Finding the right bibliographic/reference tool

Comments

• #1 Kaushik Ghose, October 14, 2006 at 3:16 p.m.

  Hi,

  I'd appreciate it if you could check out RRiki which is a rails based notes and citation manager that uses MySQL as backend.

  I wrote it during my PhD and have used it since. I'd appreciate getting usability notes/suggestions from another user.

  thanks -kaushik

• #2 Kjell Magne Fauske, October 16, 2006 at 9:06 a.m.

  @Kaushik

  RRiki looks really interesting. I will take a look at it and update the notebook entry. I just have to install a Ruby on Rails environment first.

• #3 Kjell Magne Fauske, January 2, 2007 at 9:52 p.m.

  Update: Added RRiki to the list of tools.

• #4 McMenace, January 4, 2007 at 2:05 p.m.

  Hi

  is there any tool that generates a bibtex entry from a given pdf-file by duing a litle text-mining?

  if anyone knows a good tool, please email me mcNOSPAMmenace ATTgmxDOTTnet (remove all capitals to obtain my email add)

  McMenace

• #5 Kjell Magne Fauske, January 5, 2007 at 9:27 a.m.

  @McMenace

  I'm not aware of any such tool. Jabref 2.2beta has the ability to add XMP annotations to linked PDF files. Maybe this is a step in the right direction.

• #6 jcs, January 30, 2007 at 5:56 a.m.

  Have a look at Referencer. It's a Gnome application with a slick user interface and some clever magic for fetching papers' metadata from crossref.org for papers with DOI codes, or arxiv.org for eprints.

  Please consider adding it to your growing list. A very interesting resource, by the way, thanks for keeping it maintained.

• #7 Kjell Magne Fauske, January 30, 2007 at 10:15 p.m.

  @jcs

  Thanks for the link to Referencer. Looks interesting. I'll add it to the list soon.

• #8 Kjell Magne Fauske, February 1, 2007 at 5:20 p.m.

  Update: Added Referencer to the list of tools.

• #9 R Rajagopalan, February 8, 2007 at 9:27 a.m.

  I am looking for MAC freeware for managing my references. I came across Papyrus, downloadable free from www.researchsoftwaredesign.com. They seem to have stopped further development.

  How does Papyrus compare with Bibdesk, etc.? I will be grateful for advice.

• #10 Kjell Magne Fauske, February 8, 2007 at 10:57 a.m.

  @Rajagopalan

  Unfortunately I don't have a Mac, so I haven't tried Papyrus or Bibdesk. From the feature list it seems that Papyrus is a good tool, but has some problems running on newer versions of OsX and Intel Macs.

  If you prefer to work with LaTeX and BibTex, Bibdesk or Jabref is probably a better alternative. They are both actively developed. My best advice is to download all of the tools and try them.

• #11 atom prober, March 9, 2007 at 7:57 a.m.

  Comparison of reference management software on Wikipedia might be helpful.

• #12 Kjell Magne Fauske, March 9, 2007 at 8:51 p.m.

  Thanks for the link atom prober. I think it is time to update the notebook entry again with more links.

• #13 SRK, March 26, 2007 at 12:41 a.m.

  @McMenace (and others)

  Automatic citation data extractor for PDF files

  cb2bib

• #14 Marcin, April 19, 2007 at 9:50 a.m.

  Hi there!

  First I'd like to say that I like your web site very much. As for bibliography issues: I personally quite hate BibTeX, mostly for its non-flexibility (unless you learn a weird language of the .bst files) and English-orientedness. A few years ago I discovered amsrefs, which is a really great package for making bibliographies. It would be interesting to see some GUI-type frontend for amsrefs (personally, I would prefer an Emacs module;), but I can do with what I have now). amsrefs is written entirely in TeX, and e.g. changing the style of your bibliography is very easy for, say, intermediate LaTeX users who are capable of reading manuals. (amsrefs also can import BibTeX .bib files, but I've never used this feature - I prefer the native amsrefs format, which is much better.)

  Ah, and one more thing: did I mention I like this site?

• #15 Kjell Magne Fauske, April 19, 2007 at 3:15 p.m.

  @Marcin Thank you for your comment!

  I agree that BibTeX's postfix stack language is a bit strange. I guess it runs in the family. TeX and Metafont are quite strange too. However, the I like the flexibility and simplicity of the bib file format, and as long as I don't have to modify the bst files, I'm happy.

  I have never tried alternatives like amsrefs and biblatex. I probably should. Biblatex is quite new, but looks very promising. If amsrefs work with bib files, you should be able to use Jabref as a GUI.

• #16 1sy8, April 20, 2007 at 5:55 p.m.

  Hi.

  I was also on the way to pyBibliographer for very similar reasons to yours, but unfortunately, I'm afraid it's still a bit behind JabRef for now (not to mention the fact the Gnome dependence forbids to have the same GUI on other platforms).

  So, I'm going ahead with JabRef for now. I have some fear about the work needed to take into account my big collection of already downloaded full-text materials (pdf and ps files) and to retrieve all their references. But I'll definitely enjoy the automatic Emacs insertion and customizable bibkey generation as I'm used to a certain bibkey format in all my manually filled bibfiles.

  One other promising software is zotero.org's Zotero, a Firefox extension.

• #17 Emilio García Morán, May 16, 2007 at 11:44 p.m.

  I am deeply interested in finding a suitable reference management software after recently finishing my Phd Thesis. I used BibTex, but I seriously doubt it is something to live into the future. I have just come across Bibus. It looks wonderful for a medical writer like me. It imports nicely from PubMed!!. It also integrates well into OpenOffice. (I no longer use MS Office). And about output styles, there are only a few built in, but extension from them looks easy.

  I would like to know other people's opinions on the matter.

• #18 Kjell Magne Fauske, May 18, 2007 at 9:47 a.m.

  @Emilio García Morán

  I used BibTex, but I seriously doubt it is something to live into the future.

  BibTeX has been around since 1985, and I do not think it will disappear soon. As I see it, BibTeX consists of two parts:

  1. The BibTeX bib file format
  2. Style file processing

  The bib file format is very simple and flexible. Writing custom bst style files is not easy. However, there are very promising alternatives like biblatex and Pybtex that hopefully will make it much easier.

  BibTeX is a tool for storing, formatting and sorting bibliographic information. All other necessities like database imports, organizing, note taking, and so on, has to be done by a front end. BibTeX can not help you much with such things, except with providing a flexible file format for storing the information. Having this in mind, it is up to you to find a tool that fits your workflow and requirements.

  I have never tried Bibus. It is written in Python, which is always a plus. The feature list does not mention BibTeX as output format, so it is probably not a tool suited for LaTeX users yet.

• #19 Pete Ha, May 27, 2007 at 9:30 p.m.

  Hi, I´m looking for a reference management software (freeware) for linux with a possibility to import databases from commercial Reference manager. thx a lot, Pete

• #20 Kjell Magne Fauske, May 28, 2007 at 1:15 p.m.

  @Pete Ha

  Jabref should be able to import databases from Reference manager. Jabref supports the following input formats:

  BibTeXML, CSA, Refer/Endnote, ISI Web of Science, SilverPlatter, Medline/Pubmed (xml), Scifinder, OVID, INSPEC, Biblioscape, Sixpack, JStor and RIS.

  Reference manager is not listed, but you can probably export the database from Reference manager in a format that Jabref can understand.

• #21 atom prober, May 30, 2007 at 12:08 a.m.

  @Pete Ha

  Reference Manager exports RIS, which nearly every bibliographic application can import (including JabRef, bibus, refbase, and Zotero). If you find a quirky app that can't import RIS, you can convert it to BibTeX or MODS XML or some other format with 'bibutils.'

• #22 FM, June 17, 2007 at 12:58 a.m.

  Do you have any idea of a ref manger programm that allows you to import all your text files at once; as in a batch operation kind of way? Cause it's a pain to import more than 500 ref one by one to the database. Thanks.

• #23 Kjell Magne Fauske, June 17, 2007 at 2:18 p.m.

  @FM

  Jabref lets you select multiple files when importing references. I guess that will help if you want to use BibTeX and your references are in a format that Jabref can understand.

• #24 FM, June 17, 2007 at 2:44 p.m.

  Thanks for the quick response Kjell; it will help me a lot. Thanks mate!

• #25 MT, July 26, 2007 at 11:59 a.m.

  You may also want to take a look at Zotero, a Firefox plugin that makes it a breeze to pull in bibliographic data from any document on the web. Although it maintains its own database and can format entries, it also painlessly exports its records in several formats, including BibTeX, which allows you to import these records into JabRef.

  I've only been using the Zotero+JabRef combination for two days, and I absolutely love them. There are a few shortcomings, but as of now, I'm not sure if it's because of my own lack of experience with the packages or if the features are actually missing.

• #26 michele, August 20, 2007 at 6:10 p.m.

  Good to see such reviews. I recommend that you either remove BibDesk from the list of clients, or make a note that you could not try it. I read in comments that you could not try that OS X software, and the article implies that you have tried all of the listed clients and recommend JabRef.

  I'm not affiliated to BibDesk but I believe that it is by far the most recommendable software for OS X. It is very usable, supports many databases contemporarily, can import from many formats from file, web, clipboard or drag&drop, stores publications automatically, supports keyword grouping and can search autonomously on the Web of Science, the Library of Congress and PubMed and has a definitely pleasant interface.

• #27 gnomedeplume, August 30, 2007 at 1:56 p.m.

  I have used Scholar's Aid because it is fast, free, versatile and it can output references in APA style which is important to me because I work in the field of Psychology. Their website is http://scholarsaid.com/index.html. They have both freeware and low-cost commercial versions. Cheers- G

• #28 AlleMeije, November 6, 2007 at 3:32 p.m.

  This site is great for comparing the reference managers that are available. At the moment I’m using jabref and it is so great that I don’t want to switch. But I have stopped using the Word/EndNote combination, will probably continue using a mix of LaTeX and OpenOffice, and I’m looking at the moment for a manager that

  • supports BibTeX (or better, like JabRef, uses BibTeX as its native format)
  • works within OpenOffice.

  I now saw that Zotero and Bibus both support OpenOffice, but neither of them use BibTeX as their native format. Apparently there now is something in OpenOffice itself as well (should be well integrated). Do you know of any ref managers that are OpenOffice-native and export BibTeX (or the other way around)? Thanks!

• #29 Kjell Magne Fauske, November 7, 2007 at 8:40 a.m.

  @AlleMeije. Thank you for you comment.

  Do you know of any ref managers that are OpenOffice-native and export BibTeX (or the other way around)?

  I now that Jabref can save to formats compatible with OpenOffice. On the jabref-users list there also have been some talk about a special OpenOffice plugin. I don't know the current status.

  OpenOffice has some useful bibliographic information on its wiki. Maybe you can find some tips there.

• #30 Kusmin, November 7, 2007 at 7:05 p.m.

  I wonder why don't you mention a very good reference manager RefDB. I use it for more than a year; it can do a lot of things.

• #31 Kjell Magne Fauske, November 7, 2007 at 8:30 p.m.

  @Kusmin The article is badly in need of an update. Tools like Zotero and RefDB are missing. Thank you for pointing this out.

• #32 Paul, November 7, 2007 at 11:37 p.m.

  I've been using KBibTex for a while now since I switched over to linux. For me it's quite useful because it has a simple, no fuss GUI that does one thing, i.e. let's you add and maintain references. Its also got the nice feature of being able to select the references you want to cite and copying those citations into your latex code, which as anyone writing a thesis knows can be pain if you have to remember the key you used for a particular article. I should comment that under Endnote (at least version 9, haven't used 10 yet), you can export to BibTex but the output filter has something screwy in it that I had to change otherwise Bibtex complains. Anyhow, I've long since migrated to BibTex so it's not an issue. What I would like to see though is something to generate custom bst files. Generally it's not an issue, but when your thesis advisor comes to you and asks for one specific element in your references to be in italic rather than bold it would help. Any ideas?

• #33 Kjell Magne Fauske, November 8, 2007 at 8:26 a.m.

  @Paul

  What I would like to see though is something to generate custom bst files. ... Any ideas?

  The only tool I know of is custom-bib available on CTAN. It comes with a tool called makebst. It can generate a bst file for you based on your preferences. You should give it a try. See the documentation for details.

• #34 Mike van Treek, November 10, 2007 at 12:25 p.m.

  Hi. Thanks for the information. I use LaTeX for produce my papers and my Ph.D. dissertation in biblical exegesis. I found BIBLATEX more powerfull than BIBTEX and works fine with CSQUOTES, both implemets a multilingual approach for bibliographic and quotation information. You can use JabRef as well adding some personalized fields.

• #35 Paul Sensecall, January 22, 2008 at 9:05 a.m.

  Hi. You might like to take a look at ReferenceChecker (http://www.goodcitations.com). An easy-to-use reference-checking macro that checks if references in a Word document are cited correctly

• #36 Adam Sparks, February 4, 2008 at 6:11 p.m.

  Looking over your list, you might also look at/include cb2bib, it can extract information from PDFs and write to your bibliography database.

  http://www.molspaces.com/cb2bib/

• #37 Benjamin, February 9, 2008 at 5:03 p.m.

  I'd like to add kbib, a bibtex-tool for kde, available at http://user.digisurf.com.au/~thachly/kbib/, which is very good adaptable to biblatex-specific entry types and fields and supports various search types (such as z39.50). Greetings, Ben

• #38 Kjell Magne Fauske, February 9, 2008 at 5:30 p.m.

  Thank you Paul, Adam and Benjamin for the links to the tools! I will include them in the next revision of the survey. Thank you for sharing.

• #39 Sveinung Heggen, February 26, 2008 at 10:46 a.m.

  I found a Windows program called Wibtex at http://www.wibtex.de/en/index.htm. I have not used it, but it looks interesting. It interfaces with BibTex, Tex and Word. Written by a German and translated to French, Spanish, and English.

• #40 Axel, March 30, 2008 at 5:30 p.m.

  "On the jabref-users list there also have been some talk about a special OpenOffice plugin. I don't know the current status."

  See http://www.itk.ntnu.no/ansatte/Alver_Omholt_Morten/jabref/OOPlugin.html

• #41 richard, April 18, 2008 at 1:03 a.m.

  I found this comparison of reference management software and it reminded me of this page, maybe it helps someone to get the "big picture" http://en.wikipedia.org/wiki/Comparison_of_reference_management_software

  greets, R

• #42 jen, April 21, 2008 at 5:14 p.m.

  Thanks for the breakdown, the comments and descriptions are really helpful. I just wanted to add that EndNote has gotten the face lift you mentioned (lol) and the newer versions are much more user-friendly. Might be worth looking at again. And EndNote Web too.

• #43 Basheer Chukkan, July 2, 2008 at 8:14 a.m.

  Hello there,

  Would you please advice for a selection of a software (open source) system to manage a collection of books, refeered and unfeered publications, reports & images collected and used in a library. We seek this information available for a group of staff including researchers etc., through a Microsoft Windows-based network, and administered by a librarian (multiuser). It will be very interesting if the client part can access the information through a web front-end. In addition, indexing of commonly used document types will be extremely useful. While our initial search for a suitable system, we found RefDB may provide the basic things (though we did not test it) we look for. Would you please provide your advice on this subject?

  Thank you in advance

• #44 Kjell Magne Fauske, July 5, 2008 at 7:14 p.m.

  @Basheer

  I'm afraid that I can't give much advice on that subject. I only have experience with BibTeX front end tools, and I don't think tools like Jabref is what you are looking for. Maybe some of the web based tools have the features that you are looking for.

  I recommend taking a look at the wikipedia article mentioned in the Richard's comment. The article has some very useful comparison tables.

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