6 ms·

Keeping a Bibliography

52 points by Topolomancer 7y ago

raister 7y ago
I'll leave this here https://www.mendeley.com/ https://www.mendeley.com/
- uneekname 7y ago
  I'd recommend Zotero as an easy-to-use, open source alternative. https://www.zotero.org/ https://www.zotero.org/
  - Bedon292 7y ago
    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.
    - funklute 7y ago
      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...
      - Bedon292 7y ago
        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.
- sasvari 7y ago
  This: https://news.ycombinator.com/item?id=18977461 https://news.ycombinator.com/item?id=18977461
Cenk 7y ago
If you prefer to automate most of this --> https://citationsy.com https://citationsy.com
ohmyblock 7y ago
Why not using Zotero or similar? Isn't it much more convenient?
- simlan 7y ago
  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.
- LolWolf 7y ago
  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).
- funklute 7y ago
  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.
kens 7y ago
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.
- Topolomancer 7y ago
  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.
  - supdatecron 7y ago
    I searched for this but it says it is coming soon: https://highlightsapp.net/ https://highlightsapp.net/ Did you mean something else?
    - Topolomancer 7y ago
      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.
- harrigan 7y ago
  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.
  - Topolomancer 7y ago
    Never used it myself, though, except for detecting my name in a bibliography and highlighting it (for publication lists and some such).
- calstad 7y ago
kmill 7y ago
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.
- funklute 7y ago
  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.
coliveira 7y ago
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.
- Topolomancer 7y ago
  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.
dysosmia 7y ago
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?
- henrikeh 7y ago
  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.
superflit 7y ago
I am surprise no one cited Jabref(https://www.jabref.org 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.
- funklute 7y ago
  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.
  - lmns 7y ago
    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.
    - funklute 7y ago
      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.
calstad 7y ago
If you use org mode I highly suggest org-ref (https://github.com/jkitchin/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.

52 points by Topolomancer 7y ago

raister 7y ago

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

uneekname 7y ago
I'd recommend Zotero as an easy-to-use, open source alternative. https://www.zotero.org/ https://www.zotero.org/
- Bedon292 7y ago
  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.
  - funklute 7y ago
    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...
    - Bedon292 7y ago
      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.
sasvari 7y ago
This: https://news.ycombinator.com/item?id=18977461 https://news.ycombinator.com/item?id=18977461

Cenk 7y ago

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

ohmyblock 7y ago

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

simlan 7y ago
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.
LolWolf 7y ago
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).
funklute 7y ago
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.

kens 7y ago

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.

Topolomancer 7y ago
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.
- supdatecron 7y ago
  I searched for this but it says it is coming soon: https://highlightsapp.net/ https://highlightsapp.net/ Did you mean something else?
  - Topolomancer 7y ago
    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.
harrigan 7y ago
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.
- Topolomancer 7y ago
  Never used it myself, though, except for detecting my name in a bibliography and highlighting it (for publication lists and some such).
calstad 7y ago

kmill 7y ago

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.

funklute 7y ago
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.

coliveira 7y ago

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.

Topolomancer 7y ago
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.

dysosmia 7y ago

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?

henrikeh 7y ago
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.

superflit 7y ago

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

funklute 7y ago
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.
- lmns 7y ago
  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.
  - funklute 7y ago
    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.

calstad 7y ago

If you use org mode I highly suggest org-ref (https://github.com/jkitchin/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.