The cb2Bib is a free, open source, and multiplatform application for rapidly
extracting unformatted, or unstandardized bibliographic references from email
alerts, journal Web pages, and PDF files.
The cb2Bib facilitates the capture of single references from unformatted and non
standard sources. Output references are written in BibTeX. Article files can be
easily linked and renamed by dragging them onto the cb2Bib window. Additionally, it
permits editing and browsing BibTeX files, citing references, searching references
and the full contents of the referenced documents, inserting bibliographic metadata
to documents, and writing short notes that interrelate several references.
Current version: cb2Bib 1.4.1. (See ChangeLog File for a detailed list of changes and
acknowledgments, and Release Notes
for additional notes and information.)
See also Release Note
cb2Bib 1.4.0.
Contents:
Description
The cb2Bib reads the clipboard text contents and process it against a set of
predefined patterns. If this automatic detection is successful, cb2Bib formats the
clipboard data according to the structured BibTeX reference syntax.
Otherwise, if no predefined format pattern is found or if detection proves to be
difficult, manual data extraction is greatly simplified by cb2Bib. In most cases,
such manual data extraction will provide with a new, personalized pattern to be
included within the predefined pattern set for future automatic extractions.
Once the bibliographic reference is correctly extracted, it is added to a
specified BibTeX database file. Optionally, document files are renamed to a
DocumentID filename and moved to a desired directory as a personal article library,
and their metadata is updated with the bibliographic reference. See Reading and writing bibliographic metadata
section.
The cb2Bib facilitates writing short notes related to bibliographic collections.
Notes are written using a minimalist markup on a plain text editor, and can latter
be converted to HTML. Related references and links become easily accessible on any
browser or by the embedded cb2Bib viewer. See Release Note cb2Bib 1.1.0.
Using cb2Bib
Procedure
- Select the reference to import from the email or web browser
On Unix machines, cb2Bib automatically detects mouse selections and clipboard
changes. On Windows machines, copy or Ctrl-C is necessary to activate cb2Bib
automatic processing.
- cb2Bib automatic processing
Once text is selected cb2Bib initiates the automatic reference extraction. It uses
the predefined patterns from file regexp.txt to attempt automatic
extraction. See Configuring Files section for setting the
user predefined pattern matching expression file. After a successful detection
bibliographic fields appear on the cb2Bib item line edits. Manual editing is
possible at this stage.
- cb2Bib manual processing
If no predefined format pattern is found or if detection proves to be difficult, a
manual data extraction must be performed. Select, either using mouse or
Shift+arrow keys, the reference fields from the cb2Bib clipboard area. A popup
menu will appear after selection is made. Choose the corresponding bibliographic
field. See BiBTeX Entry Types
available as cb2Bib fields. If operating with the keyboard, first letter of
the field is set as a menu shortcut. Thus, typing 'A' sets selection to 'author',
or '+A' to 'add authors'. Selection is postprocessed and added to the cb2Bib item
line edit. cb2Bib field tags will show on the cb2Bib clipboard area. Once the
manual processing is done, cb2Bib clipboard area will contain the matching
pattern. The pattern can be further edited and stored to the
regexp.txt file using Insert Regular Expression, Alt+I. See
the Extracting Data from the
Clipboard and The Regular
Expression Editor sections.
- Download reference to cb2Bib
The cb2Bib has the built-in functionality to interact with publishers "Download
reference to Citation Manager" service. Choose BibTeX format, or any other format
that you can translate using External Clipboard Preparsing Command. See
Additional, Keyboard
Functionality, Alt C. Click "Download" from your browser. When asked
"Open with..." select cb2Bib. The cb2Bib will be launched if no running instance
is found. If already running, it will place the downloaded reference to the
clipboard, and it will start processing. Make sure your running instance is aware
of clipboard changes. See Buttons Functionality. For convenience, the
shell script c2bimport, and the desktop config file
c2bimport.desktop are also provided.
- Adding documents
PDF and other documents can be added to the BibTeX reference by dragging the file
icon and dropping it into the cb2Bib's panel. Optionally, document files, are
renamed to a DocumentID filename and moved to a desired directory as a personal
article library (See Configuring Documents section).
Linked to a reference documents correspond to the BibTeX tag file.
Usual reference manager software will permit to retrieve and visualize these
files. Download, copy and/or moving is scheduled and performed once the reference
is accepted, e.g., once it is saved by pressing Save Reference button.
- Multiple retrieving from PDF files
Multiple PDF or convertible to text files can be sequentially processed by
dragging a set of files into cb2Bib's PDFImport dialog. By starting the processing
button, files are sequentially converted to text and send to cb2Bib clipboard
panel for reference extraction. See PDF Reference Import for details.
- Journal-Volume-Page Queries
Takes input Journal, Volume, and first page from the corresponding edit lines and
attempts to complete the reference. Additionally, queries consider Title, DOI, and
an <it>excerpt</it>, which is a simplified clipboard panel contents.
See Configuring
Network section, the distribution file netqinf.txt, and Release Note cb2Bib 0.3.5 for
customization and details.
- BibTeX Editor
cb2Bib includes a practical text editor suitable for corrections and additions.
cb2Bib capabilities are readily available within the editor. E.g., the reference
is first sent to cb2Bib by selecting it, and later retrieved from cb2Bib to the
editor using 'right click' + 'Paste Current BibTeX'. Interconversions Unicode
<-> LaTeX, long <-> abbreviated journal name, and adding/renaming PDF
files are easily available. BibTeX Editor is also accessible through a shell
command line. See The cb2Bib Command
Line and Embedded File
Editor.
Buttons
Functionality
- About
About cb2Bib, bookmarks, and online help
- Search references
Opens the cb2Bib's search dialog. The search is performed either on the current
BibTeX file, or for all BibTeX files on the current directory. Optionally, the
search is extended to reference's files. Hits are displayed on an editor window.
See Search BibTeX files for
references. See also Configuring Utilities section to
configure the external to text converter.
- PDFImport
Launches cb2Bib's PDFImport window. Files dragged into PDFImport window are
sequentially translated to text and sent to cb2Bib clipboard panel. The cb2Bib
automatic and manual capabilities are then easily available to extract and
supervise reference extractions. See PDF Reference Import.
- Dis/Connect Clipboard
Toggles automatic cb2Bib and desktop clipboard connection. While the automatic
cb2Bib-clipboard connection permits reducing keystrokes, the disconnected mode is
needed in cases where multiple mouse selections or copies are required to complete
a reference extraction. See also Release Note cb2Bib 0.4.1 and Release Note cb2Bib 0.2.1 if you
experience problems with this feature.
- Network Reference Query
Starts Network Query. It usually takes input Journal, Volume, and first page from
the corresponding edit lines and attempts to complete the reference. See Configuring Network network
section to customize querying. See the distribution file netqinf.txt
and also Release Note
cb2Bib 0.3.5 for the details.
- View BibTeX Reference
View current reference as will be output to the BibTeX file. Eventual manual
changes should be done on the item line edit.
- Save Reference
Inserts the current bibliographic reference to the output BibTeX file. This action
decides whether or not a reference is accepted. Scheduled actions such as PDF
downloading, copying or renaming will be performed at this time.
- Open BibTeX File
Opens the current BibTeX output file. Right click within the BibTeX Editor window
for its particular functionality. See also Embedded File Editor.
Additional, Keyboard
Functionality
- Alt A
Open cb2Bib Annote. Specify the note's filename in the dialog. A new note is
created if the file name does not exist. The cb2Bib Annote is opened as a separate
program. Exiting cb2Bib will not exit the note's viewer. On the viewer, pressing
key E launches the default text editor. The viewer will track the editor, and will
update the note's display each time the editor saves it. The viewer's
functionality is disabled if the cb2Bib was not compiled and linked against
WebKit. See The cb2Bib Command
Line to use Annote in command line mode.
- Alt B
Edits the Bookmarks and Network Query Info file netqinf.txt.
- Alt C
Preparses cb2Bib's clipboard through a user specified external script or tool.
Preparsing is necessary to catch formatted references that can not be easily
extracted using recognition patterns, or that are written in ambiguous formats.
Many available scripts or specific user-written tools can be incorporated to
cb2Bib through this external preparsing capability. In addition, simple, one-line
scripts can be used within PDFImport to provide, for instance, the journal name
when missing from the PDF first page. The cb2Bib distribution contains the sample
scripts isi2bib and ris2bib that convert ISI and RIS
formatted strings to BibTeX. See Configuring Clipboard for
details.
- Alt D
Deletes temporary BibTeX output file. This permits using cb2Bib output files as
temporary media to transfer references to a preferred reference manager and
preferred format. Caution: This feature is not intended for the users who
actually store their references in one or several BibTeX files. Remember to import
references prior to delete cb2Bib output file.
- Alt E
Edits the regular expression file. It permits an easy access and modification of
stored extraction patterns. New patterns are conveniently added to to the regular
expression file by using the RegExp Editor button functionality.
- Alt F
Launches a file dialog for selecting the source file name for the BibTeX entry
file. Selected files are displayed either, as the actual source
filename, or, as the target filename, depending on the file copy/rename/move
settings. See Configuring Documents. Alternatively
to Alt F, documents can be easily linked to a reference by dragging the
document file and dropping it to the cb2Bib panel.
- Alt J
Edits the Journal Abbreviations file.
- Alt O
Opens the currently linked document for browsing. Documents can be easily linked
to a reference by dragging the document file and dropping it to the cb2Bib panel,
or with Alt F. Linked documents correspond to the BibTeX tag
file.
- Alt P
Postprocess BibTeX output file. It launches a user specified script or program to
postprocess the current BibTeX file. The cb2Bib distribution contains two sample
scripts. One, bib2pdf is a shell script for running
latex and bibtex; this permits to check the BibTeX file
for possible errors, and to easily produce a suitable output for printing. The
other one, bib2end.bat is a batch script for running
bib2xml and xml2end, which converts references into
Endnote format. See Configuring BibTeX for details.
- Alt R
Restarts the cb2Bib automatic engine. Takes input data not from the system
clipboard but from the cb2Bib clipboard panel. This permits editting the input
stream from poorly translated PDF captions, correcting for author superscripts, or
helps in debugging regular expressions.
- Alt W
Writes current reference to the source document file. This option is intended for
writing and updating bibliographic metadata to document files without needing to
use BibTeX files. Only local and writable files are considered.
- Alt X
Check Repeated looks for existing references in the BibTeX directory similar to
the current one. The search is done for exact cite ID, and for title and author
field values, or, if empty, for booktitle and editor,using the approximate string search
pattern. See also Configuring BibTeX.
- Esc
Quits cb2Bib popup menu. The cb2Bib menu pops up each time a selection in made in
the clipboard panel. This saves keystrokes in a normal bibliographic extraction.
Press Esc or Right Click mouse button if you need to gain access to
the editor cut/copy/paste functionality instead.
Advanced features
Advanced features, and processing and extraction details are described in the
following sections:
Configuration information is described in the following sections:
Utilities and modules are described in the following sections:
Requirements
Compilation
To compile cb2Bib, the following libraries must be present and accessible:
- Qt 4.4.0 or higher from Trolltech. On a Linux platform with Qt preinstalled, make sure that
the
devel packages and Qt tools are also present.
- WebKit library (optional) to compile cb2Bib Annote viewer. It is already
included in Qt > 4.4.0 library. No special action/flag is needed during
compilation.
- LZO 2.03 library and headers available at http://www.oberhumer.com/opensource/lzo. If LZO2 were unavailable on
a particular platform, type
configure --disable-lzo or, equivalently,
qmake -config disable-lzo before compiling.
- X11 header files if compiling on Unix platforms. Concretely, headers
X11/Xlib.h and X11/Xatom.h are needed.
- The header files
fcntl.h and unistd.h from
glibc-devel package are also required. Otherwise compilation will
fail with referencelist.cpp:227: `close' undeclared.
Deployment
Although not needed for running cb2Bib, the following tools extend cb2Bib
applicability:
- The
bib2xml and xml2end BibUtils, to test the postprocess script bib2end.bat on
Windows platforms.
- ... and LaTeX and friends, to check for BibTeX file correctness and to get a
nice printing through the shell script
bib2pdf.
Credits and License
The cb2Bib icons are taken from the Oxygen, Crystal SVG, and
Noia icon sets, to be found at the KDE Desktop Environment. Several people has contributed with
suggestions, bug reports or patches. For a detailed list of acknowledgments see the
ChangeLog File.
The cb2Bib program is licensed under the terms of the GNU General Public
License version 3.
The cb2Bib, Pere Constans, Copyright © 2004-2010.
First released, version 0.1.0 on 2004-06-29.
Last updated on 2010-09-03.
