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Does cb2bib remove drudgery from bibliography creation?

By Bruce Byfield on November 11, 2008 (4:11:11 PM)

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Many academics and students share a dirty secret: They hate the drudgery of assembling bibliographies. The cb2bib utility attempts to remove some of the drudgery, at least so far as online references go. Designed primarily for use with BibTeX, cb2bib can also be used with other formats once you export the results. However, whether the application actually makes bibliographical tasks easier seems questionable.

cb2bib takes the contents of your desktop clipboard and puts it into a BibTeX database, working automatically to put information into the correct format if you are lucky, or with your manual input if you are not. Since your manual input is added to the automatic search patterns, in theory the automatic formatting should improve as you use cb2bib, although in practice I was unable to detect any improvement. Possibly I did not use it long enough for major improvements to happen.

The c2bib window is dominated by fields for bibliographical information. While that arrangement might seem reasonable at first, in practice you might wish for a larger field for viewing clipboard information if you have to do any manual formatting. As things are, the clipboard viewing field can only display three lines at a time, which can be inconvenient if you are working with more than two or three of bibliographical references at the same time. Below the clipboard viewer is a field for the path to the BibTeX database, and, below that, a toolbar of buttons. The toolbar is carelessly organized, with the exit button in the middle, but, unlike the clipboard viewer, at least large enough to be convenient for use.

Extracting references

When using cb2bib to extract references, be sure that the connection to your desktop's clipboard is toggled on, using the sixth button from the left on the toolbar; you might want to turn it off if you have to interrupt your work with cb2bib for other uses of the clipboard, but, if you fail to turn it back on, you will unable to extract references. You should also change the BibTeX database's name, to avoid having entries from several projects jumbled up in a single database.

cb2bib looks complicated, and has only minimal help available, but is easier to use than you might think at first. Essentially, cb2bib has two work cases. In the first, you copy one or more references in a file, email message, or Web page to your desktop clipboard for processing. In the second, you select any number of PDF files for cb2bib to extract information from.

According to instructions on the cb2bib site, you are supposed to be able to drag and drop PDF files onto the application window, but in practice this feature only worked in KDE. In GNOME (or if you want more control over how the PDFs are processed), you have to click on the PDF button, which is fourth from the left on the toolbar. The button opens up a sub-window in which you can choose such options as whether to open up the processed files to refer to them. In either case, cb2bib converts the PDF files to text using pdftotext and copies the resulting text to the clipboard.

In both work cases, cb2bib displays the content of the clipboard, adding color-coded comments about parts of the content that it has tentatively identified. In addition, it tries to create an entry into the database automatically. If the automatic entry is inadequate -- and, if my experience is any indication, in your first attempts it probably will be -- then you can create the database entry manually.

To create a manual entry, set the type of the reference -- for example, article, book, or conference. Then, select one part of a reference in the clipboard viewer with the mouse. As you do so, a popup list appears displaying possible fields into which you can insert the highlighted string. Choose a field, and continue with the other parts of the reference. When you finish one reference, choose another and continue, making sure that the CITEID field has a different entry for each reference.

Once you have finished all references, export them to a BibTeX file using the second button from the right on the toolbar. From there, you can convert the entry to other formats. One of the quickest ways to convert the result -- assuming that HTML is convenient -- is to copy the BibTeX file into the Online BibTeX Converter and save the resulting page.

Other functions

In addition to extracting bibliographic references, cb2bib also includes several utilities. If you want to locate a reference in the BibTeX database, you can click the third button from the left on the toolbar to open a search page in which you can use regular expressions, specify how the string you enter will be used in the search -- including approximately, all words, or any words -- and which fields and files will be searched.

You can also view the BibTeX database by clicking the toolbar's last button on the right. The resulting window lists all references, and includes an inconveniently small search field as well as bookmarks.

From the second button on the left, you can open the configuration window for cb2bib. Many of the configuration settings, such as those in the Files and Network sub-windows, should probably be left alone by most users. However, you might want to set whether BibTeX displays full or abbreviated author and journal names, or consult pdftotext's man pages to change its parameters under Utilities.

Perhaps the most useful configuration change you can make is in the Fonts window, where you can change how the clipboard viewer displays information. You might want to set a smaller font in order to display more information, or a larger one for easier viewing. I also suggest that you change the gray, yellow, orange, and cyan that cb2bib uses to add comments to the clipboard viewer into colors that are more readable.

Useful or not?

Obviously, cb2bib is most useful to BibTex users if it is useful at all, but whether it makes a bibliography easier to assemble even for them is questionable. The connection to the clipboard can save you hundreds, even thousands, of keystrokes and mouse-clicks compared to manual assembly of sources, but, if you have to do manual formatting, it might cost you as many again in setting up each entry correctly. The story might be different if the automatic extraction worked better out of the box, but as it is, cb2bib might be said to replace one sort of drudgery with another.

Still, cb2bib includes secondary functions that are useful in themselves, such as the PDF extraction, and the database searcher and viewer. If you use BibTex, you might find that these functions alone make cb2bib a worthwhile utility. If you don't, you may need to test cb2bib once or twice to compile a bibliography with it before you decide whether to continue to use it.

Bruce Byfield is a computer journalist who writes regularly for Linux.com.

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on Does cb2bib remove drudgery from bibliography creation?

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Tough competition Re: Does cb2bib remove drudgery from bibliography creation?

Posted by: Nordic on November 11, 2008 05:43 PM
Well sure, academics hate to do all the copy & paste work generated by bibliographies, and hate it even more when requirements from editors oblige you to spend hours changing the order of fields within a citation. However there is one product which basically eliminate all that pain: Endnote. As a bibliography management system it is a pretty perfect solution: change format of citations at will, create your own format, link directly to databases to import automatically references, including the abstract! BibteX and all its declensions cannot really compete, neither the clunky web-based bibliographic tools. Actually, as an academic myself, one of the last reason why I am still using Windows+Word is the perfect integration with Endnote. Don't get me wrong: I love Linux and use it as often as I can, I even enjoy LateX, I use OpenOffice and Gedit all the time, but ... for bibliography and articles I am still in chains because of Endnote. That would actually be an interesting challenge for open source communities. Create an interface for Endnote to OpenOffice and I can drop Word. Create an open source version of Endnote (for Linux) and I can convince everyone around me in academia to drop Windows. Another set of tools that could be quite useful are qualitative analysis programs such as NVivo and AtlasTi, available only under Windows.

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Re: Tough competition Re: Does cb2bib remove drudgery from bibliography creation?

Posted by: Anonymous [ip: 134.252.17.121] on November 11, 2008 06:17 PM
EndNote is a horrible program that does not run on Linux and that does not play well with the free/open source community--they are suing the creators of Zotero.

Zotero is free/open source, and cross platform. It plugs into Firefox & can import references (including the abstract, PDF copy of the article, and a web snapshot).

It plugs into OpenOffice.org Writer & into Microsoft Word & can round-trip references between the two programs. The export and citation formats work much better than in EndNote & Zotero supports EndNote citation style files.

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Re: Tough competition Re: Does cb2bib remove drudgery from bibliography creation?

Posted by: Anonymous [ip: 193.190.191.242] on November 13, 2008 07:58 AM
If you're talking about Word integration, sure, Bibtex can't compete at this time. Other than that, I find Bibtex and surrounding tools (cb2bib, JabRef, ...) much more flexible than Endnote. Citation formats? That's what BibTeX styles are all about, of course, write your own if the needed format happens to be unavailable. Auto-import? Check out JabRef, it's getting there.

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Does cb2bib remove drudgery from bibliography creation?

Posted by: Anonymous [ip: 81.191.3.44] on November 11, 2008 07:29 PM
JabRef is the tool you are looking for! Can be used with LyX for those that do not want LaTeX (w/kile or Eclipse).

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cb2bib and Endnote: working together through BibTex

Posted by: Anonymous [ip: 24.61.37.168] on November 12, 2008 04:32 AM
I use both cb2bib and Endnote -- on windows. But found this the other day. Sounds interesting.

BibTeX to Endnote converter

http://www.it.usyd.edu.au/~tapted/bib2endnote.html

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Does cb2bib remove drudgery from bibliography creation?

Posted by: Anonymous [ip: 80.222.208.215] on November 12, 2008 08:27 AM
+1 for Jabref. I don't know how awkward it is if you use OpenOffice or MS Word for writing, but for LaTeX it is excellent. I work in the biosciences and I can get practically all of the bibliographic data I need from online databases through Jabref directly. Simply paste the document ID from e.g. PubMed into Jabref and that's it. It does download the abstract as well and can integrate with a directory containing local copies of the papers in PDF format if you it want to.

The native database format is Bibtex, which really is the only way to go if you write with LaTeX. I tried Zotero, and it works, but the database must be converted from Zotero-native to Bibtex before it can be used and I found that I didn't get everything I needed in the resulting Bibtex file.

Jabref is a Java app licensed under GPL 2. The interface may not be pretty, but it works, and works very well at least for LaTeX users.

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Re: Does cb2bib remove drudgery from bibliography creation?

Posted by: Anonymous [ip: 24.5.210.198] on November 12, 2008 03:00 PM
Agree that JabRef is useful if you are using LaTeX. Word/OO.o support is lacking, though.

Zotero's BibTeX export has improved. It is definitely better than EndNote's. What issues do you have with it?

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Does cb2bib remove drudgery from bibliography creation?

Posted by: Anonymous [ip: 72.190.96.105] on November 12, 2008 04:52 PM
I use referencer. Does what I need it to do. It can create a bibtex file though I have some minor issues with the abstract component.

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Does cb2bib remove drudgery from bibliography creation?

Posted by: Anonymous [ip: 88.14.91.22] on November 12, 2008 11:14 PM
I am a scientist in the field of theoretical physics, and yes, for me the
cb2Bib removes the drudgery from bibliography creation. Not only that, after
several years of using it it has become, together with my browser, my only
bibliographic software. Why? For several reasons: 1) it extracts references
from anywhere and any format (as a scientist in a minority field I appreciate
this) 2) it links pdfs to the citation, thus I have them handy in the
reading/writing cycle 3) it easily performs internet queries, not only to
established databases but to any website, and 4) it searches the full text
article files. That's what I need and all what I need.


I found several comments in your article rather surprising. To my
understanding, they are reflecting a poor knowledge of the program you try to
describe:


- "Possibly I did not use it long enough for major improvements to happen."
Not important for how long you use it; what's important is how skilled you are
discerning patterns and writing regular expressions for them.

- I do not care on how automatically I extract a reference. Whenever I see a
relevant reference, I want to keep it with a reasonable minimal effort, and
(most important for any scientist) I want to verify it is completely correct.

- "As things are, the clipboard viewing field can only display three lines at
a time" did you resize/full-seized it?

-"The toolbar is carelessly organized" It is handy. A first block of buttons
(left) deals with searches and configuration. The right block of buttons are
properly related to reference extraction, ordered as they are needed for on a
normal extraction.

- "Drag and drop PDF files onto the application window, but in practice this
feature only worked in KDE" On windows it works fine also. Did you report not
working in Genome as bug? In my experience, the author has always been very
responsive.

- "If the automatic entry is inadequate -- and, if my experience is any
indication, in your first attempts it probably will be -- then you can create
the database entry manually" You will only have automatic PDF extraction if 1)
PDF has BibTeX metadata, or 2) you write down your own regular expressions for
your favorite journals.




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Does cb2bib remove drudgery from bibliography creation?

Posted by: Anonymous [ip: 121.44.24.231] on November 13, 2008 09:53 AM
+1 jabref -- it's really good, performs internet searches, links the database with the PDFs (people who use endnote seem amazed at that feature for some reason).

I wouldn't touch endnote with a ten foot pole. The difference between the look and feel for a word document and a latex document is quite astounding -- but most people have their feet firmly in one camp or the other. Though i find few people who have used latex that go back to using any office suite for serious writing. Rule of thumb > 5 pages of text -- latex. Everything else, office suite.

Endnote continually stuffs up references, doesn't export to bibtex properly (it *almost* does, and a quick use of sed fixes it, but you have to work it out). Doesn't link documents, isn't stable, and is horrible binary only. I have met users whose installs were continually popping up messages every five seconds when reading a document that used bibtex -- these people put up with it.

Bug fixes at jabref's site are fast and you can actually communicate with the development team -- fat chance of doing that without going through several layers of bureaucracy.

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Does cb2bib remove drudgery from bibliography creation?

Posted by: Anonymous [ip: 134.53.57.142] on November 13, 2008 08:27 PM
TeX is not a viable solution for many, and perhaps even the vast majority, of users (with some of the sciences noted above being one obvious exception). When I deal with article or book publishers, they almost exclusively insist on Word files. That's a fact of life that most of these conversations fail to recognize. BibTeX as a formatting solution only works with LaTeX, and LaTeX is only viable if a) you only care about finished (say PDF) output, or b) your publisher accepts raw LaTeX files.

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Does cb2bib remove drudgery from bibliography creation?

Posted by: Anonymous [ip: 208.65.246.240] on November 14, 2008 03:03 AM
BibTeX does not only work with LaTeX. Jabref uses BibTeX as its basic format but it will export formatted bibliographies to both Word and Openoffice.

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Re: Does cb2bib remove drudgery from bibliography creation?

Posted by: Anonymous [ip: 24.210.246.49] on November 16, 2008 01:10 AM
By "BibTeX" I meant the entire processing system. It IS LaTeX-specific.

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Does cb2bib remove drudgery from bibliography creation?

Posted by: Anonymous [ip: 202.88.84.208] on November 24, 2008 11:01 AM
This review is out of sync with my experience. I have used JabRef, kbibtex, kbib, referencer, and cb2bib, to mention a few. I use BibTeX. At present I use both JabRef and cb2bib both, sometimes at the same time. Anything I can get into the clipboard, can be worked out in cb2bib much more rapidly than with anything else I have encountered. I am still learning to use both of these tools, and each of them is quite good, each in it's own way.

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