Bookends User Guide - Michael Joseph Therapy

Transcription

BOOKENDS 10
Reference and Information Management Software
for Macintosh
Sonny Software
2703 Daniel Road
Chevy Chase, MD 20815
Sales:
Web: www.sonnysoftware.com
E-mail: [email protected]
Technical Support:
[email protected]
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THIS MANUAL IS COPYRIGHTED AND ALL RIGHTS ARE RESERVED BY
SONNY SOFTWARE. THIS SOFTWARE PRODUCT IS COPYRIGHTED AND ALL
RIGHTS ARE RESERVED BY JONATHAN D. ASHWELL. THE DISTRIBUTION
AND SALE OF THIS PRODUCT ARE INTENDED FOR THE USE OF THE
ORIGINAL PURCHASER ONLY AND FOR USE ONLY ON THE COMPUTER
SYSTEM SPECIFIED. LAWFUL USERS OF THIS PROGRAM ARE HEREBY
LICENSED ONLY TO READ THE PROGRAM FROM ITS MEDIUM INTO
MEMORY OF A COMPUTER SOLELY FOR THE PURPOSE OF EXECUTING THE
PROGRAM. COPYING, DUPLICATION, SELLING OR OTHERWISE
DISTRIBUTING THIS PRODUCT IS A VIOLATION OF THE LAW. THIS MANUAL
MAY NOT IN WHOLE OR PART, BE COPIED PHOTOCOPIED, REPRODUCED,
TRANSLATED OR REDUCED TO ANY ELECTRONIC MEDIUM OR MACHINE
READABLE FORM WITHOUT THE PRIOR WRITTEN CONSENT OF SONNY
SOFTWARE.
WILLFUL VIOLATIONS OF THE COPYRIGHT LAW OF THE UNITED STATES
CAN RESULT IN CIVIL DAMAGES OF UP TO FIFTY THOUSAND ($50,000.00)
DOLLARS IN ADDITION TO ACTUAL DAMAGES, PLUS CRIMINAL PENALTIES
OF UP TO ONE YEAR IMPRISONMENT AND/OR A TEN THOUSAND ($10,000.00)
DOLLAR FINE.
SONNY SOFTWARE MAKES NO WARRANTIES, EITHER EXPRESS OR
IMPLIED, REGARDING THE ENCLOSED COMPUTER SOFTWARE PACKAGE,
ITS MERCHANTABILITY OR ITS FITNESS FOR ANY PARTICULAR PURPOSE.
THE EXCLUSION OF IMPLIED WARRANTIES IS NOT PERMITTED BY SOME
STATES. THE ABOVE EXCLUSION MAY NOT APPLY TO YOU. THIS
WARRANTY PROVIDES YOU WITH SPECIFIC LEGAL RIGHTS. THERE MAY BE
OTHER RIGHTS THAT YOU MAY HAVE THAT VARY FROM STATE TO STATE.
PORTIONS COPYRIGHT 1998-2008 PARADIGMA SOFTWARE. POWERED BY
VALENTINA.
Apple, Macintosh, and Mac OS X are trademarks of Apple, Inc.
Microsoft Word—Microsoft Corporation
EndNote and RefViz—ISI ResearchSoft
Bookends and Sonny Software—Sonny Software
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LIMITED WARRANTY
This software and manual are sold “AS IS,” without warranties as to performance. The
entire risk as to quality and performance of the software is assumed by the user. The user,
and not the manufacturer, distributor, or retailer assumes the entire cost of all necessary
servicing, repair, or correction and any incidental or consequential damages.
THE ABOVE WARRANTIES FOR GOODS ARE IN LIEU OF ALL OTHER
EXPRESS WARRANTIES. NO IMPLIED WARRANTIES OF MERCHANTABILITY
AND FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY
OBLIGATION SHALL ARISE. SOME STATES DO NOT ALLOW LIMITATIONS
ON HOW LONG AN IMPLIED WARRANTY LASTS, SO THE ABOVE
LIMITATION MAY NOT APPLY TO YOU. IN NO EVENT SHALL SONNY
SOFTWARE OR ANYONE ELSE WHO HAS BEEN INVOLVED IN THE
CREATION AND PRODUCTION OF THIS SOFTWARE BE LIABLE FOR
INDIRECT, SPECIAL, OR CONSEQUENTIAL DAMAGES, SUCH AS, BUT NOT
LIMITED TO, LOSS OF ANTICIPATED PROFITS OR BENEFITS RESULTING
FROM THE USE OF THIS SOFTWARE, OR ARISING OUT OF ANY BREACH OF
THIS WARRANTY. SOME STATES DO NOT ALLOW THE EXCLUSION OF
CONSEQUENTIAL DAMAGES, SO THE ABOVE LIMITATION MAY NOT APPLY
TO YOU. THIS WARRANTY GIVES YOU SPECIFIC LEGAL RIGHTS, AND YOU
MAY ALSO HAVE OTHER RIGHTS THAT VARY FROM STATE TO STATE.
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TABLE OF CONTENTS
WHAT IS BOOKENDS? ........................................................................................................................ 12 REQUIREMENTS ...................................................................................................................................................... 14 REGISTERING BOOKENDS ......................................................................................................................................14 INTRODUCTION TO BOOKENDS ..................................................................................................... 15 BOOKENDS DATABASES .........................................................................................................................................15 ENTERING/IMPORTING REFERENCES ................................................................................................................. 15 VIEWING REFERENCES ...........................................................................................................................................16 THE HITS LIST ......................................................................................................................................................... 16 SCANNING A DOCUMENT AND CREATING A BIBLIOGRAPHY.............................................................................16 THE REFERENCE WINDOW .............................................................................................................. 18 REFERENCE NUMBERS...........................................................................................................................................18 Changing the unique ID...................................................................................................................................19 Use the unique ID to embed hypertext links in another application's documents ................19 Use the unique ID for Drag and Drop transfer or deletion of references...................................20 Use the unique ID to add a reference to a static group .....................................................................20 REFERENCE FIELDS ................................................................................................................................................ 20 Authors ...................................................................................................................................................................21 Title ..........................................................................................................................................................................22 Short Title..............................................................................................................................................................22 Editors.....................................................................................................................................................................22 Journal.....................................................................................................................................................................23 Vol (Issue)..............................................................................................................................................................23 Pages........................................................................................................................................................................23 Date ..........................................................................................................................................................................23 Publisher ................................................................................................................................................................23 Address/City .........................................................................................................................................................23 Abstract ..................................................................................................................................................................24 Keywords................................................................................................................................................................24 Notes ........................................................................................................................................................................24 User1 (Key), User2User18.............................................................................................................................24 URL ...........................................................................................................................................................................25 AUTOCOMPLETE...................................................................................................................................................... 26 ENLARGING REFERENCE FIELDS.......................................................................................................................... 27 CHANGE FIELD NAMES ..........................................................................................................................................28 REFERENCE TYPE ................................................................................................................................................... 28 NAVIGATION ARROWS ...........................................................................................................................................28 THE HITS AREA....................................................................................................................................................... 29 THE ATTACH POP‐UP ............................................................................................................................................29 Attaching a Wile or folder.................................................................................................................................30 Smart attachment folders ..............................................................................................................................30 Detaching a Wile or folder ................................................................................................................................31 Opening attached Wiles .....................................................................................................................................31 Attaching multiple Wiles or folders to one reference............................................................................32 Storing attached Wiles or folders automatically ....................................................................................32 Importing reference information from PubMed when attaching a pdf .....................................34 5
Downloading and attaching pdfs from a browser by drag and drop..........................................35 Attaching an image from another application by drag and drop ................................................36 Removing an attached Wile from the database ......................................................................................36 Deleting an attached Wile from the hard disk .........................................................................................37 Reveal an attached Wile in the Finder.........................................................................................................37 Show all references with or without attachments...............................................................................37 REFERENCE WINDOW DRAWER .......................................................................................................................... 37 COLOR LABEL .......................................................................................................................................................... 38 RATING .....................................................................................................................................................................38 LINKING BOOKENDS TO A WORD PROCESSOR ..................................................................................................38 COPY CITATION ....................................................................................................................................................... 40 Drag and Drop citations..................................................................................................................................42 ModiWier keys ........................................................................................................................................................42 Customizing citations.......................................................................................................................................43 POP‐UP NAVIGATION WINDOW ........................................................................................................................... 43 THE LIST VIEW WINDOW ................................................................................................................. 44 THE REFERENCE LIST PANE .................................................................................................................................45 Color Labels ..........................................................................................................................................................48 Using the List View to copy temporary citations..................................................................................49 Using the List View to copy formatted citations...................................................................................49 Using the List View to create a hypertext link to a reference .........................................................49 Emailing references.........................................................................................................................................50 GROUPS PANE.......................................................................................................................................................... 50 All ..............................................................................................................................................................................50 Hits............................................................................................................................................................................51 Groups .....................................................................................................................................................................51 Group Folders.......................................................................................................................................................56 CONCISE VIEW PANE .............................................................................................................................................58 ConWiguring the concise view ........................................................................................................................60 Editing and/or entering reference information in the concise view ...........................................62 THE DISPLAY PANE ................................................................................................................................................ 65 Formatted view...................................................................................................................................................65 Attachment view.................................................................................................................................................65 SEARCH FIELD—LIVE SEARCH AND SPOTLIGHT SEARCH ............................................................................... 67 ONLINE SEARCH................................................................................................................................... 69 Do not clear reference list between searches.........................................................................................72 Removing items from the reference list....................................................................................................72 Repeating a search ............................................................................................................................................72 PubMed...................................................................................................................................................................73 Web of Science.....................................................................................................................................................77 Library of Congress ...........................................................................................................................................80 Amazon...................................................................................................................................................................82 Z39.50 library searches ...................................................................................................................................84 SRU searches ........................................................................................................................................................86 SAVED INTERNET SEARCHES ................................................................................................................................ 86 ADVANCED PUBMED SEARCHES .......................................................................................................................... 88 AUTOMATED PUBMED SEARCHES ....................................................................................................................... 89 Preference settings ............................................................................................................................................89 Creating an automated search.....................................................................................................................89 6
IMPORT FILTERS ................................................................................................................................. 92 Designing an import Wilter..............................................................................................................................92 Type deWinitions...................................................................................................................................................95 Identifying the beginning of a reference..................................................................................................96 Parsing Authors/Editors..............................................................................................................................100 Parsing Keywords ........................................................................................................................................... 101 Replace hyphens with spaces ..................................................................................................................... 101 Removing unwanted characters............................................................................................................... 101 Parsing the Source.......................................................................................................................................... 101 Creating Wilters for existing bibliographies..........................................................................................105 Importing MARC records .............................................................................................................................107 Online Searches and importing from libraries via the Internet ................................................. 110 Adding information to imported references........................................................................................114 FORMATS AND BIBLIOGRAPHIES ................................................................................................116 New (Format) ................................................................................................................................................... 116 Edit Format........................................................................................................................................................117 Formatting Options tab................................................................................................................................117 Names................................................................................................................................................................... 118 Case ....................................................................................................................................................................... 120 When a Field is Empty................................................................................................................................... 132 Example: Stringent APA intext citation style .................................................................................... 134 Bib & Citations Options tab.........................................................................................................................135 Font and Style Hierarchy .............................................................................................................................144 SCANNING DOCUMENTS ..................................................................................................................145 BEFORE THE SCAN ............................................................................................................................................... 145 Creating removable intext citations...................................................................................................... 146 Excluding enclosing punctuation in a Winal citation ........................................................................ 147 Overriding superscript in a Winal citation .............................................................................................147 Mixing text with temporary intext citations...................................................................................... 147 Cited pages .........................................................................................................................................................148 Replace temporary intext citations with date only ........................................................................ 149 Eliminate authors from Winal citation .................................................................................................... 150 The Scan a Document Dialog ..................................................................................................................... 150 DURING THE SCAN ............................................................................................................................................... 153 Replacing citations with numbers ........................................................................................................... 154 AFTER THE SCAN .................................................................................................................................................. 155 RULES FOR SCANNING ......................................................................................................................................... 155 MICROSOFT WORD .............................................................................................................................................. 156 Go to Bookends................................................................................................................................................. 158 Find in Bookends ............................................................................................................................................. 158 Insert Citation................................................................................................................................................... 159 Scan Document................................................................................................................................................. 159 Unscan Document ........................................................................................................................................... 160 Typical use of the Microsoft Word addin with Bookends.............................................................161 Size limitation for documents scanned from within Word ...........................................................161 Problem: font sometimes changes after a citation is inserted in a Word document......... 162 MELLEL.................................................................................................................................................................. 162 Citation objects ................................................................................................................................................ 162 Bibliography palette ...................................................................................................................................... 164 7
Synchronize database ................................................................................................................................... 165 NISUS WRITER EXPRESS AND PRO MACROS .................................................................................................. 166 Bookends Find .................................................................................................................................................. 166 Bookends Go ...................................................................................................................................................... 166 Bookends Scan a Doc ..................................................................................................................................... 167 REFBASE...............................................................................................................................................169 MENUS...................................................................................................................................................171 BOOKENDS MENU..............................................................................................................................171 ABOUT BOOKENDS…........................................................................................................................................... 171 CHECK FOR UPDATES…...................................................................................................................................... 171 PREFERENCES…................................................................................................................................................... 171 Word Processor................................................................................................................................................ 172 Attachments folder......................................................................................................................................... 173 Default font ........................................................................................................................................................173 Default view.......................................................................................................................................................173 Internal cache................................................................................................................................................... 174 Hypertext links ................................................................................................................................................. 174 Journal Glossary............................................................................................................................................... 174 Window menu................................................................................................................................................... 174 Automatic backup........................................................................................................................................... 174 Reference Types ............................................................................................................................................... 175 Default new reference Type........................................................................................................................176 Keywords location in reference window...............................................................................................176 Rename attachments..................................................................................................................................... 176 Field Names .......................................................................................................................................................176 Data entry...........................................................................................................................................................177 Inserted date format...................................................................................................................................... 177 Bring reference window to front on doubleclick ............................................................................. 178 Show entire date.............................................................................................................................................. 178 Sorts based on................................................................................................................................................... 179 Sort Lists..............................................................................................................................................................179 Indicate attachments..................................................................................................................................... 179 Display of names.............................................................................................................................................. 179 Fields to display ............................................................................................................................................... 180 Color Labels .......................................................................................................................................................180 Default Summary view.................................................................................................................................. 181 Font size ..............................................................................................................................................................181 View All label colr ........................................................................................................................................... 181 Standard View organization ...................................................................................................................... 181 Temporary citations ...................................................................................................................................... 182 Cite by:.................................................................................................................................................................. 183 Multiple citations separated by: ............................................................................................................... 183 Precede with:..................................................................................................................................................... 183 Superscript & subscript ................................................................................................................................184 Bibliography font use .................................................................................................................................... 184 Sentence & Title Case..................................................................................................................................... 185 Bibliography sort: Ignore words at beginning of… .......................................................................... 185 BIBTEX.................................................................................................................................................................. 185 8
Enable BibTeX................................................................................................................................................... 185 TeX character handling................................................................................................................................187 INTERNET .............................................................................................................................................................. 188 Proxy Info............................................................................................................................................................188 Automated PubMed Searches .................................................................................................................... 189 Attaching PDFs................................................................................................................................................. 189 ReWbase................................................................................................................................................................. 189 OPENURL ............................................................................................................................................................. 189 SERVER .................................................................................................................................................................. 191 Allow Web access to databases................................................................................................................. 192 SERVICES ............................................................................................................................................................... 192 FILE MENU ...........................................................................................................................................192 NEW DATABASE… ............................................................................................................................................... 193 OPEN… .................................................................................................................................................................. 193 BACKUP….............................................................................................................................................................. 194 SYNC ....................................................................................................................................................................... 194 IMPORT REFERENCES…...................................................................................................................................... 196 Importing references from PubMed by drag and drop from a browser.................................. 198 Importing a reference from an attached PDF .................................................................................... 199 Importing references from a Mellel document (Synchronize Database)................................200 IMPORT TEXT ENCODING ................................................................................................................................... 200 IMPORT FILTER MANAGER…............................................................................................................................. 201 EXPORT REFERENCES (HITS)…........................................................................................................................ 202 GO TO URL........................................................................................................................................................... 203 ONLINE SEARCH................................................................................................................................................... 204 PAGE SETUP.......................................................................................................................................................... 205 PRINT REFERENCES... ......................................................................................................................................... 205 PRINT BIBLIOGRAPHY......................................................................................................................................... 206 DATABASE MAINTENANCE ................................................................................................................................ 206 Verify…................................................................................................................................................................. 206 Reindex….............................................................................................................................................................206 Repair… ...............................................................................................................................................................207 Rebuild (Keep User Settings)….................................................................................................................. 207 Rebuild… .............................................................................................................................................................207 Defragment & Compact… ............................................................................................................................207 When to use which method to Wix a damaged database................................................................. 207 LINK TO ................................................................................................................................................................. 208 SWITCH TO WORD PROCESSOR ........................................................................................................................ 208 QUIT ....................................................................................................................................................................... 208 EDIT MENU ..........................................................................................................................................208 UNDO, CUT, COPY, PASTE, CLEAR, SELECT ALL............................................................................................ 209 PASTE PLAIN TEXT .............................................................................................................................................. 209 COPY CITATION .................................................................................................................................................... 209 COPY FORMATTED ............................................................................................................................................... 210 COPY HYPERTEXT LINK ...................................................................................................................................... 210 SHOW CLIPBOARD ............................................................................................................................................... 211 SPECIAL CHARACTERS ........................................................................................................................................ 211 FONT AND STYLE MENUS................................................................................................................211 9
BIBLIO MENU ......................................................................................................................................211 SCAN A DOCUMENT….......................................................................................................................................... 212 SUBJECT BIBLIOGRAPHY… ................................................................................................................................. 213 BIBLIOGRAPHY FORMATTER….......................................................................................................................... 214 FORMATS MANAGER… ....................................................................................................................................... 217 DEFAULT FORMAT ............................................................................................................................................... 218 VIEW MENU .........................................................................................................................................218 REFS MENU ..........................................................................................................................................219 NEW ....................................................................................................................................................................... 221 INSERT ................................................................................................................................................................... 221 DELETE… .............................................................................................................................................................. 221 DUPLICATE ............................................................................................................................................................ 221 REPLICATE AS BOOK CHAPTER ........................................................................................................................ 222 COMPARE REFERENCES… .................................................................................................................................. 222 REMOVE DUPLICATES… ..................................................................................................................................... 224 MARK ..................................................................................................................................................................... 227 ADD TO GROUP .................................................................................................................................................... 227 New Group… ...................................................................................................................................................... 228 Group name .......................................................................................................................................................228 FIND….................................................................................................................................................................... 228 Spotlight..............................................................................................................................................................230 How a search is done ..................................................................................................................................... 230 Put matching references in the Hits List...............................................................................................231 Special Searches (for Returns, empty Wields, or nonempty Wields)............................................. 231 FIND AGAIN .......................................................................................................................................................... 231 FIND IN THIS REFERENCE… .............................................................................................................................. 232 FIND IN THIS REFERENCE AGAIN… ................................................................................................................. 232 SQL/REGEX SEARCH… ...................................................................................................................................... 232 Fields to search................................................................................................................................................. 234 Comparators ..................................................................................................................................................... 236 Characters to search for...............................................................................................................................237 Boolean searches............................................................................................................................................. 237 Regex pattern matching...............................................................................................................................238 Searching for words that include punctuation .................................................................................. 239 Sorting the result............................................................................................................................................. 240 GLOBAL CHANGE.................................................................................................................................................. 241 Find and Replace….......................................................................................................................................... 242 Change Field… .................................................................................................................................................. 243 Change Reference Type….............................................................................................................................244 Change Case… ................................................................................................................................................... 245 Move Field….......................................................................................................................................................245 Restore Default Font & Style…................................................................................................................... 246 Standardize Names…..................................................................................................................................... 246 PEEK ....................................................................................................................................................................... 247 Quick Peek ..........................................................................................................................................................249 GENERATE BIBTEX KEY ..................................................................................................................................... 249 INSERT DATE ........................................................................................................................................................ 249 OPENURL SEARCH.............................................................................................................................................. 250 LOOKUP FROM DOI............................................................................................................................................. 250 10
PUBMED ................................................................................................................................................................ 250 GET PDF ............................................................................................................................................................... 251 UPLOAD TO REFBASE…...................................................................................................................................... 252 FIRST, PREV, NEXT, LAST .................................................................................................................................. 252 GO TO REFERENCE #…....................................................................................................................................... 252 HITS MENU ..........................................................................................................................................252 SORT HITS LIST… ................................................................................................................................................ 253 CLEAR HITS LIST ................................................................................................................................................. 254 FIRST, PREV, NEXT, LAST .................................................................................................................................. 254 GO TO HIT #…...................................................................................................................................................... 254 WINDOW MENU .................................................................................................................................254 SHOW ATTACHMENT INSPECTOR ..................................................................................................................... 255 BIBLIOGRAPHY WINDOW ................................................................................................................................... 256 MINIMIZE REFERENCE WINDOW ..................................................................................................................... 257 EXTRAS MENU ....................................................................................................................................257 JOURNAL GLOSSARY ............................................................................................................................................ 257 Using the Journal Glossary ..........................................................................................................................259 PredeWined Journal Glossaries .................................................................................................................. 260 TERM LISTS........................................................................................................................................................... 261 Collapsed view .................................................................................................................................................. 261 Expanded view.................................................................................................................................................. 263 Adding/Removing a Term List .................................................................................................................. 264 HELP MENU .........................................................................................................................................265 USER GUIDE .......................................................................................................................................................... 265 VISIT SONNY SOFTWARE… ................................................................................................................................ 265 BOOKENDS SERVER..........................................................................................................................266 INTRODUCTION .................................................................................................................................................... 266 ADMINISTRATING BOOKENDS SERVER ............................................................................................................ 267 ALLOW WEB ACCESS TO DATABASES ............................................................................................................... 267 PORT ...................................................................................................................................................................... 268 MAX CONNECTIONS ............................................................................................................................................. 268 KEEP LOG............................................................................................................................................................... 268 MAX LOG SIZE ....................................................................................................................................................... 269 HTML ENCODING ................................................................................................................................................ 269 IP ADDRESS .......................................................................................................................................................... 269 AUTHORIZED ACCESS ONLY ................................................................................................................................ 269 CREATING WEB PAGES TO ACCESS BOOKENDS DATABASES ........................................................................ 271 Requesting references ................................................................................................................................... 271 Query..................................................................................................................................................................... 273 SQLQuery ............................................................................................................................................................273 REQUESTING FILES/INFORMATION FROM BOOKENDS ................................................................................. 281 COMPLETE EXAMPLE: COMMUNICATION BETWEEN A BROWSER AND BOOKENDS................................. 287 UPLOADING REFERENCES TO A DATABASE ..................................................................................................... 290 APPENDIX A. IMPORTING REFERENCES FROM ENDNOTE, PAPYRUS, AND REFERENCE MANAGER.............................................................................................................................................293 APPENDIX B. UPGRADING FROM PREVIOUS VERSIONS OF BOOKENDS..........................297 11
APPENDIX C. BIBTEX........................................................................................................................300 12
What is Bookends?
Bookends is reference management and bibliography generation software.
Bookends is a database application that allows fast and easy retrieval of reference
information. You can enter large abstracts and extensive comments, either from the
keyboard or imported from sources on the Internet. You can search Bookends databases
for authors, keywords, or any combination of words anywhere in the reference
description.
Bookends lets you directly search and retrieve information from PubMed, Amazon, the
Library of Congress, and hundreds of online libraries around the world.
Bookends also works with you to create polished manuscripts with bibliographies. If you
are using Microsoft Word X/2004 or Mellel you can access some of Bookends' features
from the word processor. For example, Bookends can scan your paper and replace
temporary in-text citations with numbers:
…as previously shown {Smith, J. Immunol., 104-109, 1989; Fredricks, Jones,
Transmembrane signaling, J. Exp. Med., 453-460}…
becomes:
…as previously shown (4, 8)…
or:
…as previously shown (Fredricks and Jones, 1990; Smith et al., 1989)…
or any reference information you like, for example:
…as previously shown (Fredricks, p. 64; Smith, p. 1024)…
Bookends can also scan and format files saved from Nisus Writer Express or Pro, or as
RTF (Rich Text Format) from any word processor, including Pages, AppleWorks, and
Mariner Write.
Bookends then generates a complete bibliography in any journal style you choose.
Reference information can be rearranged in virtually any configuration, allowing the
creation of bibliographies for papers or articles that can be submitted directly to a journal
or publisher. For example:
13
1.
Wilkenson, JD, Henderly, L and Skelton, AH. Trends in Office Computer
Training. Journal of Computer Management (March 1982). 34:123-142.
or
John D. Wilkenson, Louise Henderly & Andrew Harold Skelton. Trends in Office
Computer Training. Journ Comp Manag. March 1982. Vol. 34, pp. 123-142.
or
J.D. Wilkenson, Henderly, L., and Skelton, A.H. “Trends in Office Computer Training.”
March 1982. Journal of Computer Management.
or
Title: Trends in Office Computer Training
Authors: Wilkenson, JD, Henderly, L, Skelton, AH
Keywords: Training;CAI;Timesharing Systems
Notes: Useful review. Reprint on file.
Serve yourself!
Bookends is also an HTTP Web server. With the click of a (Preference) button you can
allow others, on any computer platform, to search your reference databases via a browser
and retrieve the results, formatted in any way you like. Remote users can also enter
references from their browsers, if you allow. Bookends Server requires an active Internet
connection and the creation of a web page to hold the search and/or reference entry
forms.
Hundreds of other features make the task of reference management easier
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Unicode-savvy (handles non-Roman fonts: Japanese, Chinese, Hebrew, etc.)
Search libraries via the Internet and directly import the hits into your databases
Autocompletion of names and terms entered from the keyboard
Any file (e.g. a pdf) can be attached to one or more references and instantly retrieved
Automatically find, download, and attach pdf available from PubMed or already on
your hard drive
Use Spotlight to search attached pdfs and return matching references
Drag and drop throughout
Many global editing options
Groups: static, smart, and virtual, with live searching. Organize in folders.
14
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Color label references
Term Lists
Duplicate reference detection and removal
Journal glossaries
and much more…
Requirements
You must have the following to use Bookends:
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A Macintosh running OS X 10.4 (Tiger) or later
Registering Bookends
Until registered, Bookends lets you enter only 50 references per database. Once you have
paid for Bookends you will receive a registration number from Sonny Software. Choose
the About Bookends menu item and click on the Register button. After you have entered
this number, Bookends will be "unlocked" and you can enter an unlimited number of
references.
15
Introduction to Bookends
Here are a few of the concepts that underlie the operation of Bookends. Each is explored
in detail later in this User Guide.
Bookends databases
Bookends stores reference information (author, title, date of publication, etc.) in
databases. The number of references you can store in a database is, in theory, essentially
unlimited. In practice, the maximum number you will find comfortable to work with
depends upon your work habits and the capabilities of your computer, but is perhaps 50100 thousand. In the event that you want to store more references, you can make
additional databases.
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We suggest you use one database rather than several smaller databases if possible.
You can make "virtual" subdivisions of the database, if you want, with static or
smart groups.
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It is important that you periodically backup databases. This can easily be achieved
by turning on "Automatic Backup" in Preferences. There is also an option to
create a backup on-demand in the File menu. Both options verify the integrity of
the database before making the backup.
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Bookends will refuse to open a database located in the same folder as itself. This
is done so that users won't inadvertently delete their databases when replacing an
older with the newer Bookends Folder when upgrading Bookends.
Entering/importing references
Reference information can be added to a database in several ways:
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Entered manually in the reference window
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Imported from
o a public online source (PubMed, the Library of Congress, Amazon)
o an online university or institutional library
o a text file exported from another reference manager or online source in
which the data are in a tagged form (e.g. RIS, Refer, etc.). You can import
this text from the clipboard as well.
o an XML file exported from another reference manager (using the EndNote
schema)
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Entered remotely by a user via browser (a Bookends Server capability)
16
These are discussed in detail in this User Guide.
Viewing references
The basic display of reference information is the List View. In addition to a row and
column view of the references in a database, this versatile window can display:
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•
•
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groups
a configurable and editable concise view (summary or all)
the reference displayed as defined by a particular format
the contents of attached pdf, image, or text file
You can double click on a reference in the List View to display its details in the reference
window, where the individual fields can be read or edited. Bookends saves entered/edited
text automatically, so there is no need for an explicit Save command.
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The reference window and the List View window are two independent ways to
view reference information. A database is open as long as either a reference
window or the List View window is open. When both are closed, the database is
closed. You can have Bookends open a database in the List View (the default) or
the reference window view by setting this option in Preferences.
The Hits List
References can be quickly added or removed from a temporary group called the Hits List.
The references in this group can then be operated on by many of the Bookends options:
sent to a bibliography, exported. edited via a Global Change, etc.
There are many ways to add references to the Hits List, including a Find, checking the
Mark button in the reference window, checking the checkbox next to the reference in the
List View, and so on.
Scanning a document and creating a bibliography
When writing a manuscript, you can have Bookends place temporary citations in the text.
These citations are enclosed in an identifying delimiter, such as curly brackets ( {} ) (the
exception is Mellel, which treats temporary citations as special objects). When it's time to
create the final manuscript, Bookends can "scan" the paper, replace the temporary
citations with their final form, and create a bibliography.
17
A bibliography is a listing of references cited in a document. It usually appears at the end
of the document, but can be placed elsewhere.
The way in which the final reference citation or footnote is inserted into the text and
arranged in the bibliography is controlled by a format. The format specifies many large
and small points, such as the appearance of the final citation, the fields to be output in the
bibliography (e.g. author, title, date of publication, etc.), the punctuation in between the
fields, whether the bibliography is numbered or sorted, and much more. Bookends is
distributed with over 150 formats, including APA 5th Edition, Chicago, Turabian, MLA,
Society of Biology Editors (Vancouver), Nature, Science, and many others. The formats
we supply can be edited or used as templates to create new formats for other sources.
Bookends can be asked to create a bibliography in a number ways:
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Scanning a Microsoft Word, Mellel, or Nisus Writer document for temporary
citations. The scan is initiated from within the word processor.
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Scanning a file containing temporary citations, saved as RTF or RTFD (for
example, exported from Pages '08). The scan is initiated from within Bookends.
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Using the Bibliography Formatter to create a bibliography of the hits.
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Using Subject Bibliography to create a bibliography of the hits.
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Using a browser to ask for a bibliography to be returned by Bookends Server.
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The Reference Window
This is a reference window and its drawer. The top part of the display (the toolbar) has
information about the reference and quick access to certain functions. The lower 4/5 of
the display (starting with the Authors and Series Editors fields) contains the actual
reference information. Note that you can choose to have the Keywords displayed in a
separate tab and have Notes shown in the main tab (a setting in Preferences, see below).
Reference Numbers
Each reference has two identification numbers. The first is the sequential number
assigned when the reference is created. The first reference is number 1, the second is
number 2, and so on. When a reference is deleted, the number of all references with a
higher number is decremented by 1. This number is shown in the title bar of the reference
window.
A unique ID is assigned to each reference when it is created. This number is generated
randomly, and will never change (unless you change it yourself—see below). It is above
and to the left of the Authors field, preceded by the ‘#’ symbol (i.e. #34737).
19
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Unique reference numbers can be used to cross-index filed copies of papers,
manuscripts, or books, and in temporary in-text citations. They are also used to
identify references saved in static groups.
•
References will usually retain their unique IDs when exported and then imported
into another Bookends database. In the rare case in which that ID is already used
in the destination database, a new ID for the imported reference will be generated.
Changing the unique ID
You can change the unique ID by clicking on it with the Command and Option keys
held down. A dialog box prompts you for a new unique ID.
If the new ID you provide is already used, you will be asked to enter another.
Use the unique ID to embed hypertext links in another application's documents
Some applications will accept a hypertext link from Bookends. When you click on that
link, Bookends will open and the corresponding reference will be highlighted in the List
View.
To do this, drag and drop the unique id from the reference window
and drop it into a compatible application's window
By default, the title will be displayed as a hypertext link. If the reference has no title, the
unique ID will be shown. You create a link that contains any text you choose by using a
format (set in Preferences, General tab).
20
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You can also insert a hypertext link to a reference in the List View by holding
down the Command and Option keys before beginning the drag.
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Hypertext links can be copied to the clipboard and pasted into another application
with Edit -> Copy Hypertext Link (as a link or as text).
Some applications that accept Bookends hypertext links are TextEdit, DevonThink,
Scrivener, Delicious Library, and OmniOutliner.
Use the unique ID for Drag and Drop transfer or deletion of references
You can copy a single reference from one database to another by dragging and dropping
the unique ID # from the source database onto the reference or List View window of the
destination database.
You can delete a reference by dragging and dropping its unique ID in the Trash.
Use the unique ID to add a reference to a static group
You can add a reference showing in the reference window to a static group in two ways:
•
Drag and drop the unique ID on the group in the List View window.
•
Control- or right-click on the unique ID and use the resulting contextual menu to
add the reference to an existing or a new group.
Reference Fields
Each reference entry consists of up to 32 fields (and one metafield: Issue, which is kept in
the Volume field, surrounded by parentheses). There is also a field for attached files, but
you access that indirectly, for example via the Attachment Inspector.
There are two or three tabs, depending on your setting in Preferences: Main, Keywords
(optional), and Notes.
The Notes field in the Main tab and in the Notes tab are identical. The latter simply
provides a more flexible field for editing and input.
If the Notes or Keywords field exist in their own tab, their name in the tab will be
followed by an asterisk if they contain any text. This allows you to see if the field has
information while you are viewing the main tab.
21
The fields in the main reference window (and Keywords, if it's in its own tab) can contain
styled text, hold an unlimited number of characters, and can be linked to Term Lists and
use autocomplete. The 14 fields in the reference window drawer contain plain text, up to
2044 characters each, and cannot be linked to Term Lists or use autocomplete.
The names of the fields vary according to reference Type. You can adjust them to suit
your needs (see Preferences). Although the names can be changed, any special attributes
a field may have (for example, the Pages field "knows" that a hyphen indicates a range of
page numbers) remain a feature of the field.
The default names for the reference Type Journal Article are:
Authors
Title
Ser Editors
Journal
Volume
Pages
Date
Publisher
Address
Short Title
User1 (user-defined)
Edition
URL
Abstract
Notes
Translator
User4
Call Num
ISSN/ISBN
Language
User8
Trans Auth
Trans Title
Orig Pub
User12
# of Vols
User14
User15
User16
DOI
PMID
Authors
Each author is placed on a separate line, entered as:
Surname, First name(s) or Initials
Bookends will attempt to handle a name entered as first name(s) or initials(s) followed by
surname (e.g., RA Heinlein). However, some features in Bookends, ranging from the
correct handling of compound surnames (e.g., von Hoffman) to proper ordering of the
sorted author/editor lists, may not work correctly! Therefore, it is recommended that you
enter names with the surname first.
Initials can be succeeded by another initial, a period, a space, or nothing. These are all
acceptable ways of entering a name:
Doe, J. M.
Doe, J M
Doe, J.M.
Doe, JM
You don’t need to put periods after initials, because you can place punctuation after the
initial when you design the format for creating a bibliography.
•
If you choose to print full names when formatting, the first names are output
exactly as entered. So, if you enter full names (e.g. Robert F. Kennedy) and want
periods and spaces after the middle initials in the formatted output, you must
include the periods and spaces after the initials.
22
If the author is an institution, place a comma after the last character and Bookends will
not attempt to format it when creating a bibliography. Commas elsewhere in the name
will be output as entered. For example, you would enter "The American Council on Diet,
Health, and Fitness" as
The American Council on Diet, Health, and Fitness,
There are times when you might want to enter information for an author other than just
the name, such as Jr., Ph.D., or M.D. This is done by following the name with a comma
and the title:
Blogget, John, Sr.
Franklin, ID, Major, USAF
Note: in Bookends 7.5 and earlier, names with titles were handled by following
the last name with a semicolon, the phrase, a comma, and the first name(s), such
as “Wilson; M.D., Diane”. The newer method is more robust because it allows for
titles that themselves contain commas (e.g. “Major, USAF”), always properly
places the title at the end of the name regardless of format, and is compatible with
other reference managers, such as EndNote. The older method usually still works
(with the limitations mentioned), but you may have to alter some entries to follow
the newer rules in some cases.
Title
The title of an article or chapter belongs here. If you are citing an entire book, its name
belongs in the Title field. If you are citing a chapter from a book, the chapter title goes
here, and the name of the book belongs in the Book Title field (by default, the label for
the Journal field, as shown above, changes to Ser. Title (Series Title) when the Type is set
to Book).
Short Title
Enter an alternative title of the reference here. This is useful for situations in which you
use the full title the first time a reference is cited and a secondary, abbreviated title for
subsequent citations (when scanning a document).
Editors
Editor names are entered just like author names.
23
Journal
The name of the journal or magazine in which the article appeared goes here. Use the
Journal Glossary (see below) to speed the manual entry of journal names. The name of
this field changes to Ser Title (Series Title) for book-related Types.
Vol (Issue)
The journal’s volume number goes here. If you want to record the issue number as well,
enter it after the volume number in parentheses, for example:
267(10)
For other reference Types, this field is named Volume and should contain the volume
number of the reference, if there is one.
•
If the reference Type is book chapter, the name of this field changes to Book Title.
Pages
The first page of the reference, or the range of pages, goes here. If you enter the range of
pages (e.g., 123-146), you can output either the first number or the range when a
bibliography is created.
Date
For the date of publication. Some examples are:
1978
March, 1978
1978 March
If you plan to sort by dates that include months and days (not just years), you should use
a special form of the date. Bookends uses an alphanumeric sort, so you need to enter the
date as year, month, day (i.e., 021103 or 02-11-03).
Publisher
A typical entry would be McGraw-Hill or Wiley.
Address/City
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This field can be used for several things. If the work has a publisher (Book, Book
Chapter, etc.) you should use it for the city where the publisher is located (by default, the
label changes to City when one of these Types is chosen). For some Types, you may use
this field for the address of the author. When importing references from PubMed, the
address of the authors (if provided) is placed in this field.
Abstract
A summary of the reference contents. A splitter control between the Notes and Abstract
fields lets you allot more space to the field you find more useful.
Keywords
Keywords should be separated by Returns.
Notes
Comments, observations, etc. A splitter control between the Notes and Abstract fields lets
you allot more space to the field you find more useful.
User1 (Key), User2-User18
These are user-defined fields. Their names are modified for particular Types (e.g. User3
is renamed Translator for some entries). The reference window drawer contains User5User18.
Here are descriptions for some of the common default labels for different reference
Types:
Translator: The translator of the work.
Edition: Edition number, e.g. 2nd.
Call Num: Call number.
ISSN/ISBN: International Serial Standard Number/International Standard Book
Number.
Language: English, French, Japanese, etc.
Edition: The edition number, such as "1st", "2nd", "Fifth", etc., as you would want it
to appear in the bibliography.
25
Reprint Edn (Reprint Edition): If the work was originally published under a different
title, you can place the original title and year in this field.
Ser Editor (Series Editor): The editor of a book series.
Trans Author (Translated Author): If the author's name is in a non-Roman language
(e.g. Chinese), you can use this field to enter the translated name.
Trans Title (Translated Title): If the title is in a non-Roman language (e.g. Chinese),
you can use this field to enter the translated title.
Orig Pub (Original Publication): For a republished work, you would put information
about the original publication here (e.g. publication date, place, publisher,).
Ser Title (Series Title): The title of a book series.
# of Vols (Number of Volumes): The number of volumes in a multiple volume work.
Volume (Multiple Volume Number): In a multiple volume work, the number of the
volume being cited. This appears in the drawer for some Types, like Book Chapter,
that place the Book Title in the reference window in the field normally used for
Volume.
DOI (Digital Object Identifier): A number assigned to a document by a publisher.
This number will always identify this particular document, regardless of where it
might be available on the Web.
PMID (PubMed ID): A unique number given to every article referenced by PubMed.
You can replace these labels with any descriptors you find useful (e.g., Cost, Secondary
Source, etc.).
To change field labels, use the References tab in Preferences.
The User1 field is renamed Key if you enable BibTeX in Preferences. See Appendix C
for details.
URL
Holds the web address (URL) of information related to the reference (such as the
published article itself). For example,
http://www.sonnysoftware.com
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The URL field can also contain an e-mail address, for example
mailto:[email protected]
To use your browser to go to the URL (or your e-mail client to create an e-mail), click on
the @ button next to URL:
You can have multiple URLs entered in this field if they are separated by Returns (rightclick or use the enlarged view to see them all). Right-clicking in the URL field will bring
up a contextual menu containing all the URLs in the field, allowing you to open the one
you want. Clicking on @ will open all of them.
Autocomplete
As you enter text into any field that has a Term List (i.e., Authors, Editors, Journal,
Keywords, or any field for which you have created a Term List), Bookends will look
through the Term List for word(s) beginning with those letters. If it finds a match, it will
show that word in gray characters, updating as you continue to type. Here is an example
of the autocomplete function while entering a name:
You have the following options:
1. Accept the text up to the flashing cursor: backward arrow or Escape.
2. Accept the full entry to the end of the line: forward arrow.
3. Accept the full entry to the end of the line and move to the next line: Return or
Enter. Note: will only move to the next line if it is a scrolling field.
4. Scroll through all the words that begin with the typed letters: up arrow (moves
forward, from A -> Z), down arrow (moves backward, from Z -> A).
5. Continue through the word: keep typing.
27
You can press the delete key while entering text without stopping autocomplete. Once a
word has been accepted, you cannot use autocomplete on it again unless it is at the end of
the field or you have deleted it entirely with the Delete key.
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Autocomplete can be turned off in Preferences.
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You cannot create Term Lists for, and thus use autocomplete with, fields in the
Reference Window drawer.
Enlarging Reference Fields
Click on the button containing the name of the field to open a separate window
containing the text of that field. For example, after clicking on the word Abstract you
might see:
Information in the extended display can be edited normally. To return to the normal
display, click on Save (to accept any changes you may have made) or Cancel.
28
When in the enlarged field view, the Refs menu will change to contain these new options:
Find In This Field and Find In This Field Again. These options let you do a word search
that is limited to just the extended field.
Change Field Names
The name of the field can be changed in a Type-dependent manner in Preferences.
Reference Type
You assign each reference a Type. This is used during bibliography creation and is
explained in detail in the section on the Bibliography Formatter. Briefly, the form of a
printed reference depends on its source. For example, in a bibliography, a journal article
usually has a volume number and a page (first or range) cited, whereas a book has the
publisher named. The Type should identify the source of the reference so that it can be
matched with the appropriate format when it is used in a bibliography.
The following 27 Types are provided:
Artwork
Audiovisual material
Book
Book chapter
Conference proceedings
Dissertation
Edited book
Editorial
In press
Journal article
Letter
Map
Newspaper article
Patent
Personal communication
Review
Internet
Unused
Unused 2
Unused 3
Unused 4
Unused 5
Unused 6
Unused 7
Unused 8
Unused 9
Unused 10
The ten “Unused” Types are placeholders that you can customize if you have reference
sources that are not already covered.
For information about how to edit the list of Types, see Preferences.
Navigation Arrows
Used to move forward or back through the references in their relative order. Holding
down the Shift key while clicking on the right or left arrow takes you to the last or first
reference in the database, respectively.
29
The Hits Area
The Hits area is in the upper-left corner of the reference display:
Below the word Hit is a button that shows the number of the current reference in the Hits
List (which may or may not be the same as the reference being displayed). Below that is
the total number of Hits.
The Mark checkbox is checked if the reference is in the Hits List. You can add or remove
the current reference from the Hits List by checking or unchecking this checkbox.
Checking it adds the current reference to the end of the Hits List. Unchecking it removes
the current reference from the Hits List. Pressing Command-M while viewing a
reference is the same as clicking on the Mark button (i.e., puts a reference in, or removes
a reference from, the Hits List).
To the right are the Hits arrows. Clicking on the Up arrowhead moves you to the next
reference in the Hits List. The Down arrowhead moves you to the previous reference in
the Hits List. If you have moved away from the last Hit (by, for example, clicking on the
Up or Down database arrows), clicking on the Hit Button takes you immediately to that
Hit. Holding down the Shift key while clicking on these arrows takes you to the first or
last reference in the Hits List respectively. Alternatively, you can use the up and down
arrow keys on the keyboard to move between references (Note: if the cursor is in a
reference field the arrow keys will move the cursor in the text).
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Holding down the Shift key when clicking on the Hit Button brings up a dialog
box asking what Hit you would like to see.
The Attach Pop-Up
This button lets you attach, view, and even open files created by other applications.
30
Files containing QuickTime-compatible graphics can be viewed from within Bookends.
Moreover, any file, regardless of type, can be attached to one or more Bookends
references and quickly opened with the application that created it. The attached files are
not stored in the database itself. Instead the name and location of the file are stored in the
database.
•
You can attach pdf files containing the papers or manuscripts to which the
reference in Bookends refers.
Attaching a file or folder
If the Attach pop-up contains a question mark, then nothing is currently attached to the
reference. If you click on this icon, a pop-up menu lets you select a file or folder to
attach. Choose the file or folder you want from the file dialog box.
When you attach a file or folder, Bookends will offer to move it to a dedicated folder and
rename it. See Storing attached files automatically below for details.
Once a file has been attached, the Attach button changes appearance:
When there is one or more attached file or folder, clicking on the Attach pop-up will
display the names of the attachments, offer to attach another, and let you open the
Attachment Inspector.
You can also attach files to a reference by dragging them from the Finder and dropping
them onto the reference window or the List View window.
•
A text file can be attached by drag and drop if you hold down the Command key.
In this case, Bookends will offer to attach the file rather than import its contents.
•
You can attach folders to references, too, by the drag and drop method.
Smart attachment folders
You can attach folders to a reference. Bookends will list all the items in the attached
folder and you can select any to view, reveal in the Finder, etc. Any files added to the
folder in the Finder are automatically made attachments (and if you remove a file from
the folder it is no longer treated as an attachment). Attachments in such a folder are one
level deep (that is, a subfolder in the attached folder will be shown, but not any files in
31
it). If you add/remove files from an attached folder, the list view will need to be refreshed
to see the change (just click on the reference is sufficient for this).
Detaching a file or folder
You can remove an attachment from a reference with the Attachment Inspector or by
right-clicking on the image (or contents, if the attachment is a text file) of the attachment
in the List View and selecting Detach…
Opening attached files
To open all of the files attached to a reference, click on the Attach pop-up (it should have
the "file attached" paper clip appearance). The pop-up menu will display a list of all of
the files or folders attached to the reference, and you can select just the one you want
opened (or open all at once).
If the List View is in front and it is indicating attachments (set in Preferences), rightclicking (or Control-clicking) on the paper clip icon will provide similar access to your
attached files or folders for that reference. You can also use Shift-Command-O to open
the attachments of all the selected references.
By default, attached files are opened in the application that created them.
If the file is a QuickTime-compatible graphic (image, pdf file, QuickTime movie, sound,
etc.), you can open it in a window within Bookends by clicking on the Attach button and
choosing its name with the Shift key held down. You can move, resize, zoom, or close
the window, just as you would in any application.
•
If you opened the attachment in Bookends, you can subsequently open it in the
application that created it by double-clicking on the image in the Bookends
window.
•
pdf attachments opened within a Bookends window will be scaled to fit the
viewing window, and you can scroll through the pdf file one page at a time.
•
If the file is not QuickTime-compatible, Bookends will attempt to open it in the
application that created it regardless of whether you held the Shift key down or
not when opening it.
For convenience, you may want to place all of your attached files in one folder
(recommended — see Storing attached files automatically, below). However, this is not
32
necessary, and you may have the pictures stored anywhere on the hard disk (or on a
server).
Attaching multiple files or folders to one reference
It is possible to attach multiple files to one reference:
1. Drag and drop the files, one at a time or as a group, from the Finder onto the
reference or List View window.
•
To avoid the dialog box that asks you to confirm each attachment, hold the
Command key down when you drop the file(s) onto the Bookends reference
window.
OR
2. Select “Attach a file…” from the Attach pop-up.
OR
3. Use the Attachment Inspector.
Bookends actually stores the aliases of all the folders in which you have attachments in
Preferences. Therefore, you can move or rename your attachments' folders and Bookends
will still find them.
Storing attached files or folders automatically
Bookends can manage the location of attached files for you. When you attach a file you
will see a dialog box like this:
33
If you check "Move to dedicated attachment folder", Bookends will move the dropped
file into a folder intended specifically for attachments. You can also have Bookends
create a copy of the file in the attachments folder, leaving the original where it was:
If you have not specified a particular folder, a folder called "Attachments" in the user's
Documents folder (~/Documents) will be created and files will be moved there. You can
designate a particular folder to hold attachments in Preferences.
Bookends will find attached files if they are in subfolders in the default attachments
folder (one level deep only). If you attach files by drag and drop, Bookends will display a
pop-up menu that lets you choose between the default folder and any subfolders you
might have created.
34
You can create these subfolders with the New Subfolder… menu option, or do it yourself
in the Finder. This means that you can organize your attachments by year, category,
database, etc. by placing them in subfolders.
You can have Bookends rename the file you are attaching. This is useful, for example, if
you download pdfs from Internet sites, which often assign unhelpful names or numbers to
them. Bookends will suggest a name based on the surname of the first author (or editor, if
there is no author), and the year in the date field (Author Date), or a name based upon the
fields specified by a format. You can tell Bookends what kind of name to suggest by
setting the "Rename attachments" pop-up menu in Preferences (Refs tab).You can use
this suggested name, edit it, or use the file's original name (by unchecking the Rename
box).
When the file is transferred to the attachments folder, Bookends will ensure that the name
is unique by appending a random number, if necessary.
Tip: We recommend that you use a dedicated attachment folder because it makes
migrating from one computer to another much easier (all the attachments can be moved
by copying that one folder). In addition, Bookends will perform Spotlight searches on
pdfs and text files in the default attachments folder (and subfolders) but not those outside
of these.
•
This feature provides a convenient way to organize your attachments. It is not
necessary to have a special attachments folder—attachments can reside anywhere
on your hard drive (or servers).
•
You can change your dedicated attachment folder in Preferences at any time—
Bookends will still find attachments in the old folder, but it will not find
attachments in a subfolder. If you change the default attachments folder, you
should move any subfolders you created to the new one.
Importing reference information from PubMed when attaching a pdf
If the pdf you are attaching is from a journal supported by PubMed and contains a doi
(Digital Object Identifier) number, Bookends will display a hypertext link to the article
online and offer to import the reference information from PubMed:
35
If "Import reference information and then attach" is checked and you have checked
Rename, Bookends will generate the pdf name automatically after the reference is
imported and then attach it to the new reference. This will work even if you don't have
access privileges to the pdf online.
This feature only works for journals surveyed by PubMed, and requires a valid doi that
Bookends can resolve via the Internet.
You can turn this feature off in Preferences (Internet tab) to avoid the slight delay caused
by checking with PubMed for availability.
Downloading and attaching pdfs from a browser by drag and drop
If your browser downloads pdf files and automatically opens them in Preview or Acrobat
Reader, you can attach them to the selected reference in Bookends by dragging and
dropping the proxy icon in the pdf's title bar onto a Bookends window. Note that in this
case the pdf file is downloaded to the user's Temporary Folder, so you must have
Bookends move it to your attachments folder.
Another way to download and import a pdf file from a browser is to drag and drop the
proxy icon (the small icon that appears at the beginning of the URL field) or a hypertext
link pointing to a pdf file onto a Bookends window. Bookends will then offer to
download and attach the pdf to the currently selected reference. If you accept, a name
will be assigned (which you can edit) and the file will be stored in the specified
attachments folder. The pdf download capability is especially useful for those using
PubMed and PubMed Central—you can go to the article of interest and drag the link to
the pdf (or view the pdf, and then drag the proxy icon) to Bookends. Here is an example
drag of the proxy icon:
36
Important: Each publisher determines how pdfs are made available. Bookends will
recognize the following URLs as indicating that the file is a pdf: (1) the URL ends in
".pdf" or (2) the dragged item contains the characters "pubmedcentral" and "=pdf".
Note that Bookends cannot know that the link is actually to a pdf, so it is possible for
links that meet one of these criteria to be imported as "pdfs" into Bookends. If you attach
an inappropriately linked file, just detach it or move it to the Trash with the Attachment
Inspector or by right-clicking on the display pane in the List View and selecting Move To
Trash from the contextual menu.
Note: not all publishers allow you to download a pdf file even if you are licensed to view
it. At the time of this writing, Blackwell Synergy lets you view the file online but not
download it. Others, like the journal Diabetes, put up indirect links that don't actually
point to the pdf file itself—in cases like these, if you can get to a page that says
"Automatic Download", dragging the link labeled "[Begin manual download]" will often
give you direct access to the pdf file, which will then be imported when you drop it on
Bookends:
You can usually verify that the link is directly to a pdf file in Safari by dragging the link
and seeing that the dragged text ends in ".pdf" (see example above).
Attaching an image from another application by drag and drop
You can attach an image from another application by dragging and dropping it onto a
Bookends reference window. Bookends will prompt you for a name, save the image to
your Bookends attachments folder as a jpeg file, and attach that file to the reference on
which it was dropped. Bookends will automatically append the extension ".jpg" to the
image file. If the name you provide is already used, you will be given the opportunity to
overwrite the older image file or cancel. The name is limited to 27 characters.
Removing an attached file from the database
Open the Attachment Inspector and click on the – (detach) button. Alternatively, you can
right-click on the attachment in the List View display pane and select Detach.
37
Deleting an attached file from the hard disk
Open the Attachment Inspector and click on the Action pop-up menu, then select Move
To Trash. Alternatively, you can right-click on the attachment in the List View display
pane and select Move To Trash.
Reveal an attached file in the Finder
Open the Attachment Inspector and click on the Action pop-up menu, then select Reveal
in Finder. You can also right-click on the references or use the Action pop-up in the List
View to reveal attachments for all selected references in the Finder.
Show all references with or without attachments
In the List View, you can do an SQL Search or make a smart SQL/REGEX group that
shows all references that do or do not have attachments. The syntax is:
Show references with attachments:
varCharField REGEX '[a-z]'
Show references without attachments:
NOT varCharField REGEX '[a-z]'
To find a specific attachment, this search will work:
Locate('my attachment name', varCharField) > 0
Reference Window Drawer
A drawer with 14 fields can be opened/closed by clicking on this icon (or pressing ShiftCommand-D):
The 14 fields in the drawer window can contain up to 2044 characters of plain text. They
cannot be linked to Term Lists or use autocomplete.
38
Color Label
A Label pop-up menu lets you assign a color label, whose meaning you define in
Preferences, to a reference. See the section on Color Labels for details.
Rating
You can assign a rating of 0 to 5 stars to a reference by clicking on the corresponding dot.
You can use the rating as a criterion when searching for a reference or creating a smart
group.
Linking Bookends to a Word Processor
You can link a database to any other currently running application. This tells Bookends in
which application to automatically insert temporary or formatted citations (usually a
word processor).
When Bookends is running, it checks to see if your word processor (which you specified
in Preferences) is also running. If it is, Bookends will automatically set the link to that
program, as shown by a check next to its name in the File -> Link To hierarchical menu.
A link will exist as long as the linked program is running.
A link can also be changed by using the File -> Link To menu. Once linked to another
program, you can switch to the linked program by
39
•
clicking on the Copy Citation button or selecting the Copy Citation/Copy Selected
Citations menu (Edit menu).
•
selecting Copy Formatted from the Edit menu.
These actions automatically switch you to the linked application.
A common sequence of events using a link would be:
1) Launch Bookends.
2) Run your word processor (make sure the word processor has been selected in
Preferences).
If using Microsoft Word X or Word 2004:
3)
In Word, select a word or phrase and use the Find in Bookends option in the Word
Tools menu or the Bookends toolbar. You will switch to Bookends.
4)
After the reference is found in Bookends, click on Copy Citation in the reference
window, or select Copy Selected Citations (Edit menu) if you want to make more
than one temporary citation at a time from the items in the List View window. You
will switch to Word with the temporary citation(s) inserted at the selection point.
If using Mellel:
3)
In Mellel, select a word or phrase and use the Find in reference database icon in the
Bibliography palette. You will switch to Bookends.
4)
After the reference is found in Bookends, click on Copy Citation in the reference
window, or select Copy Selected Citations (Edit menu) if you want to make more
than one temporary citation at a time from the items in the List View window. You
will switch to Mellel with the temporary citation(s) inserted at the selection point.
If using Nisus Writer Express:
3)
In NWE, select a word or phrase and use the Find Citation option in the Nisus
Writer Express Macros menu. You will switch to Bookends.
4)
After the reference is found, click on Copy Citation , or select Copy Selected
Citations (Edit menu) if you want to make more than one temporary citation at a
time from the items in the List View window. You will switch to Nisus Writer
Express with the temporary citation(s) inserted at the selection point.
40
Any other word processor:
3)
Find the correct reference in Bookends.
4)
Click on the Copy Citation button or select Copy Selected Citations (Edit menu) if
you want to make more than one temporary citation at a time from the items in the
List View window.
5)
You will automatically switch to your word processor. If your word process doesn't
support the necessary AppleEvents, you may have to paste the citation into the
document yourself (Command-V).
Although most often used to link to a word processor, you can link a Bookends database
to most running applications.
Copy Citation
Copy Citation can be invoked by clicking the corresponding button at the upper right of
the reference window or by selecting this menu option in the Edit menu (Command-Y).
This works in concert with Scan a Document. There are three types of automatic
temporary citations that Bookend can generate: "Content", "Author, Date, Unique ID", or
defined by a format (set in Preferences).
If you cite by content, Bookends will place the following information from the current
reference, enclosed in the temporary citation delimiters: first author, journal, pages,
volume, and date. If there is no journal or volume entry, up to 10 words of the title will be
included.
If you cite by "Author, Date, Unique ID", the corresponding fields will be placed
between the citation delimiters. The unique ID must be preceded by the # symbol—that
tells Bookends this is a unique ID and not, for example, a page number.
If you want more flexibility in how the temporary citation appears, you can "cite by
format" and Bookends will place whatever information the primary order field of the
format specifies in between the citation delimiters. To do this you would define your own
format just for citations, select it in Preferences, and use it when writing a manuscript.
o Do not use an unmodified bibliography format for your temporary citations. Such
a temporary citation will probably not be found in the database during a scan
41
because extraneous characters (like punctuation between initials) will often be
inserted. It is up to you to ensure that the output of format you use produces text
that will match the information in the cited reference.
Whichever method you choose, the items that comprise the temporary in-text citation
should unambiguously identify the reference.
After you have finished a manuscript, Scan a Document can be used to replace the
temporary citations and create a finished document. An example of reference information
placed in the clipboard by the Copy Citation button, citing by "Content" is:
{Sewell et al., Nat Med, 5, 399-404, 1999}
Note: the temporary citation delimiters (curly brackets, square brackets, tilde, or BibTeX)
are set in Preferences.
If the citation was created using "Author, Date, Unique ID", it might look like this:
{Sewell et al., 1999, #65323}
If the authors of a reference are
Smith, JR
Jones, TS
Copy Citation will generate: {Smith and Jones, …}
If the authors are
Smith, JR
Jones, TS
Carpenter, BW
Copy Citation will generate: {Smith et al., …}
The Scan a Document... feature discriminates between these, and in the latter case will
only select a reference from the database if
•
•
•
it has three or more authors AND
Smith is the first author (in this example) AND
"Smith et al." is the first entry in the temporary in-text citation
If you are linked to your word processor, clicking on Copy Citation will copy the citation
information to the clipboard, switch to your word processor, and paste it in. If you are not
linked, it will just perform the copy.
42
•
To copy citations of multiple references at once, use the List View window
(below).
•
If a reference has editors but no authors (e.g. an edited book), the first editor's
name will be used in the temporary citation.
•
Command-clicking on Copy Citation will copy and paste the formatted citation
into the linked word processor document (same as selecting the Copy Formatted
menu item).
Drag and Drop citations
You can also drag a temporary or formatted citation to your word processor.
To do this:
1.
2.
3.
4.
Click on the Copy Citation label (not the icon) and hold down the mouse button.
Drag the rectangular outline to an open window in your word processor.
Release the mouse button when the insertion point is positioned where you want it.
To drag and drop a formatted citation, perform the steps above with the Option key
held down.
•
You do not need to be linked to a word processor to drag and drop a citation to
one of its windows.
•
You can use the List View window to drag and drop multiple citations at once.
Modifier keys
If you copy a citation (button or menu selection) while the Shift key is held down, the
citation information will be placed in the clipboard without the temporary citation
delimiters. This is useful when copying multiple citations, one at a time, that are to be
placed in one set of citation delimiters:
{Coale, K., MacUser, 305-314, 1988; Smith, J., MacWorld, 101-123; 1989}
If you Copy a citation (button or menu selection) while the Option key held down,
Bookends will switch you to a linked word processor but not automatically paste it in for
you—you may then do the paste yourself. You can also use the combination of the
Option key and the Shift key to copy the citation information to the clipboard without
the enclosing citation delimiters.
43
Customizing citations
You can add instructions in temporary citations that tell Bookends to add arbitrary text
before or after the citation, output just the date in an author-date citations, and even hide
the temporary citation without inserting a final form. To learn more about these options,
see the following sections in the Scan A Document section of this User Guide:
a.
b.
c.
d.
e.
f.
Mixing text with temporary in-text citations
Replace temporary in-text citations with date only
Eliminate authors from final citation
Creating removable in-text citations
Excluding enclosing punctuation in a final citation
Overriding superscript in a final citation
Pop-up Navigation Window
If you have hidden the reference window toolbar, you can still quickly see where the
current reference is in the continuum of all references by Control-clicking (or rightclicking if you have a multi-button mouse) on "empty space" (i.e. not in a field or
control) in the reference window. This will bring up a pop-up slider window, showing the
number of the reference on display in italics:
Use the slider to navigate through the database (use the little arrows in this window for
finer control in a large database). The slider window will disappear when the cursor
leaves it or a key is pressed.
44
The List View Window
This is a multifunctional window with up to four panes: Groups, References, Info, and
Display. The List View and the reference window are two independent ways to view
reference information. A database is open as long as either its List View or a reference
window is open. When both are closed, the database is closed. Just as with the reference
window, you can import references into a database by dragging and dropping a text file
containing the references onto the List View.
Example:
•
The Page Up, Page Down, Home, and End keys scroll the reference list.
The groups and reference panes are dedicated to that particular content. The concise
view pane (on the right) can show some or all fields in either a summary or a labeled
form—clicking on the fields will open them in an editable text field. The display pane
(at the bottom) can show the reference in its formatted form (as per the currently
selected format) or show the contents of pdf, image, or text files attached to the selected
reference.
There are a variety of ways to open/close the panes, and each will be mentioned below
in the appropriate section. A common location for manipulating all of them is via the
View menu or the View pop-up in the upper right hand corner of the List View window:
45
Basic: group and reference list
Summary: Basic + concise pane (summary)
All: Basic + concise pane (all)
Formatted: Basic + display pane, formatted reference
Attachments: Basic + display pane, attached pdfs/images
The Reference List Pane
The middle (reference) pane has up to seven columns, which can show any field, the
reference Type, the relative reference number, the Unique ID, and the date added. You
specify which columns to show in Preferences. The default window has three columns:
Author, Date, and Title. The references are normally sorted alphabetically by Author.
You can sort the list of references by any column by clicking on the corresponding
heading. This sort is alphanumeric except when the column holds the relative reference
number (numeric sort), the unique ID value (numeric sort), or the date added (date sort).
Toggle the sort order between ascending and descending by clicking on the heading of
the currently sorted row (the arrowhead in the sorted column heading indicates the sort
order: ascending (arrowhead up) or descending (arrowhead down)).
•
Sorting the List View by clicking on a heading does not sort the database or the
Hits List itself, just this display. To actually change the sort order of the database
or the Hits, select the menu items Sort All References or Sort Hits List,
respectively.
•
If the first column displays the reference number (Ref #), when the List View
window opens it be sorted from highest number to lowest, so that the most
recently entered references are shown at the top. The same is true when sorting by
date added.
46
•
You can set the font and font size used in the List View window in Preferences
(default font and size for Lists).
•
Column widths can be changed by dragging a column divider. The last column
always extends to or beyond the border on the right — it should be reserved for
fields with a lot of information, like the Title.
•
Authors column: if a reference has an editor and no authors (e.g. an edited book),
the editor's name will appear in the authors column.
•
Paper clip: If Indicate attachments is checked in Preferences, any reference with
one or more attachments will be preceded by an icon of a paper clip. You can
open the attachment by right-clicking (or Control-clicking) on the reference and
selecting Open Attachment from the contextual pop-up menu. You can also type
Shift-Command-O to open the attachments of all the selected references.
•
If Indicate attachments is enabled, you can reveal the attachment in the Finder by
right-clicking on the reference or selecting the reference and using the Action
pop-up menu. If there is more than one attachment, only the first will be revealed
in the Finder.
•
Right-clicking on the paper clip icon will bring up a pop-up menu from which you
can select the name of the attachment to open (or all, if there is more than one
attachment).
•
You can display the author's names four different ways: First Only, Multiple,
First...Last, and All. See the section of this Guide on the List options in
Preferences for details.
•
Pressing Shift-Command-U will open your browser and go to the URL, if there
is one, in the selected reference's URL field. You can also use the Action pop-up
or a right-click on the right pane to Go To URL.
•
The proxy icon in the title bar let's you drag and drop the database as if you were
in the Finder. Command-click on it to see the full pathname of the database in the
Finder.
If you do not want the List View to be initially sorted when it opens, uncheck the Sort
Lists checkbox in Preferences.
•
Bookends will attempt to show just the year in the Date column. If a 4 digit
number beginning with a "1" or "2" is not found, the total contents of the Date
field will be shown. If you always want the entire data shown as entered, check
Show entire date in lists in Preferences.
47
To display a particular reference in a reference window, double-click on it or highlight it
and click on the Show Reference button. The Bring reference window to front on doubleclick setting in Preferences determines what happens when you double click on a
reference or click the Show Reference button. If Bring reference window to front on
double-click is unchecked, the reference will be shown but the List View window will
remain in front. If this checkbox is checked, the reference window will come to the front.
The checkbox that precedes each reference represents its marked status (i.e. is it in the
Hits List or not). You can add or remove a reference from the Hits List by clicking on
this checkbox or pressing Command-M. There are several convenient ways to add or
remove many references to/from the Hits List at once:
•
if only one reference is selected, click on the checkbox with the Shift key held
down and all the references in the list will assume the state of that reference (if it
was not a Hit, now it and all the references in the list are Hits; if it was originally
a Hit, all the references in the list are now not Hits).
•
if you click on a checkbox of one of several selected references with the Shift key
held down, all of the selected references assume the state of the reference whose
checkbox you clicked.
These icons along the bottom strip of the window provide a quick way to work with the
references:
Add reference
Action pop-up:
48
The Mark/Unmark All/Selected option is determined as described above when Shiftclicking on a marked checkbox (i.e., if only one selection, the operation applies to all
references in the list, if the first selection is already marked, Bookends will offer to
unmark the others, etc.).
Color Labels
You can assign a color label to the selected references via the Action pop-up, rightclicking in the right pane, or using a Control-Command-# shortcut (see Preferences,
List tab to edit the color label settings). You can use the color label as part of the search
criteria in the Find dialog or for smart groups. Here is an example of references that have
been assigned color labels:
49
If you prefer it, a setting in Preferences will have Bookends color the first column only.
• Color labels can also be assigned in the Reference Window display.
Using the List View to copy temporary citations
When the List View window is in front, the Edit menu’s Copy Citation item changes to
Copy Selected Citations. Selecting this is identical to clicking on the Copy Citation
button shown above each reference, except that it makes temporary citations of all the
references that are selected in the List View window. Just as with Copy Citation , if you
are linked to your word processor, using Copy Selected Citations switches you to the
word processor tries to paste it into your document.
•
You can also create temporary citations by dragging items from the List View
window to your manuscript.
•
Holding down the Shift key while dragging and dropping will transfer the
citations without the enclosing citation delimiters.
Using the List View to copy formatted citations
If you drag one or more references from the List View window (or a Term List, right
pane) to a word processor window with the Option key held down, Bookends will copy
the formatted reference (and place a copy in the clipboard). This is the same as selecting
Copy Selected Formatted when the List View window is in front.
Using the List View to create a hypertext link to a reference
If you drag a reference from the List View window with the Command and Option keys
held down prior to beginning the drag, Bookends will copy a hypertext link to that
reference into the receiving document. See the section Use the unique ID to embed
hypertext links in another application's documents for details.
50
•
Hypertext links can be copied to the clipboard and pasted into another application
with Edit -> Copy Hypertext Link (as a "live" link or as text). A link will be
created to the first selected reference.
•
The content of the hypertext link (the human-readable part) is the reference title
by default. You can change this by using a format, which can be set in
Preferences.
E-mailing references
A right-click (or Control-click) in the reference pane of the List View window will
bring up a contextual menu that contains the option E-Mail…. If chosen, Bookends will
copy the selected references to the clipboard in the currently active format, launch your email application, and create a new message window containing the reference(s). You can
also use the Action pop-up menu to e-mail the selected references.
The references will be displayed in your e-mail client in plain text; if you want them in
styled text, paste the references from the clipboard into the body of the e-mail.
If your e-mail client is Apple's Mail application, Bookends will include links to
attachments, so that you can easily send, for example, an attached pdf of the reference as
well.
Groups Pane
There are three submenu selections you can make from the Window -> List View menu:
All, Hits, and Groups. A column headed with the ⌘ character contains keyboard
shortcuts you have assigned to static groups (see below).
All
Lists all of the references in the database. You can permanently delete references from
the database by selecting them in the list and pressing the Delete key or selecting Clear
from the Edit menu:
51
o Shortcut: to avoid the confirm dialog, press Command-Delete. You will get no
warning before the reference is permanently deleted.
Hits
Displays the references in the Hits List. You can permanently delete Hits from the
database by selecting them in the list and pressing the Delete key or selecting Clear from
the Edit menu.
To remove a reference from the Hits List but not the database, uncheck the checkbox at
the beginning of the reference. The reference will temporarily displayed in the list so that
you can reverse the decision if you want—when the group Hits is selected again the old
"hit" will not be displayed.
To clear the Hits List, select Hits in the groups list and press the Delete key of select
Clear from the Edit menu.
If you drag a reference's unique ID from a reference window to the Hits reference list, the
reference will be made a Hit.
Groups
Bookends has two different kinds of groups, static and smart (dynamic). Virtual groups
can be created on-the-fly by selecting two or more groups at once (Hits can also be
considered a group in this context).
Static groups consists of references you have assigned to the group. The composition of
the group never changes unless you add or delete references.
Smart groups consist of references that satisfy search criteria you have defined. The
references in the group may change as references are added or deleted from the database,
or if they are edited.
52
Groups can be created in several ways. In the List View window, click on the Action
pop-up menu below Groups:
You can also right-click on an existing group to see this pop-up menu.
To create a static group when the List View is in front, you can also simply drag and drop
references to the groups pane and drop onto empty (white) space or onto the groups All
or Hits. Bookends will then offer to place them into a new static group.
Static groups
Selecting Static allows you to enter a name and tell Bookends whether you want the
group to be created empty or composed of the Hits:
The name of a static group is shown in plain text in the Groups pane. It will be preceded
by this icon:
•
Static groups store the unique ID numbers of the references. This means that the
group will be valid even if you sort the database or delete references (other than
those in the group, of course).
53
To add references to a static group when the reference window is in front, do one of
these:
–
select the Refs -> Add to Group menu item
–
drag and drop a reference's unique ID into the group's list of references
–
Control- or right-click on a reference's unique ID and select the group from the
contextual menu
To add references to a static group when the List View or Term List window is in front,
do one of these:
–
select one or more references and drag and drop onto the static group's name
–
select one or more references and then choose the Refs -> Add to Group menu
item
–
select one or more references and then Control- or right-click on the reference
list and choose the group from the contextual menu (all selected references will be
added)
•
You can copy references from one database directly into a static group in another
by dragging and dropping them on the name of the static group.
•
If a selected reference is in one or more static groups, the name(s) of the groups
will be shown in the Info Drawer.
To remove references from a static group (but not delete them from the database).
–
select the reference(s) and press the Delete key or select Edit -> Clear
Adding references to a static group with a keyboard shortcut
You can assign numbers to static groups as keyboard shortcuts to be used with the
Command key
54
o The stars in these group names were inserted via the Character Palette.
Pressing the Command-# combination will add the selected references to the
corresponding static group. If a reference is already in the group, it won't be added again.
A number can be assigned to only one static group at a time.
To add a shortcut, click in the column headed with ⌘ and enter a number from 1 to 9.
You can change the assigned keyboard shortcut at any time. If you don't want to use this
feature, you can resize the second column until it is invisible. If you decide you want it
back, you can resize it to be open later.
Smart (dynamic) groups
Select Smart or Smart (SQL) from the Add (+) pop-up menu underneath the groups list.
Smart groups are defined by filling out a window much like the Find dialog box:
55
Smart (SQL) groups are created by creating an SQL/Regex search:
The names of smart groups are preceded by this icon:
56
You can change the name of a smart search or edit the search criteria by double-clicking
its name in the groups pane.
You can delete a smart search by selecting it in the groups pane and pressing the Delete
key or selecting Clear from the Edit menu.
Virtual groups
If you select two or more groups (or the Hits) in the List View left pane, the sum or
intersection will be shown in the right pane. You can control whether you will see
references in any groups (AND) or only those present in all groups (OR) by selecting the
appropriate option from the Action pop-up menu beneath Groups:
Groups can be deleted by clicking on them and pressing the Delete key, or using the
Action menu -> Delete option.
Groups can be reordered by drag and drop:
Group Folders
57
You can create folders in which to store related sets of groups. You can drag and drop
groups to or from a folder. To add groups to a folder, slide the drag indicator to the right:
To remove a group from a folder, slide the drag indicator to the left:
If a folder contains groups, the number will be shown in grayed text:
•
Subfolders are not allowed.
58
•
Group and folder names must be unique (i.e., you can't give a folder and a group
the same name).
•
If you delete a folder, the groups it contains will be deleted as well.
Concise View Pane
The concise view pane can be opened via the View menus, Option-Command-I
(Summary) or Option-Command-N (All), or clicking on this icon underneath the
reference list:
You can close the concise view pane by selecting Basic from one of the View menus,
clicking on the concise view icon again, or double-clicking on the splitter dimple to the
left of the info pane.
The concise pane contains a highly configurable, interactive, and editable display of a
reference's content. There are two different concise views: Summary and All. Here is one
example of how a Summary view might look:
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o Bookends will highlight in red any words in the concise view that were used in
the Live Search textbox.
o The date and time the reference was entered (or imported) is displayed at the
bottom of the concise view.
Here is how the same informtion mght be shown in the All display:
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You can move between the Summary and All displays with the various View menus, or
these buttons at the bottom of the window.
Summary:
All:
Configuring the concise view
The Summary and All views can be restricted to display just the fields you want, in the
order you want them. The main difference between these displays is that Summary
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provides the information in a compact and easily readable form, and All shows the
information in a list-like form, with each field labeled.
You can set many parameters that affect how the concise view appears (Preferences).
This includes whether you want the Summary display to be Standard or that specified by
a format, the default font size, and the color of the field labels for the All display. For
details, please see the section in this User Guide on Preferences (the concise view tab).
The most important settings in Preferences include telling Bookends which fields to
display, in what order, and what text should come before or after the field (Summary
view). Here is an example of a Summary display setting in Preferences for books:
In this instance, the checked fields will be shown and the unchecked fields left out of the
concise display. The Before and After fields tell Bookends what text to output before and
after each field. If a field is empty, any before and after text is suppressed. In the example
above, a comma (and space) will be output after the publisher, if the Publisher field isn't
empty.
To output a Return character before or after a field, enter ¬ (Option-L) or the word
"return" (without the quotes).
You can change the order in which the fields are output by dragging them. This is how
you'd alter the example so that the Title was shown immediately after the Year:
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Editing and/or entering reference information in the concise view
If you are using the Standard Summary or All view, the text in the concise view pane is
editable. When you move the mouse over "live" text it will become the hand pointer (if
the Summary view is showing, the tooltip for the field will display the name of the field
the pointer is hovering over). URLs are highlighted in blue and are active (only the first
30 characters will be shown for those in the URL field. In this case, if you hover the
pointer over it the entire URL will be displayed in the field's tooltip).
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You can move through the fields in the concise view with the arrow or tab keys. Clicking
on (most) fields or pressing Return or Enter when a field is selected will open the text in
an editable field (the default size of this field is the same as for the reference window—
we recommend that you set this to at least 12 points in Preferences).
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Autocomplete will work for any fields that have Term Lists. A pop-up menu will let you
navigate between all fields you have elected to display without leaving the editable text
field. Cancel and Save buttons will appear at the bottom of the field. If you press Enter or
Tab, any changes you have made will be accepted and the field will close. Press Escape
to close the field without accepting any changes.
Clicking (or pressing Return or Enter) on the Type or Rating fields will display a pop-up
menu that lets you change the value.
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Clicking on Attachments will let you select and attach a file. Groups is a pseudo-field,
and is read-only and thus always displayed in gray.
If you are using a Summary view, you can add or modify text only to fields that already
have text. If you switch to the All view, you can enter text into empty fields by
selecting/clicking on the field's label.
The Display Pane
The display pane can be opened via the View menus, Command-E (view formatted) or
Option-Command-E (view attachments), or clicking on this icon underneath the
reference list
Formatted view
Here is an example of a formatted reference view:
o The current format is shown in the pop-up menu below the display pane. You can
change it to any format you have enabled.
o The size of the text can be increased or decreased by using the Zoom In/Zoom
Out options in the gear menu (Command- + and Command- - (Commandhyphen) are the keyboard shortcuts). You can also right-click to zoom in or out.
o Use the provided format named "Ref with Abstract" to see the reference
information plus abstract.
Attachment view
You view the attachments for the selected reference by clicking on this icon
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The name of the attachment will be displayed in a pop-up menu at the bottom of the
window, and if there is more than one attachment you can select which one to show (if
there is only one, the pop-up will be grayed out).
The display pane can show the contents of pdfs and many types of images (png, gif, jpg,
etc.). In addition, the textual contents of different file types can be displayed
• .doc (Microsoft Word)
• Mellel (XML)
• Nisus Writer Express and Pro
• rtf
• rtfd
• text
• html
The text display will contain the main body of the text only (no text styles or images, and
in the case of Mellel no note streams or footnotes).
If there is an attachment that is not a pdf, image, or compatible file (e.g. a word
processing document), Bookends will indicate that there is an attachment but that it can't
be displayed.
The displayed attachment can be resized with the pop-up menu at the lower left, scaled to
width, or scaled to fit. You can also zoom in/out with the action (gear) menu, a contextual
menu right-click, or Command- + and Command- -.
The PDF viewer will skip over damaged pages, if present, and just display the ones it
can. It will write a message to the Console application telling you which pages it couldn't
read.
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Double-clicking on the displayed attachment will open it in an application capable of
viewing it (e.g. Preview). Right-clicking on it will bring up a contextual menu that will
offer several useful options.
You can also drag the image. If to the desktop or another disk, it will be copied to there.
If you drag to a message in an email client, it will become an attachment for that email.
You can also open the attachment in an compatible application on-the-fly by dragging
and dropping it on the application's icon in the dock or on the desktop. You could, for
example, open a pdf in Preview, Acrobat Reader, Skim, or any other compatible
application this way.
Text files (identified as such by having the file type of "TEXT" or the extension ".txt" or
".text") shown in the attachment view will be shown in the encoding specified in File ->
Import Text Encoding at the time the file was loaded. The text cannot be edited, but can
be copied and pasted into reference fields or other applications. You can zoom the text in
and out as you would when viewing the formatted reference.
Attached folders are smart. The items in the folder are in an indented list beneath the
folder name in the attachment pop-up menu. Any files added to the folder in the Finder
are automatically made attachments (and if you remove a file from the folder it is no
longer treated as an attachment). Attachments in such a folder are one level deep (that is,
a subfolder in the attached folder will be shown, but not any files in it). If you
add/remove files from an attached folder, the List View will need to be refreshed to see
the change (just click on the reference is sufficient for this).
Search field—Live Search and Spotlight search
Live Search
The search field (the oval field with the magnifying glass) lets you instantly restrict the
viewable items in the reference list. Bookends will search the references in the list for any
words or phrases as you type, and update the list on-the-fly to show just those that match
(Live Search). You can use the pop-up menu next to the magnifying glass to have the live
search examine all fields in every reference or a specific field (Authors, Title, Abstract,
etc.). The total number of references and the number actually displayed (i.e., those that
meet the live search criteria) are shown at the bottom right corner of the window.
•
References that don’t match the live search criteria are still in the selected group,
they just aren’t displayed.
•
Punctuation marks are ignored in a substring search.
•
When List View is in front, pressing Option-Command-F places the cursor in
the search field.
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•
If the Option key is pressed when changing groups, any text in the search field
will be cleared. Changing groups without the Option key held down preserves the
text and applies it to the newly selected group.
•
Diacritics are ignored in the search. That is, searching for "Schütz" will find both
"Schütz" and "Schutz".
Spotlight search
If you select Spotlight in the search field pop-up menu, Bookends will use the Mac OS X
Spotlight feature to search all pdfs, .doc, text, rtf, rtfd, html, and Mellel files that you
have attached. References with an attachment in the default attachments folder (or
subfolder) that meet the Spotlight search criteria are made hits and displayed in the List
View window.
•
Bookends will find attached files only if they are in the default attachment folder
or subfolders.
•
For the Bookends Spotlight search to find Mellel attachments you must have
installed the Mellel Spotlight plug-in.
Because Spotlight searches are slower than searches within the database, they will not
begin until you have pressed the Return or Enter key (i.e. they are not live searches).
Spotlight searches are case insensitive and are performed by word. The * is the wildcard
character -- searching for
book*
will find
Bookends
bookmark
book
etc.
Search words separated by spaces will result in an AND search (meaning that all the
words must appear in the document, although not necessarily in the order you typed
them, for there to be a match).
Parentheses can be used to create complex searches. Here are examples of boolean
searches:
dog cat — finds pdfs containing the words dog and cat, not necessarily in that order
dog | cat — finds pdfs containing the words dog or cat
(dog | cat) fish — finds pdfs containing the words dog or cat and the word fish
dog -cat — finds pdfs containing dog and not cat
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Online Search
Bookends allows direct searching and retrieval of book information from hundreds of
Internet sites.
Three search options are built-in: PubMed, the Library of Congress, and Amazon.com
(US, UK, Germany, Japan, France, and Canada). You can also search hundreds of
libraries around the world that support the Z39.50 or SRU protocol. These are
international standard client/server based protocols for information retrieval. They
specifies formats and procedures governing the exchange of messages between a client
and server enabling the client to request that the server search a database and identify
records that meet specified criteria, and to retrieve some or all of the identified records.
Bookends also lets you search the ISI Web of Science (if your institution subscribes) and
the arXiv repository, a free open access site for e-prints in physics, mathematics,
computer ccience, quantitative biology, and statistics.
References you obtain from an Online Search can be imported into a Bookends database
in two ways:
•
drag and drop them onto a Bookends reference window or List View window
•
select the database from the Copy To pop-up menu at the bottom of the search
window:
If the Import to Hits List is checked, Bookends will normally replace the references in the
Hits List with the ones you imported. If you want to accumulate imports in the Hits List,
hold down the Option key (if you are importing by drag and drop, you will have to
initiate the drag first, then press Shift).
You can import directly into an existing static group by dragging and dropping the
references onto that group's name in the List View.
Images from Amazon references will be imported as attachments and their files placed in
the designated attachments folder. If you don't want the images imported, uncheck the
Display image checkbox.
This is the basic Online Search window, which can be brought up by the File -> Online
Search menu:
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It is divided into three parts: the list of books or articles retrieved (upper pane, or List
Pane), information about the selected item in the list (lower pane, or Details Pane), and a
list of saved searches (left pane, or Search List).
For PubMed and Z39.50 searches (including the Library of Congress), Bookends will
highlight the search words, if they appear in the lower pane, in red. It is possible to
retrieve references for which the information returned does not include the exact search
terms, in which case nothing will be highlighted.
The pop-up menu on the left allows you to choose between different Internet sites:
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•
The filters shown below the separator line can be removed from (or added to) the
list by unchecking (or checking) them in the Import Filter Manager window (File
menu).
You will see this in the lower left-hand corner of the main window when a search is
initiated:
If there are more than 500 matches you will be presented with the total number and asked
for the number you want to retrieve:
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When a search is complete, you will see the number or references returned and the total
found:
The results of a search can be printed by selecting the File -> Print Details Pane menu
option.
The Saved Searches pop-up menu at the bottom left corner of the window lets you save
and manipulate search strategies. See below for details.
Do not clear reference list between searches
If checked, Bookends will keep any references you have found when you do a new
search. Note that if you switch search sites, the reference list will be emptied regardless
of this setting (the exception is Amazon — the list will be retained if you switch from one
Amazon site to another).
Removing items from the reference list
You can remove items from the reference list by pressing the Delete key or using the Edit
-> Clear menu.
Repeating a search
Each search is stored in the magnifying glass pop-up. Search terms can be restored by
selecting them from the list:
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PubMed
You have the following options when searching PubMed:
Search
The simple Search works just as if you search PubMed from a browser. If you want to
limit your search to an author's name, you can put [au] after the search words:
smith jd[au]
or to a title, use [ti]
cardiovascular[ti]
You can use AND, OR, and NOT to perform boolean searches (the boolean words must
be in uppercase):
smith jd[au] AND cardiovascular[ti]
See the PubMed web site for details on searching:
http://www.ncbi.nlm.nih.gov:80/entrez/query/static/help/pmhelp.html
Advanced Search
The Advanced Search provides options and conveniences you may find useful. When you
select Advanced Search from the pop-up menu, this sheet opens:
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The sheet contains ten text entry fields, as well as the pop-up selections that that restrict
the search for the corresponding fields to these possibilities:
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The and/or/not pop-up menus let you apply Boolean logic to your searches.
The pop-up menus at the bottom of the sheet let you further limit your search to the
following:
Limit
Publication Type
Search Subset
Gender
Has Links To
Species
Publication Date
Possible Values
Clinical Trial
Editorial
Letter
Meta-Analysis
Practice Guideline
Randomized Control Trial
Review
Addresses
Bibliography
Biography
Core Clinical Journals
Dental Journals
Nursing Journals
AIDS
Bioethics
Cancer
Complementary Medicine
History of Medicine
Space Life Sciences
Systematic Reviews
Toxicology
MEDLINE
OLDMEDLINE
PubMed Central
Male
Female
Full Text
Free Full Text
Humans
Animal
Published in the last:
Published before:
Published after:
Published between:
If you elect to include a date parameter in your search, the appropriate entry fields will
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appear, for example
Dates should be entered in the YYYY/MM/DD form. The year is required, but MM and
DD are optional.
From the Advanced Search sheet you can save the search (see below) and clear the search
(reset all fields and pop-up menus to their defaults).
Indicating that the reference is already in your database
Bookends will highlight in yellow any retrieved references that are already in your
database (determined by matching PMIDs). The database must be open. If more than one
database is open, Bookends will examine the database nearest to the Online Search
window.
Working with references found on PubMed
To see any a reference in the PubMed web site, double-click on it in the list view, or
select one or more references in the list and click the PubMed button. If a single reference
is selected, Bookends will check to see if the full article is available. If it is, Bookends
will open your browser and display the article. If it is not available, Bookends will open
your browser and show the PubMed citation. Here are a few details about retrieving fulltext articles:
1. Bookends will query PubMed for the link to the full-text article. If there is none, or if a
reply is not received within 3 seconds, Bookends will display the PubMed citation.
2. If you want to see the PubMed citation, not the full-text article, hold down the Shift
key when you click on PubMed.
3. Depending on your location and/or institutional support, you may be asked for
verification and/or payment for the full-text article at the journal's web site.
4. If more than one reference is selected when you click on PubMed, Bookends will show
them all in the PubMed citation format in your browser. You can then ask for the fulltext article in the browser.
•
Note: You can automatically perform PubMed searches in the background at
defined intervals (e.g. daily, weekly, monthly) and discover references entered
since the last search. See Saved Searches below for details.
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If you check Download PDF Bookends will attempt to automatically download and
attach associated pdf files when you import references into a database:
This has the same features and restrictions as selecting a reference after import and
selecting the menu option
Refs -> Get PDF -> From PubMed (If Available)
See the section in the User Guide on Get PDF for details.
Web of Science
Your institution must have a license with ISI Web of Science for you to search this site.
The database "editions" you can search depends upon your institution's license. Only ip
authentication (not username and password) will work in Bookends.
The Web of Science filter distributed with Bookends is configured to search all database
editions to which your institution subscribeds. You can restrict searches to specific
editions, as detailed below in the section on creating an import filter (Internet tab).
You have the following options when searching Web of Science:
Search
The simple search lets you find text in the indicated fields. Source is usually the name of
the journal. Simple search will not search for date of publication.
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You can use the following wildcard characters in searches:
*
$
?
Matches zero or more characters within a word or at the end of a word
Matches zero or any one character within a word or at the end of a word
Matches any one character within a word or at the end of a word
Some examples are
enzym?
matches enzyme
sul•ur
matches sulfur and sulphur
pal*ontol* matches paleontology, palaeontology, paleontological, and palaeontological
Advanced Search
If you select Advanced Search from the pop-up menu, an ellipsis is added to the search
button name to indicate that clicking it will open a new window:
This is the advanced search sheet:
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The pop-up selections allow you to search for text as well as the year of publication:
Years are entered as 4 digits (e.g. 2007), and a range of years can be indicated by
separating two years with a hyphen (e.g. 2005-2007).
You can also limit searches to a particular document type:
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or to recent publication date:
Library of Congress
You have the following options when searching the Library of Congress:
The standard search searches all fields and allows no boolean operators.
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The advanced search allows you to specify up to three fields with boolean (AND, OR,
NOT) searches:
For both standard and advanced searches, when searching for personal names enter the
surname first:
Thurn Anne Lewis
When searching for group names, enter in direct order:
army war college
For further details on search options, visit:
http://catalog.loc.gov/cgi-bin/Pwebrecon.cgi?DB=local&PAGE=First
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Note that the Details Pane displays all reference information in MARC format (as it is
provided by the Library of Congress). If you import references into Bookends, it is this
information that Bookends will receive and parse according to the "Library of Congress"
import filter. You can edit this filter, based upon the information you see in the Details
Pane, if you want to change what information is imported (or to which field it is
imported).
The Library of Congress returns results in chunks of 50, so if you ask that more than 50
items be returned Bookends will continue to fetch them (50 at a time) until the number
you have requested, or the total number of items, has been reached.
Note: There is a limit of 10,000 records that can be identified in one search.
Amazon
You have these options when searching Amazon:
Amazon Power Searches allow you to perform boolean searches for author, title, date of
publication, type of binding (hardcover, paperback, etc.), subject matter, and more. The
Power Search option opens this drawer:
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Here are examples of some Power Searches:
Author: ambrose and Binding: (abridged or large print) and Pubdate: after 11-1996
Subject: history and (spain or mexico) and not military and Language: spanish
(Subject: marketing and author: kotler) or (Publisher: harper and Subject: "high
technology")
Keywords: "high tech*" and not fiction and Pubdate: during 1999
ISBN: 0446394319 or 0306806819 or 1567993850
For more information about Amazon Power Searches, visit this URL:
http://www.amazon.com/exec/obidos/tg/browse/-/468558/102-2591947-2010561
Note: Amazon returns books in chunks of 10, so if you ask that more than 10 items be
returned Bookends will continue to fetch books (10 at a time) until the number you have
requested, or the total number of books found, has been reached.
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Amazon searches will also fetch the cover art, if requested:
The image can be small, medium, or large (the size of the image in the thumbnail in the
lower right hand portion of the window is actually the same for medium and large, but
the latter has a higher image quality). To see the image at its actual size, double-click on
the thumbnail image and it will open in another window. Control-clicking (or rightclicking if you have a multi-button mouse) on the image gives you the option of saving
the image to disk as a JPEG file or copying it to the clipboard. You can also save the
image to disk as a picture clipping by dragging and dropping in on the Finder (or into any
folder).
You can import the picture into Bookends by dragging and dropping it on an open
Bookends reference window. Bookends will ask you for a name, and store the image as a
JPEG file in your Bookends attachment folder. The file will be made an attachment,
which you can view in Bookends. If a file of the same name already exists in your
attachment folder, you will be given the opportunity to overwrite it or to cancel.
You are given the option of downloading images or not, and at different sizes, because
downloading a large image over a slow connection (e.g. 56K modem) can take some
time. To shorten download time, you can choose the medium or small image size. To
shorten download times as much as possible, uncheck the Display image box.
To open your browser and see the book at the Amazon web site, double-click on the item
in the list view or select the book and click the Amazon button.
Z39.50 library searches
To perform a Z39.50 internet search, an import filter must be created that contains the
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information needed to connect to and search the library, and to parse the retrieved
information. These filters are discussed in the section on Import Filters.
Each site has different options. Some allow boolean searches, some do not. The fields
that can be searched on vary considerably from library to library. The import filter
contains the relevant information for each library. If boolean searches are not allowed,
you might see the following options in the right pop-up menu:
If boolean searches are permitted, you might see something like this:
Selecting Boolean Search opens a drawer, which might look like this:
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Select the fields you want to search from the pop-up menus, and the information to search
for in the fields.
SRU searches
Simple SRU searches treat spaces like a boolean AND. To look for phrases, enclose them
in quote marks. If "boolean search" is selected, the entries in one of the three fields are
treated as if they are within quote marks.
Saved Internet Searches
If you click the Action icon
(or right-click in the Search Pane) you will be given the
option to save the current search:
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Bookends will prompt you for a name for the search, and then save the logic of the search
in the import filter itself. Saved searches, therefore, are filter-specific.
Saved searches are listed, along with the day they were last run:
Searches can be reordered by drag and drop, and the column widths are adjustable, so
you can close the "Last Run" column if you don't want to see that information.
To view the contents of a search, select it from the list and the search entries will be
shown in the window. If you want to select a search without filling out the search fields,
click on it with the Shift key held down.
The Action pop-up menu offers options to edit, rename, or delete a selected search. For
example, you were to select "Tolstoy" in the example above, it would look like this:
You can use this menu (or the contextual menu) to run the search, or double click on the
search.
To edit a search, select it, change the search fields as you like, then use the "Replace"
menu item. See method for editing advanced PubMed searches in the next section.
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Searches can also be deleted by pressing the Delete key, or choosing Edit -> Clear.
•
When you create the first saved search, the filter will be moved to the Custom
Import Filters folder, in ~/Library/Application Support/Bookends/. This will
prevent you from mistakenly replacing the filter when you upgrade to a newer
version of Bookends.
PubMed searches can be restricted to find only references published since the day the
search was last run:
Advanced PubMed searches
The way these searches are created and managed differs a bit from the others. To create
an advanced search, you would fill out the advanced search form and then click the Save
Search button:
Advanced PubMed searches are indicated by a different icon:
When an advanced PubMed search is selected, you can edit it by choosing the
corresponding item from the Action pop-up menu:
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Automated PubMed searches
Saved PubMed searches can be performed automatically in the background at defined
intervals.
Preference settings
The settable options available in Preferences (Internet tab) are:
Ask before searching: You may want this option checked if you have dial-up access to
the Internet, so that you can confirm the connection is active.
Perform searches every: Whenever an automated search is run, the date and time is
recorded. Bookends will run another automated search as soon as the interval indicated
here has elapsed (if Bookend is not running when this occurs, the search will be
performed the next time you launch Bookends). Note that an interval of 0 will cause
Bookends to search PubMed every time Bookends is launched.
Retrieve max (per search): The first search may retrieve thousands of references, and this
lets you put an upper limit on the number you want to see. Unless the search interval is
very long, the number of new references Bookends finds after the initial search is usually
quite small.
Creating an automated search
The list of PubMed search contains a checkbox before each entry. If it is checked,
Bookends will perform that search at the intervals you have defined in Preferences.
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If this box is checked, this search will be performed every time the interval you chose in
Preference has passed. You can see if a PubMed search is automated, and change its
status, by selecting Search List… from the Saved Searches pop-up menu:
When a background search is performed, Bookends will report nothing if no new (since
the last search) references are found. However, if new references are found, a small
floating window will appear asking if you want to see the references or not. If you are
busy at the moment, you can leave the floating window open indefinitely and deal with it
when it is convenient. If you dismiss the window the "last search date" is updated and the
search will be performed again at the stipulated time. If you choose to see the search
results, a new window will appear containing a list like this:
Each search group is headed by a row containing the name of the search (in italics),
followed by the new references. In the example above, there are two automated search
groups (Lck and glucocorticoids).
You can remove the selected references from the list by pressing Delete or using a
contextual menu.
The bottom pane of this window is identical to the Online Search window. You can view
each reference and transfer the ones you want to your Bookends database by drag and
drop or with the Copy to pop-up menu.
The first column (headed by a •) contains just checkboxes. If checked, the reference is
considered as "viewed", and will not be shown again if it is found by the same automated
search at a later time (this is possible because some pre-publication citations in PubMed
have an entry date weeks or even months prior to their actual publication). If you want a
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reference to appear if it is found again, uncheck this checkbox. To check/uncheck the
items in an entire group, use the box next to the name of the search.
•
If you perform a saved PubMed search by selecting it from the Search Panel (and
Find new since last run is not checked), all matching references will be found as
usual (i.e. regardless of whether or not they were previously found by an
automated search), and you will asked how many you want to retrieve.
•
For automated advanced PubMed searches, the date in the Search Pane will be
ignored — automated searches always look for references added to PubMed since
the date of the last automated search.
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Import Filters
Information can be imported into Bookends from the Online Search window, files created
by many online database services, other Bookends databases, and other reference
management applications such as EndNote.
•
Direct import from the Online Search window was discussed above.
Designing an import filter
For Bookends to import references, the specific bits of information in the file must be
tagged. Tags are labels that identify the type of information that is to follow. Here are
three examples of the different ways the Authors field might be tagged:
AU - Smith AR
Author(s): Smith AR
Journal Author
Smith AR
To be recognized, a tag in the text being imported must end with a space, a colon, or a
return character.
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When filled out, the import filter will contain all the information Bookends needs to
import reference information.
On the left side of the screen is a column of field tags. Here you tell Bookends what
information you want to keep, and where it should go by entering the tag for each field of
interest. Suppose the downloaded file has the following fields:
UI:
AU:
TI:
DA:
PY:
LA:
AD:
123456789 — unique identifier
Jones, Ron — author(s)
This is my article — title
1995 — date
12-24 — page range
English — language
State University — address of corresponding author
To import the information into the corresponding fields in Bookends, you might fill out
the field tags as follows:
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•
Case matters — ‘AU:’ is not the same as ‘au:’. The exception to this rule is
BibTeX importing, where the case of the tags is irrelevant.
•
The field names to the right of the arrows are the names for the default reference
Type. If you have changed any of these in Preferences, the display will be
different. Note that Bookends will import tagged information into the
corresponding fields regardless of any names you may have given them (e.g.
Authors (Journal Article), Artist (Artwork), Inventors (Patent), etc.).
You can import more than one tagged field into any category simply by putting a comma
between the tag definitions (e.g., importing the Language and the Unique Identifier to the
Notes category in the example above).
•
If the category is a scrolling field, Bookends will put a Return character between
the imported fields.
95
•
If the category is Pages, Bookends will put a dash (-) between the imported fields
(to create a page range).
•
If the category is Issue, Bookends will surround information it finds in
parentheses and places it immediately after any data in the Volume field. So if the
Volume is 42 and the issue number is 3, the imported result in the Volume field
would be 42(3).
•
For any other field, Bookends will place a space between the imported tagged
fields.
Note: The only time you need to use the Ignore “field” is when the end-of-field is
indicated by "valid tags" (see below).
A tagged field can be imported into two different Bookends field. For example, in the
PubMed filter we supply, the PubMed ID (PMID) is imported to both the PMID and the
URL fields.
Type definitions
If the reference source has a tag that identifies the Type of reference (journal article,
book, etc.), you can map that information to the internal Type that Bookends uses.
First, enter the tag that precedes the Type in the field tags list. If the tag were "PT -" for
example, you would enter
Then click on the Edit Type definitions… button to bring up this window:
96
In the Tag column, enter the word(s) used in the file being imported that identify a
reference source next to the appropriate Bookends Type. For example, for PubMed you
would enter the words “Journal Article” in the field next to “Journal article”. A less
obvious example is EndNote Export (Refer) filter, for which “Thesis” should be entered
next to the Bookends “Dissertation” field.
o You can map multiple tags to a Bookends Type by separating them with commas.
Identifying the beginning of a reference
You must tell Bookends what constitutes the beginning of a new reference. Typically,
this will be a field tag. In the first example above, you would enter
97
•
The tagged field that identifies the start of a new reference will not be imported
into Bookends unless it is also entered in the field tags portion of the definition
window.
Numbers may sometimes be used to distinguish one reference from another in reference
files obtained from on-line services. An example might be:
1
AU Niklinska, B
TI Two years behind the mast
...
2
TI This reference has no author
...
You would indicate that a new reference begins with a number (#) and that a field ends
with a Return followed by one or more capital letters. In this case, Bookends will
recognize a number following a Return (as well as capital letters) as signifying the end of
a field and the beginning of a new reference.
•
You must enter just the # symbol. If any other characters are entered Bookends
will look for the character “#”, not a number.
If a number appears at the beginning of a line of text (that is, after a Return) Bookends
will assume that this is the beginning of a new reference and import the rest of the
information accordingly. Therefore, if fields are defined by capital letter tags, it is
preferable to define the beginning of a reference as a tag (e.g. AU) rather than as a
number (#).
Although not designed for this purpose, specifying that a reference begins with a number
can be useful if you want to import references from an existing bibliography.
For filters used in Online Searches, if you designate "references begin with" as * (an
asterisk), Bookends will import records regardless of the order of the tags. This is
especially useful if the reference information returned from a library is inconsistent (i.e.
sometimes lists the author as the first item, sometimes the title, etc.).
Note: filters that import BibTeX reference files are a special case, and you would enter
the word “BibTeX” (without the quote marks) in this field. See Appendix C for
information dealing with BibTeX import filters.
Identifying the end of a field
98
You must let Bookends know how to identify the end of a field.
All fields end after a Return character, but not all Returns indicate the end of a field!
Each time Bookends encounters a Return in the file it is importing, it checks to see if
what follows indicates the end of the field.
This is an example of a file in which spaces are used to indent information in a field (the
relevant spaces are shown as diamonds (◊), and Returns are shown as ‘¬’):
◊TI◊◊- Identification of an Epstein-Barr virus early gene encoding a second¬
◊◊◊◊◊◊component of the restricted early antigen complex.¬
◊AB◊◊- When the latent Epstein-Barr virus (EBV) genome in B95-8 cells is¬
◊◊◊◊◊◊induced into a replicative phase, two abundant early RNAs are…
Note that tags are preceded by a single space and followed by two spaces. Information
after a Return within a field is preceded by 6 spaces. The correct definition of the “end of
field” in this case would be any character in or before column 2.
In other cases, spaces may not be used and all information may begin at the left margin
(or indented the same number of spaces in from the left margin). For example:
TI◊◊- Identification of an Epstein-Barr virus early gene encoding a second¬
component of the restricted early antigen complex.¬
AB◊◊- When the latent Epstein-Barr virus (EBV) genome in B95-8 cells is…¬
induced into a replicative phase, two abundant early RNAs are…
In this case, you can tell Bookends that two capital letters after a Return indicate that the
field has ended:
99
Sometimes the capital letters are preceded by spaces. The option "ignore leading spaces"
will skip over these spaces.
•
Be careful with the "Ignore leading spaces" option, because Bookends may
mistakenly truncate a field if it encounters an acronym (e.g., DNA) following
spaces at the beginning of a new line.
•
Some sources, such as RIS, mix numbers with capital letters, such as T1 for title.
Bookends will accept these as valid when capital letters are used to determine
when a field has ended.
There are examples where neither of these rules reliably identifies the end of a field. In
these cases you can use the tags you have entered to indicate that a field has ended (and a
new one is about to begin):
For example, if “TI –” has been identified as the tag for the Title field, when these
characters are found Bookends will process the preceding text and then collect what
follows as the title.
Note that the first two methods of identifying the end of a field are rule-based—using
tags is not. Therefore, if there are tags that you have not entered in the filter definition,
they will be ignored and any text following them will be included with the preceding text
(and placed in the field identified by a previously recognized tag). To avoid this, when
using tags to identify the ends of fields you must enter all possible tags.
o Note: The use of Valid Tags is discouraged—it is easy to fail to account for a tag,
which can cause problems with the import. Use Valid Tags only if the other
methods are not able to identify the end of a field.
If there is a valid tag that you do not want to import, place it in the “Ignore field”:
This is only necessary if you are using “valid tags” to identify the end of a field—in the
other cases, tags that are not explicitly defined will be ignored.
o Source fields are ignored when valid tags are used to identify the ends of fields.
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o Unlike reference information you enter into Bookends, Import Filters must
explicitly be Saved. Bookends will prompt you if you try to leave or quit without
saving an importer that has been edited since it was last saved.
The EndNote Export (Refer) export format is a special case in which each tag consists of
two characters, the first being the % symbol (e.g. %B). Selecting
tells Bookends to use such two-letter combinations as end-of-field markers. The tag must
be followed by a space or Return for it to be recognized.
Parsing Authors/Editors
In most cases you will want Bookends to arrange the authors/editors names into the form
Bookends requires (i.e., surname, first name(s) or initial(s); each name on a separate
line). To do this, check the Parse Authors/Editors box.
Then use the pop-up menus to select how the names in the file to import are arranged,
and what punctuation character separates individual names.
If Smart is selected as the means of determining the correct surname, Bookends will try
to import compound surnames correctly. For example, the name
JG van Elden
would be imported as
van Elden, JG
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This option is especially useful for those importing from PubMed or other Medline
sources. Note that this will work only when the source provides initials instead of full
first names. If full first names are used and there is no punctuation as a guide, Bookends
will not be able to tell if a word belongs in the surname or not.
The other choice, Space, sets the surname to the first (or the last, if it is indicated that
authors are arranged in Surname last order) word in the name.
•
If the names are already arranged in the file as Surname, First Names(s) or
Initials(s), uncheck the Parse Authors/Editors checkbox.
Parsing Keywords
If you want Bookends to place each keyword on a separate line, use this pop-up menu to
enter the character that separates each keyword in the file to be imported (you can type in
a character if it does not appear in the pop-up menu).
Replace hyphens with spaces
Some database services use hyphens in place of spaces in the Authors, Editors, Journal,
and/or Keyword fields. To have Bookends replace the hyphens with spaces, check the
appropriate box.
Removing unwanted characters
You can tell Bookends to remove unwanted printing characters, such as asterisks, from
all fields by entering them in this field.
•
Bookends removes characters, not whole words. If you enter ‘hit’ in this box,
Bookends will remove every occurrence of ‘h’, ‘i’, and ‘t’ that it finds in the
downloaded file.
•
Non-printing characters (e.g. control characters) are automatically stripped out by
Bookends.
Parsing the Source
102
Many downloaded files have at least one complex field that holds the “source
information” about the reference. This may include such things as the name of the
journal, the date of publication, volume and issue number, pages, and more.
Bookends allows you to specify how two complex fields, called Source1 and Source2,
are to be parsed. Click on tab labeled Source at the top of the screen, and you will see this
screen:
Source tags
Fill in the tag for the Source box:
This is done exactly as you did above for other fields.
Collecting the Source
103
Bookends will start at the first printing character after the Source tag is found and
proceed through the Source field. By filling in the above items, you can tell Bookends
what you want to save and what you want to discard.
•
The field names to the pop-up menu are the names for the default reference Type.
If you have changed any of these in Preferences, the field names in the pop-up
menu will change accordingly.
Use the pop-up menu on the left to select the character that ends a particular section:
(CR = Return character, space = space character, number = any number, not a number =
anything but a number, letter = any letter, not a letter = anything but a letter,
alphanumeric = any letter or number, year = four digit number beginning with a 1 or 2,
end = end of Source field). You can also type in any character from the keyboard.
•
A letter is defined as A-Z, a-z, or the ASCII values 128-159 (extended ASCII
characters that have accents, such as é, ü, etc.).
Bookends will collect information from the beginning of the Source field up until the
character you enter — it will not include that character. If a section ends with a space or
104
Return, when collecting the next section Bookends will ignore this character (and any
subsequent spaces or Returns) until it finds a visible character. Bookends will also
remove any spaces or Returns that might appear at the end of a section when it places in
information in a category.
To tell Bookends what to do with the information, choose a field from the pop-up menu
on the right:
The information can be placed in any Bookends field, or it can be discarded (Ignore).
Each row starts with the character that the previous one ended with. Note that it is
sometimes desirable to Ignore several sections in a row.
This is an example Source field, and one way that it might be parsed (note that the
asterisks will be removed from the date):
SO Appl. Opt. ( ***1993*** ), 32(34), 7032-5
If you didn’t want the issue number [ (34) ] included with the volume, you could define
the Source as:
105
Creating filters for existing bibliographies
It is sometimes possible to import reference information from existing bibliographies by
using the Source parser. For example, a bibliography entry might be:
1. Smith, J. D., Jones, S. R., and Fredricks, T. V. 1995. The history of history. J. Hist.
Invest. 65: 123-145.
The first thing you must do is tell Bookends what "tag" designates a new reference.
Entering the number symbol, #, in the References start with field lets Bookends know
that each reference in the bibliography begins with a number. Then tell Bookends that
Fields end with a Return character followed by any character in or before column 1. The
rest of the first window in User-Defined Imports should be left blank. The Source
Definition window can be reached by clicking on the Source tab. You must define the
"Source tag":
106
Enter the number symbol, #, which tells Bookends that the Source begins with a number.
In the remaining fields, enter the parsing information for the Source. The entries shown
will parse the above example and will read in the authors, date, title, journal, volume, and
page range.
Note that names are not parsed when they are imported as part of the Source. In the
example above, the Authors field would contain:
Smith, J. D., Jones, S. R., and Fredricks, T. V.
rather than
Smith, J. D.
Jones, S. R.
Fredricks, T. V.
If you have an unnumbered bibliography to import, you can easily change it in your word
processor by doing a global Find and Replace, Finding Returns and Replacing them with,
for example,
return Ref:
(that is, [return character] [space] Ref: [space])
107
This will put the tag Ref: before each of your references. See your word processor
documentation for details of how to Find and Replace the Return character.
The “New reference when consecutive tags are identical” checkbox
If the button New reference when consecutive tags are identical is unchecked, Bookends
will treat consecutive lines that use the tag that defines a new reference as if the
information belongs in the same reference. This is the default behavior, and is necessary
when importing from source in which every entry in a field is on a separate line with its
own tag. For example, you would uncheck this button if you entered that References start
with AU and this was a reference to be imported:
AU - Smith, AR
AU - Jones, LL
AU - Jurgenson, S
TI - A reference with authors on separate lines.
...
If the button New reference when consecutive tags are identical is checked, Bookends
will treat consecutive lines that use the tag that defines a new reference as if each
designates a new reference. This is useful when doing a "bulk" import of a bibliography
in which each reference is imported as a chunk into one field. This is an example of an
existing bibliography for which you want to import each entry into the Abstract field.
1. Smith, AR. 1995. This is the title of an article. 12:123-321.
2. Jones, LL and Jurgenson, S, eds. This is the title of a book. Knopf, New York. 1995.
You could define a reference as beginning with # (a number), specify that a field ends
when a Return is followed by any character in or before column 1. Then indicate that the
text goes into the Abstract field. If New reference when consecutive tags are identical is
checked, Bookends will place each bibliography entry into a new reference (because the
new reference tag, #, forces the creation of a new reference, even though the # tags are
consecutive, that is, without an intervening tag of another type). If unchecked, Bookends
will place both entries into the Abstract field of the same reference (because the # tag,
used in consecutive lines, is taken to indicate information for a single reference).
Importing MARC records
MARC records, which are used by many libraries to hold reference information, are
108
highly structured and intended to be interpreted by computers. Bookends' import filters
have a section, MARC, where you can enable MARC filtering. Once MARC filtering is
enabled, Bookends follows special rules to ensure that the information is parsed properly.
Bookends understands the MARC 21 communications format. When MARC filtering is
enabled, Bookends will import these records into the usual reference fields. MARC
records begin with 3 digit numbers, and subfields within records are denoted by a
subfield identifier (usually $ or |) and (usually) a lower case letter, such as $a. Here is a
typical MARC record:
001 RIBG87-B10136
005 19870331000000.0
008 870331s1986
cau
b
001 0 eng
010
$a81021600
020
$a0893702633 (pbk.) :$c$2.95
020
$a0893701637 (hard) :$c$11.95
050 0 $aPS3572.A424$bZ85 1986
100 1 $aRawlins, Jack,$d1946245 10$aDemon prince :$bthe dissonant worlds of Jack Vance
/$cJack Rawlins.
260
$aSan Bernardino, Ca. :$bBorgo Press,$c1986.
300
$a104 p. ;$c21 cm.
490 1 $aMilford series.$pPopular writers of today,$vv. 40.
500
$aIncludes index.
504
$aBibliography: p. 97-99.
600 10$aVance, Jack,$d1916-$xCriticism and interpretation.
830 0$aMilford series.$pPopular writers of today ;$vv. 40.
The following options vary between MARC record providers, and can be changed in the
import filter: subfield identifier, the column in which the data in each record begins after
the beginning of the tag (usually 8), and the default reference Type (usually Book). They
can be entered/edited in the MARC tab:
109
To import a MARC field into a particular Bookends field, in the General tab of the
import filter enter the 3 digit tag and the one letter identifier for each item that you want
imported. For example:
would cause the first (or only) author to be imported into the Authors field.
The tag
008
is a special case. It takes no subfield identifier. If you enter this tag Bookends will import
the year (4 digits) into the requested reference field.
The following web site provides an excellent overview of MARC records and how they
are constructed:
http://www.loc.gov/marc/umb/
You should refer to this (or equivalent) documentation before attempting to write or
modify a MARC import filter.
Note: The information contained in MARC records, and where that information is held,
differs from source to source. For example, may sources place the year of publication in
tagged field
008
110
Others place it in tagged field
260c
Many place the year in both tagged fields.
In another example, many, but not all, MARC records begin with the tag
001
If the filter you are using fails to import any records, or if the date is not imported, check
the format of the MARC record and edit the import filter (or a copy) so that the MARC
record is parsed correctly.
Note: MARC records often contain annotated text describing such things as a person's
contribution to the work rather than a rigorous separation with different tags. Therefore,
authors, editors, translators, illustrators, and perhaps others are not distinguished in
machine-readable form, and you may have to move names to more appropriate fields
after importing into Bookends.
Online Searches and importing from libraries via the Internet
111
Bookends uses several protocols to connect to and query library and institutional
databases around the world: Library of Congress Z39.50 Gateway, Direct Access Z39.50,
SRU (Search/Retrieval via URL), and arXiv OpenSearch. To perform an online search,
an import filter must be created that contains the information needed to connect to and
search the library, and to parse the retrieved information.
You can often create your own online search filters. If you want to access a library for
which we do not provide a corresponding filter, you will need the following information:
1. Internet address of the Z39.50 server
2. Port number
3. Database name(s) supported (e.g. INNOPAC, Voyager, etc.)
4. Supported searches
This information should be available from your institution's library.
•
For searches using the Library of Congress gateway, SRU, or arXiv OpenSearch,
if you designate "references begin with" as * (an asterisk), Bookends will import
records regardless of the order of the tags. This is especially useful if the
reference information returned from the library is inconsistent (i.e. sometimes lists
the author as the first item, sometimes the title, etc.).
The following explains the meanings of the Internet import filter settings:
Enable Online Searching
When checked, the filter can be used by Bookends to search a library via the Internet.
The filter's name will appear in the "Import Filters" window in italics, and if checked in
that window it will also appear in the Online Search window's Search pop-up menu.
Name
The name of the library or information provider you are going to search.
Access
You can use the Library of Congress Z39.50 gateway (via HTTP) direct Z39.50 access,
SRU, Web of Science, or arXiv OpenSearch. For most Z39.50 searches it won't matter
which method (Library of Congress gateway or direct access) you use. However, in some
cases one may have an advantage over the other. For example, direct Z39.50 searches let
you specify text encoding, so that accented and non-Roman characters are displayed
properly (if supported by the library). Below is a list of the differences between the two
means of access:
LOC Gateway
Direct Z39.50 search
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Text encoding-savvy
No
Yes
Allows access to UNIMARC and
OPAC servers
No
Yes
Accessible from behind an authenticating
proxy server
Yes
No
The SRU protocol is used by a small but influtential group of libraries. These include
JSTOR, the British Library, and COPAC. Note that for the first you need to search from
an approved institutional ip address to gain access.
The arXiv OpenSearch option is used for searching the arXiv.org database. arXiv
(http://www.arXiv.org) is a premiere open access site for e-prints in physics,
mathematics, computer ccience, quantitative biology, and statistics.
The Web of Science option is used for searching ISI Web of Science.
Server address
The IP address or domain name of the library's server.
Server port
The number of the port used by the library's server. This can be left blank for some SRU
and all arXiv and Web of Sciences searches.
Database name
The name of the library's database. In the case of a source using INNOPAC as a vendor,
the name INNOPAC must be entered in this field or the searches will fail.
For Web of Science, if this field is left blank Bookends will search all database editions
to which your institution holds a license. If you want to search a particular edition, you
would fill out this field as follows:
WOS,Edition Name
The possible editions are
Code
SCI
SSCI
Description
Science Citation Index
Social Sciences Citation Index
113
AHCI
IC
CCR
Arts & Humanities Citation Index
Index Chemicus
Current Chemical Reactions
To restrict your search to the Science Citation Index, you would enter this into the
Database name field:
WOS,SCI
To limit the search to the Science Citation Index and the Social Sciences Citation Index
you would enter
WOS,SCI,SSCI
Record syntax
This setting is important only for Z39.50 searches.
MARC21 (was USMARC) – Machine-Readable Cataloging Record
SUTRS – Simple Unstructured Text Record Syntax, for plain text records
OPAC – Online Public Access Catalog
UNIMARC – International MARC
ADF – Registered by Astrophysics Data System
Record display
Most sources provide the information returned in three different forms: MARC, Full, and
Brief. Full and Brief more accessible to humans, but less useful for importing into
Bookends. Therefore, if the source provides MARC output that is usually the best option
to select.
Text encoding
Bookends will try to negotiate the text encoding with the library. Many libraries will not
accept this parameter and fail to initialize the connection. In this case, the encoding
should be set to Default, and Bookends will assume the data received from the library is
encoded as UTF-8.
114
Boolean searches allowed
Most, but not all, libraries allow boolean searches. If this checkbox is selected, Bookends
will add "Boolean Search…" to the Online Search window field pop-up. If selected, a
drawer will open and you will be able to search for up to three words or phrases.
User ID/password required
If the library requires this information, this should be checked. Bookends will prompt you
for your ID and password when you try to connect. You can store this information with
the filter, if you prefer, and that information will be used when you try to access that
library.
Very few libraries accessed via the Library of Congress gateway require this information.
Searchable Fields
These vary from database to database. This is a list of the options and, for those familiar
with the Z39.50 protocol, the Bib-1 Use Attributes they represent:
Field
Alternative name/meaning
Use Attribute
All Fields
Author
Personal Name
Corporate Name
Conference name
Title
Series Title
Keywords
Abstract
Year
Entry Date in Database
Publisher
ISBN
ISSN
LCCN
Local Control Number
Call Number
Keyword anywhere
1016
1003
1
2
3
4
5
21
62
31
1011
1018
7
8
9
12
16
Journal/Series name
Subject heading
Date of publication
LOC card number
LOC call number
Adding information to imported references
115
If specified here, Bookends will add information to up to two fields of your choosing.
The information is placed at the beginning of the field, and will be followed by imported
text (if any).
The first pop-up menu determines what will be inserted:
When nothing is checked, no information will be added to the imported references.
Dates are added in this form: Sat, Jan 25, 2003
Date and time might look like this: Sat, Jan 25, 2003, 1:19 PM
•
The exact appearance of date and time will depend upon Control Panel settings.
If text: is selected, the text field next to the pop-up menu will be enabled and any words
or phrases entered there will be added. There is a limit of 255 characters.
•
To insert a Return, enter ‘¬’ (Option-L)
116
Formats And Bibliographies
The raw reference information entered in a database can be rearranged by Bookends to
create footnotes and bibliographies. This process is called formatting, and the files that
control the final appearance are called formats.
Sonny Software supplies many common formats (e.g., APA, Turabian, Chicago, MLA,
Council of Biology Editors/Vancouver) and publication-specific formats (Nature,
Science, Cell Press, and many more).
In addition to their important role in writing academic papers, formats can be used to
define the way text is displayed in many of Bookends' operations (e.g. the concise view,
hypertext links, and suggested attachment names).
You can edit the formats that Sonny Software supplies or create your own. The following
sections describe how this is done.
New (Format)
To create a new format, you would use the Biblio -> Formats Manager menu (see below)
and click on the Plus button. You will see:
Note that the new format will be identical to the format selected in the Format window
(in this case, the format is APA 5th Edition).
You can choose to replicate just the first Format Type (usually Journal article) or all
Format Types (which may include, for example, Book, Book chapter, Edited book, etc.).
Formats distributed by Sonny Software are in the Formats folder. Formats that you create
with the New button will be placed in Custom Formats folder. This means that when you
upgrade to a new version of Bookends, you cannot mistakenly overwrite formats you
created simply by replacing the Bookends Folder.
117
•
If you simply edit an existing format, it will remain in its original folder. You
can manually move such a format to the Custom Formats folder, which
ensures that you will not overwrite it or forget to transfer it when upgrading.
•
It is possible to have two formats of the same name, one in the Formats and
one in the Custom Formats folder. This is not recommended. However, if this
occurs, Bookends will always use the version in the Custom Formats folder
when it creates a bibliography.
•
Formats in the Custom Formats folder are shown in bold face.
Edit Format
Formatting Options tab
A Format contains all of the instructions Bookends needs to scan a document and create a
bibliography. Each Format contains style information for multiple Types (Journal
Articles, Books, Book Chapters, and so on). The Types are the same as the Types used to
identify individual references.
118
At the top of the Format definition (shown above) is the Type currently on display
(default is Journal article). You use this pop-up menu to switch between different Types
in a Format. This is the Type pop-up menu for the APA format:
Add Type…
To add a new Type to a Format, choose Add Type… This will bring up a pop-up menu
from which you can select a Type (only Types not already used in the Format will be
offered).
•
To speed entry, the new Type will be an exact copy of the Type currently selected
in the Type pop-up menu (Journal article, in the example above). You must
simply change any fields that differ between that and the new Type.
Delete Type…
Deletes the Type currently selected in the Type pop-up menu from the Format.
Names
On the left side of Format display is a section for arranging author and editor names. For
these formatting features to work correctly, you must have entered the authors’ names
properly in each reference: last name, comma, first name(s) or initial(s).
119
First and subsequent author/editor. The order of the names (surname first or surname
last)
Name options. This pop-up menu offers three choices:
If Surname & Initials is selected, all names after the surname are truncated to a single
letter. For example:
Names
Arnold, Mary
Bardot, Jean-Jacque
Krieger, K.
Appears as
Arnold, M
Bardot, J-J
Krieger, K
If Full Name is selected, the output appears as you entered it, regardless of whether it was
a full name or initials.
The Others like pop-up tells Bookends how to treat names you have entered in a userdefined field (e.g. Translator). These names can be output with the ordering of Editors or
Authors (this is especially useful for Edited Book Types).
If Surname Only is selected, only the authors’ or editors’ surnames will be output.
(Any extensions of the surname, such as “M.D.” or “Jr.”, will also be output if Surname
Only is selected).
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Case
This section tells Bookends if names or titles should be output in a particular case.
Authors/Editors:
as entered —
output exactly as they were entered into the database.
ALL CAPS — every name is capitalized: SPENGLER, RICHARD.
Normal case – conventional case: Spengler, Richard.
small CAPS — every name is capitalized. The first letter will be a normal CAP, the rest
will
be capital letters that are 4 points smaller than the bibliography default
(Preferences): SPENGLER, R.
Specifying “Normal case” is useful if references you obtain have the authors in capital
letters. Note that Bookends can only guess what normal case is, and there are likely to be
a certain number of errors that will need correction. For example, “MCCAIN” or
“McCain” will become “Mccain”. Also, an author’s name that includes initials without
intervening punctuation (e.g. “LEMBECK DM) will be converted incorrectly (e.g. to
“Lembeck Dm”). Therefore, always check the results carefully if you use this option.
•
Any user-defined field can have names in them, and you can tell Bookends to
format them according to the settings for Editors by placing an * after the field
designator in the Order. See section on Special Characters below.
Title:
as entered —
output exactly as it was entered into the database.
121
Title Case —
every word in a sentence or phrase will begin with a capital letter: This
Is a Title in Title Case. Words or phrases entered in the Don’t change
case list in Preferences will be exempted.
ALL CAPS —
every word is capitalized: THIS IS A TITLE IN ALL CAPS.
Sentence case — The first letter of the first word is capitalized, all else is in lowercase:
This is a title in sentence case. Bookends will also capitalize the first
letter after a colon or period. Words or phrases entered in the Don’t
change case list in Preferences will be exempted.
Bookends will convert titles as you direct, regardless of the case of the letters in the title
as they are entered in the database (on-line services can provide titles in Sentence case,
Title Case or ALL CAPS).
This setting will apply to the Short Title field, too.
If you specify Title Case or Sentence case you may find situations in which words are
output incorrectly. For example, “Dna” instead of “DNA”, or “united states” instead of
“United States”. To avoid this, enter those words whose case should never be changed in
Preferences (Scan & Bibliography tab).
•
For Book Chapters, this setting will be applied to the title of the chapter and the
title of the book.
Punctuation
After Initial. If you have checked Initials Only, you can specify what punctuation you
want to follow the initials in the bibliography. For example, for the name Harris, John
Edward:
Punct. after initial
._
(nothing)
Results in
Harris, J._E._
Harris, JE
122
.
Harris, J.E.
Note: the underscore character _ is used to signify a SPACE.
Between Names. The sequence of characters that will separate the names of the authors
or editors. Usually, this is a comma or semicolon. Don’t forget to include a space
after the punctuation.
Between Last Names. The last two authors or editors of a citation may be separated with
different characters. Common examples include:
Separate with
,_and_
_and_
_&_
,_
Results in
Jones, E. Franklin, M. and Stanley, H
Jones, E, Franklin, M and Stanley, H
Jones, E. Franklin, M & Stanley, H
Jones, E. Franklin, M, Stanley, H
There are some publications that require the separating characters to differ if there are
just two authors as opposed to three or more. To have Bookends handle these properly,
separate the two forms with a ^ (caret): Bookends will use the characters before the caret
if there are two authors, and the characters after the caret if there are 3 or more. Do not
enter two forms in this field unless it is required by the publication.
A common example would be:
Separate with
_and_^,_and_
•
Results in
Jones, E and Stanley, H OR Jones, E, Franks, M, and Stanley, H
any words, such as 'and', in this field will be automatically converted to uppercase
if the names are output in ALL CAPPS or small CAPS.
After Surname. The punctuation separating the surname and first name of an author or
editor when the surname is output first. In most instances, this will be a comma
followed by a space.
Punct. After Surname
,_
;_
(nothing)
Format Order
Results in
Jones, E.
Jones; E.
JonesE.
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Most of the Format display is devoted to defining how the reference data is to be ordered.
The Primary Order field is where you specify which fields are to be output and in what
order. Single letters are used to represent reference categories. A summary of the singleletter codes:
Code
a
b
d
e
f
i
j
k
l
n
p
p or ps
t
u
v
y
z
h
r
g
Category
Code
Category
Author(s)
u1
User1
Abstract
u2
User2
Date
u3
User3
Editor(s)
u4
User4
Journal/Ser. Title (full)
u5
User5
Issue number
u6
User6
Journal (short)
u7
User7
Keyword(s)
u8
User8
Address or City
u9
User9
Notes
u10
User10
First page
u11
User11
Page range
u12
User12
Short title
u13
User13
Title
u14
User14
Publisher
u15
User15
Volume
u16
User16
Type
u17
User17
URL
u18
User18
Attachments
Rating (0 through 5)
Static groups to which the reference belongs
124
•
Note: For backward compatibility, w, x, c, and g can also be used for User1,
User2, User3, and User4, respectively.
Many letter symbols are the same as the first letter of the field they represent. Because
the first letters Abstract, Publisher, and Type are used for other fields, the second letter of
these words is used to represent these fields. The letters for the rest are arbitrary.
•
The names of the fields may differ from those shown if you have edited them in
Preferences. That does not matter. The letter code is what Bookends cares about,
and that does not change even if you edit the field name.
The journal name can be output in two different forms depending on its entry in the
Journal Glossary. When Bookends encounters a j or an f in the Format Order, it first
looks at the journal name in the reference, then looks in the Journal Glossary to see if
this journal name is entered there. If the journal name is in the Journal Glossary,
Bookends selects either the short (if a j) or the full (if an f) form. If the journal name isn’t
in the Journal Glossary, Bookends uses the journal name as it was entered in the
reference.
p- (dash) or p– (endash — created by pressing Option-dash, or hyphen) is used to indicate
that you want the range of pages (if entered) to be output. If you use p-, Bookends will
output whatever character is used to indicate the range in the Pages field. If you use p–,
Bookends will output an endash between the pages.
There is no specific field set aside for the issue number. If you want to enter the issue
number of a Journal Article (or Magazine, if you create such a Type), enter it in
parentheses after the volume number in the Vol (Issue) field:
125(10)
To use the issue number in a bibliography format, use the letter "i" (without the quotes)
in the Order field. Bookends will use the characters within the parentheses in the format.
It will not include the parentheses themselves.
Order is read from left to right. Each character encountered is compared with the reserved
symbols listed above. If there is a match, the field represented by that symbol is output. If
there is no match, the character is output exactly as is.
Thus, an Order of
a, t.
125
displays the author(s) in the order specified, a comma, a space, the title, and concludes
with a period.
An Order of
a t.
formats a reference like the first example, except there is no comma following the last
author(s) names.
•
If the Short Title is specified in a format and a reference has none (i.e. it is
empty), the Title will be used instead.
Entering information into the Order fields
You can use pop-up menus to enter the categories, punctuation, and special characters.
The characters in these pop-up menus that appear in curly brackets will be inserted into
the Order field when the corresponding menu item is selected. You can also type these
characters directly into the Order field without using the pop-up menus.
The three pop-up menus contain:
Fields
126
•
This example is from the default configuration for Journal Article.
•
The items in this pop-up menu may be different if you have changed field names.
Punctuation
127
Special Characters
In addition to the reserved letters, there are several modifiers you can use to further
manipulate the information. These are contained in the Special Characters pop-up menu:
Character
Meaning
$
Quote. Any characters between two dollar
signs are output as is, without any parsing.
`
Force quote (backquote). This is like $, except that the text these
symbols surround will be output even if it precedes or follows an
empty field.
~
Binding quote (tilde). Like $, except the quoted text will be
omitted if the preceding or following field is empty. The field must
128
immediately precede or follow the binding quote (no intervening
space or punctuation). E.g., with ~Title:~t, the word Title will only
be output if the Title field is not empty.
|
Break binding (pipe). Breaks the binding of text in between ~
characters. This is useful if bound text is "touching" two fields. In
this case, Bookends will consider the text to be bound to the
preceding field. But if the | character is inserted before the first ~,
Bookends will bind the text to the following field. E.g., in this
case: v|~: ~p Bookends will bind the colon-space to the Pages
field, not Volume.
#
The sequential reference number (e.g., the # symbol would be
replaced with 3 for the third reference in the bibliography).
%
The true reference number (e.g., the % symbol would be
replaced with 56 when the 56th reference in the database is
printed).
@
The unique ID number of the reference.
!
The database name (useful for Bookends Server).
^
Use the ^ in between the quote marks (dollar signs, $, or backquote
marks, `) to indicate what you want output if there is one page
(before the ^) or if there is a page range (after the ^). For example,
the format instructions
$p. ^pp. $pmight be output as
p. 123
if there is a single page, and
pp. 123-125
if there is a range of pages.
*
If the field immediately before the asterisk is a user-defined field,
the contents will be considered to be a name, and will be formatted
129
according to the instructions for the editor. For example, to have
User1 considered as a name, you would refer to it in the Order
field as w*.
++
(++)
In a bibliography format it is common to label the editors with, for
example, “Ed.”, “Editor:”, etc. In Bookends, this is done by
surrounding the label in dollar signs ($) or backquote marks(`). To
ensure that the label is singular when there is only one editor and
plural when there is more than one editor, insert two plus signs
where the “s” should go.
For example, the following format
($Ed++. $e)
could yield
(Ed. R. Roberts) [one editor]
or
(Eds. R. Roberts, W. Smith) [two editors]
• If there are no Editors, Bookends uses the Authors field to
determine if the plural should be used.
^^
This allows more flexibility than ++ for indicating what you want
output if there is one or more editors. If ^^ appears between dollar
signs ($) or backquotes (`) and there is one editor, the text before
^^ will be used. If there are multiple editors, the text after ^^ will
be used.
For example,
e $(Sole Editor)^^(All Editors)$
might be output as
Smith, JD (Sole Editor)
or
Smith, JD and Jones, WMN (All Editors)
• If there are no Editors, Bookends uses the Authors field to
determine which option to use.
130
∆ (Option-J)
Tab character.
¬ (Option-L)
Return character.
The Tab and Return characters are useful in obtaining an appropriate final look for the
bibliography. For example, if you want references to have one blank line between them,
you should end the Order with ¬.
Secondary Order: create different formats for the first and subsequent citations of a
reference
(See also the section Cite by custom citation format below).
It is possible to have a reference formatted differently depending on whether it is being
cited for the first time or subsequent to an initial citation. This is particularly useful for
footnotes or bibliographies using styles for the humanities.
The Secondary Order field determines how a reference will look when it is cited again.
To use the Secondary Order for your citations, the following must be true:
•
Information must be entered in the Primary and Secondary Order fields of the
format.
•
Cite by custom citation format must be selected (Bib & Citation Options).
•
The custom citation pop-up menu must be set to the format that will provide the
citation style definition.
If these requirements are not met, the Secondary Order will be ignored when references
are formatted.
The format can use itself to define the way citations appear or, more commonly, refer to
another format designed for just this purpose (see example below).
The authors and editors in the Secondary Order can be formatted differently from those
defined in the Primary Order. The pop-up menu next to the words "Secondary Order" has
the following choices:
131
Names Same as Primary—The authors and editors will be formatted just as they were in
the primary Order.
Surname Only—Authors and editors names will be truncated to their surnames.
Use 'et al.'—If there are three or more authors, only the first author's name will be output,
followed by 'et al.' (does not apply to the names of editors).
Surname Only & 'et al.'—Authors and editors names will be truncated to their surnames.
If there are three or more authors, only the first author's name will be output, followed by
'et al.' (does not apply to the names of editors).
•
If you want a reference cited by its Short Title after the first citation, use the 's'
character in place of the 't' in the Secondary Order definition.
Example…
Above the primary and secondary Order fields are Example buttons.
Clicking on these buttons causes Bookends to display the information of a sample
reference in a drawer as it would appear using the format information you have entered.
Clicking on the Example button will use the information (authors, title, etc.) from the
reference window (if open) or the first selected reference in the List View (if open). If
neither are open, default example information will be used. The example will update
automatically when a different reference or format is selected. Pressing Command-E
when the formats manager is in front will toggle the example pane open and closed.
•
The example format will appear as styled text, plain text, HTML, BibTeX, or
UTF-8, depending on which option you selected in the Bibliography Formatter
window.
•
If the secondary Order is empty, clicking on its Show Example button will display
data formatted as per the primary Order (which is what would occur in a
manuscript).
132
When a Field is Empty
You may on occasion make a bibliography with a reference that has an empty field.
When this occurs, Bookends tries to eliminate any unwanted output. Bookends provides
several tools to help you do this. The following rules are used to remove extra text from
the output:
Bookends searches for a space or the field before the empty field. Any characters after
the space (or, if no spaces occur, the previous field) are deleted. Any spaces enclosed in
dollar signs ($) or the backquote (`) character are ignored.
For example, if the Date field is empty in a reference, the effective format is:
Example
1.
2.
3.
4.
5.
Original order
a. t. d. p.
a. t. (d) p.
a. t. $Date: $d. p.
a. t. `Diss.` d. p.
a. t. $Diss.$ d. p.
Effective order
a. t. p.
a. t. p.
a. t. p.
a. t. `Diss.` p.
a. t. $Diss.$ p.
In example 1, the Date, the period, and the space are removed. In the second example,
Bookends removes the open parenthesis, the Date, the closed parenthesis and the space.
These are the characters between the space following the Title to the space preceding the
Page number.
In example 3, the phrase Date: is removed because the space after the colon is between
the dollar signs. Also, the period after the date is removed.
In the fourth and fifth examples, the phrase Diss. is output even if the Title and date are
both empty. That’s because there is a space before and after the word. If you wanted the
word removed if the title was empty, you would place the leading space after the tilde or
dollar sign (e.g., $ Diss.$). If you wanted it removed if the date was empty, you would
put the trailing space within the dollar signs. Finally, if you wanted the word removed if
either field was empty, you would put both spaces inside the dollar signs.
The use of spaces and the quote/force-quote metacharacters is usually versatile enough to
accommodate most situations. There are, however, times when the formatting is too
complex to allow them to handle arbitrary removal of fields. In these cases. two new
metacharacters can be helpful:
~
|
"binding quote" (tilde character)
"break binding" (pipe character)
The ~ is similar to $ in that any text between a pair of ~'s is output as is (i.e. quoted). If
the field preceding or following the ~ is empty, the text will not be output. The ~ must
immediately follow or precede the dependent field (i.e. no space or punctuation between
them). If the quoted text is in between two fields, it will be bound to the preceding field.
133
If you want it bound to the following field, insert a | (pipe character) immediately before
the initial ~.
Here are examples in which the Pages field is empty:
Example
1.
2.
3.
Original order
v: p
v~: ~p
v|~: ~p
Effective order
v:
v:
v
Notice that in example 2 the colon and space are bound to the Volume field, and so are
output because Volume contains information. In example 3 the colon and space are
bound to Pages ( | is inserted before the first ~), and are not output because Pages is
empty.
Finally, even with these tools it is sometimes impossible to avoid inappropriate
punctuation combinations when one or more fields are missing. To deal with these
situations, Bookends post-processes formatted references to eliminate unwanted
characters. Here are some combinations that Bookends handles:
Before
After
Comments
two spaces
one space
.
.
space + period replaced with period
,
.
space + comma replaced with comma
..
.
if you use three periods to indicate an ellipsis (…),
replace them with a true ellipsis character (Option-;)
..
.
;;
;
,,
,
:,
:
;.
;
?.
?
.:
.:
(;
(
(,
(
(.
(
(
(
,)
)
;)
)
;.
.
period + space + colon replaced with period + colon
open paren + space replaced with open paren
134
)
()
)
space + close paren replaced with close paren
parentheses removed
Returns and Tabs in a format are output even if they follow an empty field. This means
that if the format specifies an extra, empty line between references (with a ¬, or Return,
at the end of the format), Bookends will make sure there is one even if the last item in the
format is an empty field.
Example: Stringent APA in-text citation style
Note: The APA citation format is included with Bookends. This example is here to
show you how it is done.
The formal APA definition calls for the following in-text citation styles:
If there are fewer than six authors, cite all of them the first time and
subsequently use the first author's name followed by "et al." and the year. If a
work has six or more authors, cite only the first author's last name followed by
"et al." and the year.
You can implement this in Bookends, starting with the provided APA format, as follows:
1. Open the Formats window, select “APA 5th Edition”, and click on New.
2. Name the new format “APA citations”(this will be the format used to define the
in-text citation).
3. Set the “APA citations” fields as shown (note the pop-up menu settings, too)
4. Click on the Bib & Citations Options tab and set the “et al.” options to
135
5. Finally, go back to the APA 5th Edition format and set the custom citation format
pop-up menu to “APA citations”.
Now, when you scan a document using the “APA 5th Edition” format, the in-text citations
be in the strict APA author-date style.
Bib & Citations Options tab
136
There are a number of options that must be specified to generate a correctly formatted
bibliography. Furthermore, a number of options are available to make the best use of
scanning a document for citations.
Bibliography Options
These settings work in conjunction with Scan a Document for Citations to ensure that the
final bibliography adheres to a publication’s specifications. They are also used when one
creates a Hits List and then clicks on the Make Bib button in the Bibliography Formatter.
137
Number references If checked, references in the bibliography will be numbered
sequentially, starting with 1. You can tell Bookends what to place before and after the
number, for example parentheses (1) or brackets [1]. The default is a period and space
after the number.
Alphabetize references. If checked, the Hits List will be alphabetized before the
bibliography is generated.
•
Bookends will automatically sort the Hits List by one of three different options:
Author, Date, and Title; Author, Title; or First Author, Date, Other Authors.
•
If you want prefixes at the beginning of the first author's name, or articles at the
beginning of the Title field, ignored when sorting, check the Author or Title
checkbox, respectively. Configurable lists of words that will be ignored are found
in Preferences.
•
When a bibliography is to be sorted by author-date, if a reference has no authors
(e.g., an edited book) it will be sorted by its editors. If it has neither authors nor
editors (e.g. a reference work, such as a dictionary), it will be sorted by its title.
Remove Journal Periods. This determines if a journal name should be printed with or
without periods. In effect, an abbreviated journal name containing periods can be
output in two different forms. For example, you could enter journal names with
periods:
N. Engl. J. Med.
J. Immunol.
for the New England Journal of Medicine
for the Journal of Immunology
If you don’t want the periods printed (e.g., print N Eng J Med or J Immunol), click on
the Remove Journal “.”s button. If this option isn’t checked, the journal name is
output exactly as it is entered (or as it appears in the Journal Glossary, if it is entered
there).
•
See the section on the Journal Glossary for more information on journal
formatting options.
Include Issue # with Vol. Many on-line databases include an issue number in
parentheses after the volume number. If the reference's Type is in the same position in
the list as the default Journal Article, is "Magazine", or contains the word "Journal"
(the case of the letters is irrelevant) and the Include Issue # with Vol. button is not
checked, any data starting with a parenthesis in the Vol (Issue) field is suppressed and
the issue number will not appear in the output. If the reference's Type is not in the
same position in the list as the default Journal Article, does not contain the word
138
"Journal", and is not "Magazine", the entire contents of the Vol (Issue) field will be
output.
Don't clean up consecutive spaces. Bookends normally "cleans up" stray or aberrant
punctuation in a formatted reference, including reducing two consecutive spaces to
one. There are times, however, where consecutive spaces may be desirable. For
example, the RIS format for exporting references requires two spaces between the
field tags and the following hyphens. For cases such as these, check "Don't clean up
consecutive spaces."
Use year only for Date. If the Format has the Use year only for Date button checked and
the Format order includes a 'd' (date), Bookends will look in the Date field for a year.
If it finds one, it will output the year rather than the entire contents of the Date field.
A year is defined as a four digit number beginning with a '1' or a '2'. If Use year only
for Date is unchecked, the entire Date field is output.
Use ‘et al.’. In the first field enter the word or phrase you want Bookends to insert after
names when a certain number is reached (default is ' et al. ' —note the space before
and after). In the second field put the maximum number of authors in a reference that
should be listed before ‘et al.’ is used, and in the second field enter the number of
names that should appear before ‘et al.’ is used in the finished bibliography citation.
‘et al.’ can be used just for authors, editors, or both authors and editors. These options
are available in this pop-up menu:
If the in italic box is checked, the words in the ‘et al.’ field appear in italics (e.g., et al.).
Hanging indent. The text you are reading now has "hanging indent". When used with
reference numbers, a bibliography entry with an hanging indent would look like:
1.
James, J. E., Randolph, R., and O’Leary, F. Taxing times. The Financial
Advisor. 13:123-142 (1988).
Hanging indents will only be applied to bibliographies generated with styled text (i.e.
not plain text, BibTeX, HTML, UTF-8, or UTF-16 ) after doing a Scan. Note that
139
if you are creating a numbered bibliography, a tab will be placed after the #. at the
beginning of each reference so that the left margins of each line within a reference
align.
Page Ranges. Some formats require that both pages in a page range be shown in its
entirety (e.g. 10013-10019) while others require that the last page of the range be
abbreviated (e.g. 10013-9 or 10013-19). Use the pop-up menu to specify which of
these options you want:
Replace repeated authors with. If checked, Bookends will output whatever is in the text
box (default is three emdashes) instead of the author's name if the preceding reference
in the bibliography has the same author.
Citation Options
These settings work with Scan a Document for Citations to ensure that the final citation
entries in the revised document are correct.
Cite by number—temporary citations in a document will be replaced with numbers. The
first number is 1, and subsequent unique citations are numbered sequentially. Example:
As suggested by others (12, 13), …
or
There have been many studies on the liquidity of water (3-12), …
Superscript—if checked, citations will appear as superscripts in the final revised
document.
Styled text options—reference numbers can be output as plain text (usual), bold,
italic, or bold and italic.
140
Group references always cited together—You can specify that references always
cited together appear under one number. These references will be grouped under that
number in the bibliography, separated by punctuation that you specify in the textbox
Separate in bibliography with (typically a semicolon).
This option will generate useful citations only when the bibliography is numbered.
Three references cited in the text might appear as
(1)
and the cited references in the bibliography might look like this:
1. Jones, F et al. (2005) A title, J. Biol. Chem. 256:1045-1052; Underlie JD
(2006) A better title, Nat Immunol. 5: 45-53; Snidely, W (2007) The best title,
Nat. Cell Biol. 7: 323-326.
o If grouped references are separated by a semicolon, comma, or period, a
concluding period specified in the format will not be output for any references in
the series except the last.
Cite by author & date—temporary citation in a document will be replaced with a name
and date, e.g. (Smith et al., 1988).
When a new document file (revised file) is created, the citations are replaced with the
appropriate names (in the order cited), such as:
As suggested by others (Smith and Jones, 1989; Tobey et al., 1990), …
The rules for replacement by name are:
One author:
Two authors:
Three or more authors:
Smith, 1989
Smith and Jones, 1989
Smith et al., 1989
Punctuation in author-date citations—You can have the authors(s) and date
separated by a comma, a semicolon, or simply a space to be inserted between the
author(s) and date).
Separate two authors with—If there are two authors for a reference, can separate
them with any words or punctuation you want (e.g. " and ", " & ", " und ", etc.).
Use year-only for repeated authors— When scanning a document with a format
that creates author-date citations, this option will cause Bookends to omit the name of
an author after the first occurrence in a citation group. This means, for example, that
141
(Smith, 2004; Smith, 2005a, Smith 2005) would be output as (Smith, 2004, 2005a,
2005b). The punctuation between the years can be set in the Separate years with field.
This option requires that the repeated author names appear consecutively, and
therefore is usually used in formats where citation groups are sorted by author. This
option will be ignored for a citation group having a member with cited pages.
Handling of author-date citations with the same cited authors and date—When using
the author-date citation method, it is possible to have identical citations that refer to
different papers in the bibliography. For example, there may be two different papers
written in 1995 by Handler and colleagues cited in the document. In this instance,
Bookends will append a lowercase letter after the date of the author-date citation in the
text and in the alphabetized bibliography. The letter 'a' will be appended to the date of the
first reference in the alphabetized bibliography, the letter 'b' to the second reference, and
so on. This feature applies when scanning a document using a format in which citations
are by author-date or a custom citation format, and the bibliography is alphabetized.
Bookends will also attempt to use just the year for a citation inserted into a revised
manuscript. That is, if the Date field of the reference contains more information than the
year (e.g. Nov 3, 1995), Bookends will extract the four digit year and use that in the
citation (e.g. Smith et al., 1995). If a four digit number beginning with a '1' or a '2' is not
found in the Date field (e.g. you have entered 11/3/95), Bookends will use the
information as entered (e.g. Smith et al., 11/3/95).
Cite by custom citation format—Bookends can replace temporary in-text citations with
any information in the reference in a format designed by you.
•
Custom citations are particularly useful for replacing in-text citations in footnotes.
A custom citation format is merely a bibliography format. You create a custom citation
format just as you would create a format for a bibliography.
1.
2.
3.
4.
Select Formats Manager from the Biblio menu.
Select the format you would like to base the custom format on.
Click on the Create New Format button .
Define the format as you would like the information to appear in the revised
document.
You might use a custom citation format if, for example, you wanted the author, title, and
date used for the final in-text citations. An example of using this feature to create in-text
citations that differ depending on whether the citation is new or has been used before in
the manuscript, see Secondary Order: create different formats for the first and
subsequent citations of a reference above.
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•
If the citation format calls for a concluding period, it will be omitted from all
members of a citation group except for the last.
For repeated citations use Ibid. Some formats for citations in the humanities require the
use of "Ibid.", an abbreviation of the Latin ibidem, meaning "in the same place". Ibid.
(with the period) is used when two references to the same work follow one another
without any intervening references. This is used for footnotes, but not bibliographies. For
two different references in the database to be considered the same source, the following
fields must be identical: Authors, Editors, Title, Journal, and Volume. Some styles use a
word or phrase other than Ibid. — you can enter the appropriate text in the text field.
•
The formatted custom citation that is inserted into the document can contain
styled text. The font will be that of the paragraph's style sheet or the default font
set by the word processor.
•
When creating a custom citation format, all of the formatting options available to
you when creating a bibliography format are available with one exception:
references will not be numbered, even if this option is checked ON in the Bib &
Citations Options dialog box.
•
The pop-up menu next to the name of the custom citation format allows you to
select any format in your database to create custom in-text citations for a revised
manuscript. When inserting custom formats into footnotes, you will usually want
to use a different format from the one you are scanning with to generate the
citations. The format you are using to scan will be used for the bibliography (if
requested).
Separate multiple citations with…—If there is more than one citation between a single
pair of citation delimiters, you need a punctuation character to indicate where one citation
ends and another begins. You can choose between comma + space ( , ), semicolon +
space ( ; ), comma without a following space (, no space), and just a space (space).
Enclose citations with…—The citations in the original document are enclosed by the
temporary citation delimiters you specified in Preferences. You can replace them in the
revised document with parentheses (), square brackets [ ], or nothing (especially useful
for superscripted citations).
Order citations—When multiple references are included in a temporary citation, you can
elect to have the final citations listed in the order you entered them, sorted by year, or
sorted by author (if the items in the primary sort are identical, Bookends will subsort the
citations based upon the other item–i.e. if you are sorting by year and two citations are
from the same year, they will be subsorted by author).
For example, these citations are sorted by year:
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(Zeta et al., 1999; Alpha et al., 2002; Beta et al., 2002)
and these are sorted by author:
(Alpha et al., 2002; Beta et al., 2002; Zeta et al., 1999)
•
If a reference has an editor but no author (e.g. an edited book), Bookends will use the
editor's name(s) when it creates the final author-date citation.
Cited pages—
You define how the page or page range is displayed, and what precedes and follows the
page number(s) in the format definition:
The Display options are Page range and First page only (of course, if you only enter one
page number, only one will be displayed regardless of this setting).
Text you enter in the two fields will be output before or after the page number(s). The ^
character is used here just as it is in a format: characters before a ^ will be output if there
is only one page number, characters after the ^ will be used if there is a page range. An
example is
, p. ^, pp.
•
If you are using cited pages with a compound citation (e.g. Smith@4, 6, 10-12),
Bookends will use the text after the ^ (if present) in the before pages field.
Bookends will use Page ranges for the format to determine how a page range will be
output:
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Font and Style Hierarchy
As with any editable text field, fonts and styled text information can be specified in a
reference itself. In addition, styled text information can be applied to an entire field when
it is output to an entry in a bibliography (this is done in the Format definition). Finally,
the default font and styled text specification for the entire bibliography can be assigned in
Preferences. Here are the rules:
•
Any styled text entered in a reference is carried through to the output. Normally,
you only assign fonts and styles to special characters. These would include
symbols, Greek or mathematical characters, and phrases that need to be
underlined or italicized.
•
Styles (bold, italic, etc.) assigned in Formats are applied to all text not modified in
references. You can’t assign fonts or text size in Formats — Bookends will use
the font and size assigned by you for bibliographies in Preferences.
•
The font and text size selected in Preferences is applied to any text that hasn’t had
a font assigned in references.
•
If the reference default font and the bibliography default font differ in their
encoding (i.e. one is a Roman script, the other is a two byte script), Bookends will
use the reference font and ignore the default bibliography font.
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Scanning Documents
•
If your word processor is Microsoft Word, Mellel, or Nisus Writer Express/Nisus
Writer Pro there is no need to save an RTF file before you scan—you can scan the
document directly from within your word processor in the case of the former, and
Bookends can scan Nisus Writer files (which are already RTF) directly. See below for
details.
Before the scan
You can insert temporary citations into Microsoft Word, Mellel, RTF, and text
documents and later scan them to create a finished manuscript with formatted footnotes
and a bibliography. RTF files, sometimes referred to as Rich Text Format or Interchange
Format, are specially saved files from Microsoft Word, AppleWorks, and virtually all
word processors. In Word, you save an RTF file by choosing Save As and then selecting
Rich Text Format.
•
Bookends can scan Nisus Writer Express and Pro documents (the native Nisus
Writer file format is RTF) and RTF and RTFD (which contain graphics) files
exported from Papers '08.
For Bookends, a temporary in-text citation consists of identifying information about a
reference that is entered into a manuscript between citation delimiters. The citation
delimiters are specified in Preferences, and can be curly brackets (or braces) — ‘{‘ and
‘}’; square brackets — ‘[‘ and ‘]’; or the tilde — ‘~’. The most reliable way to enter the
temporary citation is with the Copy Citation button in the reference window or the Copy
Citation/Copy Selected Citations menu selection. This ensures that the citation is
unambiguous (unique). However, you may simply type in the citation yourself. This
means that you can insert citations into your manuscript without having a Bookends
database open. Any text in the reference can be used to specify the citation: an author’s
name, the date, a few words from the title, the journal name, etc.
Temporary in-text citations are intended for replacement by a final citation (usually a
number or the author-date, but can be almost anything). It is in the process of scanning
that this is done.
Bookends tries to find every item in the temporary citation in a reference in the database,
with four exceptions:
1. _and_
2. _et al
3. _et al.
4. _&_
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where “_” represents a space. Therefore, if you cite
{Bracken et al., 1995}
or
{Punch & Judy}
or
{Wilberry and Schwartz, 2002}
Bookends still finds the references, even though the exact words “Bracken et al., 1995”,
“Punch & Judy”, and “Wilberry and Schwartz, 2002” never appear in the references.
Even though “et al.” is stripped from the citation, Bookends recognizes it is there and
applies a special logic to the database search. A temporary citation containing a name
followed by the letters “et al” or “et al.” will find a match in a reference only when
•
•
•
the name (plus “et al.”) is the first entry in the temporary in-text citation
the name matches that of the first author of the reference
there are 3 or more authors in the reference
You can have many citations within a single set of citation delimiters. For example,
{Smith and Jones, 1993; Terry et al., 1988; Gerbil and Farrar, J. Immunol. Signal
transduction}
has three citations, each separated by a semicolon.
If BibTeX is enabled and Copy Citations copied Key field is checked (see Preferences),
the contents of the Key field will be placed between the citation delimiters, and multiple
citations will be separated by commas (no spaces are used in these temporary citations).
Creating removable in-text citations
There are instances in which you may need to enter an in-text citation to ensure that the
reference is placed in the bibliography, but do not want a citation to appear in the final,
revised document. To do this, enter an exclamation point (!) immediately after the
opening delimiter of the citation. When Bookends encounters the in-text citation, it will
look up the reference and place it in the bibliography. If you are creating a revised
147
document Bookends will remove the citation delimiters and any information between
them from the revised document. For example,
As shown by Reginald (1996) {!Reginald, J. Polygons, 82, 1996}, squares
are a subset of rectangles.
would appear in the revised document as
As shown by Reginald (1996), squares are a subset of rectangles.
Excluding enclosing punctuation in a final citation
There are times when you may want to exclude enclosing punctuation for individual
citations (for example, when a citation is placed in a footnote rather than the body of the
text). You can tell Bookends to do this by inserting an asterisk immediately after the
opening delimiter of the in-text citation. For example,
{*Reginald, Polygons, 82, 1996}
might appear after a scan as
Reginald, J. (1996). Why I love polygons. Polygon Research, 10:82.
Overriding superscript in a final citation
If the format calls for superscripted final citations, you can override this for a particular
citation group by placing an underscore (_) immediately after the opening delimiter. For
example, the following citation will not be superscripted after the scan:
{_Jones et al., 1006, The title}
This is useful, for example, when citations are by number and normally superscripted, but
you want to create a final citations like
"…(reviewed in 43)…"
or
"…which in turn activates p38 (17)…"
Mixing text with temporary in-text citations
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You may mix text with citation information. The backslash (\) is used to surround any
text you want inserted with the citation. For example, this temporary in-text citation
{Meriere, JD, How come things are?\, p. 136\}
might appear in the revised document as
(Meriere, 1997, p. 136)
Similarly,
{\see also reference \Mikelson, XN, 1996}
might yield
(see also reference 45)
Cited pages
The "quote" character, \, can be used in a temporary citation to enter a page or page
range. If you change the format, however, the page citation may no longer conform to the
desired style. You can avoid this problem by using the @ character in your temporary
citations to specify that the following numbers are "cited pages". This is how a temporary
citation with cited pages might look:
{Maguire, 2005, Russian History@45-46}
When scanned, Bookends will add the page number to the end of the final citation, such
as:
(Maguire, 2005, pp. 45-46)
or
(Maguire, 2005, pp. 45-6)
If you use an endash to separate the pages in the text of your word processor, Bookends
will use an endash in the final citation.
How cited pages appear in the scanned document is specified in the Format definition,
Bib & Citations Options tab:
149
Please refer to that section of the User Guide for details.
•
For custom citations that include pages, that field will be superseded by cited
pages. For example, if the Pages field contains 1-18 and after a scan the custom
citation would normally yield "Smith, 2002, p. 1-18", the use of cited pages in the
temporary citation (@16) would yield "Smith, 2002, p. 16").
•
Note that you can't mix Cited Pages and "quoted text" together at the end of a
citation. If you want to cite a page followed by a comment, place both after a \ as
"quoted text".
Replace temporary in-text citations with date only
If you are using a format with the Author-Date style (e.g., Smith, 1998) or a custom
citation, you can force Bookends to replace the temporary in-text citation with only the
date. To do this, place a % (the percent symbol) immediately before the citation. For
example, this in-text citation
{Anderson, 1994; %Anderson, 1995; %Anderson, Journal of Nutrition, 1997;
%Anderson, Vitamin Research, 1997}
might appear in the revised document as
(Anderson, 1994, 1995, 1997a, 1997b)
•
Bookends will not sort the citations in a group (i.e. between citation delimiters) if
one or more of them is preceded by the % symbol—the references will appear in
the same order that they were entered.
•
To have citations automatically preceded with a % symbol when you Copy
Citation/Copy Selected, check on the Precede with % (date only) checkbox in
Preferences (Scanning and Bibliography tab).
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Eliminate authors from final citation
If the first character of a temporary citation is a - (hyphen or dash), Bookends will
exclude the authors (or editors) from the final citation. For example
{-Anderson, 1994, citation information}
might appear as
(1994)
When used with an author-date format, this is identical to using a % (show date only).
But when used with a custom citation format, all the elements in the final citation will
appear except authors/editors.
The Scan a Document Dialog
When you choose to Scan a document for citations, Bookends asks you to choose an RTF
or text file and then displays the following dialog
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•
The dialog box you see when using the Microsoft Word add-in or Mellel has
some important differences. See below for details.
The options are:
Generate a bibliography after scan—If checked, Bookends will
generate a bibliography after scanning a manuscript.
Scan using the bib/document Format of…—A pop-up menu from which you can select
the format for the bibliography and the replacement for the temporary in-text citations.
•
Formats can be selected for inclusion in the pop-up menu in the Formats window.
Send the bibliography to—If a bibliography is generated, it will be saved to this
destination: Bibliography Window or Disk.
Generate bibliography as—If a bibliography is generated, it will be created either with
or without styled text (bold, italics, underline, alternate fonts such as Symbol (Greek),
152
etc.), depending on which is selected in the Bibliography Formatter. It can also be
generated as HTML, UTF-8, or for BibTeX. The setting can be changed here.
When HTML is selected, Bookends will add HTML-encoding information to the
bibliography you create and the custom citation (if one is specified in the format
definition) in the revised document. Bookends will automatically add <HTML> to the
beginning of the revised document and </HTML> at the end of the revised document. If
the document you are scanning already has these tags (i.e. is already HTML-encoded),
Bookends will not add these tags.
When BibTeX is selected, Bookends will create the bibliography in plain ASCII but add
BibTeX commands for bold, italic, super-, and subscript if these styles are encountered.
Quotation marks (") that follow a space will be converted to two backquotes (``). If
Convert to TeX is checked in the BibTeX Preferences, accented characters will be
converted to their TeX equivalents.
Create new file—Lets you create a copy of the manuscript in which the temporary
citations (e.g. {Smith et al., 1989}) have been replaced with the appropriate bibliography
notations (e.g. (1, 4)), according to the format being used. The type of file created (Text
or RTF) will be identical to the type of file being scanned.
Try to resolve ambiguous citations— If checked (the default), Bookends will pause
when it finds an ambiguous citation and allow you to specify which one you meant. If
unchecked, Bookends will collect the ambiguous citations and present them in a list after
the scan is complete. In this case, during the scan the first reference that matched the
citation will be inserted into the document and used in the bibliography, if one is
generated.
Proofreading scan—This option creates a copy of the original document in which the
citation delimiters (braces, brackets, or the tilde) are left in. It is useful if you have
entered temporary citations in the manuscript without using the Copy Citation feature. In
this situation it is possible to have unmatched and/or ambiguous entries (e.g., {Carpenter,
1990}, when there is more than one reference in the database written in 1990 and having
an author named Carpenter).
Unmatched citations: if Bookends encounters a temporary citation for which it cannot
find a match, it will display a list of all the references in the database and ask which one
you intended. The default selection shown in the list is Bookends’ best guess (it assumes
that the first word in the temporary citation is an author’s surname).
Ambiguous citations: if Bookends finds more than one possible hit while scanning the
database, it will put up a dialog box listing the references that matched and ask you to
choose the one you intended (see below).
153
After you identify the intended reference, Bookends will replace the initial temporary
citation with a correct and unambiguous citation (e.g. Carpenter et al., J. Biol. Chem.,
12323-12330, 1990).
The “proofed” manuscript can subsequently be used, and when scanned again there will
be no unmatched or unambiguous temporary citations.
During the scan
As Bookends scans your manuscript, a dialog will show you the citations as they are
encountered.
For example, the following temporary citation might be encountered:
…as previously shown {Beato, M}…
When Bookends encounters this, does a case-insensitive search the database for any
reference with “Beato” and “M” in any field. If multiple references include “Beato” and
“M” (i.e., this is an ambiguous citation), and Try to resolve ambiguous citations is
checked, Bookends puts up the dialog box:
At the top of the dialog box is the ambiguous citation. At the bottom is the text directly
preceding the ambiguous citation (the context).
The list of the references that match contains the first author, date, journal, and title of
each.
154
There are four options:
Go to ref (or double-clicking on a reference): displays the selected reference.
This one: chooses the selected reference and the scan continues.
None of these: the Scan will continue, and at the end Bookends will notify you that this
citation was not found in the database.
Stop: aborts the Scan.
If no match is found, when the scan is complete it (along with all other unmatched
citation entries) will be displayed in a floating window:
Click on Find (or double-click on an entry) to look for the reference you intended.
Punctuation, “and”, and “et al.” are stripped from the highlighted entry and the remainder
is placed in the Find dialog. You may be able to find the correct entry in the database by
editing the text in the Find dialog and doing the search.
Click Print to send the list of unmatched citations to your printer.
You must deal with the unmatched citations before closing this floating window. Once it
has been closed, the list of unmatched citations cannot be recalled.
•
There may sometimes be only a small difference between an in-text citation and
the actual reference in a Bookends database. This may occur, for example, if you
entered the page numbers in a citation as “134-142” and the reference, as
imported from the web, might have “134-42”.
•
Bookends will ignore punctuation and word-breaking characters (e.g. quote
marks, parentheses, apostrophes, commas, periods, etc.) when looking for a
match.
Replacing citations with numbers
155
If you are creating a new document in which citations are to be replaced by numbers,
citations that are replaced by three or more sequential numbers will be substituted with a
hyphenated range. For example, in a revised manuscript:
(1, 3, 4, 5, 6, 9, 11, 12, 13) will be converted to (1, 3-6, 9, 11-13).
After the scan
After Scanning a Document, one of several things may happen:
If the bibliography is sent to the Bibliography Window and a (revised) copy was made of
the original document, Bookends will automatically copy it to the clipboard and prompt
“Open the revised manuscript in your word processor?”. If this is accepted, Bookends
will launch the word processor specified by the user (in Preferences) and open the
revised manuscript. The user need only scroll to the desired location and Paste to place
the finished bibliography in the document.
If the bibliography was sent to disk and the original document revised, Bookends will
offer to “Open the revised manuscript in your word processor?” without first copying the
bibliography to the clipboard (it’s in a file on the disk). Once in your word processor, you
must open the bibliography file on the disk using the Open command in the File menu.
o The citations that were found during the scan are placed in the Hits List. This means
that if you want to generate the bibliography again (because you detected a mistake in
the format, for example) you can do so without scanning again. Just select
Bibliography Formatter from the Biblio menu, and click on Make Bib.
Rules for scanning
Here are some rules you should keep in mind when preparing a document you plan to use
with Scan a document for citations:
•
Always place citations between the citation delimiters ({ }, [ ], or ~ ~) that are
specified in Preferences.
•
Multiple reference citations must be separated by a semicolon ( ; ), a slash ( / ),
asterisk ( * ), or comma ( , ) [you can select which of these you prefer in
Preferences]. For example,
..and because the sky is blue {Henry, 1875; Schmitt-Verhulst, 1905; Castel,
1910}...
156
•
If you are not using commas as the citation separator, multiple items within a
citation (such as “author, date, journal”) should be separated by commas for
clarity—Bookends removes these before looking through the database.
•
All reference fields are searched for the words in the temporary citation.
•
Use the Copy Citation button (located in the reference display) or the Copy
Citation/Copy Selected Citations menu selection when possible, because they will
usually provide a unique, unambiguous citation.
•
You should only use a comma as the citation separator if you are using Bookends
in conjunction with BibTeX.
Microsoft Word
The Bookends add-in for Microsoft Word X and Word 2004, and AppleScripts for Word
2008, integrates this word processor with Bookends. Furthermore, the ability to retain
hidden citation information allows you to rescan or unscan a manuscript that has been
edited since it was last scanned.
When you first run Bookends it will try to find the proper locations on your startup disk
to install the add-in file and template (Word X/2004) or AppleScripts (Word 2008). If
this process fails, or if you install Microsoft Word after Bookends has already been
installed, you can install these files manually. Read the file Microsoft Word Read Me for
details.
Microsoft Word X/2004
The Microsoft Word Add-in adds five new items to the Microsoft Word X/2004 Tools
menu:
The same five Bookends options will appear (in the same order, from left to right) in a
toolbar as well:
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As for all Microsoft Word toolbars, you can change its orientation to vertical, drag it to a
new position in a tool bar, or close it. Even if you close it, the four options will remain in
the Tools menu. If you close the toolbar and decide later that you want to show it, select
it from the Toolbars hierarchical menu (under the View menu).
•
Important: Make sure that “Include formatted text in Clipboard” is checked ON
in the General tab in Preferences for Word X.
If you not see the Bookends options in the Tools menu, make sure that the Bookends two
add-in files are in the right location for Word:
Drag the file “Bookends Word X Add-in” to the folder “Office”. The path is
/Microsoft Office X/Office
Or
/Microsoft Office 2004/Office
The add-in must be placed in the Office folder, not the Startup folder!
Drag the file “Bookends Word X Template” to the folder “Word”. The path is
/Microsoft Office X/Office/Startup:Word
Or
/Microsoft Office 2004/Office/Startup/Word
Microsoft Word 2008
There are Bookends AppleScripts for Word 2008 that provide the same functionality as
the items in the Tools menu in earlier versions. They should be located in the Scripts
menu:
158
You can, if you like, change the names of these scripts in the Finder, and even move them
out of the "Bookends" subfolder, and they will still work.
If you not see the Bookends options in the Scripts menu (for example, you installed Word
2008 after installing Bookends), do the following:
Go to the folder
~/Library/Applications/Bookends/Add-ins for MS Word/Word 2008 Scripts
and drag the folder
Bookends
to
~/Documents/Microsoft User Data/Word Script Menu Items/
Go to Bookends
Brings Bookends to the front as the active application.
Find in Bookends
Brings Bookends to the front as the active application with the Find dialog box open. If
any text in a Word document is selected when you choose this option, it will appear as
the search word(s) in the Bookends Find dialog box. For example, if your document has
the following selection, when you choose Find in Bookends
the word "Gibbs" will appear in the Bookends Find Dialog box.
159
Insert Citation
This tells Bookends to insert a temporary citation for the selected references (if the List
View is in front) or the reference on display (if the Reference Window is in front) into the
Word document at the insertion point. If you hold down the Shift key, the citation will be
inserted without the surrounding delimiters (usually curly brackets). If Bookends is not
running or if no database is open, nothing will happen.
Scan Document
This option performs a scan of the active document window and creates a new window
(or replaces the contents of the currently active window) with the revised document and,
optionally, a formatted bibliography. When you select Scan Document from Microsoft
Word, you will be presented with the following dialog box:
160
These are very similar to the options available when you select Scan a Document from
the Bookends Biblio menu. There are a few differences, though. The most important is
that you are given the option to retain citation information in the document in hidden
form. This makes it possible to "unscan" and/or "rescan" a document (see below). The
options that are disabled are not available: the bibliography (if one is requested) will be
generated as styled text and will be appended to the scanned document. (You cannot
insert HTML or BibTeX formatting into a Microsoft Word bibliography using the Addin. To do this, save the document as a text file and use the Scan a Document menu
option.) You can choose to have the revised document replace the existing one or placed
in a new window.
If Retain hidden citation information if checked, Bookends will save the information in
the revised document that it needs to restore the original citations, if that is ever
requested. This makes it possible to continue working on the manuscript, adding or
deleting text or references, and then "unscan" or "rescan" the document (see below). If
this option is checked OFF, Bookends will not be able to unscan or rescan the document.
If you elect to generate a bibliography for the document, it will be appended to the end of
the manuscript. If you move the bibliography to another section of the manuscript (cut
and paste the entire bibliography, including the header, if there is one), Bookends will
remember and maintain this location if the same manuscript is rescanned.
If Create new document window is checked, scanned and revised documents will be
placed in a new window in Microsoft Word. This is the safest option, because it means
you will always have keep an unmanipulated version of your manuscript. If you prefer
the convenience of having only one version of your manuscript to deal with, check this
option OFF. If you do, please remember to keep back-up copies of your manuscript in
case the file is ever damaged!
Unscan Document
This option restores a previously scanned document to its original form (i.e., temporary
in-text citations between the citation delimiters and no bibliography). This requires that
the document was previously scanned with the Retain hidden citation option ON.
•
In addition to placing the revised document in a window in Word, the clipboard
will hold a copy of the revised manuscript when a Scan or Unscan is performed.
o The citation delimiter characters (set in Preferences) must be set to same used
when the document was scanned.
•
The Microsoft Word add-in does not work with MS Word 5.1 or earlier.
161
Typical use of the Microsoft Word add-in with Bookends
•
Launch Microsoft Word and open your manuscript.
•
Select a word or words that you expect in a reference you want to cite (e.g., a
surname) and click on the Find in Bookends button in the Bookends toolbar. This
will bring Bookends to the front (or launch Bookends and open the last-used
database) and open the Find dialog box with the word(s) you selected already
entered.
•
Find the reference(s) you want, then click on Copy Citation (or the Copy
Citation/Copy Selected Citations menu selection). If you are linked to Microsoft
Word (Preferences), this will bring Word to the front with citation inserted at the
point of the selection). Alternatively, you could select the citations you want,
switch to Word, and use the Insert Citation toolbar button or command in the
Tools menu.
•
When ready to generate a revised manuscript, click on the Scan Document button
in the Bookends toolbar. The Bookends Scan a Document dialog box will appear,
and you can select the options you want prior to the scan. Typically, you will
generate a bibliography and retain hidden citation information. Click on OK.
•
After a few seconds, the revised manuscript will replace the original or will
appear in a new window.
If you retained hidden citation information, you can continue to add to and edit the
manuscript if you like. At any time you can scan it again from Word (the changes will be
incorporated and a new bibliography generated, if desired) or unscan it (replacing the
citations with the temporary in-text citations and removing any bibliography).
If you did not retain hidden citation information, the manuscript cannot be rescanned (or
unscanned) by Bookends. Any changes you make should be to the original manuscript
(prior to the original scan).
Size limitation for documents scanned from within Word
Bookends communicates with Word via AppleEvents, and documents are passed back
and forth via the clipboard. Word has trouble copying styled text when files become very
large, and if the file exceeds a certain size it will fail. Bookends can scan very large
documents when invoked from within Word. Documents of over 10 MB containing over
230 single spaced pages and 150 complex black and white graphics have been
successfully scanned with this version. There is a theoretical file size limit of 16 MB,
which is imposed by Word.
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Workaround: Bookends is always able to scan a Word document saved as an RTF file,
regardless of its size.
Problem: font sometimes changes after a citation is inserted in a Word document
When scanning a Word document and inserting the final citation, Bookends adopts the
text style of the style sheet at that location. As a result, if you have altered the style
(changed the font, font face, etc.) from that of the style sheet in the text immediately
following the citation, this will be undone after the scan.
To avoid this, do one of the following to the affected text before a scan: (1) apply the
style sheet you want to use, (2) edit the style sheet to specify the appearance you want, or
(3) create a new style sheet and apply it.
Mellel
The word processor Mellel is "Bookends-aware", meaning that it can communicate with
Bookends to manage citations and bibliographies. To enable this, open Mellel
Preferences and set the Bibliography Application to Bookends (in the Bibliography tab).
The following is a discussion of how Mellel 2.2 or later works with Bookends.
•
For full details on how Mellel deals with citations, please refer to the Mellel
documentation.
Citation objects
Unlike other word processors, Mellel treats temporary citations as objects. This means
that temporary citations are not normal text (although they can be edited via a dialog box)
but are indivisible units. Mellel doesn't use curly brackets (or any other delimiter) to
denote citation objects. A temporary citation in Mellel might look like this:
Note that the temporary citation object is lightly colored. Another color is used for
scanned (final) citations.
If you double-click to open the citation object, you would see something like this:
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If more than one citation were inserted into Mellel, they would be separated by a
semicolon.
You can edit a citation object by double-clicking on it.
To enter a temporary citation object into a Mellel document, in Bookends make sure that
Mellel is selected as your word processor in Preferences and then
• Click on the Copy Citation button.
• Choose the Copy Selected menu item when the List View window is in front.
• Drag and drop the reference(s) you want to cite from the List View window.
or in Mellel
• Click on the Enter Citation Manually button in the Bibliography palette.
When entering a citation manually (useful, for example, if the reference has not yet been
entered in the Bookends database), you can enter more than one citation in a group,
separating each with a semicolon.
Checking the Don't Include in Final Document checkbox means that the citation(s) will
be noted and included in the bibliography but will be removed from the text of the
scanned document. This is the same as entering an exclamation point at the beginning of
a Bookends temporary citation in other word processors: {!Johannson et al., 2003,
Nature}
Don't enclose formatted citation will cause the scanned citation to appear with enclosing
parentheses or any other punctuation. This is the same as using the asterisk in other word
processors: {*Johannson et al., 2003, Nature}
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Suppress Superscript is useful if the format calls for superscripted in-text citations and
you want a particular one to be on the baseline. This is the same as using the underscore
in other word processors: {_Johannson et al., 2003, Nature}
Bibliography palette
This is the Mellel Bibliography palette:
Refresh citation list
Enter citation manually
Verify citations
Scan document
Unscan document
Find in Bookends
Switch to Bookends
The palette contains a list of temporary citations in the manuscript. Citations are added to
the list as they are inserted into the document and displayed as a sorted list (to remove
citations that were deleted from the document, click the Refresh button).
In addition to providing feedback about which citations the document contains, you can
•
•
•
•
Drag and drop a citation in the list into the document.
Double-click to insert the citation into the document at the insertion point.
Option-double-click to view the cited reference in Bookends (Bookends must be
running).
Command-double-click to scroll the document to the next occurrence of the
citation.
The buttons do the following:
Refresh citation list: Updates the citation list and removes citations that were deleted
from the document.
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Enter citation manually: Enter a citation from the keyboard (handy if the reference
hasn't been entered into a Bookends database yet). You can enter multiple citations in a
group at once by separating them with a semicolon. Do not surround a citation with curly
brackets.
Verify citations: Checks the Bookends database to ensure that the temporary citations
are valid and unambiguous. If one or more citations are not, Bookends will be brought to
the front for you to select the correct citation.
Convert text to citations: Convert temporary citations created in other word processors
to citation objects in Mellel. Useful if you are migrating manuscripts from other word
processors to Mellel.
Scan document: Initiate a scan, which will produce a finished manuscript and
bibliography. If the scan is being performed for the first time, Bookends will be brought
to the front so that you can select a format.
Unscan document: Reverts final citations to their temporary form, and if a bibliography
is present it will be removed. Mellel will reset the format to nil, and if a scan is
subsequently performed Bookends will be brought to the front so that a format can be
selected.
Find in Bookends: Bring Bookends to the front with the Find dialog box open. If text is
selected in Mellel, it will appear in the Bookends Find dialog box.
Switch to Bookends: Bring Bookends to the front.
A typical session when using citations might be:
1.
2.
3.
4.
Insert temporary citations from Bookends as needed.
Scan the document. The first time you will be asked for a format.
Continue to write and insert/remove citations.
Scan the document. You will usually not have to interact with Bookends during the
scan unless you have unscanned the document.
Synchronize database
If you are using Bookends with Mellel 2.2 or later, you can import references whose
citations have been inserted in a Mellel document. This is useful if you are, for example,
collaborating with others and want everyone involved to have the relevant references and
be able to scan the Mellel document.
To import references from a Mellel document, open a Bookends database and in Mellel
use the menu Edit -> Bibliography -> Synchronize Database. If the reference already
exists in the Bookends database (same unique ID, authors, and title), it will not be
imported.
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Nisus Writer Express and Pro Macros
Bookends can automatically insert temporary citations into and scan documents created
with Nisus Writer Express or Nisus Writer Pro. A set of Nisus Writer Express and Nisus
Writer Pro macros lets you access some of Bookends' functions from within this word
processor.
Bookends will try to find the proper locations on your startup disk to install the add-in
file. If this process fails, or if you install Nisus Writer Express or Pro after Bookends has
already been installed, you can install these files manually. Please read the file Nisus
Writer Macros Read Me for details.
For Nisus Writer, these items are added to the Macro menu:
Bookends Go
Bookends NWE Find
Bookends NWE Scan a Doc
Bookends NWP Find
Bookends NWP Scan a Doc
The macros containing "NWE" are for use with Nisus Writer Express, and the ones
containing "NWP" are to be used with Nisus Writer Pro.
Bookends Find
Brings Bookends to the front as the active application with the Find dialog box open. If
any text in the foremost Nisus Writer Express document is selected when you choose this
option, it will appear as the search word(s) in the Bookends Find dialog box. For
example, if your document has the following selection when you choose Find Citation
the word "Gibbs" will appear in the Bookends Find Dialog box.
•
Bookends must already be running when you invoke Bookends Find.
Bookends Go
Brings Bookends to the front as the active application.
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Bookends Scan a Doc
This option performs a scan of the active document window and creates a new window
with the revised document and, optionally, a formatted bibliography. When you select
this macro, you will be presented with the following dialog box:
These are very similar to the options available when you select Scan a Document from
the Bookends Biblio menu, although some items are automatically set for you and are
therefore dimmed. If you elect to generate a bibliography for the document, it will be
appended to the end of the revised manuscript.
•
The revised document (and bibliography, if generated) will automatically be
placed in a new Nisus Writer Express window.
There are a few limitations with scanning a document from within Nisus Writer Express:
•
The original temporary in-text citations cannot be retained as hidden text.
Therefore the scanned document cannot be unscanned. For this reason, the revised
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document and bibliography are always placed in a new document window. You
must keep the original document if you think you might want to make changes
and rescan it (highly recommended!).
169
Refbase
Refbase is a web-based bibliographic manager for literature, references and citations.
Refbase can import and export references in various formats (including BibTeX,
Endnote, Reference Manager, ISI, PubMed, CSA, MODS XML, and OpenOffice.org). It
can make formatted lists of citations in HTML, RTF, PDF, or LaTeX, and offers
powerful searching, and RSS support. An overview of the main features can be found at
http://refbase.sourceforge.net/features.html
There is a public Refbase server (http://www.refbase.org). In addition, Refbase can be
downloaded and installed by institutions, at no charge, to allow exchange of information
from collaborating individuals.
You may want to user a local Refbase server if:
o a research group wants to restrict the database content to references that are
relevant to their own group, research, or institution.
o a research group wants to control user access to their Refbase database, and
fine tune user permissions for each user individually (such as permissions for
adding/editing records or file upload/download).
o Note that, due to legal concerns, file upload is currently disabled at
refbase.org, and this may be the biggest reason for users/groups to install their
own Refbase server.
o one wants to use Refbase locally or behind a firewall and not with public
access.
The installation process of the Refbase server is described in the 'INSTALL' file that
comes with the Refbase package. More information (requirements, troubleshooting) is
available online at:
http://install.refbase.net/
Pointers to the Refbase forums and mailing lists as well as direct contact information can
be found at:
http://support.refbase.net/
The Refbase online documentation is available at:
http://wiki.refbase.net/
Using Refbase is described here in detail:
http://wiki.refbase.net/index.php/Documentation#Usage
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To apply for a Refbase user name and password, go to http://www.refbase.org and click
on the Register link.
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Menus
Bookends Menu
About Bookends…
Displays the version of Bookends you are using. You can register Bookends by clicking
on the Register button in this window.
Check For Updates…
If you enabled this option when Bookends is first run, Bookends will use the Sparkle
framework to check for, download, and install new versions. Bookends will check for a
new version each time it is run or when you use the Check For Updates menu option.
If you elected not to use Sparkle when asked, this menu opion will still be available and
will check the Sonny Software web site to see if there is a version of Bookends that is
more recent than the one you are using. If a newer version is available, Bookends will tell
you what the version number is and for which users it is a free upgrade. A Download…
button will launch your browser and take you to a page on the Sonny Software web site
where you can download Bookends and install it yourself.
Preferences…
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•
You can type Command-1 through Command-8 to show the corresponding tab.
General
Word Processor
Brings up a dialog asking you to find your word processor. When you have located it,
click on the Open button (Bookends will not “Open” your word processor, but will obtain
its full pathname). The Creator field is filled in for you automatically when you select the
word processor. You can restore the value to "None" by clicking the Set To Default
button.
This is an important setting in Preferences. Your word processor preference determines:
•
The Creator for files that are written to disk (so that double-clicking them opens
your word processor).
•
When to implement the auto-linking feature.
173
Attachments folder
You can select a folder to hold files attached to references by drag and drop. When you
drag and drop a file on a reference or List View window, you will asked if you want
Bookends to move the file to your attachments folder. The default folder is
~/Documents/Bookends/Attachments (the tilde indicates that the file path is that of the
user who is logged in). The Set To Default button will restore this setting if you have
changed it.
•
Most people will find the default attachments folder satisfactory. We do
recommend that you have all your attachments in one place so that you can easily
include them if you share your database with others or move Bookends to another
computer.
•
See the section "Storing attached files automatically" for details on how to have
Bookends move attached files to one folder.
Default font
You can set the default font and size for bibliographies, references, and lists (Term Lists
and the List View).
Toggle with
You can toggle between the default font for references and any other font with the key
combination Command-Shift-G. You can set the alternating font here. This only applies
to text you are entering in the reference window. This is useful if you routinely enter
information in more than one text encoding.
Default view
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When you open a database, it can be displayed in the List view or the reference window
view (the default for Bookends 7). If a database is empty, it will always open in the List
view, even if you have selected the reference view.
Internal cache
This setting determines how much memory (RAM) is allocated to Bookends for database
operations. The lowest setting is 8 MB, which is more than enough for most databases.
However, when a database become very large some operations may become sluggish
because of inadequate cache. In this case, increasing the amount of internal cache can
dramatically improve performance. You can adjust the cache to suit your particular
needs. A reasonable rule of thumb is that 2 MB of additional cache should be allocated
for every 1000 references over the first 3000-4000 (i.e. 10 MB for a 5000 reference
database). Another is 1 MB of additional cache for every 3-4 MB of data in the database.
•
Changes do not take effect until you quit and re-launch Bookends.
Hypertext links
You can define the visible portion of a hypertext link that you create in Bookends (via
drag and drop or copying to the clipboard). The default is the title of the reference, but
you can use any active format. If you use a format, it is likely you will want to create
your own for this purpose (and name it accordingly, such as Hyperlink Format).
Journal Glossary
Bookends automatically replaces an abbreviated journal name entered in the Journal field
if it finds a match in the Journal Glossary. This option controls whether the short journal
name or full journal name is substituted.
Window menu
The Window menu shows the names of open database windows only or the names of all
open windows regardless of their kind, depending on this setting.
Automatic backup
175
When this is enabled, Bookends will check each database when it is opened to see if the
specified interval between backups has been exceeded. If it has been, Bookends will offer
to make a backup (if the Prompt box is checked) or will make the backup without asking
(if the Prompt box is unchecked). The database will be verified before being backed up,
and if there are any problems the backup process will be aborted and you will be alerted.
Automatic backups are made to this folder: ~/Documents/Bookends/Backup. The date
and time of the backup will be recorded in the database, and can be seen by using File ->
Database Maintenance -> Verify.
References
Reference Types
To change a reference Type, click on its entry in the list. The ten Types starting with
“Unused” are meant to be altered if you have a reference source that is not already
covered. You can also change a Type that you don’t use (e.g. Audiovisual material) to
one that you do (e.g. Manual).
176
Default new reference Type
Any new reference you create, or any reference you import that does not have a defined
Type, will be assigned the default Type.
Keywords location in reference window
In the reference window, the Keywords field can be displayed in the main tab or in its
own tab. If it is placed in its own tab, it will be replaced by the Notes field in the main tab
(Notes will also appear in its own tab, regardless of this setting).
Rename attachments
When Bookends offers to rename an attachment it will suggest the reference's author and
year of publication (Author Date). You can create your own suggested name by
specifying a format. If you do this, it is likely you will want to create a special format for
this purpose, and name it accordingly (for example, Attachment Name Format).
The checkbox Rename local pdfs on Find & Attach tells Bookends to rename pdfs as
directed (Author Date or by format) when they are attached using the Refs -> Get PDF > Find & Attach Local PDF option.
Field Names
You can change the name for any field as a function of reference Type. To change a
name, select the Type you want to edit from the pop-up menu and then click on the
relevant entry in the list.
If you want to change the name for the field in all Types (e.g. you may want to use
"Auteurs" rather than "Authors"), click on the entry, edit it, and then click the Apply
button.
•
The names you assign will be used throughout Bookends if the reference Type
can be determined by Bookends. If it can't, Bookends will use the field names of
the default reference Type. For example, if you bring up the Find dialog box, the
pop-up menu containing the fields you might search in will contain the names of
the default reference Type unless you elect to search only a particular Type. In
this case, the pop-up will contain the field names of the corresponding Type.
•
Bookends will access a particular field correctly even if it has different names in
different reference Types. For example, if you perform a Find for an "Author" and
177
do not specify a reference Type, Bookends will find the name if it is in the
"Artist" field (Artwork), or "Inventor" field (Patent).
•
Note: these changes only affect the words you see in the name, i.e., the name you
see in Bookends. The internal names for the fields are unaffected. This is
important if you perform an SQL/Regex search — the field name popup menu in
that dialog box will always show you the internal and fixed field name.
Data entry
The Autocomplete check box lets you turn on or off the autocomplete function (described
in the Reference Display section).
You can assign the keyboard shortcut Command-V to Edit -> Paste (default) or Edit ->
Paste Plain Text. The Paste menu item that is not given this shortcut will be assigned
Option-Command-V. You may find this useful if you often use the keyboard to
copy/paste styled text from other sources (like a browser) and want it to be inserted as
plain text.
Inserted date format
This controls the format of the date inserted in a reference with Refs -> Insert Date. You
can choose between the setting in System Preferences and yyyy-mm-dd (year-monthday). The advantage of the latter is that it will sort correctly by date when you do an
alphanumeric sort.
Lists
178
These options deal with the List View and the Term Lists windows.
All Lists
Bring reference window to front on double-click
When the List View or Term Lists window is in front, double-clicking on a reference will
show that reference in the reference window. If Bring reference window to front on
double-click is unchecked, the reference you selected will be shown in the reference
window, but the list window will remain in front. If this checkbox is checked, the
reference window will come to the front.
Show entire date
Lists display only the four-digit year (if available) in a Date column. If you want the
entire date to be shown, as entered, check this option.
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Sorts based on
Bookends can sort lists by ASCII or Unicode values. ASCII sorts are approximately
twice as fast as Unicode sorts. If you don't have Unicode characters (accented or nonRoman) the ASCII sort is preferable. If you do use Unicode and want correct sorting
(e.g., "é" to sort after "e" and before "f"), select Unicode sorting.
The Unicode sort is the same one the Finder uses, and is also smarter about numbers (for
example "Chapter 9" sorts before "Chapter 10").
List View Window
Sort Lists
When checked, the All and Hits groups will be automatically sorted when the List View
window opens. If this box is not checked, the display order will be the order in the
database or in the Hits List, respectively.
•
You can always sort the list on-the-fly by clicking on the desired column heading.
•
Term Lists are always sorted.
•
The lists are sorted by the first column and then by date (in ascending order). If
the first column is the date, the list will be sorted in descending date order (from
most recent to oldest).
Indicate attachments
When checked, references that have one or more attachments will be preceded by an icon
of a paper clip.
Display of names
Bookends will display author/editor names one of four ways:
one
First Only
Multiple
First...Last
All
Doe, J
Doe, J
Doe, J
Doe, J
Number of authors
two
Doe, J
Doe, J & Smith, W
Doe, J & Smith, W
Doe, J & Smith, W
three or more
Doe, J
Doe, J et al.
Doe, J...Henry, SR
Doe, J, Smith, W &
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Henry, SR
Fields to display
The List View window can display up to seven columns. You can view any of the
reference fields as well as the Type, unique ID, and reference number in a column.
Color Labels
These labels can be assigned to references. In the List View, the entire row can be
colored, or just the first column (typically the Authors), depending upon your preference
setting. Click on the color in the first column to bring up the Color Picker and change the
color (the color setting for Normal is black, and can't be changed). Edit the meaning of
the color label by clicking in the second column. The keyboard shortcuts (ControlCommand-#) are shown for your information and cannot be modified.
Concise View
181
Default Summary view
You can choose between Standard and a bibliography format. Standard is preferred,
because in this case the Concise View is interactive and editable.
Font size
This is the size to be used for Summary and All displays.
View All label colr
Sets the color of the field labels in the All display.
Standard View organization
The pop-up menu lets you choose three concise views to alter: All, Summary (Books),
and Summary (Others). Only checked items will be displayed in the corresponding view.
Drag reorder the items in the list to tell Bookends in what order you want them output.
For Summary displays, you can specify what text you want before and after a field. If the
field is empty, the before and after text is omitted.
To output a Return character before or after a field, enter ¬ (Option-L) or the word
"return" (without the quotes).
Click the Set To Default button to return the list that is showing to the factory default.
For more information about configuring and using the concise view, see the section in
this User Guide on the List View window, concise view Pane.
Scan & Bib
182
Temporary citations
Temporary in-text citations can be delimited by curly brackets ({}), square brackets ([]),
the tilde (~), or BibTeX (i.e. \cite{ } or \nocite). Only one type of delimiter is allowed at a
time. Examples are:
{Grunenfelder et al., 2001, Proc Natl Acad Sci U S A, 98(8), 4681-6}
[Grunenfelder et al., 2001, Proc Natl Acad Sci U S A, 98(8), 4681-6]
~ Grunenfelder et al., 2001, Proc Natl Acad Sci U S A, 98(8), 4681-6~
\cite{Grunenfelder2001}
•
To unscan a Word document, this setting must be the same as when the document
was scanned.
•
During a scan Bookends will replace the temporary citation delimiters with those
specified in the definition of the format you are using.
•
The BibTeX delimiters will only scan properly if they are used in a plain text
(ASCII) file.
183
Copy Citation
Cite by:
When you use Copy Citation to create a temporary in-text citation, Bookends will use the
reference’s content (Authors, Journal, Volume, Pages, Date [and title if necessary to
create a unique citation]), the Author, Date, and unique ID, or any combination of fields
specified in a format. See the section on Copy Citation for details.
Multiple citations separated by:
Bookends will use this character to determine when one temporary in-text citation has
ended and another begins within one set of citation delimiters. You can choose between
semicolon, slash, asterisk, and comma. For example, if the semicolon is used, the
following contains two citations:
{Mittelstadt et al., 2001, J Biol Chem; Li et al., 2002, Nature}
The comma is only useful for separating BibTeX citations:
{jones2001,edwards2002b}
It should not be used for citations by content, author/date/uniqueID, or defined by format.
o If you want a comma to separate citations in a group after a scan (the final
citation), set the "Separate multiple citations with" pop-up menu in the format
definition, second tab.
Precede with:
This options lets you tell Bookends to include certain modifiers in temporary citations by
default.
Some in-text citation styles require that the authors appear in the text followed by the
year of publication in parentheses [e.g. Jones (2003)]. You can force the citation to
contain only the date by preceding it with the % symbol. If you want to use this
throughout a document, a setting in Preferences tells Bookends that all citation(s) are to
be preceded by a % symbol when you use Copy Citation/Copy Selected.
•
This applies to formats using Author-Date citations or custom citations. Formats
in which citations are by number ignore this command.
184
Temporary citations that are preceded with the ! character will be recognized by
Bookends and included in the bibliography, but will not appear as a final citation in the
final, scanned document. If you would like temporary citations created in Bookends to
default to this form, select '! (do not show)' from this pop-up menu.
Superscript & subscript
Bookends can’t display superscripts or subscripts in a field. It is possible, however, to
embed special symbols (escape characters) in reference information that, when included
in a bibliography file or in the clipboard, will cause the text to be displayed as
superscripted or subscripted in a word processor. The symbols you may use are:
Superscript:
Subscript:
^, @, or ~
|, \, or _ (underline)
To create a subscript (with the bar symbol: |) you might type, for example:
CO|2 -> CO2
Superscripts and subscripts are terminated by one of three things:
•
•
•
a space
the end of line
another superscript or subscript symbol
Some examples are:
H|2|O ->
H2O
^3^H ->
3H
If you select None, Bookends will not superscript or subscript any characters.
Bibliography font use
If Default font overrides field settings is checked, Bookends will ignore any font settings
in individual fields when creating a bibliography, and output all text in the default font.
This may be useful if you have imported styled text from other applications (via XML or
copy/paste) and want the imported font information to be ignored when creating a
bibliography.
185
Sentence & Title Case
A list of words that will always appear in the entered form when using a bibliography
format that stipulates that titles be output in Sentence or Title Case. You can add or delete
words from this list. Combinations of words (e.g. “United States”) can also be entered.
Bibliography sort: Ignore words at beginning of…
There are two lists: Author and Title.
Words (name prefixes) entered in the Author list will be ignored when sorting by author.
For example, if 'van' is entered, the name 'van Beethoven' will sort with the 'Bs', not the
'Vs'. The corresponding option must be checked in the format itself for these prefixes to
be ignored. This is case-insensitive ('Von' is the same as 'von') and applies to the first
author only.
Words in the Title list will be ignored, if they are at the beginning of a title, when sorting
bibliographies. The corresponding option must be checked in the format itself for these
words to be ignored. This function is case-insensitive ('The' is the same as 'the'). In the
title itself, the word must end with a space or a hyphen to be ignored.
BibTeX
Enable BibTeX
Enabling BibTeX turns on features that make working with BibTeX references and
citations easier.
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When BibTeX is enabled:
1. The User1 field is renamed Key, and is used to enter the reference’s unique id/key.
2. The Key field will not accept spaces, commas, or apostrophes.
3. If you enter an id in the Key field that is not unique, you can have Bookends:
•
Do nothing.
•
Warn you (you will be given the opportunity to change the entry or proceed).
•
Automatically append a lowercase letter to the entry to make it unique. If the last
letter is already a lowercase letter, it will be incremented to the next (e.g.
jones2001b becomes jones2001c).
Note: Duplicate checking is performed only for typed (or imported, see next)
entries — text pasted into this field is not checked.
4. When Create Key value when importing is checked, Bookends will create a key for
you when references are imported. The value will consist of the first author’s surname
and the year of publication. If there are no authors, the first editor’s surname will be
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used. If there is no four digit year number in the Date field, the entire contents of the
Date field will be used (spaces will be removed).
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•
•
A key value will not be generated if one already exists.
If the key value is not unique, Bookends will either do nothing, warn you, or
append a lowercase letter until the value is unique, according to what you
specified in the pop-up menu above this Preference choice.
This option does not work when importing tab-delimited files.
5. If “Copy Citation” copies Key field is checked, invoking Copy Citation (or Copy
Citations if there are selections in the List View window) copies the entry in the Key
field and pastes it into the linked word processor. If there is more than one reference
selected in the List View window, the citations will be separated by a comma:
{Hurley1999,Franks2002,Graf2001}.
When turned on, you will be asked if the comma should be used as the citation
separator when scanning a document (the default is OK).
6. Any text can automatically precede the temporary in-text citation generated by
Bookends. The default is “\cite”.
7. Holding down the Shift key when selecting Copy Citation puts the citation in the
clipboard without the preceding text and citation delimiters.
8. BibTeX requires that certain fields be filled out for each reference Type. Bookends
can indicate which fields are required in two ways: underline the field names or color
the field backgrounds. The default color is light yellow—you can change the color to
one of your choice by clicking on the text below the pop-up menu. The Bookends
reference Types that will have required fields indicated are: Journal article, Book,
Book chapter, Edited book, Dissertation, Conference Proceedings, Letter, In press,
and Personal communication. You can rename the Unused reference Types to add
other BibTeX types. Bookends will recognize and indicate the required fields for the
following Types you might add: Booklet, Technical Report, and Manual.
TeX character handling
Importing: Convert from TeX. When checked and using a BibTeX import filter,
Bookends will convert imported TeX-formatted accented characters to their 8-bit
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("extended ASCII") form: e.g. \"{u} will be converted to ü ('u' with an umlaut). Double
backquotes (``) will be converted to quotation marks (").
Bibliographies: Convert to TeX. When checked, when creating a bibliography as BibTeX
Bookends will convert accented characters to their TeX equivalents: e.g. ü will be
converted to \"{u}.
Bracket acronyms in title, e.g. {DNA}. If selected, Bookends will try to wrap acronyms in
the title field in curly brackets. Words that begin with a single number will be wrapped
(e.g. {3D}), but those beginning with more than one number will not be (e.g. 32P).
Internet
Proxy Info
If you are using a proxy server to access the Internet, Bookends will retrieve that
information from the System Preferences. However, if your server requires
authentication, the User Name/ID and Password can be entered here. Otherwise leave
these fields blank.
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The checkbox "Use proxy info" is useful if you are switching from one environment
where an authenticating proxy server is used and another where it is not.
Automated PubMed Searches
These settings control the behavior and how often automated PubMed searches are
performed. Please see the section below on Automated PubMed Searches for details.
•
If you have not created any automated PubMed searches, you can ignore these
settings.
Attaching PDFs
If you don't attach pdfs that might be listed on PubMed, uncheck this option to avoid the
slight delay caused by checking for reference availability from PubMed.
Refbase
Enter a Refbase server URL (the default is the public Refbase server,
http://www.refbase.org, but you may have access to an institutional server). Once you
have applied for and received a user name and password, enter them in the corresponding
fields. Once this has been done, the Refs -> Upload To Refbase menu will become
enabled, and you will be able to automatically upload references to the Refbase server.
Furthermore, you will be automatically logged in when you File -> Go To URL to go to
your Refbase server with your browser.
You can choose to upload references to Refbase using with EndNote XML (styled text
will be preserved, but not configurable) or RIS (plain text only, but configurable by
editing the RIS format).
To apply for a Refbase user name and password, go to http://www.refbase.org and click
on the Register link.
o You can read more about Refbase and what it does in the section in this User
Guide called Refbase.
OpenURL
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OpenURL is a protocol provided by many institutional libraries that allows you to look
up information about a reference, often including the full text of an article. If you have
entered one or more OpenURL server paths and the arguments for searching, Bookends
will enable a Refs -> OpenURL Search menu.
The OpenURL information you enter here has two parts: the library server paths (URLs)
and the search arguments.
You can add or remove OpenURL servers with the + and - buttons. The server URL is
entered or edited directly in the list.
At this time, Bookends supports the following arguments:
aufirst: first author's (if no author, editor's) first name or initials
aulast: first author's last name (if no author, editor's)
issn: ISSN
isbn: ISBN
atitle: title of an article
title: journal (if an article), book title if a book
volume: volume number if an article
date: year
spage: starting page
epage: ending page
genre: type of work (article, book, bookitem, conference proceedings)
Any other arguments you enter will be sent to the library's OpenURL server as you
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entered them, so you can provide, for example, the name of a library database to search.
The arguments must be entered in the form
argument=
with each argument being separated with an ampersand.
For example:
&aufirst=&aulast=&issn=&isbn=&atitle=&title=&volume=&issue=&date=&spage=
&epage=
Bookends will replace the argument with the relevant information from the selected
reference.
The default settings in Bookends point to the 1Cate server. It is for demonstration
purposes, and you will probably want to add servers with arguments supported by your
institution's library (the information you require should be obtained from your library).
Server
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Set and edit parameters important for serving your own reference databases over the
Internet.
Allow Web access to databases
This turns on or off Bookends Server. When on, Bookends will open a port and "listen"
for attempts to access one of your databases over the Internet. The rest of the settings
control different aspects of Bookends Server. You can read about their functions in the
User Guide section Administrating Bookends Server.
Services
Bookends supports OS X services. To use a service, select the text that you want to act
upon and then the service you want to use from the Services menu. If the Services options
are disabled, it means that you have not selected any text.
File Menu
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Bookends automatically saves any text you type as you enter it. Therefore, there
is no Save menu item in the File menu, and no dialog will appear asking you if
you want to save the changes when you close a database or quit Bookends.
New Database…
Creates a new, empty database.
Bookends will recognize a file with the suffix ".bdb" as a Bookends database. That means
that if you transfer a database with from one computer to another via a protocol that does
not preserve the file's metadata (Type and Creator), you can still have Bookends
recognize it by adding ".bdb" to its name. This is otherwise unnecessary.
Open…
Opens an existing Bookends database. The names of the five databases most recently
opened are shown, and you can instantly open any of them by selecting them from this
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hierarchical menu. The Clear Menu option removes the names of the most recently
opened databases.
Backup…
Verifies the integrity of the selected database, and if there are no problems creates an
exact copy of the current database. If there are any problems, the backup process will be
aborted and you will be alerted. Manual backups "reset the clock" for that database with
regard to automatic backups. We strongly recommend that you make backup copies of
your databases. Automatic backup (see Preferences) is a convenient way to ensure that
backups are made without your intervention.
Sync
Synchronize Bookends databases across a network or the Internet. Each database can be
configured to sync with a designated remote copy (File -> Sync -> Configure).
The date of last sync is kept in the database, as is the last modification date for each
reference. In most cases syncing between two or more databases goes through an
intermediary database, known as the "remote" (as opposed to "local") database. When a
sync is performed, one database is designated as the "master" and the other as the
"client". Any references found in the master but not the client will be added to the client.
Any references found in the client but not the master will be deleted from the client. The
same is true when syncing groups. When a reference is found in both databases but with
different modification dates, the database with the older version will be updated to the
newer one, regardless of whether it is the master or the client. Before the sync is actually
performed you will be shown the intended operations and will be allowed to any or all
(via a Permit checkbox).
You can tell Bookends how the master/client relationship is decided with a pop-up menu
in the File -> Sync -> Configure dialog. If Use last sync dates is selcted, Bookends will
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designate the most recently synced database as the master—if both databases have the
same last sync date the local database will be the master. The other options are This
(local) database is always the client and This (local) database is always the master. If
you are part of a group and want one person to be in charge of maintaining a central
database and the rest to be clients, you should select always master for the person
maintaining the database and always client for all others. Be aware, however, that
modified references are always synchronized to the most recently edited, regardless of
which database is the master and which the client.
We recommend that the remote database never be modified directly when the
master/client relationship is based on the last sync date. If you do, you may lose
references you added if you sync the database with that has a more recent last sync date
(and therefore the edited database is the client).
Use scenarios:
1. You are the only person using sync to maintain your database. You have a client
database at work or school, a client at home, and a remote database on a server. Cofigure
the two databases so that Bookends will Use last sync dates. References can then be
added/deleted/edited at work, synced with the remote database, and when you go home
you sync the database there with the remote database.
2. You are a member of work group and are in charge of maintaining the central database.
You configure your database so that This (local) database is always the master. The other
members of the group configure their copies to This (local) database is always the client.
You can then sync your database to the remote central database to add/delete references
and groups and the others can sync their databases to the central database to receive the
changes. The latest edits performed by either you or members of the group will be added
to the central database unless you/they uncheck the modify reference Permit checkbox at
the time of sync.
3. You are a member of a work group in which anyone is allowed to add references to a
remote central database, and you want everyone in the group to obtain those references
when syncing. All members of the group should configure their databases so that
Bookends will Use last sync dates. When each member does a sync they will have the
opportunity, if they are the client database, to download any new references (uncheck the
corresponding Permit checkboxes for delete or modify if they are enabled). Once that is
done, they can do another sync and, since their database will now be the master, any
references they added will be uploaded to the central database.
• You must have read/write permission for the remote database.
• Bookends identifies each reference by unique id.
• Although not designed for this purpose, sync can also be used to maintain incremental
backups to a remote database if you configure the sync to Always use this (local)
database as client.
• Ancillary files, such as attachments, must be synchronized separately.
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Import References…
Information can be imported into Bookends from text files created by many internet
database services, other Bookends databases, and other reference management
applications such as EndNote.
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Direct import from the Online Search window is discussed above.
To ensure that reference information is imported correctly, Bookends must know the text
encoding of the imported data. This is specified in the File -> Import Text Encoding
submenu. The encoding information is relevant when importing via a filter or importing
Bookends tab-delimited text files.
References can be imported from files, directly from the clipboard, or from other
reference management applications by drag and drop.
•
If Import to Hits List is checked, the imported references will replace any existing
hits in the Hits List. If you want to accumulate imports in the Hits List, hold down
the Option key when clicking OK.
•
When the group All is selected in the List View, imported references are
immediately selected and the list scrolls to the first one imported. Any text
entered in the Live Search box will remain, which means that if imported
references do not match the Live Search criteria they will not immediately appear
in the reference list, even though they are in the database.
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•
The Import References dialog box will appear whenever you drag and drop a text
file onto a Bookends database window or the List View window. You can drag
and drop several files at once.
•
You can import a reference file exported from any version of Bookends into a
Bookends database by dragging and dropping it from the Finder onto the database
reference window or the database’s List View window.
•
References imported from a Bookends 7 export file will be assumed to be in the
encoding of the Bookends default reference font (selected in Preferences). If you
have used Bookends with a two-byte (non-Roman) font, it is essential that this
font be set as the default for references when you import, or the characters will be
displayed incorrectly.
•
If a file has the extension ".txt", it will be treated as a text file regardless of its
Macintosh file type when it is dropped on a Bookends database window. This
means that Bookends will offer to import references from files downloaded from
the internet even if the Finder does not recognize them as text files (you may have
to add “.txt” to the file name yourself). A short cut is to hold down the Shift key
when you drop the file—Bookends will treat it as a text file and offer to import it.
•
If you hold down the Shift key when clicking on OK to begin an import,
Bookends will not filter the files shown in the Get File dialog. This allows you to
select text files downloaded from the Internet that lack the usual identifiers (like a
.txt extension).
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Some internet sources incorrectly assign the TEXT file type to pdf files when they
are downloaded. To avoid an erroneous attempt to import these files, Bookends
will treat a file with the ".pdf" extension as a pdf file, regardless of its Macintosh
file type, and offer to attach it if it is dropped on a reference or List View window.
Bookends will automatically move the file to the Trash when the import is complete if
you check Move to Trash after import.
To import from other reference management applications (such as EndNote) by drag and
drop, drag references from that application that have been displayed using a tagged
format and drop them on a Bookends List View window or reference window, and select
the appropriate import filter from the pop-up menu. In EndNote, for example, you might
select EndNote Export as the style, then drag the references with the Option key held
down to Bookends.
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If dropping on a reference window, do not drop into an editfield because text will
be inserted into the editfield rather than imported.
EndNote 7 or later lets you export references as XML. These files contain both text and
the style information for each field. The Bookends Import References dialog pop-up
menu has an XML (EndNote). If selected, the file will be parsed as an XML document
and imported into Bookends with styles intact (italic, bold, and underline; shadow and
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outline are ignored). Superscripted or subscripted text will be preceded by the Bookends
superscript/subscript escape characters. Fonts and font sizes will be preserved for
EndNote 7 XML files. Font sizes will be preserved for EndNote 8 or later XML files, but
fonts will be set to the Bookends default value. Author/editor names in surname-last form
(e.g. John Doe) will be converted to surname-first form (e.g. Doe, John) on import.
Affected fields will be set to plain text, and compound surnames will have to be corrected
manually (e.g. 'Ralph Vaughan Williams' will be converted to 'Williams, Ralph
Vaughan').
Bookends will import pdf links in XML files created with EndNote 9 or later as
attachments. For Bookends to locate these attachments you must either place them in the
Bookends default attachments folder (or subfolder), or set the Bookends default
attachments folder to the folder containing your pdfs. If they are scattered among many
folders, you will have to reattach just one file from each folder.
The Bookends Tab-Delimited import option is intended to be used only with files
exported from Bookends in a tab-delimited format. Bookends will refuse to import tabdelimited files from other sources. It may be possible to create an import filter to handle
the files in those cases.
Note: The file format for Bookends files was changed between version 7.5 and previous
versions to accommodate references containing large amounts of styled text. As a result,
Bookends files created with Bookends 7.5 or later cannot be imported into previous
versions of Bookends. However, Bookends 7.5 or later can successfully import files
created with previous versions.
Importing references from PubMed by drag and drop from a browser
You can import from PubMed into Bookends by dragging and dropping the proxy icon
(the small icon that appears at the beginning of the URL field) or the hypertext link itself
onto a Bookends database window. The reference will be automatically imported using
the Bookends PubMed import filter. Bookends will not be brought to the front, making it
easier to perform several imports in a row (or follow up by importing the associated pdf).
If you drop onto the name of a static group, the reference will be imported into that
group.
Here are examples of a drag from PubMed using Safari, dragging the actual link
or the proxy icon:
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You can also drag and drop links to pdf files from your browser for downloading
and attachment. This is especially useful for PubMed and PubMed Central
articles. See the following section in the User Guide for details: Downloading and
attaching pdfs from a browser by drag and drop
Importing a reference from an attached PDF
If you attach a pdf that includes a doi (Digital Object Identifier) that Bookends can
resolve and that is listed on PubMed, Bookends will offer to download the reference
information from PubMed and attach the pdf to the new reference. This will work even if
you don't have access privileges to the pdf online.
If you check Import reference information and then attach, the rename function (if
checked) will create the file name based upon the imported reference.
A live hypertext link to the article online is displayed in the attach dialog.
•
Importing reference information when attaching will only be offered when the pdf
contains a valid doi that Bookends can extract and the reference is listed on
PubMed.
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Importing references from a Mellel document (Synchronize Database)
If you are using Bookends with Mellel 2.2 or later, you can import references whose
citations have been inserted in a Mellel document. This is useful if you are, for example,
collaborating with others on a paper and want everyone involved to have the relevant
references and be able to scan the Mellel document.
To do this, open a Bookends database and in Mellel use the menu Edit -> Bibliography ->
Synchronize Database. If the reference already exists in the Bookends database (same
unique ID, authors, and title), it will not be imported.
Import Text Encoding
You can select the encoding of a file you are importing.
Note that for plain ASCII text (values ≤ 127), these choices work identically. It is only
when character values are greater than 127 (e.g. accented characters, such as é) or when
Unicode is involved that these choices make a difference.
Western (Mac OS Roman): best for text created on a Macintosh.
Western (ISO Latin1): best for text created on a Windows PC or imported from most
Internet sites.
UTF-8: the only option that works for Unicode text (encoded in UTF-8 format).
Bookends assumes the text is in the selected encoding when using an import filter to
import from a text file, the clipboard, or a browser. This does not apply to text imported
using the Online Search window—the encoding in that case is always ISO Latin1
(because that is what is currently provided by the Library of Congress Internet gateway).
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References imported from a Bookends 7 export file will be assumed to be in the
encoding of the default reference font used in Bookends.
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Import Filter Manager…
Import filters tell Bookends how to import reference information obtained from a wide
variety of sources. These filters are kept in the folders Import Filters and Custom Import
Filters. Import Filters must be in the same folder as Bookends. Custom Import Filters is
created when you run Bookends, and is placed in ~/Library/Application
Support/Bookends.
When you select this menu item, you will see something like this:
On the left is a list of the filters in the Import Filters and Custom Import Filters folders.
A check mark next to a name means that it will be included in the Import References popup menu. An unchecked filter can still be edited, but it won't appear in that pop-up menu
until you check it.
If the name is in italics, that means the filter is capable of performing and importing
references obtained with a Bookends Online Search. If the name is in bold, that means
the filter is in the Custom Import Filter folder.
You can create a new filter (based upon the one currently selected) by clicking the Plus
button. A filter created in this way will automatically be placed in the Custom Import
Filters folder.
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Clicking the Minus button, pressing the Delete key, or selecting Clear from the
Edit menu will cause Bookends to offer to move the selected filter to the Trash.
Filters distributed by Sonny Software are in the Import Filters folder. Filters that you
create with the New button will be placed in Custom Import Filters folder (in
~/Library/Application Support/Bookends). This means that when you upgrade to a new
version of Bookends, any filters you created cannot be mistakenly replaced by replacing
your old Bookends Folder.
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If you simply edit an existing filter, it will remain in its original folder. You can
manually move such a format to the Custom Import Filters folder, which ensures
that you will not over-write it or forget to transfer it when upgrading. The
exception to this is filters for which you have saved search strategies—these will
be moved to the Custom Import Filters folder for you.
•
It is possible to have two filters of the same name, one in the Import Filters and
one in the Custom Import Filters folder. This is not recommended. However, if
this occurs, Bookends will always use the version in the Custom Import Filters
folder when it imports references.
Export References (Hits)…
You can save the information contained in references as a file that can be read by a
variety of other programs.
You have the option of saving them in different forms:
Bookends—A proprietary format that exports the references with full style information.
The file can only be read by Bookends 10 or later.
Bookends 7-9—A proprietary format that exports the references with full style
information. The file can only be read by the named version or later.
Tab-delimited text—A Tab is placed after each field, and a Return is placed after each
reference. The first “field” is the unique ID, the second is the reference Type. These
are followed by the fields in the order that you tab through them in Bookends, i.e.
Authors, Title, Editors, etc. This type of file is used by many database applications,
such as Excel and FileMaker.
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Note: This is intended to be used for moving data to a third party application for
manipulation and then importing back into Bookends.
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Bibliography format—This brings up the Biblio Formatter dialog box, which allows you
to selected any format that you have enabled in Bookends. The destination is set to
“Disk”, and you can output the references as styled text, plain text, HTML, UTF-8,
or BibTeX.
XML (EndNote 7), XML (EndNote 8 or later)—Export references as XML. Files
exported in this way conform to the EndNote 7 or 8 or later XML schemas. This
means that XML files exported from Bookends can be imported by EndNote 7 or
later, with styled text information intact.
Bookends XML extends EndNote 7 XML in that it is encoded in Unicode (UTF-8)
and can therefore handle characters in non-Roman languages (Japanese, Chinese,
Hebrew, etc.). EndNote 7 will not read these characters correctly, but will handle
accented Western characters (é, ü, etc.) properly. This is not an issue with later
versions of EndNote, which understand Unicode.
If the Date field contains a 4-digit year beginning with 1 or 2, Bookends will output
that to EndNote's Year field, and any other information will be output to EndNote's
Date field. If no recognizable year is found, the Bookends Date field will be output
to the EndNote Date field. If the Bookends Volume field for a Journal Article
contains parenthesis [e.g. 263(13)], the number to the left will be output to the
EndNote Volume field and the number in parentheses will be output to the Issue
field. If no parentheses are found, the contents of the field will be output to the
EndNote Volume field.
•
Text that is preceded by a superscript or subscript metacharacter will be
exported with the corresponding style information, so that when imported into
EndNote the text will be super- or subscripted and the escape character will be
removed.
•
Not all fields in Bookends have corresponding fields in EndNote (e.g. Trans
Author does not exist in EndNote 7). In such cases, the information in those
fields will not be imported by EndNote.
•
References exported as EndNote 8 XML or later will retain links to attachments
on the local hard drive if imported into EndNote 9 or later.
Go To URL
The Go To URL menu choice lets you quickly open bookmarked web sites in your
browser.
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Selecting Edit Bookmarks brings up this dialog box, where you can add/edit bookmarks:
•
An entry in the Site column is helpful but optional.
To remove a bookmark, check the Delete checkbox. The bookmark will be deleted when
you click OK.
Refbase is a special case. If you have entered a URL for Refbase in Preferences, it will
appear in the Go To URL list (so that you can go to the Refbase web site via your
browser). You can delete the Refbase URL in the Edit Bookmarks dialog window or edit
the URL, but you can't change the name (which is indicated by Refbase appearing in
italics).
Online Search...
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Page Setup...
Brings up the standard printing options.
Print References...
You can print information from the reference currently being viewed, the references in
the Hits List, or all references in the database.
When the List View window is in front, selecting Print References gives you the option
of printing the selected references, all Hits, or all references.
•
If elect to print all Hits, the order may not be the same as that shown in the List
View window if you have sorted it (or have Sort Lists checked in Preferences).
You can print the reference(s) in any format style that is checked in the Biblio -> Formats
menu. Sonny Software supplies a format called "Printout" that outputs all the reference
information in tagged form, i.e.,
Unique ID: #12323
Authors: Johnson, AP, Motley, F
Title: The rise and fall of the western omelet.
etc.
Note that the standard print dialog lets you send the output to a pdf file.
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Print Bibliography...
This option is enabled only when the Bibliography Window is the frontmost window.
Database Maintenance
These options let you determine the integrity of your database and fix problems that arise.
Among them, the most useful are Verify (checks for database integrity), Repair (tries to
fix damaged directories and fields), and Rebuild (exports all reference data and imports
into a fresh database, with or without keeping user information like groups, window
locations, etc.). Each is discussed in detail below.
Verify…
This function checks the integrity of the selected database. This is useful if you are
experiencing crashes or other aberrant behavior. If problems are found, regardless of how
small, Bookends will report it and offer to Rebuild the database (keeping user
information, such as groups, intact). If no problems are found, Bookends will report that
as well as the date of the last backup.
Reindex…
The internal indexes that Bookends uses for rapid retrieval of references can become
corrupted if the database is being written to during a crash. This results in odd or erratic
behavior, such as the inability to find a reference even though it is in the database, or
misnumbering of the references. If this occurs, it is sometimes possible to recreate
functional indexes with this command.
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Repair…
This function may allow you to recover databases that have become corrupted and can't
be opened. Select this option, find the database to repair in the Open File dialog, select a
destination, and name the repaired copy of the database to be created. Bookends will
attempt to make a copy of your database in which any corrupted references have been
repaired or, if that is not possible, deleted. The length of time this takes depends upon the
size of the database (e.g., a 20 MB database might take several minutes).
Rebuild (Keep User Settings)…
This creates a temporary copy of the data and imports it into a new database with styled
text information intact (and then deletes the temporary file). All preferences and user data
associated with the database (groups and window size and placement being the most
important) will be retained. This also clears the index and compacts and defragments the
database. Note that if the retained user information is corrupted in the original database,
they will be corrupted in the rebuilt database, too. Therefore, if there are problems with
the rebuilt database, perform a complete Rebuild (see next). Note: this can be a lengthy
process for a large database.
Rebuild…
This creates a temporary copy of the data and imports it into a new database with styled
text information intact (and then deletes the temporary file). All preferences and user data
associated with the database (groups, window size and placement, etc.) will be lost. This
also clears the index and compacts and defragments the database. This operation can
often repair a corrupted database. Note: this can be a lengthy process for a large database.
Defragment & Compact…
Over time a database can become fragmented and accumulate wasted space (especially if
many references have been deleted). This command defragments and reclaims wasted
space, which can increase speed and reduce database size.
When to use which method to fix a damaged database
If you have having problems with a database and believe it might be damaged, we
suggest the following guidelines:
1.
If searches are erratic, but everything else appears to be OK, try reindexing first.
2.
If you can open the database, try Rebuild (Keep User Data) first (Repair would be a
reasonable choice as well).
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3.
If you cannot open the database, try Repair (and select the database from disk).
Link To
This menu displays a list of running applications. A checkmark will appear next to the
name of the application to which Bookends is linked, typically the word processor you
selected in Preferences. You can use this menu to quickly change the linked application
(for example, if you are alternating between your word processor and note taking
application) or to unlink Bookends from any other application.
Switch To Word Processor
If you have selected a word processor in Preferences (or from the Link To menu) and it is
running, use this menu item to bring it to the front. This will occur without Bookends
copying or pasting any reference information.
Quit
Any changes to the database are automatically saved.
Edit Menu
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Undo, Cut, Copy, Paste, Clear, Select All
The standard Macintosh text editing options. When the List View window is in front,
choosing Select All selects all of the references in the list. In Preferences, you can assign
the keyboard shortcut Command-V to Paste or Paste Plain Text.
Paste Plain Text
Pastes text without style information (no italic, size, color, etc.). This is useful if you are
copying and pasting text from outside of Bookends, for example a browser or word
processor, and you want the text to conform to the settings in Bookends. In Preferences,
you can assign the keyboard shortcut Command-V to Paste or Paste Plain Text.
Copy Citation
Selecting this is identical to clicking on the Copy Citation button in the Reference
window.
When the List View is in front, this item changes to
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Selecting it will cause temporary citations to be made of all of the references selected in
the List View window.
Copy Formatted
Creates a formatted version of the reference being viewed and places it in the clipboard.
The Copy Formatted function will automatically paste the formatted reference into your
word processor (the default for this can be set in Preferences). The word processor must
be running and linked, and be able to accept the appropriate AppleEvent. Automatic
pasting works with Word, Mellel, Nisus Writer Express, Pages '06 or later, and Mariner
Write.
The format currently selected in the Default Format menu item will be used as the
template. This feature is especially useful for creating footnotes that contain reference
information.
•
If the Option key is held down when Copy Formatted is selected, you will switch
to your word processor with the formatted reference in the clipboard but without
pasting.
When the List View window is in front, this item changes to
Selecting it will cause all of the references selected in the List View to be formatted and
placed in the clipboard, and you will switch to your linked word processor.
You can also place formatted references in your word processing document when the List
View or a Term List window is in front by dragging and dropping one or more references
with the Option key held down.
•
Holding down the Shift key while invoking Copy Formatted will tell Bookends to
try to use the Secondary Order field for formatting. If the Secondary Order field is
empty, Bookends will use the Primary Order field.
Copy Hypertext Link
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Copies a hypertext link to the reference to the clipboard, from where it can be pasted into
a window of another application. If the receiving application is capable, clicking on the
link will take you to the corresponding reference in Bookends. See the section Use the
unique ID to embed hypertext links in another application's documents for details.
The link can be "live" (clickable) or just the text of this link:
•
You can also drag and drop hypertext links from the reference window (drag the
unique id) and the List View (holding down the Command and Option keys and
then drag the reference).
Show Clipboard
Displays the contents of the clipboard. Clicking on the Show invisibles check box allows
you to see spaces (◊), Tabs (∆), and Returns (¬).
•
The ability to see the contents of the clipboard may be especially useful when you
are importing references from the clipboard.
Special Characters
This displays up the Mac OS X Character Palette.
Font and Style Menus
Set these attributes in reference fields.
Biblio Menu
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This menu contains options for scanning manuscripts and creating formatted
bibliographies.
Scan a Document…
This brings up the dialog box for scanning files (RTF (including Nisus Writer files),
RTFD files (which contain graphics) exported from Pages '08, or text files).
See the section Scanning Documents for details on how to prepare documents for
scanning and then to scan them.
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Subject Bibliography…
A subject bibliography is on in which references are grouped and listed by subject. This
is a convenient way, for example, to list all of the references written by a specific author,
or to segregate references by keyword, label, etc. Bookends will offer to create subject
bibliographies for references in the hits list, based on any of the criteria shown in the
Subject pop-up menu:
Once selected, Bookends will display all of the possible groups (in the example above,
the authors) based upon the information contained in the references (for example, the
different authors, keywords, etc.). You can elect to use any number of these as subject
groups. You can also choose any format for the references. Bookends will create a
bibliography in which subject appears as a title, in bold face, followed by the references
belonging to that subject. The subject bibliography will appear in the Bibliography
Window, from where you can print it or copy/paste it into your word processor.
o Note that if the format specifies hanging indents, Bookends will insert tabs.
Therefore, when you paste it into your word processor you can see the hanging
indent simply by adjusting the left margin and word wrap marker in the ruler.
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Here is an example of a subject bibliography by Author, in the Cell format:
Bibliography Formatter…
Bookends can automatically rearrange reference data in virtually any style necessary for
bibliographies or citation lists. This capability, called formatting, can also be useful in the
creation of special reports, such as alphabetized lists of all of the titles with dates. A
format is used by Bookends to determine how the selected references (the Hits List) are
to be displayed in a bibliography or report.
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Bookends is distributed with over 150 formats already defined. They are located in the
Formats folder.
Some of the formatting capabilities of Bookends are accessed via the Bibliography
Formatter… dialog box (others reside in the format definition: see below).
With this dialog box you can tell Bookends which format to use, whether to create the
bibliography with styled text, without styled text (plain text), or in HTML, and designate
where the bibliography is to be sent. You can also "manually" generate a bibliography (as
opposed to having one generated automatically when you Scan a Document for
Citations).
Select the format for the bibliography from the pop-up menu. It is initially set to the same
format that is selected in Format window (you can find this in the Biblio menu).
Changing the selected format here will also change it in the Format window.
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You have the option of creating the bibliography with or without styles (multiple fonts,
bolding, underlining, etc.), as plain text, HTML, BibTeX, UTF-8, or UTF-16. For a
typical bibliography, you will want to use the styled text option. If you are exporting
references to be imported into another program, you might choose plain text. If the
bibliography is to be included in a web page or a LaTeX document, you might choose
HTML or BibTeX, respectively. UTF-8 and UTF-16 may be useful for exporting to other
Unicode-aware applications (without styles).
If “as HTML” is selected, Bookends will generate a formatted bibliography that is
preceded by the <HTML> command and followed by the </HTML> command. This tells
a browser that the information in between contains HTML-style information.
Furthermore, Bookends will add the appropriate HTML commands to the bibliography so
that the references are displayed as you specify.
If “as BibTeX” is selected, Bookends will generate the bibliography as plain text but with
these changes to accommodate BibTeX styled text commands:
1.
2.
3.
4.
5.
6.
7.
Bold text will be output as \textbf{the bold text}
Italic text will be output as \emph{the italicized text}
Superscripted text will be output as $^{the superscripted text}$
Subscripted text will be output as $_{the subscripted text}$
A hyphen in a range of pages will be output as two hyphens
Quotation marks that follow a space ( ") will be output as ``
If Convert to TeX is checked in Preferences, accented characters will be output as their
TeX equivalents.
You can send the formatted references to the Bibliography window (where they may be
viewed, edited, printed, or copied to the clipboard) or to a file.
When you send the output directly to disk, there are several different ways the file can be
saved. The saved file will be in RTF when With Styles is selected. If the bibliography is
made Without Styles, a plain text file is generated, using the Creator of the word
processor specified in Preferences.
Clicking on the button Make Bib starts the formatting process. If you have used this
dialog box just to change the default settings, click on the Set Defaults button when you
are finished. If you don't want any changes remembered, click Cancel.
If you direct the formatted output to the Bibliography window, this is the window that
will be displayed when bibliography is created.
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Formats Manager…
Select this to see a list of the available formats:
On the left a list of all the formats in the Formats and Custom Formats folders. Formats
must be in the same folder as Bookends. Custom Formats is stored in
~/Library/Application Support/Bookends.
The default format (the last one used) is highlighted. The Show check box tells Bookends
to include this format in pop-up menus that list formats. Check the checkbox for the
formats you use, and check OFF those for formats that you don't. This avoids very long
pop-up menus filled with options that you don't want.
•
Clicking the Minus button, pressing the Delete key, or selecting Clear from the
Edit menu will cause Bookends to offer to move the selected format to the Trash.
See the section Formats And Bibliographies for details on how to create and use formats.
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Default Format
This menu holds the names of all the formats that are currently enabled. A checkmark
appears before the active format. You can change the active format to another by
selecting it from the menu.
View Menu
All items in this menu are enabled when the List View is in front. The options determine
which panes of the List View are open, and which of the various pieces the panes can
display are shown:
Basic: only groups and references are shown
Concise: the concise summary is shown in the info pane
Notes: the notes are shown in the info pane
Formatted: the formatted view of the reference is shown in the display pane
Attachments: the attachments are shown in the display pane
•
Except for Basic, these options toggle the view.
•
These same options are available in the View icon at the top right of the List View
window.
When the reference window is open, the Formatted menu option is still enabled. If
selected, it displays the current reference in its formatted form in a separate window. The
reference will be shown in the currently selected format.
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You can change the format with the pop-up menu or the Default Format menu item.
You can change the way that styled text is handled (output as styled text, plain text,
HTML, BibTeX, or UTF-8) with the rightmost pop-up menu.
•
Using these pop-up menus to change the format or styled text output will change
the default settings accordingly.
The Show invisibles check box lets you see spaces (◊), Tabs (∆), and Returns (¬).
•
The formatted reference will automatically be copied to the clipboard, so after
viewing you can paste it into a manuscript.
If the example window is left open, it will update silently (i.e., will not come to the front)
if you edit a field in the reference and press Tab, or if you move to a different reference.
Refs Menu
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221
New
Creates a new empty reference at the end of the database. If invoked from the List View
and a static group is selected, the new reference will automatically be added to that static
group.
Insert
Creates a new empty reference immediately after the reference being displayed. This
menu option is only enabled in the reference window view.
Delete…
Permanently deletes reference(s) from the database. If the reference window is in front,
selecting this option (or pressing Command-D) will bring up this dialog box:
Deleting references is NOT undo-able. Make sure you really want the references to be
permanently removed from the database.
If the List View window is in front, Bookends will open a sheet asking if you want to
delete the selected references from the database.
Duplicate
Creates an exact copy of the open reference (if the reference window is in front) or the
selected reference(s) (if the List View is in front).
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If the reference window is in front, the duplicate is placed in the database immediately
after the reference. If List View is in front, the duplicated reference(s) are placed at the
end of the database. The unique id of a duplicate will be one greater than that of the
original (if that unique id is already used, the number will be incremented by one until it
is unique or until 10 attampts have been made). If a static group is selected and a
reference in it is duplicated, the new reference will automatically be added to that group.
he date and time of duplication will be used as the date added
Replicate As Book Chapter
This option is enabled when the reference Type is Edited Book, Book, or Conference
Proceedings. When invoked, Bookends will create a new reference of Type Book
Chapter that includes the relevant information placed in the correct fields (for example,
an edited book's Title is placed in the book chapter's Book Title field).
Compare References…
If more than one reference is selected in the List View, you can use this menu option to
view the first two selected references side-by-side in a new window.
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Only fields that have information in either reference will be shown. In this window you
can move between references using the stepper control arrows or enter the numbers of the
references you want to compare. You can mark/unmark the references in this window to
add/remove them from the hits list, and assign ratings. Field names will be preceded by a
clickable blue symbol: ❖. When clicked, a dialog containing that field from both
references will allow you to copy/paste or drag and drop text from one to the other.
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Remove Duplicates…
You can choose which fields must match for two references to be considered duplicates.
Be sure to choose enough fields to guarantee uniqueness.
In addition to specifying the fields that must be examined to determine if references are
duplicates, in some cases you can control what information in each field is used.
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Here are some important things to know before you Remove Duplicates:
•
Spaces and the case of the letters are ignored.
•
If two references are duplicates, the one with the shorter Abstract field is
removed. If the Abstracts are of the same length, the one that has no (or the fewer)
attachments is removed. If they have the same number of attachment, the
reference that appears earlier in the database (i.e. has a lower sequential number)
is removed.
•
Reference removal is irreversible, so you may want to backup the database before
doing this.
•
This operation clears the Hits List.
When you click the Proceed button, database is examined and the number of duplicates is
reported:
You can have the duplicates automatically removed. If you choose to Preview & Verify
Duplicates, Bookends will display all of the references that meet the criteria you set for
defining a duplicate:
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The references that have been identified as duplicates are listed, and the one that
Bookends proposes to eliminate is checked. You can click on a reference to select it and
its duplicate. Alternatively, you can use the arrows at the top to move you through the list
of duplicates.
Two fields at the bottom of the window allow you to compare the selected references
side-by-side. Fields that contain information that differs between the references are
highlighted in red.
❖
Each field is preceded by the symbol . Clicking on this symbol will bring up a dialog
box that lets you move text from one reference to the other (by drag and drop or
copy/paste).
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Once you press Save, the modified field will be saved to the database.
•
No references will actually be deleted from the database until you press the Delete
Marked button and click OK when asked to confirm your decision.
•
Take care not to mark all the duplicate references, or you will delete all copies of
the reference from the database (the "duplicate" and the "original").
Mark
There are two options:
Mark All References puts all of the references in the Hits List, in their order in the
database.
Mark Range… brings up this window:
The references will be placed in the Hits List in the order specified (e.g. 1-10 and 10-1
select the same 10 references, but they will have reverse orders in the Hits List).
You can also mark/unmark all or selected references in the List View with an Action
pop-up or a contextual menu command.
Add To Group
Add references to a static group (see section on List View window for more details on
groups).
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New Group…
When selected, Bookends will open the List Views window as for the name of the new
static group.
Group name
The static group names, if any, will be shown in this submenu. You can add the selected
references (if the List View is in front), or the reference showing in the reference window
if it is in front, to any existing static group. If the List View is in front and a static group
is already selected, its name will be disabled in the submenu. If you try to add a reference
to a static group in which it is already a member, it will not be added again.
An alternative to using this menu is to Control-click (or right-click if you have a multibutton mouse) on a reference's unique ID, or in a List View reference list, and a
contextual menu with these options will appear.
You can also drag and drop one or more references from the list of references onto a
static group name in the List View.
Find…
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You can perform boolean (and/or/not) searches to find references that contain any word
or combination of words.
From the first pop-up menu you can choose to search All fields or any particular field.
You can also choose to search for a reference by unique ID.
The second pop-up menu specifies whether you want to search the entire database or the
references that are already in the Hits List (this option will not be available if the Hits
List is empty).
The third pop-up menu lets you choose to search for
words beginning with…
whole words
characters
You can further restrict your search to references that are or that are not a particular
Type, color label, or rating.
You can specify up to ten items you want to search for. Individual search items are
entered in separate fields. The pop-up menus between lines let you specify boolean
“AND”, “OR”, and “NOT” searches (see below).
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•
Shortcut: if the Shift key is held down while a boolean option (AND, OR, or
NOT) is selected from one of the pop-up menus, all of the pop-up menus will be
set to the same boolean search option.
•
To delete search items that have already been entered, click on the Clear Search
Items button.
Spotlight
If a word or phrase is entered in the Spotlight field, Bookends will search pdfs and text
files in the Bookends attachments folder (or subfolder) that are attached to references in
the database. The results of this search are combined with any other criteria in the Find
dialog (for example, references written in 2006 by Jurgenson and whose pdf attachment
has the words "Bach cantata").
How a search is done
The Find function allows you to perform up to 10 independent boolean AND, OR, and
NOT searches to be done at once. Bookends lets you search for words that begin with
certain characters, whole words, or a string of characters anywhere in the word.
Important: The “words beginning with…” and “whole words” searches use an internal
index, and therefore are extremely fast. However, these searches ignore punctuation. If
you need to find words containing punctuation symbols, use the “characters” search.
A words beginning with search for
Search Word
cat
blue paint
blue paint
Smith, AB
Smith,
Matches
cat and catsup
blue paint
paint blue
Smith, AB
Smith, Allan
Doesn’t Match
meercat
blue (or paint)
blue (or paint)
Smith
Arrowsmith
Matches
cat
blue/paint
Smith, AB
Smith, Allan
Smith, AB
Doesn’t Match
catsup
blue (or paint)
Smith
Asmith
Smithson
A whole words search for
Search Word
cat
blue paint
Smith, AB
Smith,
Smith
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A characters search for
Search Word
cat
blue paint
Smith, AB
Smith,
Matches
meercat
blue paint
Smith, AB
Smith, Allan
Doesn’t Match
dog
blue/paint
Smith
Smith; AB
•
Searches are not case sensitive.
•
Most searches ignore diacritics. For example, searching for "Schütz" will find
both "Schütz" and "Schutz". The exception is a Find search by character, in which
case searching for "ü" will not find "u".
Put matching references in the Hits List
Replaces the Hits List with the new hits and brings the List View window to the front. If
you want to save the Hits List prior to a new search, you can do so by making it a static
group (List View window, see below).
When unchecked, the first reference that matches the search criteria that follows the
current reference will be shown, without bringing up the List View window.
You can use the pop-up menu beneath this option to have the new hits replace the current
hits or be appended to the current hits. The pop-up menu will not offer the second choice
if there are no hits when you perform the Find.
Special Searches (for Returns, empty fields, or non-empty fields)
•
Use the ¬ character (Option-L) to find the Return character (ASCII 13). This will
work only with a character search!
•
To search for references with empty fields, leave all fields in the Find dialog
blank.
•
To search for references in which a field is (or All fields are) not empty, enter just
an asterisk (*) in the first field of the Find dialog.
Find Again
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Finds the word or phrase used in the last Find operation. If no previous Find was
performed, selecting Find Again will bring up the Find dialog box. Find Again will go to
the next matching reference in the database without showing the List View window.
Find in This Reference…
Will find and highlight a word or phrase in the current reference (or the first selected
reference, if the List View window is in front). The search begins from the current
insertion point in the reference. If no match is found, you will hear a beep. This search is
equivalent to the characters search (see Find), and will find the matching characters
anywhere in a word. For example, a character search for "ion" will find and highlight
these three letters in
"ion"
"cation"
"cationic"
This function is useful if you have done a Find and want to see the location of the
word(s) you searched for in the resulting hits.
•
Enter the ¬ character (Option-L) to find the Return character.
Find in This Reference Again…
Use this option to do repetitive finds within a reference without bringing up the dialog
box. Words or characters entered into the Find dialog will automatically appear in the
Find in This Reference dialog box.
SQL/Regex Search…
•
For complete documentation of Regex as used in Bookends, visit:
http://icu.sourceforge.net/userguide/regexp.html
The syntax of SQL and Regex searches may change as the database engine
evolves. If that occurs, saved searches may have to be updated to reflect the new
syntax.
Note: Using direct SQL and Regex searching is an option for power users. These
searches are extremely flexible, but they are also very finicky (a misplaced comma,
apostrophe, or parenthesis can give erroneous results). Therefore, before you use this
feature please read the documentation below.
SQL (Structure Query Language) lets you manipulate conforming databases, such as
Bookends, in a near English-like syntax. These searches do not use the database indexes
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(with one exception, noted below) and therefore the time required for a search increases
linearly with the size of the database. Nonetheless, for most purposes search speed is
more than adequate.
You enter the query in this window:
The Searches pop-up menu lets you save and instantly retrieve SQL/Regex searches you
have defined.
The Fields pop-up menu will insert the name of fields you can search (listed below). This
is for your convenience only — you can simply type in the field names if you wish.
•
The names of the fields shown in the Fields pop-up are the internal ones used by
Bookends. Do not use any names you may have assigned in Preferences: they will
not be recognized.
To begin the search, click on the Search button or hit the Enter key (not Return).
Searching
A SQL query always begins with the words
"SELECT * FROM references WHERE…"
(the * is an SQL metacharacter that means that Bookends should return all the
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information associated with that reference).
Bookends automatically provides the "SELECT * FROM references WHERE…" when
you do a search, so you should not type this in yourself or the search will fail!
You must provide the search criteria, in the form:
fields to search
comparator
'characters to search for'
Note that you cannot do an SQL search in indexed fields with phrases that contain work
break characters (e.g. space, comma, semicolon, etc.). Only characters one would find in
a word are allowed (because you are searching an index, and the index only contains
word characters).
To search an indexed field for multiple words, you must search for each one and connect
the searches with AND: authors='John' AND authors='Doe'
REGEX searches can include non-word characters: authors REGEX 'John Doe'
•
An empty field does is considered NULL, and has no length value. If you want
to search for records without a title, 'WHERE length(title)=0' will not work. But
'WHERE title IS NULL' will.
Fields to search
Individual indexed text fields:
You can search any field, combinations of fields, as well as some reference-specific
information associated with a Bookends reference. The names of the fields are fixed and
must be entered as follows (case is irrelevant):
authors
title
editors
journal
volume
pages
thedate (note: date is a reserved word and cannot be used)
publisher
location (address or city)
url
title2
abstract
keywords
notes
user1
user2
user3
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user4
user5
user6
user7
user8
user9
user10
user11
user12
user13
user14
user15
user16
user17
user18
•
Use these field names even if you have changed the way they are labeled in your
database.
Example:
authors = 'Frantino '
•
These fields contain alphanumeric values, so you cannot use > or < as
comparators (see below).
allFields (indexed) pseudo field:
The name of this “field” is fixed and must be entered as follows (case is irrelevant):
allFields
allFields is "pseudo field", meaning when you search it you are searching all of the text
fields in a reference. In addition, allFields is indexed, meaning that the searches are very
fast. An example that will find a record with 'Waterloo' in the title, abstract, or elsewhere:
allFields = 'Waterloo'
Numeric (integer) fields:
The names of the fields are fixed and must be entered as follows (case is irrelevant):
id
hit
type
uniqueID
rating
Example:
(relative reference number: 1, 2, 3, etc.)
(Hit number. If the reference is not a Hit, this value will be 0)
(position in the Type pop-up menu, starting at 0)
(unique ID of the reference)
(an integer from 0 to 5)
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hit > 0
type = 9 (this would find references of Type ‘Journal article’)
rating >= 3 (finds references assigned three or more stars)
Comparators
The following can be used to compare the values of two fields (the meaning is in
parentheses):
SQL:
=
IS
<>
IS NOT
>
<
(equal)
(equal)
(not equal)
(not equal)
(greater than)
(less than)
REGEX
(is contained in)
Regex:
=, <>, >, <, IS, IS NOT
SQL searches using =, <>, >, and <, are always case insensitive. They are also indexed
searches, so that only one word can be searched for in a set of apostrophes. Therefore,
title = 'Days of Glory'
will not find a reference with the title
"Days of Glory"
The proper indexed SQL search would be
title = 'days' AND title = 'of' AND title = 'glory'
Of course, this search would find a reference where the title field was
"Glory of Days"
If you want to find an exact string, including spaces, you must do a REGEX search.
REGEX:
REGEX is used to indicate a Regex search. These can be case sensitive or insensitive,
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match any words or letters in a field, and use Regex pattern matching. Because of this
flexibility, most searches you perform will probably be ‘REGEX' searches.
REGEX searches are case sensitive by default.
Example:
title REGEX 'days of glory'
will not match
"Days of Glory"
but
title REGEX '(?i)days of glory'
will.
“allFields” is a special case. This search is indexed, so any (capitalized or not) word can
be matched with =.
Example:
SELECT * FROM references WHERE allFields = 'MEMBRANE'
will find any reference in which any field has the word “membrane”, regardless of case.
This can also be accomplished with the REGEX comparator
SELECT * FROM references WHERE allFields REGEX '(?i)membrane'
• Tip: You cannot use 'NOT REGEX as a comparator. To negate the REGEX
comparison, use the NOT boolean operator like this:
NOT title REGEX 'motion'
Characters to search for
Words or characters being searched for must be surrounded by apostrophes (single quote
marks): 'characters' not "characters"
Boolean searches
You can create complex Boolean searches by using logical parentheses. Reserved
boolean operators are:
AND
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OR
NOT
Example:
((authors REGEX 'Henson, J') AND NOT (title REGEX '(?i)equator')) OR (abstract
REGEX '(?i)mercator')
Regex pattern matching
Queries using the REGEX comparator can contain regular expression metacharacters and
perform complex pattern matching.
Below is a subset of the Regex capabilities of Bookends that you may find useful.
Metacharacters:
\B
\A
\Z
matches a word boundary (transitions between word (\w) and non-word (\W)
characters).
matches the string within a word (any position that's not word boundary).
matches the beginning of the target string.
matches the end of the target string.
^
$
matches at the beginning of a line.
matches at the end of a line.
\b
\w Matches a word character.
\W matches a non-word character.
\r
\n
\t
carriage return (ASCII 13)
line feed (ASCII 10)
tab (ASCII 9)
Character classes ([...])
A character class, also known as a "list" or "bracket expression", is a list of one or more
items. The list is defined by the items included between the square brackets, "[...]". For
example,
[abc] matches "a" or "b" or "c".
The dash indicates a range of characters. A range is formed by placing a dash between
two characters. The range represented falls between the beginning and ending elements in
the ASCII sequence.
Examples
1. '[a-z]' is equivalent to "[abcdefghijklmnopqrstuvwxyz]"
2. '[0-9]' is the same as "[0123456789]"
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Shortcuts:
\d = Digit (Match any digit. It is equivalent to '[0-9]')
\D = Non-digit (Match any character that is not a digit. It is equivalent to '[^0-9]')
Alternation:
A regular expression can contain a list of subexpressions, anyone of which might match
the target. The list of subexpressions is delimited by "|"
Example:
'one|two|three' will match "one" or "two" or "three".
Since regular expressions are greedy (i.e., they match the longest possible first match),
the alternation metacharacter operates on the largest possible surrounding regular
expression.
Example:
'this and|or that' will match "this and" or "or that".
To limit alternation, grouping brackets can be used.
Example:
'this (and|or) that' will match "this and that" or "this or that".
Searching for words that include punctuation
Because REGEX searches use punctuation to indicate special pattern matching features,
you cannot search for words containing punctuation marks directly. You must "escape"
them by preceding them with the backslash (\) symbol. For example,
title REGEX '\$12'
will find a reference in which the Title contains
...$12...
and
abstract REGEX 'comprised of \[sic\]'
will find a reference in which the Abstract contains
...comprised of [sic]...
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Sorting the result
The results of a search can be sorted by using the words ORDER BY followed by the
field(s) to sort and, optionally, the direction of the sort. Note that because the fields are
indexed, to generate a correct sort the name of the field must be followed by the
characters 'SortMethod', or it will not work properly. These would be proper ways to
indicate a field to ORDER BY:
authorsSortMethod
thedateSortMethod
titleSortMethod
The default order for sorting is ascending (A -> Z) — you can specify a descending sort
(Z -> A) with the word DESC. For example
authors REGEX ‘Smythe, R’ ORDER BY thedateSortMethod, titleSortMethod DESC
•
Note that you can sort on fields you didn’t search in.
Example queries and their results:
Query
•
Finds references where…
Remember, “WHERE” is automatically added by Bookends.
hit > 0
the reference is in the Hits List
uniqueID > 10000
the unique ID is greater than 10,000
authors is NULL
there is no author
authors is not NULL
there is an author
length(thedate) IS NULL
There is no date
length(thedate) > 0
There is a date
authors is not NULL AND editors is not NULL
there is an author(s) and an editor(s)
title = 'My Life as a Dog'
the Title is "My Life as a Dog" (case
insensitive)
left(title, 2) = 'My'
Title starts with "My Life" (case
insensitive)
title REGEX 'Life'
Title contains the letters "Life" (case
sensitive)
title REGEX '(?i)Life'
Title contains the letters "Life" (case
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insensitive)
title REGEX '\b(?i)life'
Title contains a word beginning with
"life" (case insensitive)
authors REGEX '\bSmith\b'
Authors contains the whole word
"Smith" (case sensitive)
authors REGEX '\Bsmith\b'
Authors contains a word "smith", but
is NOT the whole word "smith"
sensitive)
(case
authors REGEX 'Smith, RA\Z'
"Smith, RA" is the last (or only)
author (case sensitive)
authors REGEX 'Henry, KB\rGeorge, D'
the authors are Henry, KB and
George, D, in that order, on two lines
(case sensitive)
abstract REGEX '\AMedicine'
Abstract begins with the word
"Medicine" (case sensitive)
abstract REGEX '(?i)medicine\Z'
Abstract ends with the word
"medicine" (case insensitive)
abstract REGEX '\AMedicine\Z'
Abstract contains the whole word
"Medicine" (case sensitive)
notes REGEX '(?i)defen[sc]e'
Notes contain the characters
"defense" or "defence" (case
insensitive)
notes REGEX 'A[0-9]'
Notes contains the characters 'A#'
(where # = a number) (case
sensitive)
notes REGEX '(primary|secondary) example'
Notes contains the letters "primary
example" or "secondary
example" (case sensitive)
id > (select max(id) - 15 from thereferences)
the 15 most recently entered
references
Global Change
Warning: Global Change operations are NOT undo-able!
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This is a hierarchical menu with five choices:
•
All global change operations can be performed on the selected references (if the List
View is in front), the references in the Hits List, or all the references in the database.
You can select which via a pop-up menu in each of the dialog boxes corresponding to
the particular change operation being performed (see below).
Find and Replace…
The search will match if the characters appear anywhere in the word. For example, “ion”
would match with its counterparts in “ionophore” and “information”.
Use the pop-up menus at the top of the dialog box to choose between searching for
characters in a particular field or in any field, and for choosing to search the entire
database or just the references in the Hits List (if the Hits List is empty, that option will
not be available).
•
The Find is case insensitive. Replace inserts the text just as you typed it, including
case.
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•
Enter the ¬ character (Option-L) to match the Return character.
The Style pop-up menu that let's you specify the style of the replacing text:
As found will leave the text in the style of the original.
The Font pop-up menu is used to specify the font of the replacing text.
Use target case will cause Bookends to convert the text to match the case of the text it
replaces. This conversion will occur if the target word is in normal capital form (e.g.
“Paris”), all caps, or all lowercase. Words in other forms of mixed case will be replaced
with the text as it appears in the replace text box.
Change Field…
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Any word(s), spaces, and punctuation marks entered in the text field will be placed
before, after, or into the specified field in each reference that is in either the Hits List or
in the entire database, depending on the options that are selected. Placing words into a
category will replace any text that may exist in that field.
Words placed in any field will be added immediately after the existing text. If you want
them to be on a separate line, precede them with the return character, ¬ (Option-L). If the
field you are adding the text to is empty, the initial return character will be suppressed.
o To delete an entire field, don’t enter any text in the dialog box and then choose to
put the (empty) text into the field to be deleted.
•
Enter the ¬ character (Option-L) to insert a return character.
Change Reference Type…
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You can change the reference Type (journal article, book, edited book, etc.) for the
references in the Hits List or in the entire database.
Change Case…
Change the case of any field in the database or just the Hits to Sentence case, Title Case,
UPPERCASE, or lowercase. For Sentence case and Title Case, Bookends will convert
any words in the list of words whose case should not be changed (Preferences, Scan &
Bibliography tab) to the case specified. This process is not undo-able. Command-. to halt
the operation.
Move Field…
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This option works just like Change Field, except you are moving the contents of one field
into (or before or after) the contents of another. If Empty source field is checked ON, the
contents of the field you are moving text from will be emptied after the move is done.
Restore Default Font & Style…
Removes any changes you may have made to the default reference font alone, or to the
font and text styles (font size, font face [italics, bold, etc.]) and sets these to the default
settings. This can be applied to all references in the database or just those in the Hits List.
Standardize Names…
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Bookends will search the Authors/Editors fields or any user-defined field (in all
references or just those in the Hits List) for names in surname-last form (that is, without
commas, such as John Doe) and change them to surname-first form (e.g. Doe, John).
Note that changed fields will revert to the default reference font and plain text style, and
that compound surnames will have to be fixed after conversion (e.g. Ralph Vaughan
Williams will be converted to Williams, Ralph Vaughan).
You can restrict this to a particular reference Type so that if, for example, you want to
standardize name if the Translator field for Books it will no affect on data in the User3
field in Journal articles.
Peek
You can copy information from a field in a previously entered reference to a reference
you are entering. When Peek is selected, this dialog box appears:
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The field that is shown by default is the active field in the reference just before the
current reference. If no field is active, the Keywords field will be shown. In the example
above, the user was entering data in reference 12 (the “base” reference), and the category
being peeked at is the Authors from reference 8.
You can change the field being peeked at with the pop-up menu. You can change the
reference you are peeking at with the arrowheads. You can also go to a particular
reference by typing its number into the text box and pressing the Tab key or clicking
anywhere in the box in which the field’s items are listed.
To copy information from another reference into the current reference, select the line(s)
of text and click Insert. The selected lines will be appended to the corresponding field in
the base reference. As usual, multiple lines can be selected by holding down the Shift or
the Command key when clicking.
The Peek window will stay open until dismissed with the Done button.
You can also bring up the Peek dialog box by:
1. Selecting Peek from the Refs menu.
2. Holding down the Shift key and clicking on the name of the field you want to peek at.
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3. Clicking on the Peek button in the palette.
Quick Peek
If you want to quickly copy the contents of a field from one reference to another, place
the insertion point where you want it and press Command-' (apostrophe). This will copy
the entire contents of that field from the preceding reference.
Generate BibTeX key
Creates a key (id) for BibTeX entries and puts it in the Key field (normally User1). The
key consists of the last name of the first author followed by the year of publication. For
example:
Anfinson2002
If there are no authors, the last name of the first editor is used. Any spaces, commas, and
apostrophes are removed.
BibTeX keys created by Bookends will be encoded as ASCII. If the author's name has
accented characters, Bookends will try to convert them to their non-accented counterparts
(e.g. é becomes e). If no conversion can be made, the character will be replaced by a
question mark (?).
If the reference window is in front, a key will be generated only for the reference being
edited. When the List View is in front, applying this command will generate a key (if
there is none already) for the selected references.
If selected in Preferences, Bookends will check to make sure the key is unique, and if not
will either warn you or append a lowercase letter to make it unique.
•
This menu item is only available if BibTeX has been enabled in Preferences.
Insert Date
Inserts the current date at the insertion point. This may be useful if you want to keep track
of when references were manually entered. A similar option is available for imported
references (in the Misc tab of the Import Filter).
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OpenURL Search
OpenURL is a protocol provided by many institutional libraries that allows you to look
up information about a reference, often including the full text of the article. If you have
entered one or more OpenURL server paths and the arguments for searching in
Preferences, Bookends will enable the OpenURL Search menu (and add an OpenURL
Search command to the List View Action pop-up menu and the contextual menu for the
reference list). If invoked, Bookends will send the necessary reference information to the
selected OpenURL server (such as your library) via your browser, which will then
display the results of the search.
Lookup From DOI
If the selected reference has a doi (digital object identifier), this will open your browser
and go to the address pointed to by the doi resolver at http://dx.doi.org/.
PubMed
If the first selected reference (List View) or the reference showing in the Reference
Window has a number in the PMID field or has a link to the PubMed entry for the article
in the URL field, this hierarchical menu is enabled:
You can use it in conjunction with your browser to access the full text of the article (this
may require a subscription to the journal for you or your library), the PubMed LinkOut
feature, or search for related articles on PubMed. You can also copy the PMID to the
clipboard without opening the reference itself.
Update From PubMed will fetch the reference again. If the information in any field you
are importing differs from that currently entered, the newer information will replace the
old. Fields that aren't identified in the PubMed import filter will be untouched. This is
useful if you import pre-publication reference information from PubMed and want to
update the record once the paper is published. It also means that if you enter just the
PMID, Bookends can download the entire reference for you.
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A similar feature is available in the List View's Action pop-up menu and via a contextual
menu (right-click) in the reference list.
Get PDF
This hierarchical menu offers two ways to find and attach pdfs to the selected references:
From PubMed (If Available)
Bookends will attempt to find and download the pdf(s) for the selected article(s) from
PubMed. To be successful, you must have access privileges (e.g. the article must be
freely available or you or your institution has a subscription to the journal).
Articles downloaded and attached this way will automatically be filed in your default
attachments folder. The name will be the author name, year, and PubMed ID (e.g.
Johnson et al 2006 33434245.pdf).
Note: It is not possible to retrieve articles from some publishers even if you have access
privileges, and the retrieval process will simply end without a pdf being downloaded. If
this occurs, you can download the pdf via your browser and attach it manually.
Find & Attach Local PDF
Bookends will perform a Spotlight search and try to find pdfs that match the reference
entry. If more than one pdf is found to be a likely match, a list of possibilities will be
presented and you can select one to attach or stop the process.
Attachments found in this way are copied to the default attachments folder; the original is
left where it was found.
Note: The local search may fail even when there is a matching pdf if Spotlight has not
indexed it properly. By the same token, an incorrect match might occur if the information
in the reference matches indexed text of another article (for example, if the reference only
contains an author's name and that name appears in an unrelated pdf). Therefore, if a
local pdf is found and attached it is prudent to confirm it is correct with the Attachment
Inspector.
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Upload To Refbase…
Once you have applied for and received a user name and password and entered them in
Preferences, the Refs -> Upload To Refbase menu will become enabled, and you will be
able to automatically upload references to your Refbase server. Furthermore, you will be
automatically logged in when you use File -> Go To URL to go to your Refbase server
with your browser.
o You can read more about Refbase and what it does in the section in this User
Guide called Refbase.
First, Prev, Next, Last
Navigates through the database. You can also click on the arrowheads at the top of the
Reference window, and go to the first or last reference by holding down the Shift key
while clicking on the Down or Up arrowheads, respectively.
Go to Reference #…
Displays a dialog box asking for the number of the reference you want to view.
•
Quick Navigation shortcut: Control-click or right-click on a reference window in
any "empty space" (i.e., not in a field or control). A small pop-up window with a
slider allows you to quickly navigate through the database. The window will
disappear when the cursor leaves it or a key is pressed.
Hits Menu
This menu deals exclusively with the references in the Hits List.
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Sort Hits List…
Alphabetizes the Hits List. You are presented with the dialog:
If you don’t want a multiple sort, select None for the secondary and tertiary sort choices.
•
Sorting the Hits does not rearrange the references in the database. It simply sorts
the Hits List. If you want your references to be permanently arranged in
alphabetical order, use Sort All References in the Refs menu.
•
You can sort the Hits List by Type (article, book, etc.). Note that the reference
Type is stored internally as an integer, so if you have edited or added reference
Types they may not sort alphabetically. However, sorted Types will always be
grouped together.
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Clear Hits List
Empties the Hits List without affecting any references in the database.
First, Prev, Next, Last
Navigates through the Hits List. You can also do this by clicking on the arrowheads in
the Hits area, and go to the first or last Hit by holding down the Shift key while clicking
on the Down or Up arrowheads, respectively.
Go to Hit #…
Displays a dialog box asking for the number of the Hit you want to view. The number is
its order in the Hits List, not its order in the database.
•
You can also bring up this dialog box by holding down the Shift key and clicking
on the button displaying the number of the current Hit in the reference window.
Window Menu
This menu displays the names of all open reference database windows or of all open
windows regardless of their kind (set in Preferences). You can switch from one window
to another by selecting its name.
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Show Attachment Inspector
The Attachment Inspector is a floating window that allows you to view and manage
attachments for your database. The Attachment Inspector can be opened from this menu,
the List View Action pop-up menu, right-clicking on the references in the List View, and
the Attach pop-up menu in the reference window. The Attachment Inspector will remain
open until you close it (Option-Command-A is a toggle that will open/close it) or the
associated database is closed.
The Attachment Inspector looks like this:
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The controls along the top will perform the following operations:
+
add an attachment
–
detach the selected attached files
The Action pop-up menu offers the following operations on the selected attachments:
Note: the image can be dragged and dropped. If you drop it in the Finder, a copy of the
attached file will be placed there. If you drop it on an e-mail message, it will be attached
to that e-mail. If you drop it on an open word processor document, the image will be
inserted.
You can collapse/expand the Attachment Inspector by clicking on its disclosure triangle.
Bibliography Window
If you create a bibliography from within Bookends (that is, without Scan a Document, but
using the Bibliography Formatter), it can be viewed in this window and, if desired,
copied to the clipboard. Text pasted into Microsoft Word, Mellel, Pages, or Nisus Writer
Express retains its formatting.
•
When the bibliography field is copied, the escape super- and subscript characters
are removed and the appropriate super- or subscript styles for your word
processor are inserted.
•
To print the bibliography, select the Print Bibliography menu item in the Files
menu. Super- and subscripting are not printed correctly from within Bookends. To
print them properly, copy the bibliography to the clipboard, paste it into your
word processor, and print it from there.
The bibliography window doesn’t change until you make another bibliography, or you
delete or edit the field manually. You can return at any time to the most recent
bibliography you created.
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Minimize Reference Window
This command moves the frontmost reference window (the one checked in the Window
menu) to the dock. This is especially useful if you want to hide the reference window and
use the List View window as the primary means of accessing information in a database.
To bring a reference window back into view, in the List View window double-click on a
reference or click the Show Reference button, in the Term List window double-click on a
reference, select its name in the Window menu, or simply click on the reference window's
icon in the dock.
Extras Menu
Journal Glossary
The Journal Glossary provides a rapid means of entering journal names and customizing
bibliographies. Glossaries are kept in a special folder called Journal Glossaries, which
must be in the same folder as Bookends itself. Any Journal Glossaries you create are
stored in Custom Journal Glossaries, which can be found in ~/Library/Application
Support/Bookends/.
The Journal Glossary menu contains a list of the glossaries in the Journal Glossaries and
Custom Journal Glossaries folders:
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Select the name of the glossary to make it active.
To create your own glossary, chose New. After giving the glossary a name, you will see:
Journal glossaries distributed by Sonny Software are in the Journal Glossaries folder.
Formats that you create with the New button will be placed in Custom Journal Glossaries
folder. This means that when you upgrade to a new version of Bookends, you cannot
mistakenly overwrite any glossaries you created by replacing the old Bookends Folder.
•
If you simply edit an existing journal glossary, it will remain in its original
folder. You can manually move such a glossary to the Custom Journal
Glossaries folder, which ensures that you will not overwrite it or forget to
transfer it when upgrading.
•
It is possible to have two glossaries of the same name, one in the Journal
Glossaries and one in the Custom Journal Glossaries folder. This is not
recommended. However, if this occurs, Bookends will always use the version
in the Custom Journal Glossaries folder.
A Journal Glossary entry contains 3 items: your abbreviation for the journal, the
journal’s short name, and the journal’s full name.
The buttons at the bottom of the dialog let you:
1. Add—Add a new journal entry.
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You can enter your own abbreviation for the journal in the Abbreviation field, the
accepted short name in the next field, and the full journal name in the last field. For
example
Abbrev.
Short Name
Full Name
ji
J. Immunol.
Journal of Immunology
pnas
Proc. Natl. Acad. Sci. USA
Proceedings of the National Academy of
Sciences USA
nyt
New York Times
2. Edit —Edit an existing entry.
Brings up the Journal Glossary Entry dialog box filled out with the current item.
3. Delete—Remove the currently selected journal entry.
Using the Journal Glossary
The Journal Glossary has several distinct functions:
Entering journal names into references
To use the Journal Glossary while entering a reference, enter the abbreviated journal
name (e.g., “ji”, without the quotes) in the Journal category. When you “leave” the
Journal field (by pressing Tab or clicking outside of the field), Bookends replaces the
abbreviation with either the short or the full journal name. You specify which you want
substituted in Preferences:
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Selecting journal names in a bibliography
The Journal Glossary allows you to automatically generate bibliographies that contain
either the short or the long form of the journal name. In the Order field of each Format,
the letter "j" tells Bookends to use the short form and the letter "f" the full form of the
journal name. When Bookends is making a bibliography and encounters a "j" or an "f" in
the Format, it fetches the journal name from the reference and looks to see if it is entered
in the Journal Glossary. If so, Bookends selects either the short (if a "j") or the full (if an
"f") form to put in the bibliography. If the journal name isn’t in the Journal Glossary,
Bookends uses the name as it was entered in the reference.
•
The form of the journal name entered in the reference itself (short or full) doesn’t
matter when a bibliography is being created. If the journal name is in the Journal
Glossary, Bookends finds it regardless of whether it is the short or the full form.
Adding periods to journal names in a bibliography
If a journal name in a reference lacks periods (e.g. J Biol Chem, the style used in Medline
databases) but the Journal Glossary version has periods (e.g. J. Biol. Chem.), periods will
be added when the bibliography is generated.
•
Even if the Journal Glossary short journal forms are entered with periods, you
always have the option of selecting the Remove Journal “.”s in the actual Format
if periods are not desired.
Using the Journal Glossary to enforce upper/lowercase
The case of a journal name in the Journal Glossary overrides the case in an individual
reference. For example, if you imported a reference with the journal name “NATURE”
but it is entered in the Journal Glossary as “Nature”, the latter will be used in the
bibliography.
Pre-defined Journal Glossaries
Sonny Software provides glossary files named Concise Medline (which contains over
750 of the most commonly used Medline abbreviations), Chemistry, Humanities, and
Society Biblical Lit. The short names in the Concise Medline and Chemistry files include
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periods after abbreviations (e.g. J. Biol. Chem.). This means that the periods will be used
in your bibliographies (unless you specify in the format that periods in journal names
should be excluded).
Term Lists
Selecting the Term Lists menu item
displays an alphabetical list of the authors, keywords, editors, or journals in the database.
In addition to these four default lists, you can create a Term List for any field in the
database (see below).
•
•
•
The font and font size used in lists are set in Preferences.
You can drag and drop items from the list into a reference field.
You can navigate the lists with the Page Up, Page Down, Home, and End keys.
Items are added automatically to Term Lists as they are entered into a reference database.
Items are not removed from Term Lists automatically. If you have deleted a Term and
don’t want it to show in the Term List, you must explicitly Update the Term List (see
below).
There are two Term List views:
Collapsed view
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The small disclosure triangle at the top right of this window is pointing down. To see the
expanded view, click on it once (see below).
At the top of the window, a pop-up menu shows the list currently being shown and the
number of unique items in the database. To change from one list to another, simply select
the one you want from the pop-up menu.
Next to each item in the list is the number of times it is used in the database. The list can
be sorted in ascending (arrowhead up) or descending (arrowhead down) fashion by
clicking on the heading of the column you want to sort by (the sort direction toggles).
Typing the first letter(s) of an item will quickly scroll to that item (or the closest in
spelling in the list) and highlight it.
The buttons perform these functions:
Find:
Brings up the Find dialog with the selections already entered. The field to
search is set to the field shown in the Term List.
Insert: Places the selected words at the end of the corresponding field of a reference.
Save:
Saves the list (the first column only) to a text file.
Update: Rebuilds all lists and displays the updated list. Tip: if you press the Delete key
when the Term List window is in front, regardless of whether the view is
collapsed or expanded, Bookends will offer to update the lists.
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Expanded view
The disclosure triangle is pointing to the right. To see the collapsed view, click on it once
(see above).
The scrolling list on the right shows each reference in the database that contains the term
selected on the left. Double-clicking on an item in the list will show that reference—
whether the reference window is brought to the front or not depends upon the setting of
the Bring reference window to front on double-click checkbox in Preferences.
You can select multiple terms (left pane) by holding down the Shift or the Command
key when you click. If more than one term is selected, the references shown in the right
pane will be those in which all the terms appear (AND) or those in which any one of the
terms appear (OR), depending on which option is selected in the Multiple selections popup menu in the lower left corner of the window.
The checkbox that precedes each reference in the right pane is its marked status (i.e. is it
in the Hits List or not). You can add or remove a reference from the Hits List by clicking
on this checkbox. There is a convenient way to add or remove many references to/from
the Hits List at once:
•
if only one reference is selected, click on the checkbox with the Shift key held
down and all the references in the list will assume the state of that reference (if it
was not a Hit, now it and all the references in the list are Hits; if it was originally
a Hit, all the references in the list are not Hits).
•
if you click on a checkbox of one of several selected references with the Shift key
held down, all of the selected references assume the state of the reference whose
checkbox you clicked.
You can find the term or reference you want by typing the first few letters. To change the
focus (indicated by the focus ring) from one list to the other for this purpose:
•
click on the list you want
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•
press the right or left arrow keys
•
press the Tab key
You can change column widths by clicking on a column divider and dragging to the left
or right.
When in the expanded view, you can drag and drop references from the list (right pane)
just as you can references in the List View window. This means they can be used to insert
temporary citations (or formatted citations, if the Option key is held down during the
drag), into word processing documents, copy references between databases, and add
references to a group. You can also drag and drop items from the Term List (left pane).
Adding/Removing a Term List
To create a new Term List, select Add List from the Term Lists menu and select the field
you want to add from the pop-up menu. Bookends will create a Term List and populate it
with the items from that field. To see the new Term List, select it from the Term Lists
menu or from the pop-up menu in the Term List window.
•
Autocomplete works in any field that has a Term List.
•
You cannot make Term Lists with the fields in the reference window drawer.
•
The Return character is used to delimit terms. The maximum number of
characters that Bookends will use per item/line is 128.
To remove a Term List, select Remove List from the Term Lists menu. Highlight the
list(s) you want to remove in the resulting dialog box and click on Remove.
•
You cannot remove the four default lists: Authors, Editors, Journals, and
Keywords.
You can add references from a Term List to a static group two ways:
•
drag and drop the references onto the List View window when a static group is
showing
•
Control- or right-click on the Term List references — you can add the selected
references to a new group or an existing group
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Help Menu
User Guide
If Bookends User Guide (a separate download from the Sonny Software web site) is in
~/Documents, ~/Documents/Bookends, or the same folder as Bookends, it will open in
Adobe Acrobat Reader or Preview. If it is not, a dialog box will appear and offer to
download the User Guide (via your browser). You must then drag the drag the Bookends
User Guide to ~/Documents, ~/Documents/Bookends, or the Bookends folder.
Visit Sonny Software…
Launches your browser and takes you to the Sonny Software home page:
http://www.sonnysoftware.com
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Bookends Server
Introduction
The Web is an Internet-based communications system with a standardized language
known as Hypertext Markup Language (HTML). An HTML document consists of text
and embedded commands that specify how the text (and images that are available in
separate files) should be presented. The applications that make this content available to
the Web are known as servers. Browsers, such as Safari or Microsoft Internet Explorer,
render this information into a human-understandable form and are known as clients. To
ensure reliable communication between servers and clients, a set of rules (or a protocol)
called HTTP (Hypertext Transport Protocol) was created. The most commonly used
HTTP-compliant server on the Mac is Apache. These are flexible applications that make
it possible to host a Web site on one’s computer.
In addition to its other functions, Bookends is an HTTP server that allows Web-based
access to its databases. That means that anyone, on any platform, can access your
Bookends databases and retrieve formatted references and bibliographies in real time
without themselves having a copy of Bookends. Bookends also has the ability to also
serve files, so that, for example, individuals searching your databases over the Web can
retrieve pdf documents or images associated with a reference. Bookends also lets you
return HTML commands. This means that in addition to returned the details of a
reference to the client browser, Bookends can send back a hypertext link to that
reference’s abstract or to a pdf file associated with the reference. Finally, you can allow
users to enter references into a database via their browser.
Bookends server is threaded, meaning that it can handle multiple requests
simultaneously. It is fairly robust, and should be able to easily handle thousands of
requests an hour. It will almost certainly drop some requests, however, if there are many
hundreds per minute.
Many safeguards have been built into Bookends server to protect your data. When
accessing Bookends via the Web:
•
With the exception of adding references to a database (if allowed), it is not
possible to modify files on the server.
•
Users can only use databases and files that are at (or below) the root level of
~/Library/Application Support/Bookends/Server. This means that you must move
all files (including default.html) to this folder or they cannot be accessed by
Bookends Server. Attempts to access the invisible directory file ".DS_Store" will
be denied.
•
A username and password can be required, and access can be allowed or denied
based upon IP address.
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•
Open databases cannot be accessed. This means that you cannot be interrupted by
a Web access while working with a database (but databases that are not open can
be accessed while you are working with another database).
It is beyond the scope of this manual to delve further into the particulars of HTTP servers
and HTML. What follows are the details of the capabilities of Bookends and a
description of the syntax you must use to allow communication between a browser and
Bookends.
•
For a quick start, see the contents of the folder Serve databases in 5 minutes (or
less).
Administrating Bookends Server
Bookends Server functions are administrated from the Server tab in Preferences.
Allow Web access to databases
If checked, Bookends will allow you or others to access your databases via the Web.
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Port
All internet-based communications depend upon an IP address (provided by your ISP or
institution) and a port. Each communications protocol has a standard port number. For
HTTP, typically the server “listens” on port 80. For a variety of reasons, we suggest that
you do not use 80 as the port number. First, this would conflict with other HTTP servers
you might run on your Mac (e.g. Apache, which is also used for personal Web serving).
Second, in OS X only applications running with root permissions can bind to a port of
less than 1024. Therefore, we strongly suggest using a port 1024 or greater. However, the
choice of which port to use is yours to make. The Bookends default port is 2001.
•
If you change the port number while Web access is enabled, the change won't take
effect until you disable/enable Web access or relaunch Bookends.
If the port is not set to 80, the port number must be supplied (along with the IP address)
when accessing Bookends from a browser. E.g.,
http://www.yourdomain.com:2001
or
http://193.232.43.21:2001
Max connections
This is the maximum number of connections that Bookends can handle simultaneously.
You can increase this number, but of course response times will increase as more
requests are handled simultaneously.
The smallest value permitted is 2.
Keep log
When checked, Bookends will maintain a log of each Web access, recording the time, the
IP address of the requester, and the number of bytes returned by Bookends. The log file
("Bookends Server Log") is a tab-delimited text file kept in ~/Library/Application
Support/Bookends/Server. Newer requests are added to the beginning of the file and
older requests are moved down.
The log can be read or cleared with the corresponding buttons (the log can also be opened
in any word processing application or spreadsheet).
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Max log size
As requests are logged, Bookends will make sure that the file does not exceed this limit
by removing the oldest entries. This ensures that the file does not grow to an enormous
size with a great deal of use over time.
HTML encoding
This setting determines the encoding of the text sent to the browser. There are two
options: Unicode (UTF-8) and Western (MacRoman).
UTF-8 (Unicode) allows any characters in any language to be sent to the browser. Use
UTF-8 if your database contains characters not found in Western languages (Japanese,
Greek, etc.). All modern browsers should be able to render UTF-8 characters properly,
but some old browser may fail or the appropriate glyphs may not be available on certain
computers or operating systems.
MacRoman is the standard Macintosh character set for Western languages (English,
French, German, etc.). If your database contains only characters common to these
languages (including accents, umlauts, etc.) and your users only have older browsers that
do not support Unicode, use MacRoman.
Note: the HTML encoding you set here is also used by Bookends when you create a
bibliography as HTML, even when not actively serving on the Web.
IP Address
This is the IP address of your computer, and can be used in the URL field in a browser to
access your computer. If your computer is linked to the Internet via a router it may have a
local IP address (as in the example above: 10.0.1.2). In this case, to allow computers not
on your local network to access your computer you need to use the appropriate
configuration utility to perform port mapping between the inbound port number and the
internal address of Bookends Server. Users can then connect using the IP of the router
followed by a colon and the port number.
•
For AirPort, you would use the AirPort Admin Utility -> Port Mapping tab. The
router IP address can be found in AirPort Admin Utility -> Configure toolbar icon
-> Internet tab.
Authorized access only
You can restrict Web access to your databases in the following ways:
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1. Username/password
If there are entries in this list, Bookends will tell the browser initiating the request to ask
for a username and password. Once submitted, these will be compared with the list you
have entered, and if a match is made the request will be permitted. If there is no match,
the user will received a “request denied” message.
•
Username and password comparisons are case sensitive.
2. Allow IP address
Enter the IP address(es) of those you want to have access to your databases. Access from
any non-listed IP address will be denied. This is a convenient way to allow access to
anyone in a particular school, institution, or organization.
Matching is from left to right, so that
255.230.34.
will allow anyone with an IP address beginning with “255.230.34.”to access your
databases. You can use an asterisk to make this clearer, if you like:
255.230.34.*
3. Deny IP address
Enter the IP address(es) of those you do not want to have access to your databases.
Access from any listed IP address will be denied.
The rules for matching are the same as for allowing IP addresses, above.
If there are entries of all three kinds of permission, Bookends uses the following logic:
1. Any IP address in the deny category is refused, regardless of the other settings.
2. If not in the deny group, any IP address in the allow category is permitted access.
3. If not in the deny or allow group, the user will be asked to provide a
username/password.
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Note: the access protection provided by Bookends is good but not invulnerable. If the
information in your databases is sensitive, you may need security measures in addition to
those provided by Bookends. Or don’t share these databases on the Web, of course.
Use the + and – buttons to add and delete entries, respectively. Double-click on an
existing entry to edit it.
Creating Web pages to access Bookends databases
Users will typically access your databases from Web pages you have designed (and
served by Bookends). In addition to whatever information you want to present, these
pages will contain forms or hypertext links (or both) that tell Bookends what information
to retrieve (and how to format it) or what information can be uploaded to your databases.
The following section will present, in great detail, all you need to know to create Web
pages to use with Bookends. It may appear daunting at first glance, but it is actually
rather simple once a few basic concepts are grasped. You can use the file default.html,
distributed with Bookends in the folder Serve databases in 5 minutes (or less), as a
template that can be modified to quickly create your own Web pages. We estimate that
you can be up and running a simple server for your own databases in 15-30 minutes.
Remember that while HTML and HTTP communication are not difficult to understand,
they are quite exacting. You must strictly adhere to HTML punctuation rules — attention
must be paid to small details, because a misplaced space or punctuation mark can cause
an otherwise valid request to fail.
_________________________________________________________________
Requesting references
There is required and optional information to be included with the user’s request.
If you are asking Bookends to serve a file (html, pdf, etc.), there is only one element
(required): the URL of the file.
If you are asking Bookend to retrieve references from a database, there are nine elements
(two required):
Element
Required:
Representation
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• name of the database to search:
• words or phrases to search for:
DB
Query or SQLQuery
Optional:
• name of the format
• field in which to search, or All
• boolean search options
• maximal number of references to return
• header above the references
• footer after the references
• show the number of hits
• sort the result
• sort direction
• send to file
Format
Field
Bool
HitLimit
Head
Foot
ShowHitNum
SortBy
SortDirection
sendToFile
Below are detailed examples of how to use each element, and how they might appear in a
browser window.
_________________________________________________________________
Name of the database to search
Element: DB (required)
HTML example (pop-up menu):
Choose a database to search:
<SELECT NAME="DB">
<OPTION>Database1
<OPTION>Second database
<OPTION>Third database
</SELECT>
You can allow the user to select the database to be searched (but only one can be
searched at a time!). Because users usually can't be expected to know the names of your
databases, the names would typically be supplied by you in a pop-up menu. If you only
have one database to search, you can include the DB information in a hidden field.
Errors:
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DB was not defined: No Bookends reference database was specified.
Database is open: The database X can't be accessed at the moment because it is in
use on the server.
Database could not be found: Can't find database X.
Database could not be opened: Can't open database X.
_________________________________________________________________
Word or phrase to search for
Element: Query or SQLQuery (required)
Bookends allows two different kinds of searches, a Query and an SQLQuery.
Query
A Query is similar to using the Bookends Find dialog, meaning that Bookends will take
the information and create an SQL query from it. This is the type of search you are likely
to offer users via a form. You can also use one or my Query statements in a hypertext
link that you create in a Web page.
The Query should consists of words or combinations of words (alphanumeric characters).
You can have multiple query fields, connected by boolean operators. Typically, the word
or phrase to search for will be entered by the user in an editable text field (or perhaps
selected from a pop-up menu). You can have multiple Queries per request. All Queries
are case insensitive.
HTML example (editable text field):
Word or phrase to search for: <INPUT SIZE=50 NAME="Query">
SQLQuery
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An SQLQuery is a raw search request, similar to using the SQL/Regex search feature in
Bookends. You are unlikely to offer an SQLQuery to your users unless they are quite
knowledgeable about this feature. It is likely that you will use SQLQueries to create
hypertext links in which, for example, you can have a direct link based upon a reference’s
unique ID number.
There can only be one SQLQuery per request. If a request contains both Query's and an
SQLQuery, the SQLQuery will be performed. SQLQueries can be case sensitive or case
insensitive — it's up to you (or the user) to indicate which (use the REGEX comparator
and (?i) in the query to make an SQLQuery case insensitive).
HTML example (hypertext link):
<A
HREF="http://193.232.43.21:2001/$BEGet?DB=Database1&Format=Chicago&SQLQue
ry=uniqueID=134312">Click on this link</A>
If there are no hits, Bookends returns No matches were found.
Errors:
There were no words to search for: There are no search words!
_________________________________________________________________
Name of the format
Element: Format (optional)
Format the references in the style of:
<SELECT NAME="Format">
<OPTION>Chicago
<OPTION>APA
<OPTION>Medline
</SELECT>
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The user may select the name of the format in which to display the reference information
or you may provide it in a hidden field. If no format is requested, Bookends will use the
format that was last used. You can use a format even if it is not checked in the Format
dialog list in Bookends.
Errors:
The format cannot be found: Can't find format X.
The format cannot be opened: Can't open format definition!
_________________________________________________________________
Name of the field to search
Element: Field (optional)
<p>Find in field:
<SELECT NAME="Field">
<OPTION VALUE = "allFields">All
<OPTION>Authors
<OPTION>Title
<OPTION>Editors
<OPTION>Journal
<OPTION>Volume
<OPTION>Pages
<OPTION>Date
<OPTION>Publisher
<OPTION>Location
<OPTION>Keywords
<OPTION>Abstract
<OPTION>Notes
<OPTION>User1
<OPTION>User2
</SELECT>
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This is the name of the field in which to search for the information. The name of the field
must be the same as in an unmodified Bookends database (that is, even if you have
changed them in Preferences, the field names in the form must be those provided with the
original Bookends). If Field = allFields or All, Bookends will look through all of the
fields for a match.
If Field is undefined, Bookends will perform an “All” search.
_________________________________________________________________
Boolean search options
Element: Bool (optional)
<p>Boolean:
<SELECT NAME="Bool">
<OPTION>AND
<OPTION>OR
<OPTION>NOT
</SELECT>
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The following boolean values are legal: AND, OR, NOT, AND NOT, OR NOT
The Bool element can be useful if you are performing a Query and have more than one
editable text field that can be used. When Bookends builds the SQL search from the
Query from multiple fields, the first field is always used for a simple “is it there” search.
Subsequent fields, however, can be modified by the value of the Bool element. Consider
a case in which there are three fields in the Query and two pop-up menus asking for a
boolean value. If the three fields are filled out as “A”, “B”, and “C” and the two pop-up
menus are set to “AND” and “OR” then the search done by Bookends might be
select references from database X where allFields = ‘A’ AND allFields = ‘B’ OR
allFields = ‘C’
If there are fewer Bool values then there are fields to which they would apply, Bookends
will keep using the last supplied Bool value (so if you want to do only OR searches, you
need to set the Bool element to OR only once, not repeatedly for each field).
_________________________________________________________________
Maximum numbers of hits to return
Element: HitLimit (optional)
Maximum number of references to return:
<SELECT NAME="HitLimit">
<OPTION>1
<OPTION>2
<OPTION>5
<OPTION>10
<OPTION>Unlimited
</SELECT>
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You may want to limit the number of references returned. Bookends will check the value
of HitLimit, and if it is non-zero, will limit the number of references it can return
accordingly. If the number of hits is less than the value of HitLimit, all of the hits will be
returned.
If HitLimit is undefined or is not a number ("Unlimited" in the example above),
Bookends will return all the hits.
_________________________________________________________________
Header above the references
Element: Head (optional)
HTML example (hidden text field, defined by you):
<INPUT TYPE="Hidden" NAME="Head" VALUE=
"<h1>Search Results</h1>">
You can specify the header (title) that will appear above the bibliography returned by
Bookends. In the example above, the header would be “Search Results” (without the
quote marks).
The <h1> and </h1> instructions tell the browser to display the text as the largest header
type.
If Head is undefined, Bookends does not return a header.
_________________________________________________________________
Footer following the references
Element: Foot (optional)
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<INPUT TYPE="Hidden" NAME="Foot" VALUE="<A
HREF=http://yourURL/yourHomePage.html>Return to home page</A>">
You can specify the footer (text or hypertext links) that will appear after the bibliography
returned by Bookends. In the example above, the footer would be a hypertext link that
would display the words “Return to home page” (without the quote marks). Clicking on
this would return the user to your home page (you would, of course, supply the URL and
name of your home page in place of “yourURL” and “yourHomePage.html”).
If Foot is undefined, Bookends does not return a footer.
_________________________________________________________________
Show the number of hits
Element: ShowHitNum (optional)
<INPUT TYPE="Hidden" NAME="ShowHitNum" VALUE="true">
A value of true instructs Bookends to return the number of hits found for display in the
browser. If HitLimit is defined and the number of hits is greater than that value,
Bookends will return both the number of hits returned and the total that were found:
If ShowHitNum is undefined or false, Bookends will not return this information.
_________________________________________________________________
Sort the result
Element: SortBy (optional)
Sort the references by:
<SELECT NAME="SortBy">
<OPTION>Authors
<OPTION>Title
<OPTION>Date
</SELECT>
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You can specify multiple levels of sorting by separating the fields by commas (sorting
hierarchy is from left to right, e.g. "Authors,Date" will cause the references to be sorted
first by author, then by date.
Make sure that the format you use has "alphabetize references" turned off. If it is on, an
author-date sort will supersede any instruction set in the query.
_________________________________________________________________
Sort direction
Element: SortDirection (optional)
Sort direction:
<SELECT NAME="SortDirection">
<OPTION>Ascending
<OPTION>Descending
</SELECT>
This used in conjunction with sorting the results (SortBy). If you choose to sort the
results and SortDirection is unspecified, an ascending sort (A to Z) will be done.
Specifying a descending sort is especially useful if you are sorting by Date and want the
most recently published references returned first.
_________________________________________________________________
Send to file
Element: sendToFile (optional)
<label for="SendToFile">Send results to:</label>
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<select name="SendToFile">
<option>Screen</option>
<option value="RIS Download">Text File</option>
</select>
When this element specifies a file name, the results will be downloaded to a text file.
Bookends will automatically append .txt to the file name. This may be useful for
returning references in a tagged plain text form, like RIS or EndNote Refer, that others
may import into their reference manager.
_________________________________________________________________
Requesting files/information from Bookends
•
If you tell a browser access the URL of the Bookends server, Bookends will send
back the page named "default.html". Therefore, you should alter the
"default.html" page distributed with Bookends to suit your own purposes.
•
Tip: in the examples given below, when testing on a single computer you can use
“localhost” instead of an IP address:
http:// localhost:2001/…
A. Requesting a file
To request a file, send Bookends the URL of the file you want returned.
Example:
http://175.34.232.1/the file name.html
Bookends will correctly send five types of files:
Type
Extension
text
html
pdf
jpeg
.text, .txt
.html., .htm
.pdf
.jpeg, .jpg
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gif
.gif
To make sure these files are handled properly, they should have the corresponding
extension. If the file type is undefined (i.e., there is no extension) Bookends will return
the file, but the browser may not know what to do with it.
•
Bookends does not use the Macintosh file type to determine what kind of file it is
sending.
•
Depending the settings for your Mac, file extensions may be hidden. Even if so,
they are still present, and if the browser requests a file, the file name must include
the extension or you will get a “file not found” error.
•
Bookends will only return files that are in ~/Library/Application
Support/Bookends/Server (or in a subfolder of that folder). This is a security
measure that prevents someone from typing in the name of any file on your hard
drive and retrieving it.
B. Accessing Bookends via an HTML form
An HTML “form” consists of one or more fields a user fills out and then submits to a
Web site. HTML forms can be used to search Bookends databases. A form designed for
use with Bookends should begin with the following HTML code:
<form method=POST action="http:// 175.34.232.1:2001/BEPost">
The word BEPost tells Bookends that this is message is coming from a form (a POST) so
that Bookends knows what to do with the instructions that follow.
HTML Sample Forms
All forms are assumed to begin with the source code:
<form method=POST …
and end with:
</form>
The visible (to the user) elements in a form typically include text and fields, and are
terminated by buttons, such as
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<INPUT TYPE=Submit VALUE="Submit Search">
<INPUT TYPE=Reset VALUE="Start Over">
1) Including the opening and closing source code above, what follows is the simplest
form you can create. It specifies the database to search and asks for the word/phrase to
search for; all other elements are undefined:
<INPUT TYPE="Hidden" NAME="DB" VALUE="Database1"
<INPUT NAME="Query">
2) This is a form in which you define Query, but allow the user to specify the database to
search and the header for the results:
<INPUT TYPE="Hidden" NAME="Query" VALUE="Hoover">
<SELECT NAME="DB">
<OPTION>American Presidents
<OPTION>Appliance Vendors
</SELECT>
<INPUT NAME="Head" VALUE="What I Found">
C. Accessing Bookends via a hypertext link
You can embed a hypertext link to Bookends in your Web page—the link typically
appears as underlined and colored text. When the user clicks on this text a request,
specified by you, will be sent to Bookends. Bookends will attempt to find the requested
references and return them. This is different from the “form” access described above
because the user has no control over the search.
You might use a hypertext link, for example, in the following way:
Here is a list of the works of Sir Francis Bacon.
To create this hypertext link, instead of BEPost (which is used for forms) you use the
instruction BEGet?. You might use the following HTML code (note the use of the
ampersand to separate elements):
<A HREF="http://
175.34.232.1:2001/BEGet?DB=Database1&Query=Francis
Bacon'">Francis Bacon</A>
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Instead of a Query, you could also supply an SQLQuery, in which case you have total
control over the search:
<A HREF=" http:// 175.34.232.1:2001/BEGet? DB=Database1&SQLQuery=authors
LIKE 'Francis' AND authors LIKE 'Bacon'">Francis Bacon</A>
Elements in an BEGet must follow the question mark and be terminated with an
ampersand (&):
<A HREF=" http:// 175.34.232.1:2001/BEGet?DB=Music
History&Format=Turabian&Head=Citations&HitLimit=5&Query=flight of the
bumblebee">the flight of the bumblebee</A.
The user will see
The flight of the bumblebee
Clicking on this hypertext link will retrieve the indicated references from the database
named “Music History” and format them according to the Turabian style. The word
"Citations" will appear above the references, which will be limited to a maximum of 5.
D. Returning a hypertext link to your Bookends databases
One very useful feature is the ability of Bookends to return text that includes a hypertext
link. For example, you can have Bookends send a list of references (a bibliography) to a
user in reply to a search. At the end of each reference you can include a hypertext link
that, when clicked on by the user, sends another message to Bookends to fetch and return
the abstract of that particular reference. Here is an example of how this can be done, with
a detailed breakdown of each element:
Create a format. At the end of the format include the following:
`<A HREF="http:// 283.14.150.9:2001/$BEGet?DB=`!`
&Format=AbstractOnly&SQLQuery=uniqueID=`@`">abstract</A>`
(Note: In place of AbstractOnly you would provide the name of the format you want to
use for this reply—in this example the format Order will just consist of the letter “b”,
indicating that only the Abstract field is to be returned by Bookends).
Here is what the parts of this hypertext link instruction, embedded in a Bookends format,
mean:
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` —The backstroke is the Bookends "force quote" instruction. Bookends will output
any characters between ` characters exactly as you entered them.
<A HREF="$BEGet?—<A HREF is an HTML command that means a hypertext link
is to follow. BEGet tells Bookends to perform an SQL query.
DB=` !`& — The name of the database to search (the ! directive tells Bookends to supply
the name of the database creating the bibliography.
Format=AbstractOnly&—AbstractOnly is the name of the format that Bookends will
use when it fetches the abstract.
SQLQuery=uniqueID=` — Here you assign the actual SQLQuery to be performed (it
follows the first = sign). In this case, the query is 'uniqueID=' followed by the
unique ID.
`@` — After turning off the force quote, @ is a Bookends formatting instruction that
causes the unique ID of the reference to be output.
">abstract</A>` —The word "abstract" will be visible to the user as the hypertext
link. The </A> means "end of hypertext link instruction", and the final `
characters tells Bookends to end the "quote".
Here is how the hypertext link that Bookends returns might actually look when it is
returned to a browser:
<A HREF=" http://
283.14.150.9:2001/$BEGet?DB=Database1&Format=AbstractOnly&SQL
Query=uniqueID=9702">abstract</A>
Here is what will happen when the user retrieves a reference produced with this format:
The reference information you have specified in your format will be followed by the
underlined word abstract. Clicking on abstract will cause the browser to contact
Bookends again. In the example above, Bookends will fetch the reference with the unique
ID of 9702 and arrange the information as defined in the AbstractOnly format (in this
case, just the Abstract field will be output). This information (the Abstract) will be
returned to the browser.
E. Returning a hypertext link to another URL from Bookends
You can have Bookends return the URL of another site as a hypertext link. One example
where this is useful is when the full reference is available on the Internet and you want to
make it available to the user.
286
Here is an example of how you would might return a URL to another site from
Bookends:
1. Enter the full URL of the site you want to link to into the URL field in Bookends.
2. Conclude the format definition you want to use with the following:
$<A HREF="$z$">Full article</A>$
That's it! When Bookends outputs a reference in this format to a browser, it will be
followed by the words Full article. Clicking on Full article will cause the browser to link
to the URL entered in the URL field.
Note that by using the $ sign as the "quote" character (as opposed to the ` "force quote"
character) the user will not see this link if there is no URL entered in the URL field. This
means that you can use the same format for references that are and those that are not
available on the Internet.
F. Returning a Hypertext Link to your own Web pages
Bookends can return a hypertext link to your own Web pages (served by Bookends) by
placing the URL after the Head or Foot element. For example, if you put this in your
Web page (note that there is a space after the initial <A ):
<A
HREF="http://localhost:2001/$BEGet?DB=Database1&Query=Henry&Que
ry=Jones&Foot=<A
HREF=http://www.mylocation.com:2001/default.html>Return to home
page</A>">Jones, 1996</A>
your Web page will display a hypertext link Jones, 1996. When the user clicks on this,
Bookends will return the reference followed by a hypertext link to your home page (you
would, of course, supply your own URL in place of “www.mylocation.com” and the port
you are using (if you have changed it from the default of 2001).
•
The same strategy can be used to create a hypertext link to an ftp-able file. In this
case, replace the words "http://" in the format with "ftp://".
G. Returning a hypertext link to a pdf file attached to a database
287
You can have Bookends automatically generate a hypertext link to a pdf file (or any other
kind of file, for that matter) attached to a reference. If you have a single attachment, you
might create a format that concludes with this:
$<A HREF=" http://localhost:2001/$h$">download pdf</A>$
(the letter h is the code for the attachment field).
When the user clicks on the link download pdf, Bookends will send the pdf file.
Complete Example: Communication between a browser and Bookends
Here is a complete example of how you might have a browser and Bookends
communicate with one another. In this case the browser requests a list of references by a
particular author. After each reference, Bookends returns a hypertext link to the abstract
and, if one is indicated in the reference, a hypertext link to a pdf file. At the end of the
bibliography, Bookends returns a hypertext link to the home page, Return to home page.
The user can see a reference's abstract by clicking on the abstract hypertext link, which
will again be followed by a hypertext link offering to return to the home page. The URL
and port for Bookends server is assumed to be
232.21.134.1:2001
Step 1.
Somewhere in your Web home page is the following HTML instruction (note that
there is a space after the initial <A ):
<A HREF="http:// 232.21.134.1:2001/$BEGet?Head=<h1>Recent
Publications</h1>&Foot=<A HREF=default.html>Return to home
page</A>&Format=Chicago2&DB=Current Literature&Query=Hildegard,
RM">Recent publications</A>
Meaning:
<A HREF="http:// 232.21.134.1:2001/$BEGet?—A hypertext link to Bookends.
Head=<h1>Recent Publications</h1>&—The header that
Bookends will return, in this case the bolded words Recent Publications.
Foot=<A HREF=home.html>Return to home page</A> —The footer that
Bookends will return after the bibliography. It is, itself, a hypertext link!
288
Format=Chicago2&—Tells Bookends to arrange the hits in the Chicago2 format.
DB=Current Literature&—The name of the database to search is “Current
Literature” (Note that the database must be closed to be available.)
Hildegard, RM"—The name of the author whose references Bookends will
display, followed by a close quote.
>Recent publications</A>—The hypertext link the user sees on your Web
page: Recent publications
Step 2.
This is the Order field for the Chicago2 format for the Journal Article Type in
Bookends (based on Chicago).
a. "t." f v (d): p-.
`<A HREF="http://10.0.1.3:2001/$BEGet?DB=`!`&Format=AbstractFormat
&SQLQuery=uniqueID=`@`">abstract</A>` $<A HREF="$h$">pdf file</A>$
Each reference returned by Bookends in the Chicago2 format will be followed by a
hypertext link to itself, with instructions to use the "AbstractFormat" format if
clicked upon.
Viewed with a browser, a retrieved reference might look like this:
Meaning:
a. "t." f v (d):p-.—The standard Bookends instructions that orders the reference
information: the Chicago format.
289
`$<A HREF="http://10.0.1.3:2001/—It is at this point that we see the hypertext
link that Bookends will return to the browser. The initial ` is the "force quote"
symbol that tells Bookends to output the following characters as is. The hypertext
line begins with <A HREF=", which is followed by IP address of your computer
(the server) followed by the port Bookends is bound to.
$BEGet?—Tells Bookends that this is a BEGet procedure for a direct search of a
database (as opposed to BEPost, which is used for forms in which the user types in
the word(s) to search for).
DB=`!`&—Provides "DB=" followed by the name of the database to search. When
the ! is encountered in a format, Bookends outputs the database name. The & marks
the end of this instruction.
Format=AbstractFormat &—Tells Bookends to output the reference information
in the format “AbstractFormat” (defined below).
SQLQuery=uniqueID=`@`—This specifies that the SQLQuery (the direct SQL search
of Bookends, will be "select * from references where uniqueID=" followed by the
unique ID of the corresponding reference (provided by Bookends when it encounters
the @ symbol in the format). The pair of backquotes surrounding the @ (`@`) turns
off, and then back on, the "force quote" feature so that Bookends will output the
unique ID in place of the @ symbol.
">abstract</A>—This is the text ("abstract") that the user will see after each
reference in the bibliography when using the Chicago2 format.
$<A HREF="$h$">pdf file</A>$—A second hypertext link that may or may not
be returned to the browser when this format is used. The h is the instruction
that tells Bookends to output the attachment name. For the purposes of this
example, it is assumed that this field will (or may not) hold a single attached pdf
file.
• Remember, whereas Bookends allows you to attach retrieve files anywhere on
your hard disk (or a server), when accessed over the Web Bookends will only
return files that are in ~/Library/Application Support/Bookends/Server (or
subfolder). This is a security feature.
Be sure to note that one or more spaces separate this instruction from the previous one.
This ensures that if the Keywords field is empty, nothing will follow the hypertext link
to the abstract!
Step 3.
290
When the user clicks on the abstract hypertext link, Bookends will format the
associated reference in the style of the format “AbstractFormat”. Here is the
AbstractFormat format:
t ajd
¬
b
¬
`<A HREF="default.html">Return to Home Page</A>`
This format will output the title (in bold), authors, journal, and date. After a forced
return (the ¬ character, option-L), the abstract will be output, and after another forced
return a hypertext link back to your default page.
Meaning:
t a j d¬b¬—Standard formatting instructions.
`<A HREF="default.html">Return to Home Page</A>`— A hypertext link
instruction that will be returned after the abstract.
Uploading references to a database
You can upload references to a Bookends database by submitting the reference in a
tagged format that a Bookends import filter can parse (e.g. RIS, EndNote Refer, BibTeX,
etc.). The reference information can be entered into a form as individual fields, as
complete tagged references, or uploaded as a text file. An example web page that
demonstrates each of these techniques is included in the file "import.html", found in the
folder Serve a Bookends database in 5 minutes (or less).
Element
Representation
Required:
• name of the database to import to
• the filter to use
DB
Filter
Optional:
• uploading each field individually
IndividualFields
291
Below are examples of how to use each element.
_________________________________________________________________
Name of the database to import to
HTML example (hidden field):
<label for="DB"><b>Database to send references to</b>: Database1</label>
<input type="hidden" id="DB" name="DB" value="Database1"/>
If you only have one database to search, you can include the DB information in a hidden
field.
_________________________________________________________________
The filter to use
<label for="Filter"><b>Use filter</b>: RIS</label>
<input type="hidden" id="Filter" name="Filter" value="RIS" />
If you use only one import filter, you can include the information in a hidden field.
_________________________________________________________________
Uploading individual fields
Element: DB (optional)
<label for="IndividualFields"></label> <input type="hidden" name="IndividualFields"
value="true" />
292
This value is set to true if each field is sent to Bookends as a separate entity. If the user is
uploading a single text file for importing this value should be false (or simply excluded).
If you are uploading individual fields, they should be named with the tag used by the
import filter for that field. For example, to upload authors via an RIS filter, you might use
this in your web page:
<p>Author: <INPUT cols="30" rows="1" name="AU " value="Hemingway, E">
</INPUT></p>
_________________________________________________________________
293
Appendix A. Importing references from EndNote, Papyrus,
and Reference Manager.
You can export references from EndNote in either the EndNote Export style or as XML.
XML has the advantage of retaining styled text information, but you cannot edit the filter.
The EndNote Export style will not include styled text information, but you can edit the
Bookends import filter to import specific fields where you like.
Perform these steps to transfer references from EndNote to Bookends.
For EndNote 7 or later:
In EndNote:
•
•
•
Use the File -> Export menu.
Set the “Save file as type” pop-up menu to XML.
Click Save.
In Bookends:
•
•
•
Choose File -> Import References…
Select XML (EndNote 7) or XML (EndNote 8/9) from the pop-up menu, then click
OK.
Use the Get File dialog to select the XML file exported from EndNote, then click
Open.
Note: You can also drag and drop the exported file onto a Bookends reference or List
View window.
For EndNote 6 or earlier (also works with EndNote 7 or later):
In EndNote:
•
•
•
•
•
•
•
Examine the File -> Output Styles menu.
If “EndNote Export” is not listed, select Open Style Manager…
Find the “EndNote Export” style and check it ON. Close this window.
Make sure that “EndNote Export” is now checked in the File -> Output Styles
menu.
Select the references you want to transfer.
Choose File -> Export…
Make sure you are exporting the references as Text Only, then click OK.
In Bookends (note that the filters are different for EndNote 6 and EndNote 7 and later):
294
•
For EndNote 6 or earlier:
• Select EndNote 6 Export (Refer) from the pop-up menu, then click OK.
For EndNote 7 or later:
• Select EndNote Export (Refer) from the pop-up menu, then click OK.
•
Use the Get File dialog to select the file exported from EndNote, then click Open.
Note: Book Sections imported from EndNote 6 will have the book title imported into
the Series Title field. You can move them after importing using the Global Change ->
Move Field menu option.
Note: If you have custom fields in EndNote, you may want to edit the Bookends
import filter to place them in the closest corresponding field.
Note: Other Refer export styles can be called Refer Export and Refer Export with
Records.
Note: You can also drag and drop an exported file onto a Bookends reference or List
View window.
Alternative drag and drop method:
In EndNote:
•
•
Set the out style to "EndNote Export", as above
Drag and drop references onto a Bookends window with the Option key held
down.
In Bookends:
Note: Other Refer export styles can be called Refer Export and Refer Export with
Records.
Note: the drag and drop method works best for a small number of references (< 200).
Perform these steps to transfer references from Papyrus to Bookends.
In Papyrus:
•
•
•
If BibTeX is not already in your format list, open the Windows -> Formats
window.
Click on the Open… button.
Find the file "BibTeX formats" (you may have to download this file from the
Research Software Design web site).
295
•
•
•
•
•
•
Drag "BibTeX output" to the Formats window and drop.
Close these windows, then select the references you want to export.
Select the File -> Print/Export menu item.
Click on the Format button and choose "BibTeX output".
Set Print/Export dialog to create a new text document in plain text.
Save the file.
In Bookends:
•
•
•
•
Make sure the "BibTeX" import filter is active (it should be checked in the Import
Filters dialog box).
Select BibTeX from the pop-up menu, then click on OK.
Use the Get File dialog to select the file exported from Papyrus, then click Open.
Note: You can also drag and drop the exported file onto a Bookends reference
window.
Important: The Papyrus BibTeX export automatically converts extended ASCII
(e.g., accented characters) to their TeX equivalents, which you may not want
imported into Bookends. If the Papyrus database contains extended ASCII characters,
duplicate the Papyrus “BibTeX output” format and rename it so that the first word is
not “BibTeX” (for example, “Bookends BibTeX output”). When you use this format
for exporting, Papyrus will output extended ASCII characters without conversion.
Perform these steps to transfer references from Reference Manager
to Bookends.
In Reference Manager:
•
•
Select the references you want to transfer.
Export the references in "RIS" format (make sure you are exporting the references
as Text Only).
In Bookends:
•
•
•
•
Make sure the "RIS" import filter is active (it should be checked in the Import
Filters window).
Select RIS from the pop-up menu, then click on OK.
Use the Get File dialog to select the file exported from Reference Manager, then
click Open.
296
Note: You can also drag and drop the exported file onto a Bookends reference
window.
297
Appendix B. Upgrading from previous versions of
Bookends.
• from Bookends 10
There are two ways to upgrade: use the Bookends implementation of Sparkle, or perform
a manual upgrade.
Sparkle:
1. If Bookends alerts you that an upgrade is available and shows you the new features
available page on the Sonny Software web site, then you are using Sparkle.
2. Click on Install Update.
3. After the files are downloaded and you have confirmed the update, Bookends will
quit and reopen with the new version. Your old files can be found in the Trash.
• from Bookends 9
Bookends will offer to convert your Bookends 9 databases to Bookends 10 format when
they are opened. It will make a copy of and then convert the older database, and leave the
older (original) file untouched.
1.
2.
Move any formats, import filters, or glossaries you modified (i.e. edited, but did
not create, and so are not in one of the Custom folders) to the corresponding
Custom folders.
Open the older Bookends 9 database with the newer version.
• from Bookends 8
Note: As of Bookends 8.0.2, any formats, import filters, or journal glossaries you create
in Bookends will be stored in folders starting with the word Custom. These folders can
be found in ~/Library/Application Support/Bookends/.
The default attachments storage folder is ~/Documents/Bookends/Attachments. You
may have subfolders in the default attachments folder (one level deep, only).
Move the following from the older to the new Bookends Folder:
1.
2.
Databases you have created (only if you store them in the Bookends Folder,
which is not necessary).
If you are migrating from 8.0 or 8.0.1: move the folders Custom Formats,
Custom Import Filters, and Custom Journal Glossaries to
298
~/Documents/Bookends/Attachments
If you haven't run the updated version of Bookends, you can create these folders
yourself (Bookends will do so automatically when it is first run, if you prefer).
3.
Move any formats, import filters, or glossaries you modified (i.e. edited, but did
not create, and so are not in one of the Custom folders) to their corresponding
folders.
Now:
4.
5.
Run Bookends 9.
Open your older Bookends 8 database. Bookends will offer to convert it to
Bookends 9. Your database will be copied first, and then converted, so you will
not lose the original. Bookends 9 databases (created in Bookends 9 or converted
from Bookends 8) cannot be opened in Bookends 8.
• from Bookends 7
The internal database and format structures in version 8 are not compatible with version
7. This means that Preferences will be reset to their defaults, and that any settings stored
in databases (the most important of which is Groups) will be lost and have to be reentered. You will, however, be able to retain your references, import filters, formats, and
journal glossaries.
Bookends 7 references can be transferred to a Bookends 9 database by
exporting/importing.
Note for non-Roman font users: Bookends 9 will assume that the references it is
importing from Bookends 7 use the same encoding as the Bookends 9 default reference
font (selected in Preferences). If you have used Bookends 7 with a two-byte (non-Roman)
font like Osaka (Japanese), it is essential that this font be set as the default for references
when you import your Bookends 7 references, or the characters will be displayed
incorrectly. After you have finished importing, you can change the default font to
anything you like (e.g. Times New Roman) and perform a Global Change -> Restore
Default Font & Style on the database. From this point on you can use the International
Input Menu to change font encodings as necessary.
Bookends 7 formats will be converted automatically when you open them in Bookends 9.
Once converted, a format cannot be opened in Bookends 7. Therefore, you should place a
copy of any format you want converted in the Bookends 9 Custom Formats folder, in
case you want to use the format again with Bookends 7.
Bookends 7 import filters and journal glossaries need no conversion.
299
Begin by:
1.
Launch Bookends 7, and for each database you have select all references (Refs–
–> Select References -> Select All References) and export them (File -> Export
References (Hits)) as a Bookends 7 file.
Move the following from the old to the new Bookends Folder:
2.
3.
4.
5.
Attachments folder (if present).
Copies of formats you have created or modified (to the new Custom Formats
folder).
Import filters you have created or modified (to the new Custom Import Filters
folder).
Journal glossaries you have created or modified (to the new Custom Journal
Glossaries folder).
Now:
6.
7.
Run Bookends 9 and create a new database.
Import the reference file(s) you exported from Bookends 7 (the easiest way to
do this is to drag and drop each file onto a new Bookends 9 List View or
reference window). You can also use the Import References menu, select
Bookends from the pop-up menu in the dialog box, and proceed with the import.
If you used non-Roman fonts in Bookends 7, adjust the default reference font
accordingly before importing (see above).
• from Bookends Pro/Plus (6.0.1 and earlier)
Bookends 9 cannot read databases made with Bookends 6 or earlier. Any custom formats,
import filters, or journal glossaries you made will have to be recreated. To move your
references to Bookends 9:
1.
2.
3.
4.
5.
6.
Launch your older version of Bookends and open a database.
Choose All references.
Export the Hits as a Bookends file (File -> Export References (hits)).
Copy the new Bookends Folder to your hard drive.
Launch Bookends 9 and, if necessary, create a new database.
Import the references exported from Bookends Pro/Plus (this is pop-up menu
selection in the File -> Import References dialog box).
300
Appendix C. BibTeX.
Bookends has options for entering, citing, importing, and formatting BibTeX references.
Entering and citing BibTeX references
You can enable BibTeX features in Preferences. Once you have done this, the User1 field
will be renamed “Key” and is intended to hold the key (id) value for the reference. You
cannot enters spaces, commas, or apostrophes in this field.
The Generate BibTeX key (Refs menu) menu will create a key for you and place it in the
Key field. The key consists of the last name of the first author (or editor, if there are no
authors) followed by the year in the Date field (or the contents of the Date field if no 4
digit year is entered). Similarly, if requested in Preferences, when importing a reference
Bookends will generate a key value for it. Checks for uniqueness will be performed as
specified in Preferences. No key will be generated if one already exists.
If requested in Preferences, after entering a value in the Key field (or having Bookends
generate one) Bookends will check to make sure it is unique, and if not will either warn
you or automatically append a lowercase letter that makes it unique.
When using Copy Citation(s), Bookends can place the text in the Key field, surrounded
by the temporary citation delimiters, in your linked word processor document. Multiple
citations will be separated by commas (no spaces). Any text (or none) can be placed
immediately before the citation in the word processor—the default is “\cite” (without the
quote marks).
See the section on Preferences and other relevant sections in this manual for more details
on these features.
Importing BibTeX references
It is possible to import BibTeX references into a Bookends database (a filter is supplied
with Bookends). Importing BibTeX references is a special case, because the 13 possible
tags that indicate a new reference and the reference Types are fixed.
To have Bookends recognize that the source is a BibTeX file, enter the word “BibTeX”
(without the quotes—case is irrelevant) in the “References start with” field in the filter
definition:
Bookends will recognize the following BibTeX tags as indicating a new reference:
301
@Article
@Inproceedings
@Techreport
@Misc
@Book
@Incollection
@Manual
@Inbook
@Mastersthesis
@Unpublished
@Proceedings
@PHDThesis
@Booklet
Unlike other filters, the case of the tags is irrelevant.
The BibTeX id/key will be imported into the Key field (named User1 field if BibTeX is
not enabled). For example, for this reference
@Article{nabu2002,
author = Nabu, R. S.
…
the letters “nabu2002” would be placed in the Key field.
Because the import filter supplied with Bookends uses “valid tags” to detect the end of a
field, all possible tags that might be encountered in the body of the reference must be
accounted for. The tags included in the filter supplied by Sonny Software and their
mapping to Bookends fields are:
302
Tag
Bookends Field
Author
Authors
Title
Title
Editor
Editors
Journal
Series
Volume
Booktitle
Number
Chapter
Journal
Pages
Pages
Year
Month
Date
Publisher
School
Address
Organization
Publisher
Location
Affiliation
City
URL
Address or City
Misc
Price
Size
Edition
LCCN
lib-congress
mrnumberd
ISSN
ISBN
Language
User2
Abstract
Abstract
Keywords
Keywords
Note
Annote
Howpublished
Contents
Notes
DOI
User17
Volume
URL
User4
User6
User7
303
The following tags are ignored:
type
crossref
key
If you have tags that are not listed here, you should modify the filter to include them. If
there are tags here that you do not want imported, move them to the “Ignore” field
The BibTeX filter maps the reference Types as follows:
@Article -> Journal Article
@Book -> Book
@Inbook -> Book chapter
@Proceedings -> Conference proceedings
@Inproceedings -> Conference proceedings
@PHDthesis -> Dissertation
@Mastersthesis -> Dissertation
@Unpublished -> In press
You can add your own Types in Preferences. When indicating required fields, Bookends
will recognize the following Types you might have added: Booklet, Technical Report,
and Manual.
All other Types are mapped to Journal Article. You can edit this in the import filter
definition window (Edit Type definitions) and/or set the default reference Type in
Preferences.
•
Double hyphens are replaced by a single hyphen when imported into the Pages
field.
•
If the Importing: Convert from TeX option is checked in Preferences, Bookends
will convert BibTeX-formatted accented characters to their 8-bit ("extended
ASCII") form: e.g. {\"u} will be converted to ü. Double backquotes (``) will be
converted to quotation marks (").
•
The BibTeX import filter supplied by Sonny Software assumes that author and
editor names are “surname-first” (e.g. Anderson, RS). If you want to import
BibTeX references in which the names are “surname-last”, you must edit the
import filter accordingly:
304
Formatting BibTeX references for bibliographies
A BibTeX format is supplied with Bookends. It includes formats for the following Types:
Journal article
Book
Book chapter
Conference Proceedings
Dissertation
These can be edited if they not exactly fit your needs, and new Types can be added. In
particular, although not supplied as defaults with Bookends, if you add the following
Types Bookends will recognize them an indicated the required fields (if that option is
selected in Preferences): Booklet, Technical Report, and Manual.
If the Bibliographies: Convert to TeX option is checked in Preferences, when creating a
BibTeX bibliography Bookends will convert accented characters to their TeX
equivalents: e.g. ü will be converted to \"{u}.
Creating a .bib file
Here is a series of steps you might take to create a .bib file.
1.
Write your paper using Bookends to insert citations in the manuscript (in
Preferences: BibTeX enabled, Copy Citation uses the Key field, BibTeX chosen as
the Temporary Citation Delimiters)
2.
When ready, Scan the document with Bookends (Biblio -> Scan a Document). Do
not make a new file, do not generate a bibliography.
3.
After the Scan, the Hits List contains the cited references.
4.
Select the Biblio -> Biblio Formatter menu item. Make a bibliography in the
BibTeX format, using BibTeX styled text conventions, and send it to disk:
305
The resulting file can be used with LaTeX or other TeX-savvy applications.

Bookends User Guide - Michael Joseph Therapy

Transcription

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