BOOKENDS v10.6.

1
Reference and Information Management Software
for Macintosh

Sonny Software
2703 Daniel Road
Chevy Chase, MD 20815

Sales:
Web: www.sonnysoftware.com
E-mail: sales@sonnysoftware.com

Technical Support:
support@sonnysoftware.com
 2

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
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WILLFUL VIOLATIONS OF THE COPYRIGHT LAW OF THE UNITED STATES CAN RESULT IN CIVIL
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DAMAGES, PLUS CRIMINAL PENALTIES OF UP TO ONE YEAR IMPRISONMENT AND/OR A TEN
THOUSAND ($10,000.00) DOLLAR FINE.

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ENCLOSED COMPUTER SOFTWARE PACKAGE, ITS MERCHANTABILITY OR ITS FITNESS FOR
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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
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PORTIONS COPYRIGHT 1998-2009 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 ...................................................................................................................................................23
Journal ..................................................................................................................................................23
Vol (Issue) ..............................................................................................................................................23
Pages .....................................................................................................................................................23
Date .......................................................................................................................................................23
Publisher ...............................................................................................................................................24
Address/City ..........................................................................................................................................24
Abstract .................................................................................................................................................24
Keywords ...............................................................................................................................................24
Notes......................................................................................................................................................24
User1 (Key), User2-User18 ..................................................................................................................24
URL .......................................................................................................................................................26
AUTOCOMPLETE..........................................................................................................................................26
ENLARGING REFERENCE FIELDS.................................................................................................................27
CHANGE FIELD NAMES ...............................................................................................................................28
OPENING URIS IN ANY FIELD ......................................................................................................................28
REFERENCE TYPE........................................................................................................................................29
NAVIGATION ARROWS.................................................................................................................................29
THE HITS AREA...........................................................................................................................................29
LINKS..........................................................................................................................................................30
THE ATTACH POP-UP..................................................................................................................................30
Attaching a file or folder .......................................................................................................................31
Folders as attachments..........................................................................................................................32
Detaching a file or folder ......................................................................................................................32
Opening attached files ..........................................................................................................................32
Attaching multiple files or folders to one reference ..............................................................................33
Storing attached files or folders automatically .....................................................................................33
Automatic attachment of PDF documents you print from other applications ......................................36
Importing reference information from the Internet when attaching a pdf ............................................36
Downloading and attaching pdfs from a browser by drag and drop ....................................................37
Attaching an image from another application by drag and drop..........................................................38
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Removing an attached file from the database .......................................................................................38

Deleting an attached file from the hard disk .........................................................................................38
Renaming an attachment .......................................................................................................................38
Reattaching a file ..................................................................................................................................39
Reveal an attached file in the Finder ....................................................................................................39
Find references that do or do not have attachments .............................................................................39
REFERENCE WINDOW DRAWER ..................................................................................................................39
COLOR LABEL.............................................................................................................................................39
RATING........................................................................................................................................................40
LINKING BOOKENDS TO A WORD PROCESSOR ............................................................................................40
COPY CITATION ...........................................................................................................................................42
Drag and Drop citations .......................................................................................................................44
Modifier keys .........................................................................................................................................44
Customizing citations ............................................................................................................................44
POP-UP NAVIGATION WINDOW....................................................................................................................45
THE LIST VIEW WINDOW ......................................................................................................................46
THE REFERENCE LIST PANE........................................................................................................................47
Color Labels ..........................................................................................................................................50
Using the List View to copy temporary citations ..................................................................................51
Using the List View to copy formatted citations....................................................................................52
Using the List View to create a hypertext link to a reference ................................................................52
E-mailing references .............................................................................................................................52
GROUPS PANE .............................................................................................................................................52
All ..........................................................................................................................................................53
Hits ........................................................................................................................................................53
Attachments ...........................................................................................................................................54
Groups ...................................................................................................................................................54
Group And Folders................................................................................................................................59
Instantly see the groups to which a reference belongs ..........................................................................60
CONCISE VIEW PANE ..................................................................................................................................61
Configuring the concise view ................................................................................................................62
Editing and/or entering reference information in the concise view ......................................................64
NOTE STREAM PANE...................................................................................................................................65
THE DISPLAY PANE .....................................................................................................................................68
Formatted view......................................................................................................................................68
Attachment view ....................................................................................................................................68
SEARCH FIELD—LIVE SEARCH AND SPOTLIGHT SEARCH............................................................................72
THE INSPECTOR........................................................................................................................................75
ATTACHMENT INSPECTOR ...........................................................................................................................75
LINK INSPECTOR .........................................................................................................................................76
ONLINE SEARCH .......................................................................................................................................79
Do not clear reference list between searches ........................................................................................82
Removing items from the reference list .................................................................................................82
Repeating a search ................................................................................................................................82
Download pdf ........................................................................................................................................82
Indicating that a reference is already in your database........................................................................83
PUBMED......................................................................................................................................................83
WEB OF SCIENCE.........................................................................................................................................87
LIBRARY OF CONGRESS...............................................................................................................................90
Amazon ..................................................................................................................................................91
GOOGLE SCHOLAR......................................................................................................................................93
BOOKENDS BROWSER .................................................................................................................................94
Z39.50 LIBRARY SEARCHES.........................................................................................................................94
SRU searches ........................................................................................................................................95
SAVED INTERNET SEARCHES.......................................................................................................................95
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Saved Advanced PubMed, Web of Science, and Google Scholar searches ...........................................97
AUTOMATED PUBMED SEARCHES ...............................................................................................................97
Preference settings ................................................................................................................................98
Creating an automated search ..............................................................................................................98
DETERMINING AN H-INDEX..........................................................................................................................99
REFERENCE SURFING ................................................................................................................................100
EZProxy and reference surfing/Bookends browser .............................................................................104
JSTOR and reference metadata detection ...........................................................................................105
Reference data detection and COinS ..................................................................................................105
Data detection and indication of references you already have ...........................................................107
IMPORT FILTERS ....................................................................................................................................107
Designing an import filter ...................................................................................................................107
Type definitions ...................................................................................................................................110
Identifying the beginning of a reference..............................................................................................111
Parsing Authors/Editors......................................................................................................................115
Parsing Keywords ...............................................................................................................................116
Replace hyphens with spaces ..............................................................................................................116
Removing unwanted characters ..........................................................................................................116
Parsing the Source ..............................................................................................................................116
Creating filters for existing bibliographies .........................................................................................119
Importing MARC records ....................................................................................................................122
Online Searches and importing from libraries via the Internet ..........................................................124
Adding information to imported references ........................................................................................129
FORMATS AND BIBLIOGRAPHIES .....................................................................................................131
New (Format) ......................................................................................................................................131
Edit Format .........................................................................................................................................132
Formatting Options tab .......................................................................................................................132
Names ..................................................................................................................................................133
Case .....................................................................................................................................................135
When a Field is Empty ........................................................................................................................145
Example: Stringent APA in-text citation style......................................................................................147
Name Punctuation tab .........................................................................................................................148
Citation Options tab ............................................................................................................................150
Bibliography Options tab ....................................................................................................................155
Font and Style Hierarchy ....................................................................................................................158
COinS ..................................................................................................................................................158
Book chapter [Book] metatype............................................................................................................159
SCANNING DOCUMENTS ......................................................................................................................162
BEFORE THE SCAN.....................................................................................................................................162
Creating removable in-text citations ...................................................................................................163
Excluding cited references from the bibliography...............................................................................164
Excluding enclosing punctuation in a final citation............................................................................164
Overriding superscript in a final citation ...........................................................................................164
Mixing text with temporary in-text citations .......................................................................................165
Cited pages ..........................................................................................................................................165
Replace temporary in-text citations with date only.............................................................................166
Eliminate authors from final citation ..................................................................................................167
The Scan Document Dialog ................................................................................................................167
DURING THE SCAN ....................................................................................................................................170
Replacing citations with numbers .......................................................................................................172
AFTER THE SCAN.......................................................................................................................................172
RULES FOR SCANNING...............................................................................................................................172
MICROSOFT WORD....................................................................................................................................173
Go to Bookends ...................................................................................................................................175
Find in Bookends ................................................................................................................................175
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Insert Citation .....................................................................................................................................176

Scan Document....................................................................................................................................176
Unscan Document ...............................................................................................................................177
Typical use of the Microsoft Word add-in with Bookends ...................................................................177
Size limitation for documents scanned from within Word ...................................................................178
Problem: font sometimes changes after a citation is inserted in a Word document ...........................178
MELLEL.....................................................................................................................................................179
Citation objects ...................................................................................................................................179
Bibliography palette ............................................................................................................................181
Synchronize database ..........................................................................................................................182
NISUS WRITER PRO (VERSION 1.4 OR LATER)............................................................................................183
Switch to Bookends..............................................................................................................................183
Find Reference… .................................................................................................................................183
Insert Citation .....................................................................................................................................184
Insert Bibliography Placeholder .........................................................................................................184
Scan Document....................................................................................................................................184
Unscan Document ...............................................................................................................................185
APPLE PAGES '08 AND ‘09.........................................................................................................................186
Apple Pages Scripts ............................................................................................................................187
REFBASE ....................................................................................................................................................187
MENUS ........................................................................................................................................................189
BOOKENDS MENU ..................................................................................................................................189
ABOUT BOOKENDS… ...............................................................................................................................189
CHECK FOR UPDATES… ...........................................................................................................................189
PREFERENCES… .......................................................................................................................................189
Word Processor ...................................................................................................................................190
Attachments folder ..............................................................................................................................191
Default font..........................................................................................................................................191
Default view ........................................................................................................................................192
Internal cache......................................................................................................................................192
Hypertext links ....................................................................................................................................192
Journal Glossary .................................................................................................................................192
Window menu ......................................................................................................................................193
Automatic backup ................................................................................................................................193
Reference Types ...................................................................................................................................194
Default new reference Type .................................................................................................................194
Keywords location in reference window .............................................................................................194
Rename attachments............................................................................................................................195
Field Names ........................................................................................................................................195
Data entry............................................................................................................................................195
Inserted date format ............................................................................................................................196
Bring reference window to front on double-click ................................................................................197
Show entire date ..................................................................................................................................197
Sorts based on .....................................................................................................................................197
Sort Lists..............................................................................................................................................197
Indicate attachments ...........................................................................................................................198
Display of names .................................................................................................................................198
Fields to display ..................................................................................................................................198
Color Labels ........................................................................................................................................198
Notecard color ....................................................................................................................................199
Default Summary view ........................................................................................................................199
Font size ..............................................................................................................................................199
View All label color .............................................................................................................................200
Standard View organization ................................................................................................................200
Temporary citations ............................................................................................................................201
Cite by: ................................................................................................................................................202
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Multiple citations separated by:..........................................................................................................202

Precede with:.......................................................................................................................................202
Superscript & subscript ......................................................................................................................203
Bibliography font use ..........................................................................................................................203
Sentence & Title Case..........................................................................................................................203
Bibliography sort: Ignore words at beginning of… ............................................................................204
Link Relationships ...............................................................................................................................205
Format for linked reference display ....................................................................................................205
Enable BibTeX .....................................................................................................................................206
TeX character handling .......................................................................................................................208
INTERNET..................................................................................................................................................208
Proxy Info ............................................................................................................................................209
Automated PubMed Searches..............................................................................................................210
Attaching PDFs ...................................................................................................................................210
Refbase ................................................................................................................................................210
OPENURL & COINS .................................................................................................................................210
OpenURL ............................................................................................................................................211
COinS ..................................................................................................................................................212
SERVER .....................................................................................................................................................212
Allow Web access to databases ...........................................................................................................213
SERVICES ..................................................................................................................................................213
FILE MENU ................................................................................................................................................214
NEW DATABASE… ....................................................................................................................................214
OPEN….....................................................................................................................................................214
BACKUP… ................................................................................................................................................215
SYNC.........................................................................................................................................................215
IMPORT REFERENCES… ............................................................................................................................217
Importing references from PubMed by drag and drop from a browser ..............................................219
Importing a reference from an attached PDF .....................................................................................220
Importing references from a Mellel document (Synchronize Database) .............................................221
IMPORT TEXT ENCODING ..........................................................................................................................221
IMPORT FILTER MANAGER… ....................................................................................................................222
EXPORT REFERENCES (HITS)… ................................................................................................................223
Export attachments too........................................................................................................................224
EXPORT ATTACHMENTS… ........................................................................................................................224
GO TO URL ..............................................................................................................................................224
ONLINE SEARCH... ....................................................................................................................................225
PAGE SETUP... ..........................................................................................................................................226
PRINT REFERENCES... ...............................................................................................................................226
PRINT BIBLIOGRAPHY... ............................................................................................................................227
DATABASE MAINTENANCE........................................................................................................................227
Verify… ................................................................................................................................................227
Reindex… ............................................................................................................................................227
Repair… ..............................................................................................................................................227
Rebuild (Keep User Settings)… ..........................................................................................................228
Rebuild… .............................................................................................................................................228
Defragment & Compact… ..................................................................................................................228
When to use which method to fix a damaged database.......................................................................228
LINK TO ....................................................................................................................................................229
SWITCH TO WORD PROCESSOR ................................................................................................................229
QUIT..........................................................................................................................................................229
EDIT MENU................................................................................................................................................229
UNDO, CUT, COPY, PASTE, CLEAR, SELECT ALL ......................................................................................230
PASTE PLAIN TEXT....................................................................................................................................230
COPY CITATION .........................................................................................................................................230
COPY CITATION AND MODIFIERS… ..........................................................................................................231
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COPY FORMATTED ....................................................................................................................................232

COPY HYPERTEXT LINK/COPY NOTECARD AS HYPERTEXT LINK .............................................................232
SHOW CLIPBOARD.....................................................................................................................................233
SPECIAL CHARACTERS ..............................................................................................................................233
FONT AND STYLE MENUS ....................................................................................................................233
BIBLIO MENU ...........................................................................................................................................233
SCAN DOCUMENT… .................................................................................................................................234
UNSCAN WORD RTF DOCUMENT… .........................................................................................................235
SCAN OPEN APPLE PAGES DOCUMENT… .................................................................................................235
SUBJECT BIBLIOGRAPHY… ......................................................................................................................235
BIBLIOGRAPHY FORMATTER… .................................................................................................................237
FORMATS MANAGER….............................................................................................................................239
DEFAULT FORMAT .....................................................................................................................................240
VIEW MENU ..............................................................................................................................................241
REFS MENU ...............................................................................................................................................242
NEW ..........................................................................................................................................................243
INSERT.......................................................................................................................................................244
DELETE… .................................................................................................................................................244
DUPLICATE................................................................................................................................................244
REPLICATE AS BOOK CHAPTER ................................................................................................................245
SHOW WITH CHAPTERS ............................................................................................................................245
COMPARE REFERENCES… ........................................................................................................................245
REMOVE DUPLICATES… ...........................................................................................................................247
MARK........................................................................................................................................................249
ADD TO GROUP ........................................................................................................................................250
New Group… .......................................................................................................................................250
Group name .........................................................................................................................................250
FIND…......................................................................................................................................................250
Spotlight ..............................................................................................................................................251
How a search is done ..........................................................................................................................252
Put matching references in the Hits List .............................................................................................253
Special Searches for Returns ..............................................................................................................253
FIND AGAIN ..............................................................................................................................................253
FIND IN THIS REFERENCE…......................................................................................................................253
FIND IN THIS REFERENCE AGAIN… ..........................................................................................................254
SQL/REGEX SEARCH… ............................................................................................................................254
Fields to search ...................................................................................................................................255
Comparators........................................................................................................................................257
Characters to search for......................................................................................................................259
Boolean searches ................................................................................................................................259
Regex pattern matching ......................................................................................................................260
Searching for words that include punctuation ....................................................................................261
Sorting the result .................................................................................................................................262
Example queries and their results:......................................................................................................262
Search for the last 15 references entered ............................................................................................263
Search for references that were edited within the last 2 weeks ...........................................................264
Search for references that do or do not have attachments ..................................................................264
GLOBAL CHANGE......................................................................................................................................264
Find and Replace… .............................................................................................................................265
Change Field… ...................................................................................................................................266
Change Reference Type…....................................................................................................................267
Change Case… ....................................................................................................................................267
Move Field… .......................................................................................................................................267
Restore Default Font & Style… ...........................................................................................................268
Standardize Names… ..........................................................................................................................268
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Remove Orphaned Attachments….......................................................................................................269

PEEK..........................................................................................................................................................269
Quick Peek...........................................................................................................................................270
GENERATE BIBTEX KEY............................................................................................................................271
INSERT DATE .............................................................................................................................................271
AUTOFILL FROM INTERNET.......................................................................................................................271
GET PDF ..................................................................................................................................................272
From Internet (If Available) ................................................................................................................272
Find & Attach Local PDF ...................................................................................................................273
AUTOCOMPLETE PAPER… ........................................................................................................................273
PUBMED....................................................................................................................................................276
DOI...........................................................................................................................................................276
Lookup Article From DOI ...................................................................................................................277
Get DOI ...............................................................................................................................................277
OPENURL SEARCH ...................................................................................................................................277
UPLOAD TO REFBASE… ...........................................................................................................................277
FIRST, PREV, NEXT, LAST .........................................................................................................................278
GO TO REFERENCE #… .............................................................................................................................278
HITS MENU................................................................................................................................................278
SORT HITS LIST….....................................................................................................................................278
CLEAR HITS LIST ......................................................................................................................................279
FIRST, PREV, NEXT, LAST .........................................................................................................................279
GO TO HIT #… ..........................................................................................................................................279
WINDOW MENU .......................................................................................................................................280
SHOW INSPECTOR......................................................................................................................................280
BIBLIOGRAPHY WINDOW ..........................................................................................................................280
MINIMIZE WINDOW ..................................................................................................................................281
EXTRAS MENU .........................................................................................................................................281
JOURNAL GLOSSARY .................................................................................................................................281
Using the Journal Glossary.................................................................................................................283
Pre-defined Journal Glossaries ..........................................................................................................284
TERM LISTS ..............................................................................................................................................285
Expanded view ....................................................................................................................................286
Collapsed view ....................................................................................................................................289
Adding/Removing a Term List .............................................................................................................290
HELP MENU ..............................................................................................................................................290
USER GUIDE..............................................................................................................................................291
FAQ… ......................................................................................................................................................291
VISIT SONNY SOFTWARE….......................................................................................................................291
BOOKENDS SERVER...............................................................................................................................292
INTRODUCTION..........................................................................................................................................292
ADMINISTRATING BOOKENDS SERVER......................................................................................................293
Allow Web access to databases ...........................................................................................................293
Port......................................................................................................................................................294
Max connections..................................................................................................................................294
Keep log ..............................................................................................................................................294
Max log size.........................................................................................................................................295
HTML encoding ..................................................................................................................................295
IP Address ...........................................................................................................................................295
Authorized access only ........................................................................................................................296
CREATING WEB PAGES TO ACCESS BOOKENDS DATABASES.......................................................................297
Requesting references..........................................................................................................................297
Query ...................................................................................................................................................299
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SQLQuery............................................................................................................................................300
REQUESTING FILES/INFORMATION FROM BOOKENDS ................................................................................307
COMPLETE EXAMPLE: COMMUNICATION BETWEEN A BROWSER AND BOOKENDS ....................................313
UPLOADING REFERENCES TO A DATABASE.................................................................................................316
EDITING/UPDATING REFERENCES IN A DATABASE ......................................................................................318
APPENDIX A. IMPORTING REFERENCES FROM ENDNOTE, PAPYRUS, AND REFERENCE MANAGER 320
APPENDIX B. UPGRADING FROM PREVIOUS VERSIONS OF BOOKENDS .............................323
APPENDIX C. BIBTEX .............................................................................................................................327
 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, Web of Science, Google Scholar,
Amazon, the Library of Congress, and hundreds of online libraries around the world (access privileges may be
required).

Bookends also works with you to create polished manuscripts with bibliographies. If you are using Microsoft
Word, Mellel, or Nisue Writer Pro 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 Apple Pages '08 and ’09, OpenOffice, or as RTF (Rich Text
Format) from any word processor, including Mariner Write and TextEdit.

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 and edit 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

• Unicode-savvy (handles non-Roman fonts: Japanese, Chinese, Hebrew, etc.)

• Search libraries via the Internet and directly import the hits and associated pdfs into your databases
• Use the built-in web browser to surf to references of interest and download them and their associated pdfs
and/or web pages with a single click
• Find reference details of a pdf you already have with reference autocomplete
• 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
 14

• 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 a folder hierarchy.
• Color label references
• Term Lists
• Duplicate reference detection and removal
• Journal glossaries
• and much more…

Requirements

You must have the following to use Bookends:

• 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 50-100 thousand. In the event that you want to store more references, you can make additional
databases.

· 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.

· 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.

· 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:

· Entered manually in the reference window

· Imported from
o a public online source (PubMed, Google Scholar, the Library of Congress, Amazon, etc.)
o commercial sources, if you have access privileges (e.g. Web of Science, JSTOR, OVID)
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, BibTeX, etc.). You can import this text from the clipboard as well.
o an XML file exported from another reference manager (using the EndNote schema)

· Entered remotely by a user via a 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:

· groups
· a configurable and editable concise view (summary or all)
· a note stream consisting of virtual notecards
· 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.

· 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 160 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:

· Scanning a Microsoft Word, Mellel, or Nisus Writer document for temporary citations. The scan is
initiated from within the word processor.

· Scanning a file containing temporary citations saved in Apple Pages '08 and ‘09 or OpenOffice 3.x
format, RTF, RTFD, or text. The scan is initiated from within Bookends.

· Using the Bibliography Formatter to create a bibliography of the hits.

· Using Subject Bibliography to create a bibliography of the hits.

· Using a browser to ask for a bibliography to be returned by Bookends Server.

 18

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

· 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

· You can also insert a hypertext link to a reference or a group in the List View by holding down the
Command and Option keys before beginning the drag.

· 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. The Notes field can be used to create virtual notecards, which are described here.
 21

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.

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 Pages User1 (user-defined) Translator User8 # of Vols

Title Date Edition User4 Trans Auth User14
Ser Editors Publisher URL Call Num Trans Title User15
Journal Address Abstract ISSN/ISBN Orig Pub PMCID
Volume Short Title Notes Language User12 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.
 22

· 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.

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).

· Short Title shortcut: if you Control- or right-click in the Title field, Bookends will offer to put the
selected text in the Short Title field.
 23

Editors

Editor names are entered just like author names.

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).
 24

Publisher

A typical entry would be McGraw-Hill or Wiley.

Address/City

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. The Notes field is also placed in its own tab in the reference window display.
The Notes field can hold virtual notecards, which are described here.

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 User5-User18.

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.

 25

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.

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.

PMCID (PubMed Central ID): A unique number given to every article referenced by PubMed Central. This
must be cited in by scientists applying for NIH-funding grants.

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. Right-clicking in the
DOI field will allow you to select a url that will open the reference (if you have access privileges) in your
browser.

PMID (PubMed ID): A unique number given to every article referenced by PubMed. Right-clicking in the
PMID field will allow you to select a url that will open the PubMed entry in your browser.

You can replace these labels with any descriptors you find useful (e.g., Cost, Secondary Source, etc.).
 26

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

The URL field can also contain an e-mail address, for example

mailto:steve@mac.com

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 (right-click or use the
enlarged view to see them all). This will open all URLs contained in the field.

Right-clicking in any field will bring up a contextual menu containing all the URLs in the field, if they are on
separate lines, allowing you to open the one you want.

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:
 27

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.

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.

· Autocomplete can be turned off in Preferences.

• 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:
 28

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.

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.

Opening URIs in any field

Right-click on any field in the reference window that contains a URI to bring up a contextual menu containing
that URI. This will allow you to, for example, use links to items in DevonThink 2 and access them while you
are in Bookends. If the URI is in a field that normally contains multiple lines of text (e.g. the Abstract field), it
must reside on its own line or Bookends won't recognize it.
 29

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 37 Types are provided:

Artwork Editorial Personal communication

Audiovisual material In press Review
Book Journal article Internet
Book chapter Letter Unused
Conference proceedings Map Unused 2–20
Dissertation Newspaper article
Edited book Patent

The twenty “Unused” Types are placeholders that you can customize if you have reference sources that are not
already covered.

There is also a "metatype" called Book chapter [Book], which is defined in formats only and lets you cite
information from a book chapter and its book in one place.

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.

The Hits Area

The Hits area is in the upper-left corner of the reference display:

 30

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).

· Holding down the Shift key when clicking on the Hit Button brings up a dialog box asking what Hit you
would like to see.

Links

This button is enabled if the reference has linked references and is disabled if it does not.

Clicking the enabled button will bring up the Link Inspector, with the reference as the parent.

The Attach Pop-Up

This button lets you attach, view, and even open files created by other applications.
 31

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 or folders 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 edit an attached text file in the List View window lower pane or the reference window
Attachment tab. When leaving the field (e.g. by tabbing) you be asked if you want to save the changes.
Note that if the text file is open in another application it may not be possible to save the changes.

· You can attach folders to references, too, by the drag and drop method.
 32

Folders as attachments

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 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).

· If a reference’s first attachment is a folder, Bookends will show the first item in the folder, rather than
the folder itself, when the reference is selected.

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), right-clicking (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 when the List View
is in front, and the attachments of the reference being displayed if the reference window is in front.

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.
 33

· 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 or folders automatically). However, this is not 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:
 34

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 (or subfolders in the
subfolders). When you attach files, Bookends will display a pop-up menu that lets you choose between the
default folder and any subfolders you might have created (each subfolder levels is indented).
 35

You can create these subfolders with the New Subfolder… menu option, or do it yourself in the Finder. If you
create the subfolders in Bookends, they will be placed in the folder that was selected in the pop-up menu. This
means that you can organize your attachments by year, category, database, etc. by placing them in subfolders.

The folder hierarchy in the pop-up menu is cached for speed and updated only if you create a new subfolder
with the New Subfolder command. If you add/delete an attachment subfolder the Finder, use the menu item
Rebuild Folder List to update the pop-up menu.

You can also use the Browse button to select a subfolder in the default attachments folder hierarchy. This may
be faster than using the pop-up list if you have many subfolders and sub-subfolders. If you select a folder
outside of the default folder hierarchy, you will receive an error message. If you create a new folder with this
dialog, make sure its name is unique in the default folder hierarchy or Bookends may not be able to find
attachments in it.

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.

If you check Attach this file to a new empty reference Bookends will create a reference and attach the file. If the
file is a pdf or web page, you can then select portions of text (e.g. the authors) and have Bookends copy that to
the corresponding field in the reference. This processed is described in the section Direct entry of pdf/web page
text to reference fields.
 36

Automatic attachment of PDF documents you print from other applications

A menu item, "Bookends", will be added the Print -> PDF pop-up menu of all applications running on your
Mac. If used, the document will be saved as a PDF and sent to Bookends. Bookends will present the attach
dialog and allow you to attach the reference to the first selected reference or a new empty reference (if the List
View is in front) or the reference showing in the Reference Window (if it is in front).

Importing reference information from the Internet when attaching a pdf

If the pdf you are attaching contains a doi (Digital Object Identifier) number, Bookends will display a hypertext
link to the article online and offer to import the reference information:

Bookends will first try to get the information from PubMed. If the article is not listed on PubMed, Bookends
will retrieve it from Google Scholar.

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 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 for
availability.
 37

If there is no doi, Bookends will still offer to attach the reference to a new (empty) reference and let you
autocomplete the paper:

Autocompletion lets you quickly search PubMed, Google Scholar, or JSTOR for the reference details, and
import that information into the new reference.

See the section Autocomplete Paper for details on how this works.

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:

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".

If you attach an inappropriate 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:
 38

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.

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.

Renaming an attachment

You can tell Bookends to rename an existing attachment. When you do, any reference in the database that
attaches that file will be updated to reflect the new attachment name. Note that this will break links to that
attachment, if they exist, for references in other databases. Rename attachment can be invoked in the List
Window action pop-up menu, by right-clicking on the image of the attachment in the List View attachment
pane, or in the Attachment Inspector.

The name Bookends suggests will follow the setting you have made in Preferences for renaming (that is, Author
Date or according to a format).
 39

Reattaching a file

If an attachment has been renamed in the Finder and Bookends can no longer locate it, you can select
"Reattach" from the List Window action or a contextual menu that appears when you click on the attachment
pane. Once a file has been reattached, the obsolete name will be removed from the reference.

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.

Find references that do or do not have attachments

There is a special smart group called Attachments that shows you all references that have attachments. You can
also perform your own SQL Search or make a smart SQL/REGEX group that shows all references that do or do
not have attachments. Here are some example searches.

Reference Window Drawer

A drawer with 14 fields can be opened/closed by clicking on this icon (or pressing Shift-Command-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.

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.
 40

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

· 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:

 41

1) Launch Bookends.

2) Run your word processor (make sure the word processor has been selected in Preferences).

If using Microsoft Word:

3) In Word, select a word or phrase and use the Find in Bookends option in the Word Tools menu (Word
2004),the Bookends toolbar (Word 2004), or the Scripts ( ) menu (Word 2008). 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 Pro (version 1.4 or later):

3) In NWE, select a word or phrase and use the Insert -> Bibliography -> Find Reference option. 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 with the temporary citation(s) inserted at the selection point.

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.
 42

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 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.

· 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 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.
 43

After you have finished a manuscript, Scan 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 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 try to paste it in. If you are not linked, it will just perform the
copy.

· 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.
 44

· 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).

· If you are linked to OpenOffice, Bookends will switch to it but you must perform the paste manually
because OpenOffice does not support AppleEvents at this time. You can also insert the citation by drag
and drop into OpenOffice.

Drag and Drop citations

You can also drag a temporary or formatted citation to your word processor.

To do this:

1. Click on the Copy Citation label (not the icon) and hold down the mouse button.
2. Drag the rectangular outline to an open window in your word processor.
3. Release the mouse button when the insertion point is positioned where you want it.
4. 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.

Customizing citations
 45

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 Document section of this
User Guide:

a. Mixing text with temporary in-text citations

b. Replace temporary in-text citations with date only
c. Eliminate authors from final citation
d. Creating removable in-text citations
e. Excluding enclosing punctuation in a final citation
f. Overriding superscript in a final citation
g. Cited pages
h. 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 right-clicking 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.
 46

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, web page, RTF, .doc, Mellel, or text files
attached to the selected reference.
 47

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:

Basic: group and reference list

Summary: Basic + concise pane (summary)

All: Basic + concise pane (all)

Note Stream: Basic + notecards

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, the date added, and the date last modified. 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 or modified (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)).
 48

· 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 or modified.

· You can sort the list by label (color) by choosing “Sort By Label” from the Action pop-up menu or by
right-clicking on the list of references. The sort is descending, so unlabeled (uncolored) references are
listed at the end, and there is a secondary sort based on the first column (usually Authors).

· 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. Bookends
will not try to uncompress attached .zip files.

• 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.
 49

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.

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 double-click 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:
 50

The Mark/Unmark All/Selected option is determined as described above when Shift-clicking 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, right-clicking 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:
 51

If you prefer it, a setting in Preferences will have Bookends color the text instead of the background:

or just 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.
 52

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.

If you hold down the Command and Option keys and drag and drop a notecard, the contents of the notecard
are used to create the hypertext link.

· 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 or group.
If a notecard is selected, the menu will change to Edit -> Copy Notecard As Hypertext Link.

· The content of the hypertext link (the human-readable part) for a reference is the reference title by
default. You can change this by using a format, which can be set in Preferences. For groups, it is always
the name of the group.

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 e-mail 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 default 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
 53

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:

If Move attachments to the Trash is checked, Bookends will move any attachments it finds to the Trash. Use this
carefully, because it is possible to have more than one reference, perhaps in more than one database, attach the
same file.

· Shortcut: to avoid the confirm dialog, press Command-Delete. You will get no warning before the
reference is permanently deleted.
· The setting for Move attachments to the Trash is ignored when you remove delete references with
Command-Delete.

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.
 54

If you drag a reference's unique ID from a reference window to the Hits reference list, the reference will be
made a Hit.

Attachments

Displays all references that have attachments (usually pdfs, but can be any file type).

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.

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.

• If a folder or a group in a folder is selected, a new group created with this menu (or contextual menu) will
be placed in the same folder.
 55

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).

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)
 56

• 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

To add a shortcut, click in the column headed with ⌘ and enter a number from 1 to 9:

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.

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 window:
 57

For a description of how these settings are used, see the section on Find. In addition, you can further restrict
your search to references that do or do not belong to marked static groups. If you check Any Group, Bookends
will find any reference that does or does not belong to any static group, regardless of whether they are checked
or not.

Note that the group criterion is applied to references after they are found using the other search criteria, so you
can't have an otherwise empty smart group that finds references based on their presence in particular static
groups. If you want to to do a smart search simply based on static group inclusion, you should set the first
search to Text and find "field is empty" while searching "All fields". This will find all references that have text
in at least one field, and then will check to see if they do or do not belong to the marked groups.

Smart (SQL) groups are created by creating an SQL/Regex search:

 58

The names of smart groups are preceded by this icon:

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.

Smart groups can be copied and pasted. Select a smart group and click on the Action pop-up menu or right-click
on the group list to bring up then contextual menu option Copy Smart Group.

Chose the Action pop-up menu or right click again and the option Paste Smart Group will appear.

The smart group may be pasted into the same database to duplicate it, or into another database to copy it. If the
group name is already used, a number will be appended to the name of the pasted version to make it unique.

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, or by right-
clicking on the Groups pane:
 59

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 And Folders

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:
 60

If a folder contains groups or subfolders, the number will be shown in grayed text.

· You place folders within folder (subfolders). The number of subfolders is unlimited.

· 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 and subfolders it contains will be deleted as well.

If you hold down the Option key when clicking on a folder's expand/collapse triangle, all the subfolders under
that folder will be expanded or collapsed. This is a convenient way to quickly show or hide all of the items a
folder contains.

If the group/folder hierarchy ever becomes disordered, the folder hierarchy can be instantly flattened (that is,
each group and folder/subfolder will be listed at the root level of the list) using the Action pop-up menu Flatten
Groups List Hierarchy.

This will enable you to recover all groups/folders, which you can then rearrange as you like. This is undo-able.

Instantly see the groups to which a reference belongs

Hold down the Shift and Option keys together to highlight in yellow the groups (static and smart) to which the
selected reference belongs. If more than one reference is selected, groups containing all will be highlighted. The
reference or group list must have the focus when the Shift and Option keys are pressed. If the group is in a
closed folder, that folder (or its topmost closed parent) will be highlighted.
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Concise View Pane

The concise view pane can be opened via the View menus, Option-Command-I (Summary) or Option-Shift-
Command-A (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:

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 information might be shown in the All display:
 62

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 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
 63

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 (including the URL Bookends
will create if the reference has a DOI) are highlighted in blue and are active (only the first 30 characters will be
shown for those in the URL field). E-mail addresses will also be active. In this case, if you hover the pointer
over it the entire URL will be displayed in the field's tooltip).

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).
 65

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.

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.

Note Stream Pane

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A note stream displays virtual notecards created from the Notes field. Notecards are useful for collecting,
reviewing, and organizing information, and for citing the paper (with or without the note, with or without cited
pages) in a document.

A note stream looks like this

Each notecard represents a paragraph entered in the Notes field—each paragraph must be separated from the
other by a blank line (i.e. two Returns in a row). For example, this Notes field would have 3 notecards:
 67

You can show the note stream by clicking on this icon at the bottom right of the List View window

or by using the View -> Note Stream menu. In addition to creating/editing notecards in the Notes field, you can
add a notecard with the + button, or by pressing Shift-Enter while the note stream is selected. Furthermore, if
you drag text from a Bookends reference, a selection from a PDF in the display pane, or another application,
and drop it on the note stream it will be used to create a new notecard.

You can remove a notecard by deleting the text from the Notes field, but generally you would do so by selecting
the notecard and pressing the - button or pressing the Delete key. To avoid the warning dialog, hold the
Command key down when you do this. Edit a note in the note stream by double clicking on it, or selecting it
and pressing the Enter key. To save the edited note click on the Close button (bottom right) or press Enter. To
abort press the Cancel button (bottom right) or press Escape. You can reorder notes by drag and drop.

Notecards offer a versatile way to enter temporary citations, with or without the note and with or without the
cited pages, into your word processing document. To insert the notecard as a temporary citation, select one or
more and use Copy Citation (Command-Y). To insert the notecard contents followed by the temporary citation,
use Edit -> Copy Note And Citation (Command-K). Notably, if you have entered the pages in the text the note
concerns, and you wanted it added to the temporary citation as cited pages, precede the note with an @ and the
pages. For example, if the notecard consisted of

@7-12 These are my thoughts.

and you invoked a Copy Citation, the temporary citation it created might look something like

{Smith, 2009, #123432@7-12}

If you are doing a Copy Note And Citation, the cited pages will not be included in the note, but only at the end
of the temporary citation.

• Bookends will include anything after the @ and before a space or the end of the line as cited pages.

• You can also drag and drop notecards into your word processor document to create a temporary citation,
or with the Option key held down to copy the notes and the citations.

• A contextual menu (right-click on the note stream) lets you access many of these functions. In addition,
the contextual menu will contain any URIs in the notecard, which you can then select and open. This
includes URIs to other references in Bookends, created with the Edit -> Copy Hypertext Link -> Copy As
Text menu
 68

You can set the font, font size, and color for notecards in Preferences.

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 Action
(gear) menu (Command- + and Command- - (Command-hyphen) 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 (often pdfs) by clicking on this icon
 69

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, web pages (webarchives), 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

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.
 70

Web pages are displayed in an active pane—that means that hypertext links are active. There are no navigation
controls in the List View, but a right-click on the web page brings up a contextual menu that lets you move back
or forward, if applicable.

PDFs can be displayed with WebKit (links are active, certain WebKit contextual menus are enabled) or in a pdf
pane (links inactive). You can toggle between these with the Action pop-up menu:
 71

· Note that some versions of the Adobe pdf plug-in can interfere with the WebKit display of pdfs. To
uninstall the Adobe pdf plug-in, launch Adobe Reader, open its preferences, click on the Internet label in
the left column, then uncheck “Display PDF in browser using :...”. Close the preferences window.

Text can be copied from pdfs if you are using WebKit for the display. Hold down the Option key when you
select to allow cropping of the text.

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 menu, a contextual menu right-click, or Command- + and
Command- -.

Double-clicking on an image 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. To open pdfs and web
pages in another application press Shift-Command-O or select “Open Attachment” from the Action menu.
Bookends will not try to uncompress attached .zip files.

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 an image 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.

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).

Direct entry of pdf/web page text to reference fields

If the attachment is a pdf (in WebKit view) or a web page, you can use Bookends to semi-automate the process
of entering reference information. To do this, select some text (e.g. authors) in the pdf, for example, and use the
Action pop-up menu and select the Copy Selected Text To menu option:
 72

Select the appropriate field and the text will be copied to it. Note that Bookends will attempt to parse names if
the text is sent to the Authors or Editors field. It assumes the names are separated by commas and are surname
last.

• Note: pdfs often contain invisible characters (often spaces) that are copied to the clipboard. These will appear
when you copy the text to Bookends, and you will have to remove them manually. Accented characters
usually are composed of the character, the accent, and a space, and will need to be repaired after the copy.

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.
 73

You can exclude references containing given words by placing a dash (minus sign) before a word in the live
search textbox. For example,

shakespeare -william

will find references containing the word "shakespeare" but not the word "william". The minus sign must
precede each word that is to be excluded, as in

blue green -red -purple

The dash must be the first character in the field or be preceded by a space for the NOT search to be performed.

• 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.

• 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".

• Press Escape to clear the search field.

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, so searching
for
 74

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

 The Inspector
The Inspector is a floating window that allows you to view and manage attachments or links for references in
your database. The Inspector can be opened from the Window menu, the List View Action pop-up menu, right-
clicking on the references in the List View, the Attach pop-up menu in the reference window. The Inspector will
remain open until you close it or the associated database is closed.

Attachment Inspector

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:
 76

Note: the image in the lower pane 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 tell Bookends to rename an existing attachment. When you do, any reference in the database that
attaches that file will be updated to reflect the new attachment name. Note that this will break links to that
attachment, if they exist, for references in other databases. Rename attachment can also be invoked in the List
View action pop-up menu or by right-clicking on the image of the attachment in the List View attachment pane.

Multiple attachments are normally listed in the order in which they were added. You can change that order by
rearranging (via drag and drop) the names in the list.

Link Inspector

A link is a relationship between two references. To establish a link, open the Link Inspector:

The reference that was selected in the List View (or the one in the opened reference window) will appear in an
image well at the top. Consider this to be the “parent”. To add a link, drag and drop a reference from the List
View (or drag its unique id from an opened reference window) to the listbox:
 77

There are two columns in the listbox. The first, Link Type, defines the relationship between the references. To
assign a relationship, use the pop-arrows on the left and select the one you want:

The first term references to the parent, the second to the reference in the list. For example, the parent could be a
review article, and the linked reference a work reviewed in that article. Note that in this case, when you view
the work reviewed as the parent, the relationship will be inverted (Work Reviewed : Review). You can edit and/
or add up to 10 link relationships in Preferences.

The second column shows the linked reference. The format for both the parent and the linked reference is set in
Preferences (the default is APA 5th Edition).

You can link one reference to as many references as you like. Use the checkbox to add or remove that reference
from the Hits List. Double-click on either the parent or a linked reference in the list to immediately go to that
reference in the List View.

Remove a reference link by selecting it and pressing the Delete key (press Command-Delete to bypass the
confirmation dialog sheet).
 78

You can change to a different parent by:

• dragging a new reference to the parent image well

• dragging an item in the linked reference list to the parent image well (“elevating” it)
• selecting a reference in the List View and using Window -> Inspector (Option-Command-A)

If you view more than one parent while the Link Inspector is open, forward and back arrows at the top left of
the Link Inspector let you scroll through the viewing history.

The Comments field in the Link Inspector is where to add your thoughts about the relationship between the two
references (for example, about the cogency of a rebuttal), quotes from the references, or any other information
you might find helpful.

You can see which references have links, and how many, by selecting "Links" as a List View column in
Preferences.

• When you use Replicate As Book Chapter to create a reference, the new reference will automatically
inherit a link to the book that contains is, with a link type of “Book:Book Section”.
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Online Search
Bookends allows direct searching and retrieval of book information from hundreds of Internet sites. Reference
surfing lets you go to web-capable sites (e.g. PubMed, Web of Science, JSTOR, etc.) via a built-in browser
(Bookends browser) and acquire pdfs and/or web pages related to references you find.

These search options are built-in: PubMed, the Library of Congress, Google Scholar, and Amazon (US, UK,
Germany, Japan, France, and Canada). Bookends also lets you search the ISI Web of Science and JSTOR (if
your institution subscribes) and the arXiv repository, a free open access site for e-prints in physics,
mathematics, computer science, quantitative biology, and statistics. 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.

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 Import button at the bottom of the search window:

If more than one database is open, you will instead see an Import pop-up menu, and you can
select which database to import to:

If the Import to Hits List is checked, Bookends will normally add the references you imported to any that might
already be in the Hits List. If you want to replace the current hits with the references you are importing, 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:
 80

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 most searches 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 and the built-in Bookends
browser:
 81

· 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:
 82

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.

Download pdf

When searching PubMed, JSTOR, and Web of Science a new checkbox appears at the bottom of the window:
Download PDF. If you check Download PDF Bookends will attempt to automatically download and attach
associated pdf files when you import references into a database using the Import button or pop-up menu, or drag
and drop:

This has the same features and restrictions as selecting a reference after import and selecting the menu option
 83

Refs -> Get PDF -> From Internet (If Available)

See the section in the User Guide on Get PDF for details.

Indicating that a reference is already in your database

If you are searching PubMed, Web of Science, or JSTOR, Bookends will highlight in yellow any retrieved
references that are already in your database. This is determined by matching PMIDs, DOIs, and JSTOR URLs,
respectively. The database must be open. If more than one database is open, Bookends will examine the
database nearest to the Online Search window in Z-order.

Right-click on the reference list and tell Bookends to select just the references that are not already in your
database (the ones highlighted in yellow). This is handy if you want quickly select and import the references
you don't already have.

If you select a reference highlighted in yellow and right-click on in the Online Search reference list, a
contextual menu will give you the option to Find This Reference In Database (Shift-Command-J), which will
take you to that reference.

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]

 84

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:

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:
 85

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 Possible Values

Publication Type Clinical Trial

Editorial
Letter
Meta-Analysis
Practice Guideline
Randomized Control Trial
Review
Addresses
Bibliography
Biography
 86

Search Subset 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
Gender Male
Female
Has Links To Full Text
Free Full Text
Species Humans
Animal
Publication Date 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 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).

PubMed Central ID number

 87

The User16 field for Journal Articles is used to store the PubMed Central ID number, and is named PMCID.
The PubMed import filter will import the PubMed field containing the PMC into PMCID. If you are creating a
bibliography for an NIH-funded grant application, you can add this field to the output.

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 full-text 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 full-text 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.

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 subscribes. You can restrict searches to specific editions, as detailed below in the section on creating
an import filter (Internet tab).

Some journals covered by the Web of Science do not use page ranges, but rather article numbers. These will
now be displayed in the search window and imported to the Pages field in Bookends (using the AP tag). The doi
for such articles, if present, will also be resolved properly.
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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.

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:
 89

This is the advanced search sheet:

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:

 90

or to recent publication date:

Library of Congress

You have the following options when searching the Library of Congress:

The simple search searches all fields and allows no boolean operators.

The boolean search allows you to specify up to three fields with boolean (AND, OR, NOT) searches:
 91

For both simple and boolean 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

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 boolean searches allow you to perform searches for author, title, date of publication, type of binding
(hardcover, paperback, etc.), subject matter, and more:
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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.

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 right-clicking 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.

To shorten download times, or to prevent the import function from downloading and attaching the cover art,
uncheck the Display image box.
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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.

Google Scholar

You have the following options when searching Google Scholar:

For information on how Google Scholar handles search terms, see this link

http://scholar.google.com/intl/en/scholar/help.html

Tip for names: Enter the author's name in quotations: "d knuth". To increase the number of results, use initials
rather than the full first name.

• Google Scholar results are often incomplete or truncated. Bookends will show as much of the relevant
data as it can.

Bookends will attempt to locate and import the best information Google Scholar offers about the reference. If
none additional information cannot be found, Bookends will import the information available on the web page.

· Note that if you import by drag and drop (rather than with the Import pop-up menu), Bookends will
import the information from the web page.

When you click on the Advanced Search button you'll be presented with this form:
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Bookends Browser

When selected, the entire online search window is devoted to the built-in browser. This is particularly useful for
reference surfing to web sites of libraries, publishers, or reference aggregators (e.g. CiteULike and OCLC
WorldCat).

Z39.50 library searches

To perform a Z39.50 internet 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. 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:
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If boolean searches are permitted, you might see something like this:

Selecting Boolean Search reveals these options:

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

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If you click the Action icon (or right-click in the Search Pane) you will be given the option to save the
current search:

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.

Searches can also be deleted by pressing the Delete key, or choosing Edit -> Clear.
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• 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:

Saved Advanced PubMed, Web of Science, and Google Scholar 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 searches are indicated by a different icon:

When an advanced search is selected, you can edit it by choosing the corresponding item from the Action pop-
up menu:

Automated PubMed searches

Saved PubMed searches can be performed automatically in the background at defined intervals.
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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.

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
 99

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 Import 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 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.

Determining an h-index

The h-index, sometimes called the Hirsch number, is a method that attempts to quantify the productivity and
impact of a scientist based upon his or her most cited papers. As defined by Hirsch:

A scientist has index h if h of his Np papers have at least h citations each, and the other (Np - h) papers have at
most h citations each.
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You can learn more about the h-index here: http://en.wikipedia.org/wiki/Hirsch_number

When you search Web of Science or Google Scholar in Bookends Online Search, you have the option of asking
Bookends to display the h-index for the papers you have selected in the list. You can do this by using the action
menu or right-clicking on the reference list:

After selecting the references you want included, at the bottom of the Online Search window you might see

Remember that you can remove unwanted references from the list by selecting them and pressing Delete.

Disclaimer: Sonny Software does not guarantee the accuracy of the h-index, which can vary depending on the
site used and the completeness and accuracy of the reference selected. If you want to use this value for a serious
purpose, we suggest you confirm it on one or more web sites such as Web of Science, Scopus, and/or Google
Scholar.

Reference surfing

When you access a web-capable site, a toggle button appears in the search window:

• Web-capable sites allow browser-access to references. Such sites include PubMed, Web of Science,
JSTOR, Google Scholar, Amazon, and arXiv.

When clicked, the image changes from the text to the Web icon, and some new controls appear:

From left-to-right they are: bookmark pop-up menu, URL field, data detector icon (appears when embedded
references are found), proxy icon (for drag and drop), text size decrease/increase, and forward/back navigation
arrows.
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The blue bookmark icon brings up a list of any sites you have bookmarked so that you can quickly go to them
while doing an online search. You can edit/add/delete bookmarks as well. This is functionally the same as the
File -> Go To URL menu, but more convenient if you are already reference surfing.

Here is an example of a search:

The hypertext links are live, and you can navigate the web site as if you were in your browser. Clicking on the
pdf link yields this
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The forward/back buttons allow you to move between pages—if you click and hold on an enabled arrow, a
contextual menu will appear that lets you move to specific pages before or after the page you are currently
viewing. The a/A buttons decrease or enlarge the HTML font size, respectively (they have no effect on the text
size of a displayed pdf).

The proxy icon ( ) is a drag-and-drop control that appears whenever there is web content in the display
pane. You can drag it onto a Bookends database, in which case it will be downloaded and attached according to
the options you select in the ensuing dialog:
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If you check "Attach to a new reference and autocomplete", Bookends will create a new reference, attach the
pdf (or webarchive), and bring up the Autocomplete Paper sheet so that you can locate the reference's metadata
online and import it

If you drop the pdf proxy icon onto the Desktop in the Finder, the web page or pdf will be downloaded and
placed where you dropped it.

When there is web content, right-clicking on the proxy icon brings up a contextual menu that lets you save the
pdf/page as follows:

· Attach Web Page To Selected Reference. This is the same as dragging and dropping the proxy icon on a
database window.

· Attach Web Page To New Empty Reference And Autocomplete. Creates a new reference and attaches
the pdf/web page to it. Then it opens the Autocomplete Paper sheet so that you can locate the reference's
metadata online and import it.

· Attach Web Page To New Internet Reference. Creates a new reference of Type Internet and attaches the
pdf/web page to it. Some of the fields in the reference will be filled out automatically, including Title,
URL, and Month and Year Accessed.

The Import popup menu also changes to reflect the presence of web content:

This allows you to import just the reference data, or to import the reference data and then download and attach
the web content displayed.

The URL field on the left contains the address of the web content. It is also editable and you can enter arbitrary
addresses of your choosing. Thus you can visit sites other than those for which there are filters. Note that any
content there can be downloaded and attached to references in your database, but the reference importing
feature will only operate on sites for which there are filters. When the Online Search window is in front, the File
-> Go To URL menu will use the Online Search browser instead of your default browser (to make it use the
default browser, hold down the Shift key when selecting the menu option).
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You can enlarge the browser view to encompass the entire window by selecting Bookends Browser from the
pop-up menu at the upper left:

· JavaScript is enabled in the Web browser. This can cause interface problems, such as incorrectly
rendered web pages, in some cases, and is selectively turned off at sites that are known to be
problematic. If you encounter such a problem, please contact us and provide the URL of the affected
web page.

· Note that you cannot download pdfs/web pages to Bookends or the Finder if the Adobe pdf plug-in is
installed. To uninstall the Adobe pdf plug-in, launch Adobe Reader, open its preferences, click on the
Internet label in the left column, then uncheck “Display PDF in browser using :...”. Close the
preferences window.

EZProxy and reference surfing/Bookends browser

If your institution uses EZProxy, you can use reference surfing/Bookends browser to access restricted web sites
even if you are off campus. Enter the EZProxy URL in Bookends Preferences Internet tab. The EZProxy
address must end in the characters %@.

To start an EZProxy session, open Online Search and either perform a search in Bookends browser or perform a
search with Google Scholar or PubMed (not JSTOR or Web Of Science, which require ip authentication) and
then click on the Web toggle icon to surf references. You will be asked for your name and password, and then be
taken to the article's web site. You can navigate to the article's pdf and use the Import With PDF import option.
For direct download of pdfs from these sites (that is, without using Bookends browser), you still require ip
authentication. If you leave the proxy space (the URL doesn't include the proxy information), you can start it
again by clicking in the URL field and pressing Return, or by pressing Option-Command-L.

· EZProxy is for Bookends browser/reference surfing access only. It will not allow you to perform direct
searches of restricted sites—you need to be on campus, or have a VPN client, for that.
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JSTOR and reference metadata detection

The Bookends browser has a JSTOR reference data detector. This means that you can use Bookends browser to
navigate to JSTOR even if you have username/password access (rather than ip authentication) and import
references you find into Bookends.

After you perform a search on JSTOR, the metadata detector icon

will appear. When clicked, you will be presented with a list of the references embedded in the web page that
you can import:

Automatic pdf download still requires ip authentication, but the drag and drop import and attaching of the pdf
will work with the Bookends browser proxy icon.

Reference data detection and COinS

Many web sites embed reference metadata in their HTML pages. A popular protocol for this is COinS
(ContextObject in Span, http://ocoins.info/). When you navigate to a web site in the Online Search window,
 106

Bookends will automatically detect the presence of COinS references embedded in the web page. You will be
alerted to this by the appearance of the data detector icon:

When clicked, you will be presented with a list of the references embedded in the web page:

Check the references you want to import and then use the Import pop-up menu (Bookends will offer to
download the associated pdfs, if it can locate them on the Internet and you have access privileges). Among the
many sites that embed reference metadata are

CiteULike (http://www.citeulike.com)

Copac (http://copac.ac.uk/)

OCLC's Open WorldCat (http://www.oclc.org/worldcat).

These sites can be accessed via the File -> Go To URL menu.

Here's one way in which you can combine reference surfing with data detection:

1. Add compatible sites of interest to your URL Bookmarks (File -> Go To URL -> Edit Bookmarks).
2. Open the Online Search window.
3. Choose the site from File -> Go To URL (for example, Open WorldCat).
4. Perform the search in the Bookends browser.
5. Click on the data detector's green icon, check the references to import, then use the Import pop-up menu to
import them (with or without their pdfs) into an open Bookends database.

· Bookends and Bookends Server can also embed COinS in bibliographies it generates for web sites. See
the section on COinS for details.
 107

· There are also data detectors for JSTOR that work in a similar fashion.

Data detection and indication of references you already have

The data detector sheet will indicate references you already have in the open database by displaying the titles in
yellow. This works with JSTOR and CiteULike, which provide their own unique identifiers, and with COinS
sites for references that have a doi (not all do).

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.

· You can also automatically import reference metadata using Autofill From Internet.

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.
 108

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: 123456789 — unique identifier

AU: Jones, Ron — author(s)
TI: This is my article — title
DA: 1995 — date
PY: 12-24 — page range
LA: English — language
AD: 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:
 109

· 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.

· 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.
 110

· If t he category is Pages, Bookends will strip out the following trailing characters, if present: " p", " p.",
" s", and " s.".

· Press Command-S to save an edited import filter.

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:
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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.

· 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

· 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.
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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

You must let Bookends know how to identify the end of a field.
 113

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:

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.
 114

• 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.

· 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.

· Source fields are ignored when valid tags are used to identify the ends of fields.

· 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
 115

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

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.
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· If the names are already arranged in the file as Surname, First Names(s) or Initials(s), uncheck the Parse
Authors/Editors checkbox.

Regardless of whether you are parsing authors/editors or not, Bookends will strip off any non-letter that are
found after a name (such as a trailing number).

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

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:
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Source tags

Fill in the tag for the Source box:

This is done exactly as you did above for other fields.

Collecting the Source

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:
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(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 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.
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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:

Creating filters for existing bibliographies

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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":

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
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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])

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
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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 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 $aRawlins, Jack,$d1946-
245 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:
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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
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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

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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:
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LOC Gateway Direct Z39.50 search

Text encoding-savvy No Yes

Allows access to UNIMARC and No Yes

OPAC servers

Accessible from behind an authenticating Yes No

proxy server

The SRU protocol is used by a small but influential 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 (or use Bookends Browser).

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 science, 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
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The possible editions are

Code Description
SCI Science Citation Index
SSCI Social Sciences Citation Index
AHCI Arts & Humanities Citation Index
IC Index Chemicus
CCR 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
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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.

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 Keyword anywhere 1016

Author 1003
Personal Name 1
Corporate Name 2
Conference name 3
Title 4
Series Title Journal/Series name 5
Keywords Subject heading 21
Abstract 62
Year Date of publication 31
Entry Date in Database 1011
Publisher 1018
ISBN 7
ISSN 8
LCCN LOC card number 9
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Local Control Number 12

Call Number LOC call number 16

Adding information to imported references

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.
 130

· To insert a Return, enter ‘¬’ (Option-L)

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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.).
 132

Formats distributed by Sonny Software are in the Formats folder. Formats that you edit or 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.

· 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

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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.

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). You can also use this pop-up menu to
add the Book chapter [Book] metatype.

· 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 (or Book chapter [Book] metatype) currently selected in the Type pop-up menu from the
Format.

Names
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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).

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 Appears as
Arnold, Mary Arnold, M
Bardot, Jean-Jacque Bardot, J-J
Krieger, K. 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 user-defined field (e.g.
Translator). These names can be output with the ordering of Editors or Authors (this is especially useful for
Edited Book Types).
 135

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).

If a particular name should not be parsed, for example 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,

Case

This selection 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.
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· 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.

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.

Format Order

Most of the Format display is devoted to defining how the reference data is to be ordered.
 137

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 single-letter codes:

Code Category Code Category

a Author(s) u1 User1
b Abstract u2 User2
d Date u3 User3
e Editor(s) u4 User4
f Journal/Ser. Title (full) u5 User5
i Issue number u6 User6
j Journal (short) u7 User7
k Keyword(s) u8 User8
l Address or City u9 User9
n Notes u10 User10
p First page u11 User11
p- Page range u12 User12
s Short title u13 User13
t Title u14 User14
u Publisher u15 User15
v Volume u16 User16
y Type u17 User17
z URL u18 User18
h Attachments
r Rating (0 through 5)
g Static groups to which the reference belongs

• Note: For backward compatibility, w, x, c, and g can also be used for User1, User2, User3, and User4,
respectively.
 138

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– (en dash — 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 en dash 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.

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.
 139

· 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

· 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.
 140

Punctuation

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.
 141

~~ Binding quote (tilde). Like $, except the quoted text will be omitted if the preceding or
following field is empty. The field must 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).

{} Conditional formatting group. This gives you a high level of control over what is output
when reference fields are empty.

^ 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. $p-

might be output as

p. 123

if there is a single page, and

pp. 123-125
 142

if there is a range of pages.

^ can also be used in a conditional formatting group (see above).

* 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 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
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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.

∆ (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).
 144

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:

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…

Bookends displays the information of a sample reference as it would appear in the bibliography at the bottom of
the window.

The information (authors, title, etc.) is taken from the reference window (if open) or the first selected reference
in the List View (if open), if the Types match. If neither are open, or if the selected reference's Type does not
match the Type selected in the format window, default example information will be used. The example will
update automatically when the format is edited or a new format is selected.

· 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.

· Bookends will not display hanging indents in the example, but they will appear in the word processor.
 145

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.

Use of spaces

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 Original order Effective order

1. a. t. d. p. a. t. p.
2. a. t. (d) p. a. t. p.
3. a. t. $Date: $d. p. a. t. p.
4. a. t. `Diss.` d. p. a. t. `Diss.` p.
5. a. t. $Diss.$ d. 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
 146

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. 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 Original order Effective order

1. v: p v:
2. v~: ~p v:
3. v|~: ~p 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
,) )
;) )
;. .
) ) space + close paren replaced with close paren
 147

() 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.

Conditional groups

Conditional groups give you a high level of control over what is output when reference fields are empty.
Conditional groups are enclosed by curly brackets, and the conditional fields are separated by the caret, ^. You
can place as many conditional separators as you want, and you can include punctuation and quoted text in the
conditional statements.

For example, if you wanted the title output in quote marks, and if no title was present the journal name output,
and if neither are present the publishers name preceded by the label "Published by", you could use this construct
in the Order field:

{"t"^j^`Published by `u}

The logic is: if there is a title output it in quote marks, if there is no title output the journal name, if there is no
journal name output the words "Published by " followed by the publisher's name. If there is more than one field
in a conditional group, all must have data or that group will be ignored.

Example: Stringent APA in-text citation style

Note: The APA citation format is included with Bookends. This discussion is 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)
 148

4. Click on the Bibliography Options tab and set the “et al.” options to

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.

Name Punctuation tab

Here you tell Bookends how author and editor names are to be punctuated. If Editors same as authors is
checked, you only need to enter this information for authors (and you will not be able to edit the editors’
setting).
 149

If a format order begins with an editor (e.g. an Edited Book), Bookends will punctuate the editors’ names as
specified for authors.

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 Results in

._ Harris, J._E._
(nothing) Harris, JE
. Harris, J.E.

Note: the underscore character _ is used to signify a SPACE.

After surnames. 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 Results in

,_ Jones, E.
;_ Jones; E.
(nothing) JonesE.

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 Results in

,_and_ Jones, E. Franklin, M. and Stanley, H
_and_ 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 Results in

_and_^,_and_ Jones, E and Stanley, H OR Jones, E, Franks, M, and Stanley, H
 150

• 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.

Citation Options tab

These settings work with Scan Document 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), …

 151

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.

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: Smith, 1989

Two authors: Smith and Jones, 1989
Three or more authors: 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.).
 152

Italicize et al.—If there are three or more names, Bookends will output the first followed by et al.

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 (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.

Letters for repeated years—For author-date citations and repeated authors, Bookends will output repeated
years and distinguishing letters (2006a, 2006b) unless this option is checked, in which case it will output
simply the letters (2006a, b).

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. Select Formats Manager from the Biblio menu.

2. Select the format you would like to base the custom format on.
3. Click on the Create New Format button .
4. Define the format as you would like the information to appear in the revised document.
 153

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.

• 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 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).

For ambiguous citations—This tells Bookends what to do when two identical citations refer to different
references. Append letter to year works identically to how citations are resolved for author-date citations. Add
initials/names/short title to citation until unique will use whatever is needed to distinguish the citations, starting
with initials, full name (if necessary), and finally the italicized short title (if necessary—the italicized full title
will be used if there is no short title entry). The last method is used in the MLA citation style.

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).
 154

Order grouped 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.

When using an author-date citation style, the sort will be based on the data in the final citation. For example,
these citations are sorted by year:

(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.

When ordering grouped citations in a custom citation format, the date sort will be alphanumeric and based on
the date information entered for the reference. For the sort to be chronologically correct, therefore, the date
should consist of just the year, or the year first, as in '2008 Feb 2'.

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
 155

, 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.

· If the final citation contains no text before a cited pages entry, any spaces or punctuation that begin the
before pages text will be suppressed. This will prevent, for example, a space from being output before a
page number in the MLA format when the author's name is not output.

Bookends will use Page ranges for the format to determine how a page range will be output:

Bibliography Options tab

These settings work in conjunction with Scan Document 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.
 156

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. New England Journal of Medicine

J. Immunol. 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 "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
 157

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 (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 and your money. 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 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:
 158

Replace repeated authors with. If checked, Bookends will output whatever is in the text box (default is three
em-dashes) instead of the author's name if the preceding reference in the bibliography has the same author.

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.

COinS

It is possible to embed reference metadata (which includes details such as reference type, authors, title, etc.) in
an HTML page using a protocol known as COinS (ContextObject in Span, detailed here http://ocoins.info/).
Applications that have COinS-aware data detectors will alert you to the presence of such information. The most
popular example of this is the combination of the Firefox browser (http://www.mozilla.com/en-US/firefox/) and
the free Zotero plug-in (http://www.zotero.org/).

You can choose to have Bookends include COinS metadata in HTML bibliographies it generates. This could be
a bibliography you create to be included in a web page, or a bibliography dynamically generated by Bookends
Server. This means that anyone using Zotero, for example, would be able to capture the references you have
posted.

To enable this feature, check Embed reference metadata (COinS) in HTML output in Preferences (OpenUrl &
COinS tab). Bookends will include the COinS automatically with no further input from you.
 159

Book chapter [Book] metatype

A metatype is a "compound Type", meaning that it allows you to combine information from two references in
one citation. Bookends offers a metatype that fuses information from a book chapter and its book in a single
footnote and/or bibliography entry. Such a citation/bibliography entry might look like

Smith, The Way Things Are, In: Jones, RR (ed.) 2009.

or

Johnson, EW In The Way We Were, p. 69-71

where parts of the citation are taken from the book chapter and parts from the book that contains it. You can
control under what circumstances this metatype is to be used (for example, only if 3 or more chapters are cited
from the same book). In addition, the book will be added to the bibliography, even if it is not explicitly cited in
the document (it is implicitly cited when you cite a book chapter that uses this metatype). You can have the
metatype determine the appearance of a final citation (e.g. footnote), an entry in the bibliography, or both (and
the footnote and bibliography entry can be formatted differently).

Creating and using a metatype may seem complicated, but it is actually relatively straightforward if you follow
these steps:

1. You must be using a custom citation format to create the citations. You can't use metatypes with the built-in
numbered or author-date citations.

2. In the format, use the "Add Type" popup menu to add a "Book chapter [Book]" type in the main format (if
you want it to be used in the bibliography) and/or to the custom citation format (if you want it to be used for
footnotes and in-text citations). If the format doesn't have a Book chapter [Book] metatype defined, it will not
be used even if you instruct Bookends to do so in the Citation Options tab.
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3. In the Book chapter [Book] metatype window, fill in the Order fields and name punctuation settings as you
would for a normal Type, with an asterisk separating the format you want for the book chapter from that for
the book. In the example above, you might enter this in the Primary Order field:

The author and title (not enclosed in square brackets) will be taken from the Book chapter, the quoted text,
editor, and date (all enclosed by square brackets) will be taken from the Book.

You can alternate information between the Book chapter and the Book, such as
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In this case, the author of the Book chapter will be followed by the title of the Book, and finally by the page
range of the Book chapter.

4. In the Citation Options tab in the format, tell Bookends when to use the Book chapter [Book] metatype. The
options are shown here:

This should be set just once, in the main format (the one that creates the bibliography, not the custom citation
format).

5. Finally, you must tell Bookends what books the chapters you are citing belong to. This is done with the
reference link feature. Use the Link Inspector to assign a "Book: Book Section" relationship between each
book and the chapters you are citing:

If you don't do this Bookends will not know the book to cite and will treat the reference simply as a book
chapter when it is formatted.

• If you are using the Refs -> Replicate As Book Chapter to create chapter entries, Bookends will do this for
you.

If you are creating a formatted reference without scanning, for example in the List View window lower pane,
Bookends will use the Book chapter [Book] metatype if all of the requirements above are met and the format is
set to use the metatype (that is, the pop-up menu is not set to Never).
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Note: you should not create a new reference Type in Preferences. Bookends chapter [Book] is a metatype and
only has meaning for a format. It will work with the existing Book chapter Type and Book Type (e.g. Edited
book, Book, Conference Proceedings) if the above conditions are fulfilled.

Scanning Documents

Before the scan

You can insert temporary citations into Microsoft Word, Mellel, Pages '08 and ‘09, Nisus Writer Pro,
OpenOffice, 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 or any other word processor. In Word, you save an RTF file by
choosing Save As and then selecting Rich Text Format.

· Bookends can scan files in Apple Pages '08 and ‘09, OpenOffice, and Nisus Writer Express or Pro
format. It can also scan an RTF file saved from any word processor.

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.

• Note that if you want the citation to be placed in a footnote, you must create the footnote in your word
processor first, then insert the temporary citation in the footnote text area.

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 document
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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 cited references from the bibliography

You may want to cite a reference such as letter or a personal communication in a footnote but not in the
bibliography. To do this, precede the temporary citation with a $. For example,

{$Smith, 2009, What I did last summer}

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}

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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

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:
 166

(Maguire, 2005, pp. 45-46)

or

(Maguire, 2005, pp. 45-6)

If you use an en-dash to separate the pages in the text of your word processor, Bookends will use an en-dash in
the final citation.

How cited pages appear in the scanned document is specified in the Format definition, Bib & Citations Options
tab:

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)

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· 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).

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 Document Dialog

When you choose to Scan Document, 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 or a Subject
Bibliography after scanning a manuscript, depending on which you selected from the pop-up menu. The
bibliography will be placed at the end of scanned RTF file after the first scan. If you are doing a rescan of an
RTF document and Retain hidden citations was enabled, the bibliography will be placed wherever you had
previously moved it. Subject Bibliographies are placed in the clipboard, to be pasted into the scanned RTF file
after opening it in your word processor.

Retain hidden citations—If checked, Bookends will retain the temporary citations in the new RTF document
in an invisible form. This means that you can rescan the new document and Bookends will automatically
incorporate any changes you have made since the last scan. You can also unscan the RTF document, which will
remove any hidden citations and the bibliography. Note that hidden citations are only recognized and saved by
Microsoft Word. If you open the RTF file in another word processor and save it, the hidden citation information
will be stripped out and you will not be able to rescan/unscan the RTF document. In addition, this should be
unchecked if you scan TextEdit RTF documents, because it may result in unexpected truncation of the
document.

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.
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· 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 appended to a new RTF file.

Generate bibliography as—If a bibliography is generated, it will be created either with styled text. If you scan
a plain text file, you will be given additional options such as save as generate s HTML, UTF-8, or BibTeX.
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 styling is selected for formatting, Bookends will create the bibliography in plain ASCII but add
BibTeX commands for bold, italic, super-, and subscript if these styles are encountered. Smart open quote
marks (“) will be converted to two backquotes (``) and smart close quote marks (”) will be converted to two
apostrophes (''). If Convert to TeX is checked in the BibTeX Preferences, accented characters will be converted
to their TeX equivalents.

Create new file (not shown)—This option is available when you scan a plain text file. It 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.

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
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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).

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:
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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.

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 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 or to a PDF file.

You must deal with the unmatched citations before closing this 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.
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Replacing citations with numbers

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 Document:

· 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}...
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· 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

· Do not place the add-in or the template in the corresponding

Microsoft Word 2008 folders. They will not work with Word 2008.

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:
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· Note that there is no Bookends toolbar in Word 2008. Word 2008 does not let you invoke AppleScripts
from a toolbar.

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 10 Folder/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
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the word "Gibbs" will appear in the Bookends Find Dialog box.

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:
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These are very similar to the options available when you select Scan 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 Add-in. To do this, save the document as a text file and
use the Scan 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.

Typical use of the Microsoft Word add-in with Bookends

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· 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 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.

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

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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
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other punctuation. This is the same as using the asterisk in other word processors: {*Johannson et al., 2003,
Nature}

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:

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Refresh citation list: Updates the citation list and removes citations that were deleted from the document.

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. Insert temporary citations from Bookends as needed.

2. Scan the document. The first time you will be asked for a format.
3. Continue to write and insert/remove citations.
4. 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 Pro (version 1.4 or later)

Bookends can automatically insert temporary citations into and scan documents created with Nisus Writer Pro.
Nisus Writer Pro has a set of command in the Insert -> Bibliography menu that all it to work directly with
Bookends.

Switch to Bookends

Brings Bookends to the front as the active application.

Find Reference…

Brings Bookends to the front as the active application with the Find dialog box open. If any text in the foremost
Nisus Writer 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 Find Reference.

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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.

Insert Bibliography Placeholder

Places the text

<Bibliography placed here after document scan>

at the insertion point. When you scan the document, this is where bibliography will appear.

If there is no placeholder, the bibliography will appear at the end of the document.

Scan Document

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, you will be presented with the
following dialog box:
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These are very similar to the options available when you select Scan Document from the Bookends Biblio
menu, although some items are automatically set for you and are therefore disabled.

The options are the same as those available for scanning a Microsoft Word document, and you can read about
them here.

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.

• The citation delimiter characters (set in Preferences) must be set to same used when the document was
scanned.
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Apple Pages '08 and ‘09

Bookends can scan Pages '08 and ‘09 files and replace temporary citations with final citations. Do do this, use
the Biblio -> Scan Document menu, select a Pages '08 and ‘09 document, and then scan as you would an RTF
file.

A new Pages document will be created, and after the scan is completed it will be opened in Pages and the
formatted bibliography pasted in.

By default, the bibliography will be placed at the end of the document. If you want it placed elsewhere, enter

<bibliography>

in the document at that site. If there is an AppleScript error during this phase, you can still perform a manual
paste to place the bibliography where you want it.

If the final citation contains styled text (e.g. a superscripted number or a custom citation as in a footnote), the
font will be the default font for the text element. You can change this for one or all elements in the document by
using the Pages Styles drawer.
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You can also scan an open Pages document with the menu Biblio -> Scan Open Apple Pages Document.

• Although Bookends can scan Pages documents saved with track changes active, the results may be
unpredictable and it is strongly recommended that you turn off track changes and then save the document
prior to a scan.

Apple Pages Scripts

Sonny Software provides scripts for the following interactions with Apple Pages: Go To Bookends, Find In
Bookends, Insert Citation From Bookends, and Scan Open Pages Document In Bookends. These scripts can be
accessed while you are running Pages via the Scripts menu on the right side of the menu bar (it's an icon, not a
word). If you don't see the Scripts menu, you can enable it by running AppleScript Utility and checking "Show
Script menu in menu bar". If you are running Bookends for this first time, these scripts will be automatically
installed in ~/Library/Scripts/Pages. If you have run Bookends before, you'll need to move the scripts there
manually.

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:

· a research group wants to restrict the database content to references that are relevant to their own group,
research, or institution.

· 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).

· you want to use Refbase locally or behind a firewall and not with public access.

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.
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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

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…

Mac OS X 10.4 (Tiger) and 10.5 (Leopard):

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 option 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.

Mac OS X 10.6 (Snow Leopard):

This menu option 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 Go To Download Page 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. This usually means replacing your old Bookends 10 folder with the new one on the .dmg.

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.

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Attachments folder

Default 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 or folders automatically for details on how to have Bookends move
attached files to one folder.

Remove Paths to Arbitrary Attachment Folders

Bookends stores the paths to any folder in which you have attachments if they are outside of the default folder.
On occasion this can cause problems, for example a very long pause as the Finder tries to locate a folder on a
server that is no longer available. In such cases you can clear the internal list of paths by clicking this button.
Note that you will have to reattach one file for every folder if you want to reestablish the path. This does not
apply to any attachments in the default folder or its subfolders—they will always be found.

Default font

You can set the default font and size for bibliographies, references, lists (Term Lists and the List View), and
notecards.

Toggle with
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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

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 10 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. 12 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).

• This setting applies to linked references. If you link to a group, the group's name will always be used.

Journal Glossary
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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

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.

Refs
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Reference Types

To change a reference Type, click on its entry in the list. The twenty 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).

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

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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 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
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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-month-day). The advantage of the latter is that it will sort
correctly by date when you do an alphanumeric sort.

Lists
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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.

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 non-Roman) 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.

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· 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 eight ways:

Number of authors
one two three or more
First Only Doe, J Doe, J Doe, J
Multiple Doe, J Doe, J & Smith, W Doe, J et al.
First...Last Doe, J Doe, J & Smith, W Doe, J...Henry, SR
All Doe, J Doe, J & Smith, W Doe, J, Smith, W &
Henry, SR

Check Surname only to have only the name before the comma output.

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, the number of other references a reference is linked to, the date added or last modified, and the
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 (Control-
Command-#) are shown for your information and cannot be modified.

The color can be applied to the text or to the background of the labeled references.
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Notecard color

Select the background color for notecards. If you make changes that you don't like, use the Set To Default button
to restore the original (yellow).

Concise View

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.

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View All label color

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

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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.

Copy Citation
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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.

· 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.

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.
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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: ^, @, or ~
Subscript: |, \, 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.

Sentence & Title Case

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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.

For some romance languages, contractions in front of a noun (such as d' and l') should be left as lower case.
When using Title Case, Bookends will treat the apostrophe as a word break character unless it occurs prior to a
word-terminating letter "s" (the possessive case). Therefore, for the examples above, entering the letter d or l in
the list of words to be unchanged when applying Title Case would cause a word such as "d'etat" to be output as
"d'Etat".

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 ignored word must end with a space, hyphen, or
apostrophe to be ignored.

Links
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Link Relationships

These are the relationships you can assign when you link two references in the Link Inspector. You can have up
to 20 link relationships. You should define only one pair for each relationship: Bookends will automatically
generate both the forward and backward link options for you (e.g. if you enter Review and Work Reviewed in
preferences, Bookends will let you also select the reversed relationship, Work Reviewed and Review, from the
Link Type pop-up menu).

You can edit and/or add your own relationships. Note that they are stored internally by their place in the list, so
if you move a relationship to another row, the Link Inspector will change the wording of the relationship to
what you enter in the old row.

Check the Link Type you want to be the default when a link is made (or don't check any if you want the default
to be undefined).

You can see which references have links, and how many, by selecting "Links" as a List View column (Lists tab).

Format for linked reference display

The references display in the Link Inspector will be in the format selected here.
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BibTeX

Enable BibTeX

Enabling BibTeX turns on features that make working with BibTeX references and citations easier.

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.
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· 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 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).

· 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,
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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 ("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
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Proxy Info

If you are using a proxy server to access the Internet, Bookends will retrieve that information from the System
Preferences. If you want Bookends to use a different proxy setting from the rest of your applications, check
Override system proxy settings and enter the proxy server address and port that you want Bookends to use. This
setting will be used by Online Search but not by Bookends browser (reference surfing), which always uses the
settings in System Preferences.

If your server requires authentication, the User Name/ID and Password must be entered here. Otherwise leave
these fields blank.

The checkbox Proxy server authentication is useful if you are switching from one environment where an
authenticating proxy server is used to another where it is not.

EZProxy is an HTML-based protocol many university libraries use to allow students to access restricted
publications from off campus. You can use Bookends browser with EZProxy by checking this option. The
EZProxy address must end in %@, as in

http://offcampus.lib.washington.edu/login?url=%@
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Bookends will replace the %@ with the URL you are trying to reach. If the address does not end in %@, the
proxy will not work.

More information about how to use EZProxy can be found here.

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 contain dois and might be listed on PubMed or Google Scholar, uncheck this option
to avoid the slight delay caused by checking for reference availability.

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.

· You can read more about Refbase and what it does in the section in this User Guide called Refbase.

OpenURL & COinS

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OpenURL

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
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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 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).

COinS

COinS (ContextObject in Span) are reference metadata embedded in HTML pages. Bookends can automatically
generate and insert COinS into HTML bibliographies created with the Bibliography Formatter or Bookends
Server. See the section on COinS for details.

To enable this feature, check Embed reference metadata (COinS) in HTML output.

It is recommended that each COin contain a referrer id that identifies your web site, in the form

<your domain>:<your-id>

(for reference, see: http://ocoins.info/cobg.html)

To do this, enter your referrer id here and Bookends will include it in the COinS output.

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.
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File Menu

· 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 suggest a name that ends in ".bdb". Bookends will recognize a file with the extension ".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…
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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 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
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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 selected, Bookends will 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.

If you check the corresponding checkboxes, Bookends will perform a sync automatically when the database is
opened and/or closed.

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 one 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. Configure 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.
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· Ancillary files, such as attachments, must be synchronized separately.

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.

• 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).

· You can import text files into Bookends by dragging and dropping it on the Bookends icon in the Dock.

· 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.

• 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;
 219

shadow and 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 tab-delimited 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.
 221

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 many 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).

· References imported from a Bookends 7 export file will be assumed to be in the encoding of the default
reference font used in Bookends.
 222

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 pop-up 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.

· 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.
 223

Filters distributed by Sonny Software are in the Import Filters folder. Filters that you edit or 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.

· 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.

• Note: This is intended to be used for moving data to a third party application for manipulation and
then immediately importing back into Bookends. It will not work for exporting/importing between
different versions of Bookends.

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.
 224

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 from Bookends as "EndNote 8 XML" or later will retain links to attachments on the
local hard drive if imported into EndNote 9 or later.

Export attachments too

If this checkbox is marked, Bookends will export any attachments belonging to the hits to the same folder a the
exported hits file. Export rules are the same as for Refs -> Export Attachments (immediately below).

Export Attachments…

This menu will be enabled when the first selected reference in the List Window (or the reference in the
reference window that is in front) has attachments. Bookends will create of a copy of each attachment (in the
case of the List View window, for each selected reference that has attachments) in the selected destination
folder. The original attachments will remain where they were. An attachment will not be copied to the
destination folder if the folder already contains a file with the same name.

Go To URL

The Go To URL menu choice lets you quickly open bookmarked web sites in your default browser or the Online
Search browser.
 225

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 Remove checkbox. The bookmark will be removed from the list when you
click OK.

If the Online Search window is in front, the destination web page will be loaded into the Bookends browser. In
this case you can force it to use the default browser by holding down the Shift key when selecting the menu
option.

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).

· You can access the same menu options and edit bookmarks with the bookmark pop-up menu when you
are reference surfing.

Online Search...
 226

Brings up the Internet search window. See the section on Online Search in this user guide for more information.

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.
 227

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.

Repair…
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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 check mark 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

Selecting it will cause temporary citations to be made of all of the references selected in the List View window.
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Copy Citation And Modifiers…

This brings up a dialog box that simplifies the generation of temporary citations that contains special formatting
instructions:

If text is entered into the first textbox, it will be added as Cited Pages (preceded by the @ symbol) in the
temporary citation.

· If there is any selected text in the frontmost reference window, Bookends will use that as the default
value for Cited Pages.

Any text in the second textbox will be inserted in front of the temporary citation, as in {\See also \Smith et al.,
2009, whatever}

You can also tell Bookends if you want the citation treated in a special manner after the scan (the punctuation in
the square brackets tells you what character will be added to the temporary citation by Bookends):
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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 Pro or Express, Pages '06 through '09,
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/Copy Notecard As Hypertext Link

Copies a hypertext link to the selected reference or group 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 or group 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:
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· 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).

If a notecard is selected, the menu changes to Edit -> Copy Notecard As Hypertext Link. This is identical to
Copy Hypertext Link, except the contents of the notecard will be displayed as the link.

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 Document…

This brings up the dialog box for files on your hard disk (Apple Pages '08 and ‘09, OpenOffice, Nisus Writer
Pro or Express, RTF, RTFD , or text files).

You can choose to generate a normal bibliography or a Subject Bibliography (see next) after the scan.
 235

See the section Scanning Documents for details on how to prepare documents for scanning and then to scan
them.

Unscan Word RTF Document…

You can unscan a Word RTF document that was previously scanned with Retain Hidden Citations checked. The
result of the unscan will be an RTF file in which final citations and the bibliography have been removed and
temporary citations have been restored. Note that you can rescan without doing an unscan first.

· Only Microsoft Word and Nisus Writer Pro v10.3.1 or later will recognize hidden citations in RTF files.
If you open and save an RTF file in any word processor other than Word, the hidden citations will be
lost and you will not be able to unscan it.

Scan Open Apple Pages Document…

If Apple Pages is open, Bookends will enable this menu. Bookends will scan the last saved version of the
document open in Pages '08 or '09. If the document has never been saved, Bookends will offer to switch to
Pages so you can save it. If the document has unsaved changes, Bookends will offer to save the file before
doing the scan. If you choose not to have Bookends do this, the scanned and formatted document will not
include the unsaved changes.

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:
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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. Both static and smart groups will be available if you choose Group.
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.

· 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.

Here is an example of a subject bibliography by Author, in the Cell format:

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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.

Bookends is distributed with over 200 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).
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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
Document).

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.

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 Embed reference metadata (COinS) in
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HTML output is checked in Preferences, Bookends will include this in the HTML output. See the section on
COinS for details.

If “as BibTeX” is selected, Bookends will generate the bibliography as plain text but with these changes to
accommodate BibTeX styled text commands:

1. Bold text will be output as \textbf{the bold text}

2. Italic text will be output as \emph{the italicized text}
3. Superscripted text will be output as $^{the superscripted text}$
4. Subscripted text will be output as $_{the subscripted text}$
5. A hyphen in a range of pages will be output as two hyphens
6. Quotation marks that follow a space ( ") will be output as ``
7. 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.

Formats Manager…

Select this to see a list of the available formats:

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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.

Default Format

This menu holds the names of all the formats that are currently enabled. A check mark appears before the active
format. You can change the active format to another by selecting it from the menu.
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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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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.
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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).

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 attempts 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
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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).

The new reference you create in this way will automatically be linked to the book that contains it, with the link
type of “Book:Book Section”.

Show With Chapters

This is enabled if the reference window in front, or the first selected reference in the List View, is a book
chapter, book, edited book, or conference proceeding. When a book or variant selected, Bookends will find and
list the book and any chapters it has (they are identified as such if they are of Type Book Chapter and have the
book's title in their Book Title field). If a Book Chapter is selected, Bookends will list all of the other chapters
you have from the same book. You can also invoke this in the List View with a right-click or with the Action
menu pop-up.

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.

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 fewer attachments is removed. If the number of
attachments is of the same, the one that has less information in Notes attachments is removed. If the
Notes are the same, 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:
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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:

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").

· This window will not appear if the static groups to which a reference belongs is to be shown, because
this is not a property of the reference itself.

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).
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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).

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 multi-button 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 pop-up menu at the upper left you can choose to search the database or, if there is one, the existing
Hist List.

Beneath that is up to 12 rows of searches you can perform (click on the or the button to add or
remove a row, respectively).

The first column lets you set the boolean search conditions.

The second lets you set what you are searching for (Text, Type, Label, or Rating).

The third pop-up column contains comparators (is, is not, etc.) as well as the conditions for a text search:

words beginning with…

whole words
characters
field is empty
field is not empty

Note that the last two possibilities are metasearches, and search for a condition rather than specific text. If you
are searching "All fields", a reference with text in any field will be ignored if you select "field is empty", and
will be found if you select "field is not empty".

The fourth column contains the information you are searching for. If it is not text, a pop-up menu appears with
the appropriate possibilities (as list of Types, Labels, or star ratings). A text search allows you search for

The final (fifth) column appears only if you are performing a text search. In addition to any particular field, you
can search all fields or the unique id field. The field names are those of the default reference Type set in
Preferences (typically Journal article). If you are searching for information in another Type (e.g. Book) you
would search the corresponding field in the reference window.

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").
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How a search is done

The Find function allows you to perform up to 12 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. You can also search for references that do or do not have text in particular
fields or anywhere in the reference (All fields search).

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 Matches Doesn’t Match

cat cat and catsup meercat
blue paint blue paint blue (or paint)
blue paint paint blue blue (or paint)
Smith, AB Smith, AB Smith
Smith, Smith, Allan Arrowsmith

A whole words search for

Search Word Matches Doesn’t Match

cat cat catsup
blue paint blue/paint blue (or paint)
Smith, AB Smith, AB Smith
Smith, Smith, Allan Asmith
Smith Smith, AB Smithson

A characters search for

Search Word Matches Doesn’t Match

cat meercat dog
blue paint blue paint blue/paint
Smith, AB Smith, AB Smith
Smith, Smith, Allan 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".
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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

· Use the ¬ character (Option-L) to find the Return character (ASCII 13). This will work only with a
character search!

Find Again

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.

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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 (Structured Query Language) lets you manipulate conforming databases, such as Bookends, in a near
English-like syntax. These searches do not use the database indexes (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:

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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 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'

• 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
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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] (note: pages is a reserved word and must be surrounded by brackets to be used)
thedate (note: date is a reserved word)
publisher
location (address or city)
url
title2
abstract
keywords
notes
user1
user2
user3
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:

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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 (relative reference number: 1, 2, 3, etc.)

hit (Hit number. If the reference is not a Hit, this value will be 0)
type (position in the Type pop-up menu, starting at 0)
uniqueID (unique ID of the reference)
rating (an integer from 0 to 5)

Example:

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:

= (equal)
IS (equal)
<> (not equal)
IS NOT (not equal)
> (greater than)
< (less than)

Regex:
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REGEX (is contained in)

=, <>, >, <, 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, 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'

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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
OR
NOT

Example:

((authors REGEX 'Henson, J') AND NOT (title REGEX '(?i)equator')) OR (abstract REGEX '(?i)mercator')
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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 matches a word boundary (transitions between word (\w) and non-word (\W) characters).
\B matches the string within a word (any position that's not word boundary).
\A matches the beginning of the target string.
\Z matches the end of the target string.

^ matches at the beginning of a line.

$ matches at the end of a line.

\w Matches a word character.

\W matches a non-word character.

\r carriage return (ASCII 13)

\n line feed (ASCII 10)
\t 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]"

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]')
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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)

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[pages] = '1-10' Pages field is “1-10” (pages must appear in brackets)

title REGEX 'Life' Title contains the letters "Life" (case sensitive)

title REGEX '(?i)Life' Title contains the letters "Life" (case 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" (case sensitive)

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 andGeorge, 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
"secondaryexample" (case sensitive)

Search for the last 15 references entered

id > (select max(id) - 15 from thereferences)

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Search for references that were edited within the last 2 weeks

For US systems:

dateModified > datediff( now(), '01/01/1904 00:00:00', 'second' ) - (14 * 24 * 60 * 60)

For European systems:

dateModified > datediff( now(), '01-01-1904 00:00:00', 'second' ) - (14 * 24 * 60 * 60)

· Change 14 to the number of days you want as the interval since last edited.

Search for references that do or do not have attachments

To find references with attachments:

varCharField REGEX '[a-z]'

To find references without attachments:

NOT varCharField REGEX '[a-z]'

To find a reference with a specific attachment:

Locate('my attachment name', varCharField) > 0

Global Change

Warning: Global Change operations are NOT undo-able!

This is a hierarchical menu with five choices:

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· 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.

· 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:
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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…

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.

· 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.
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· Enter the ¬ character (Option-L) to insert a return character.

Change Reference Type…

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.

Remove Orphaned Attachments…

This option removes an attached file from a reference if the file cannot be located.

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:

· Selecting Peek from the Refs menu.

· Holding down the Shift key and clicking on the name of the field you want to peek at.

· Clicking on the Peek button in the palette.

Quick Peek
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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).

Autofill From Internet

This option automatically imports or updates reference metadata in selected articles and books. If the first
selected reference in the List View (or the one in the reference window) has a PubMed ID (pmid), Digital
Object Identifier (doi), or ISBN, the menu Refs -> Autofill From Internet is enabled. When invoked, Bookends
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will use the pmid, doi, or isbn to find the reference metadata (author, title, etc.) and fill in the corresponding
fields in the reference. Bookends will try to find the reference on PubMed first (even if you only have the doi),
and if the reference is not there will try Google Scholar. If the reference has an ISBN and no pmid or doi,
Bookends will use it to find the book on Amazon.com. This option also useful for updating references,
especially those in PubMed, whose metadata can change after the initial electronic publication.

• You can also create a new reference and autofill it in one step by dragging and dropping a doi, or a
browser’s HTML link to a reference on PubMed, onto a database window. If a doi, it must begin
with the characters "10." (without the quote marks) and only the doi must be present in the drag.

• You can also use Autofill to fetch the reference again, for example to update a reference on PubMed
that has changed as new publication information was added. 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 corresponding import filters (PubMed, Google Scholar, or Amazon) will be
untouched.

Get PDF

This hierarchical menu offers two ways to find and attach pdfs to the selected references:

From Internet (If Available)

Bookends will attempt to find and download the pdf(s) for the selected article(s) from the Internet. 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).

To find the pdf, some unambiguous identification information must be entered in the reference record.
Bookends looks for the following information and searches compatible sites for the pdf:

· PMID (in PMID field or as part of a PubMed URL in the URL field)

· JSTOR link in the URL field (begins with http://www.jstor.org/stable/)

· DOI in the DOI field

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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, or
the Spotlight engine simply isn't capable of locating the file based on the text entered in the Bookends reference.
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.

Autocomplete Paper…

This menu item is enabled if the selected reference has a pdf or webarchive attachment. When invoked, it brings
up a dialog sheet that shows the attachment and provides several fields in which you can enter information from
the pdf (author, title, year, etc.). Different reference sources support different search options, and Bookends will
enable search fields that are appropriate for the selected source (PubMed, Google Scholar, Web of Science, or
JSTOR).
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An Action pop-up action menu near the top left of this dialog copies selected text from the attachment to the
search fields or to the reference itself:

If you copy the text to an autocomplete field, in the case of authors or year Bookends will attempt to clean up
the raw text to a form suitable for submission to the search engines. Bookends will use the information to search
PubMed, Google Scholar, or JSTOR (selected from the pop-up menu at the lower right), and give you a list of
the first 20 references that match. You can refine the search, if necessary, until you find the reference. Select it
from the list, click on Import, and it will be downloaded to your database and the attachment associated with it.
Only fields that have tags in the corresponding import filters will be imported.
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If the attachment has a doi, Bookends will insert it in the DOI field and do a search automatically. if it does not
have a DOI, you will have to enter information in one or more search fields and then do a search.

Note that you can also perform an Autocomplete Paper on a pdf when it is being attached.

• To autocomplete from JSTOR or the Web of Science you need access privileges and ip authentication.

• If you close the Autocomplete dialog sheet without finding a match, Bookends will display the empty
reference window for you to edit manually.

If you cannot find the paper’s metadata online, you can still copy pieces of text from the pdf to individual
references fields with the Action pop-up menu Copy Selected Text to Reference Field.

The selected text will replace any text that might already be in that field (which is usually empty if you are
autocompleting a paper). If the text is sent to the Authors, Ser. Editors, or Translator field, Bookends will
assume it contains names and will try to clean it up. It will assume that words separated by commas represent
names, and that the names are surname-last. Bookends will also remove punctuation not normally association
with names, as well as numbers and common superscript symbols. Click the Close button when finished.

Search tips:
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• More is usually not better. Use the minimum number of criteria to locate the reference. Using too many (for
example, entering each word in a long title) can result in the reference not being found.
• If a search containing an accented character fails, try it again with the corresponding unaccented character.
• You can search for more than one author by separating the names with a semicolon. However, usually
searching for one author (especially the first author) is more likely to find the reference you want.
• Bookends will try to eliminate confounding characters (such as numbers and superscripts) from the authors'
name when you use the action pop-up menu, but you may still need to clean up the text before doing the
search.
• Each source has slightly different search optimizations. For example, PubMed likes names as "surname
initials" ("smith aj"), although for publications since 2002 the full name can be used if it's included in the
article. Using punctuation (such as a comma) in a name can result in failure to find the article.
• Bookends lets you enter text only in search fields that make sense for the source. For example, PubMed and
JSTOR let you restrict searches to title words, but Google Scholar does not. PubMed lets you restrict by the
first page of an article, but neither JSTOR nor Google Scholar do. Search fields that do not work with the
selected source will be disabled.

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.

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.

DOI

This hierarchical menu brings up these options:

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Lookup Article 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/.

Get DOI

Bookends will request the reference's digital object identifier (doi) from CrossRef (requires an Internet
connection). If found, the doi will be added to the selected reference(s) in the List View window or to the
reference showing in the Reference Window. To locate the doi, CrossRef requires some of the reference fields to
have accurate information. These include an author, journal or book title, first page, year of publication, and
sometimes the article title. The doi you obtain can then be used for features such as Autofill and Get PDF From
Internet.

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.

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.

· You can read more about Refbase and what it does in this section of the User Guide.
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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.

Sort Hits List…

Alphabetizes the Hits List. You are presented with the dialog:
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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.

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.
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· 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.

Show Inspector

The Inspector is a floating window that allows you to view and manage attachments or links for references in
your database. The 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 Inspector will
remain open until you close it or the associated database is closed.

This menu toggles, so that when the Inspector is open it will read

Hide Inspector

The Inspector handles two different kinds of reference metadata: attachments and links. Read this section for
full details about how the Inspector is used.

Bibliography Window
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If you create a bibliography from within Bookends (that is, without Scan Document, but using the Bibliography
Formatter), it can be viewed in this window and, if desired, copied to the clipboard. Text pasted into a word
processor document 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.

Minimize Window

This command moves the frontmost window (the one checked in the Window menu) to the dock. To bring a
window back into view, select its name in the Window menu or click on the 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 periods after abbreviations (e.g. J. Biol. Chem.). This means
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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).

The action menu (gear icon) at the bottom left of the Term List window performs these functions:

Insert: Places the selected words at the end of the corresponding field of a reference.
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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.

Save: Saves the list (the first column only) to a text file.

Replace: Brings up a dialog that allows you to do a global Find/Replace for this term in the corresponding field
in the database. This is the same as performing a Global Change -> Find And Replace, but with fewer
options. The advantage it offers is convenience if you simply want to correct a misspelling in a term or
want to normalize the spelling of a term, such as a journal name.

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.

Multiple Selections: When two or more terms are selected, this tells Bookends whether to show only references
common to all terms (AND) or references found that contain any of the terms (OR). This applies only
when the Term List is shown in the expanded view.

· All of these options can be accessed in a contextual menu by right-clicking on the list of terms.

There are two Term List views:

Expanded view
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The disclosure triangle is pointing to the right. To see the collapsed view, click on it once (see below).

At the top left 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.

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.

Type into the textbox below the pop-up menu to filter the terms. Bookends performs character matching, so that
the characters "cog" will match the keywords "cognitive science" and "neurocognition".

To the immediate right of 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).

To the left of each item is the image of a pin. If you click on this, the term is temporarily "pinned" and treated
like a selection (until unpinned, or the term list is dismissed). You can accumulate terms in this fashion to
perform boolean AND/OR searches. When multiple terms are selected or pinned, the actual search Bookend is
performing is shown. You can pin or unpin all terms, or deselect all unpinned terms, with an option in the
Action menu or by right-clicking on the term list.

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 submenu in the Action menu in lower left corner of the window.

When multiple terms are selected (or pinned), Bookends will display the exact boolean search being performed.

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.

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.
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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

· 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.

You can change the relative sizes of the terms list and the reference list by dragging a splitter:

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).

Pressing Command-M when the reference pane is selected will toggle the Marked status of the selected
references, using the value of the first selected reference as the toggle value.

This is an example of a Term List with two pinned items and a filter applied simultaneously
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Collapsed view

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).
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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

Help Menu
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User Guide

This User Guide (Bookends User Guide.pdf) is included in the Bookends download. When first run, Bookends
will move it to ~/Documents/Bookends/. When you use the menu Help -> User Guide, it will open in Adobe
Acrobat Reader or Preview. If it is not found, 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/Bookends/
(although it will also be found if it is in the Bookends folder).

FAQ…

Launches your browser and takes you to the Sonny Software FAQ (Frequently Asked Questions) page:

http://www.sonnysoftware.com/faq/faq.html

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 or edit references in 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).

Bookends Server will automatically embed reference metadata (COinS) in the HTML it generates if you have
checked Embed reference metadata (COinS) in HTML output in Preferences (OpenUrl & COinS tab). See here
for more information about COinS.

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.
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Authorized access only

You can restrict Web access to your databases in the following ways:

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.
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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.

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.
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If you are asking Bookend to retrieve references from a database, there are nine elements (two required):

Element Representation

Required:

• name of the database to search: DB

• words or phrases to search for: Query or SQLQuery

Optional:

• name of the format Format

• field in which to search, or All Field
• boolean search options Bool
• maximal number of references to return HitLimit
• header above the references Head
• footer after the references Foot
• show the number of hits ShowHitNum
• sort the result SortBy
• sort direction SortDirection
• send to file 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>
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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:

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">

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SQLQuery

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&SQLQuery=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)

HTML example (pop-up menu):

Format the references in the style of:

<SELECT NAME="Format">
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<OPTION>Chicago
<OPTION>APA
<OPTION>Medline
</SELECT>

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)

HTML example (pop-up menu):

<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
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<OPTION>Abstract
<OPTION>Notes
<OPTION>User1
<OPTION>User2
</SELECT>

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)

HTML example (pop-up menu):

<p>Boolean:
<SELECT NAME="Bool">
<OPTION>AND
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<OPTION>OR
<OPTION>NOT
</SELECT>

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)

HTML example (pop-up menu):

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)

HTML example (hidden text field, defined by you):

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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)

HTML example (hidden text field, defined by you):

<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)

HTML example (pop-up menu):

Sort the references by:

<SELECT NAME="SortBy">
<OPTION>Authors
<OPTION>Title
<OPTION>Date
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</SELECT>

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)

HTML example (pop-up menu):

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)

HTML example (pop-up menu):

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<label for="SendToFile">Send results to:</label>

<select name="SendToFile">
<option value="">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 .text, .txt

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html .html., .htm

pdf .pdf
jpeg .jpeg, .jpg
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:

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</form>

The visible (to the user) elements in a form typically include text and fields, and are terminated by buttons, such
as

<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):
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<A HREF="http://175.34.232.1:2001/BEGet?DB=Database1&Query=Francis
Bacon'">Francis Bacon</A>

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).
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Here is what the parts of this hypertext link instruction, embedded in a Bookends format, mean:

` —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&SQLQuery=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.
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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&Query=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

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$">download pdf</A>$

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(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!

Format=Chicago2&—Tells Bookends to arrange the hits in the Chicago2 format.

DB=Current Literature&—The name of the database to search is “Current

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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.

`$<A HREF="http://10.0.1.3:2001/—It is at this point that we see the hypertext link that Bookends will
return to the browser. The initial ` is the "force quote" symbol that tells Bookends to output the following
characters as is. The hypertext line begins with <A HREF=", which is followed by IP address of your
computer (the server) followed by the port Bookends is bound to.
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$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.

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:

tajd
¬
b
¬
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`<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 DB

• the filter to use Filter

Optional:

• uploading each field individually IndividualFields

Below are examples of how to use each element.

_________________________________________________________________
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Name of the database to import to

Element: DB (required)

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

Element: DB (required)

HTML example (hidden field):

<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)

HTML example (hidden field):

<label for="IndividualFields"></label> <input type="hidden" name="IndividualFields" value="true" />

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:
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<p>Author: <INPUT cols="30" rows="1" name="AU " value="Hemingway, E">

</INPUT></p>

Editing/updating references in a database

You can edit references to a Bookends database by submitting the name of the database, the unique id of the
reference to be edited, and the fields that are to be changed.

Element Representation

Required:

• name of the database to import to DB

• the unique id of the reference updateUniqueID
• fields to be updated authors
editors
title
journal
volume
pages
date or thedate
publisher
location
url
shorttitle or title2
rating
keywords
notes
abstract
user1 through user18

• Rating should contain a number from 0 to 5.

• Fields in the target database that are not assigned values in the HTTP request will be left as is. The
font and text style of a field updated in this manner will be set to the defaults.

Here is an example for the settings in a form in which the authors’ field is edited:
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<input type="hidden" id="DB" name="DB" value="Database1" />

<input type="hidden" name="updateUniqueID" value="25232" />
<p>Author: <INPUT cols="30" rows="1" name="authors"></INPUT></p>
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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):

• Choose File -> Import References…

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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).
· Drag "BibTeX output" to the Formats window and drop.
· Close these windows, then select the references you want to export.
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· 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).
· Choose File -> Import References…
· 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).
• Choose File -> Import References…
• 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.

Note: You can also drag and drop the exported file onto a Bookends reference window.
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Appendix B. Upgrading from previous versions of Bookends

• from Bookends 10

There are two ways to upgrade: use the Bookends implementation of Sparkle (only on Mac OS X 10.4 and 10.5
— it will not work in 10.6 (Snow Leopard), or go to our web site (http://www.sonnysoftware.com/download/
download.html) and download Bookends to your hard drive.

If you are using Mac OS X 10.4 (Tiger) or 10.5 (Leopard):

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.
4. When you use the Sparkle automatic update, the new User Guide will be installed in ~/Documents/
Bookends/.

If you are using Mac OS X 10.6 (Snow Leopard):

1. Use Bookends -> Check For Updates…

2. Bookends will alert you if a new versioin is available, and if you’re eligible for a free upgrade.
3. Click on the Go To Download Page button and Bookends will launch your brower and take you there.
4. Download Bookends.
5. Replace the Bookends 10 Folder in your Applications folder with the new Bookends 10 Folder. The
Bookends User Guide will be automatically moved to ~/Documents/Bookends/ when you next run
Bookends.

• 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. 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.
2. Open the older Bookends 9 database with the newer version.
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• 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 (and subfolders in the subfolders).

Move the following from the older to the new Bookends Folder:

1. Databases you have created (only if you store them in the Bookends Folder, which is not necessary).
2. If you are migrating from 8.0 or 8.0.1: move the folders Custom Formats, Custom Import Filters, and
Custom Journal Glossaries to

~/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. Run the newer version of Bookends.

5. Open your older Bookends 8 database. Bookends will offer to convert it. Your database will be copied
first, and then converted, so you will not lose the original. Newer Bookends databases cannot be
opened in Bookends 8.

• from Bookends 7

The internal database and format structures in newer versions of Bookends 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 re-entered. You will, however, be able to retain your
references, import filters, formats, and journal glossaries.

Bookends 7 references can be transferred to a newer Bookends database by exporting/importing.

Note for non-Roman font users: Bookends will assume that the references it is importing from Bookends 7
use the same encoding as the Bookends default reference font (selected in Preferences). If you have used
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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. 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 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.

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. Attachments folder (if present).

3. Copies of formats you have created or modified (to the new Custom Formats folder).
4. Import filters you have created or modified (to the new Custom Import Filters folder).
5. Journal glossaries you have created or modified (to the new Custom Journal Glossaries folder).

Now:

6. Run the newer version of Bookends and create a new database.

7. 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 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:

1. Launch your older version of Bookends and open a database.

2. Choose All references.
3. Export the Hits as a Bookends file (File -> Export References (hits)).
4. Copy the new Bookends Folder to your hard drive.
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5. Launch Bookends and, if necessary, create a new database.

6. Import the references exported from Bookends Pro/Plus (this is pop-up menu selection in the File ->
Import References dialog box).
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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:
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@Article @Book @Inbook @Proceedings

@Inproceedings @Incollection @Mastersthesis @PHDThesis
@Techreport @Manual @Unpublished @Booklet
@Misc @Collection

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:
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Tag Bookends Field

Author Authors
Title Title
Editor Editors
Journal Journal
Series
Volume Volume
Booktitle
Number
Chapter

Pages Pages
Year Date
Month

Publisher Publisher
School
Address
Organization

Location Address or City

Affiliation
City
URL URL
Misc User2
Price
Size
Edition
LCCN User4
lib-congress
mrnumberd
ISSN User6
ISBN
Language User7
Abstract Abstract
Keywords Keywords
Note Notes
Annote
Howpublished
Contents

DOI User17

The following tags are ignored:

type
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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:

Formatting BibTeX references for bibliographies

A BibTeX format is supplied with Bookends. It includes formats for the following Types:
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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 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:
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The resulting file can be used with LaTeX or other TeX-savvy applications.