographic salvation.

I switched from JabRef to Zotero a while ago, mainly because JabRef seemed to be extremely buggy. I'm broadly using the same feature set on both, but Zotero is a lot less buggy, and it's faster and easier to add new references.

If JabRef was more stable, I think I would have stuck with that, because of the inherent simplicity.

EDIT: I'm an exclusive linux user, and as you can maybe tell, I like JabRef because of the unix-ish philosophy: a tool that does exactly what it needs to do, and nothing more.


Bibtex is the true standard for bibliographies. Practically every scientific publisher uses it. This shows how well designed the bibtex format was: nearly 30 years after it was created, we see it used everywhere.

In particular with BibLaTeX it truly is a joy to use for me! I am saddened by seeing how little some publishers care about providing good output, though.

I am surprise no one cited Jabref(https://www.jabref.org).

The author does cite it on *6.

It works nicely, cross-platform. It can work on Lyx, Latex, Bibtex, and Word.


Unfortunately I've found it rather buggy (on linux) in the past. It really could be a super nice tool, if they traded some features for more stability, in my opinion.

This is also my experience with JabRef on macOS. If I remember correctly, I had some problems where it silently corrupted parts of my bibliography. I'm not sure if it was related to me using it with subversion or some other problem, but I was a little bit surprised to say the least.

Ouch, that sounds pretty bad... Thankfully I didn't have that issue - mostly my problems were to do with java libraries, glitchy UI, and the "add reference" tool often didn't work.

I'll leave this here https://www.mendeley.com/

I'd recommend Zotero as an easy-to-use, open source alternative.

https://www.zotero.org/


I have used both extensively. And I really want to love Zotero, but to me Mendely is just so much better I have to use it.

Am really curious about JabRef though that other people are mentioning. Haven't used it before.


For me the key drawback about Mendeley is a very limited ability to control the citation keys. Even on Zotero this is a second-class citizen, since you have to install a plugin.

Have you been able to control the citation keys on Mendeley? It's been a while since I've tried it now...


Sorry, slow response. Every item has a Citation Key field on it in the details. Just put whatever you want in there. Annoyingly it doesn't show up until after you try and export or copy it the first time. I just hit Ctrl-K to copy the citation and then change it if needed.




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