NEW in Version 11.3.7 (May 10, 2013)

Get DOI was updated to deal with changes made by CrossRef
This includes dealing with changes made in the way CrossRef encodes accented characters.

Updated Import From Existing Bibliography to deal with changes made by CrossRef

Updated Bookends browser to detect DOIs on the Google Scholar web site to deal with changes made by Google

Bug fixes
Fixed a bug that could cause the last character of an in-text citation to be dropped in scanned LibreOffice files. Fixed a bug that caused an error if you invoked Copy Formatted while a field was being edited. The Get DOI progress window updates properly now. Fixed a bug that caused the style of an italicized et al. to bleed into the open parenthesis if the author was placed in front. Fixed a rare bug that could cause an error to be thrown when looking for attachments. Fixed a bug where Autofill From Internet did not update the date modified setting, so affected references were not uploaded to Bookends On Tap when synced with Bookends. Fixed a bug in which references deleted by removing duplicates were not subsequently deleted from Bookends On Tap when synced. Fixed a problem with formats like Turabian where citations with cited pages could have .: instead of just : output before the cited page numbers. Fixed a bug that could cause an error to be thrown when scanning a Pages document for citations in footnotes. Escaping characters in SQL Search works again.

NEW in Version 11.3.6
(March 2, 2013)

Improvements in adding formats and import filters supplied by others
If you receive a format or import filter from another individual or from our anonymous ftp site, you can automatically add it by double-clicking on the file or dragging and dropping it on the Bookends library window. The file will be moved to the corresponding custom folder and enabled for use. If a format/import filter of the same name already exists in the custom folder, the new file name will be modified with a sequential number and you will be informed.

A new smart group that finds the last X references entered is more accurate and much faster
If you already have added this smart (SQL) group, delete it and reinsert it from the Add -> Smart Group (SQL) pop-up menu.

Improved Remove Duplicates
When performing a preview and manual deletion, a red X will be displayed in the bottom pane to indicate which reference will be deleted. This indicator will change in real time if you check/uncheck references in the reference list.

Backslashes will be replaced with dashes in automatically-generated attachment names
This is done to ensure compatibility with DropBox.

When BibTeX is enabled in preferences, the BibTeX format will automatically be enabled
This means that if you have unchecked BibTeX in the Formats Manager, it will be checked once again when you enable BibTeX, and therefore available in format-selection pop-up menus.

Updated formats for American Society of Microbiology journals
Also added a generic format called American Society of Microbiology that can be used instead of the individual journal formats.

In the library window column view, a tertiary sort will be performed by title if the author and date are the same
This will only occur if the authors are shown in the first column and the date and title are shown in subsequent columns.

If "Idem" is used for a reference in a citation group, that group will not be sorted even if the format calls for it
This ensures that the "Idem" reference follows the correct reference.

Bug fixes
Fixed a problem that could cause a sync with Bookends On Tap to fail with an error message. Fixed a bug that would cause an error message to appear when adding a folder to the group's pane. An remote library that is open is now accurately detected when syncing Bookends libraries. Fixed a bug where all items in a duplicate reference group weren't selected when doing a preview and manual remove of duplicates. Fixed a bug where dragging and dropping a PubMed reference link from a browser onto the library window would cause an error. Right-clicking on a pdf to open it with a specific application works again. Warnings that a format is too new to be used by the current version of Bookends no longer appear in an endless loop. Fixed several bugs in the use of metatypes when formatting references. Fixed a bug in which an error could be incorrectly thrown when opening a library. Fixed a bug in the Format Catalog that caused two examples of every reference Type to appear.

NEW in Version 11.3.5
(January 12, 2013)

Improved groups
Selecting a folder in the groups pane will show the references of all the groups it contains as well as those that are contained in any subfolders.

Import Zotero libraries and pdf attachments
Export the library from Zotero in RIS format (File -> Export Library -> RIS (and tick the Export Files checkbox)). Zotero will create a folder that contains a text file with the extension ".ris", which contains the reference metadata. A subfolder called "files" contains a copy of pdf attachments. In Bookends, import the ".ris" file (by drag and drop or using the Import References menu item) using the RIS import filter. Bookends will import the reference metadata and attach the corresponding pdfs in the "files" folder after moving a copy of each pdf to the default attachments folder. Once you have assured the import went well, you can use pdfs exported by Zotero for another purpose or Trash them. Note that the "files" folder must be in the same folder as the .ris file or Bookends will not find the pdfs.

Updated JSTOR parser in Bookends Browser to deal with changes made by JSTOR

Improved Autocomplete Paper
If Autocomplete Paper can't locate the reference online, any text you searched for will be entered in the corresponding field in the new reference when you close the sheet.

When attaching pdfs in batch, CrossRef has been added as a source of metadata to fill out reference fields

The boolean setting (AND/OR) for virtual groups is remembered between launches

Added an AppleEvent that returns the modification date of the indicated references
The dates are represented by the number of seconds elapsed since January 1, 1904. If more than one unique id is submitted, the returned dates are separated by ASCII 0.

Bug fixes
Fixed a problem with escaped characters that could affect multiple functions in which REGEX searches are performed. After using Autocomplete Paper, the new reference is once again selected in the reference list. Fixed a bug where adding a term to multiple references would fail after finding one reference in which that term already existed. The first text field in the Find sheet is once again selected when the sheet is opened (Command-F). Colons are not allowed in names you assign to files you are attaching. Fixed a bug that could cause an error to be thrown when scanning a Pages document with comments in footnotes.

NEW in Version 11.3.4
(December 23, 2012)

Autofill ISBN from any Amazon source
In preferences, select which Amazon site (US, UK, Japan, etc.) to use to autofill references using the ISBN. This was previously limited to Amazon US. Note that many sites do not provide summary information.

Automatically exclude author and title from a citation or footnote
If the temporary citation begins with &, Bookends will exclude the author and title (or secondary title) in the final citation or footnote.

The font size delta for small caps has been changed to 3 points (from 2)

Search Web Of Science for grant number and funding agency

JSTOR parser in Bookends Browser was updated to deal with changes made by JSTOR

Perform a Spotlight boolean NOT search by putting a minus sign directly in front of a word
For example, to search for an attached pdf written by Smith and not Jones, search for "Smith -Jones" (without the quote marks).

Bookends Browser will detect DOIs on the Web Of Science web site and allow you to import references and pdfs by clicking on the green icon
If not already present, the Web Of Science web site will be added to the Bookends Browser bookmarks.

Keywords shown in a column in the list view will be separated with semicolons
Previously, only the first keyword was shown.

Bug fixes
Improved check for a valid PMID in the PMID field when doing an Autofill From Internet. Fixed a bug that prevented text in fields being edited from being saved if some of the Action pop-up menu commands were invoked. Fixed a bug that could result in incorrect author-date sorts in citation groups if the name and date was separated by a space. Fixed a bug that caused an error when renaming a Type in preferences when a format window displaying that Type was open. The Reveal In Finder contextual menu now works in the reference pane view of the library window. Fixed a bug that could cause an error when syncing pdfs with Bookends On Tap. Fixed a problem where trying to open a pdf in Preview using the right-click hierarchical menu could result in an error. Fixed an error that could occur when changing the pop-up menu to select different search options in the Find dialog. Fixed an error that was generated with exporting a tab-delimited text file with attachments. Fixed a bug where the pdf display pane was not updated properly when replicating a Book as a Book Chapter.

NEW in Version 11.3.3
(October 20, 2012)

Edited pdf attachments will be synced with Bookends On Tap

Autofill single fields from the Internet
To autofill a single field instead of an entire reference, use Refs -> Autofill From Internet -> Selected Field or right-click on that field in the reference pane (or the standalone reference window) and select "Autofill This Field From Internet". A PMID, DOI, or ISBN must be present for this to be enabled.

Web of Science searches restored
The new search function replaces an older one that was discontinued by the service provider. If you don't have ip authentication, you can now still search the Web of Science if you have a valid username and password entered in the Web of Science import filter (Internet tab).

When tying to find a pdf online, if Bookends can't resolve the ip address it will skip to the next selected reference rather than showing an error dialog

In response to an AppleEvent asking for more than one formatted reference to be returned at once, they will be separated with a null character (ASCII 0)
Previously, they were separated with the return character (ASCII 13).

Added an AppleEvent that returns the contents of a specified field
The Event id RFLD takes two parameters: the unique id (if more than one, separated with commas or Returns), and the name of the field to return. If the field name is unspecified or incorrect, the Title field will be returned. Field information from multiple references will be returned as a null (ASCII 0)-delimited string.

The punctuation separating authors' names is full sized when output as small caps

Small caps in author names are slightly larger

Copy Notecard and Citation will include cited pages if they occur after a header, and will not include tags

Updated the Google Scholar parser to deal with changes made by Google

Bug fixes
Fixed a bug where dragging and dropping multiple pdfs with the Command key held down would not bring up the dialog offering to attach all to a new reference and autocomplete data if a doi was found. Fixed a rare bug where using smart quotes could cause a hang if the field it was applied to had a large amount of text. Fixed a problem where sorting of author-date citation groups by year would give inconsistent results if a citation included cited pages or quoted text. Fixed a rare case where misuse of the backslash in Cited Pages could cause problems in citations when scanned with Mellel. Fixed a bug in Subject Bibliography -> groups that could have incorrect group names shown. Fixed a bug that prevented a straight single quote from begin converted to a smart single quote if it is the first character of a citation or a bibliography entry. Fixed a bug where the wrong library was selected for Database Maintenance when more than one was open..

NEW in Version 11.3.2
(September 1, 2012)

Better integration with DEVONthink and DEVONthink Pro 2.4 and later
Use the DEVONthink script "References from Bookends" for batch import of references, drag and drop references from Bookends to DEVONthink with the Command and Option keys held down to add full rich text summaries, and have reference data shown in smart templates. Some features require DEVONthink Pro.

AppleScript support for obtaining the names of user-created groups in a Bookends library
In response to the AppleEvent "RGPN", Bookends will return an ASCII 13-delimited list of all groups in the frontmost library window. AppleScript example: return «event ToySRGPN».

Changes in the format definition layout to make options more clear

Improved ability of Bookends Browser to detect a valid doi in a web page

For Get PDF from the Internet, if a site doesn’t respond within ~30 seconds Bookends will move to the next selected reference

If Bookends has been set to generate BibTeX keys for imported references, it will do so for references imported from Bookends On Tap

Assign ratings by clicking on the Ratings column in the library window
You can choose to show ratings in this view in preferences.

Updated Get PDF from Internet to deal with changes made by some publishers

Emailing a reference no longer puts the formatted reference in the clipboard

Updated the PMID detector in Bookends Browser to deal with changes made by PubMed

File -> Import From Existing Bibliography updated to deal with changes made by CrossRef

Bug fixes
Fixed a bug in which a Type added in the format Bibliography tab would not immediately show up in the Type pop-up menu in the Citation Options tab. Fixed a problem where some internal formatting in a Pages document would prevent Bookends from finding temp citations in that section. Fixed a bug that could cause an error message when parsing reference found on JSTOR or the Library of Congress. Fixed a bug that caused some bibliography settings to be used for custom citation situations when scanning a document. Fixed a bug where the order of the duplicates displayed in the Preview and Verify window could be switched if you edited one reference before deleting the other. Fixed a number of issues with metatypes. Fixed a bug that caused extra characters to be output in a scanned citation if the author's name was placed outside and the year had to be disambiguated. Fixed a bug in formatting where changes to the alphabetize bibliography setting weren't honored. Fixed an unscan bug that could cause a temp citation's font size to become 12 point regardless of the initial value. Fixed a bug where scanning a Pages document with tracked changes could be halted because of an error.

NEW in Version 11.3.1
(July 28, 2012)

Unified format window
The information necessary to create a custom citation is now contained in the same file as the information for creating the bibliography. Creating a custom citation is no different form creating a numbered or author-date citation (although much more flexible). Any existing formats will be automatically converted to the new scheme, and will no longer be able to be edited in Bookends 11.3 (although they can be viewed). Versions of Bookends before 11.3.1 had a different user interface, and bibliography (parent) formats and custom formats were stored in different files. These older formats will be automatically converted when opened in 11.3.1 or later. Old custom citation format files are now obsolete. If a Type exists in the parent but not the custom citation, a custom citation will be created for that type that is identical to the first custom citation Type. If a Type exists in a custom format but not in the parent, that custom citation Type will be ignored.

Replace authors repeated in consecutive footnotes with Idem (or your own text)
This feature works with custom citations when two consecutive citations from different works have the identical authors. It will not be invoked if the previous citation was the last in a group, and the optional sorting of a group that has a repeated citation will be disabled (so that “Idem” does change its position and follow the wrong citation).

Live Bibliography (with Mellel)
If enabled in Mellel, citations and bibliographies will be updated as you type. This feature was actually added in an earlier release, but we held back the announcement until Mellel 3.0 was released.

Convert PMID to PMCID has been updated to deal with changes made by PubMed Central

Open pdf with PDFpen added to the "Open Attachments With" hierarchical menu

When formatting, Bookends can output Ibid. (or the equivalent) in italic

Single column sort settings are remembered between launches

If a text file with the extension .ris is dropped on the library window, Bookends will offer to import it using the RIS filter
The RIS filter must be enabled in the Import Filter Manager.

New AppleEvents for obtaining unique ids from Bookends libraries and performing SQL searches

Retrieve multiple references at once with the GUID AppleEvent

A selection of pre-defined smart groups is provided
When adding a smart SQL group, you can choose to design it yourself (Empty), or select from a group of pre-defined smart searches (e.g. most recent 15 references added, edited in the last 2 weeks, etc.). You can also use these as templates that you modify (e.g. to find references edited in the last 4 weeks).

You can perform an autocomplete paper for only one dropped pdf at a time

BibTeX scans will recognize "\onlinecite{" as indicating a temporary citation

The temp citation metacharacter "[" will work with Mellel 3.0.1

The maximum database cache is now 50 MB
Levels above this could slow launch times without benefiting performance.

Updated the Google Scholar parser to deal with changes made by Google

Bug fixes
Fixed a bug where an "et al." in a temporary citation quoted text could result in an unmatched citation during a scan with Word or Nisus Writer Pro. Fixed a bug where doing a Find for a color label would fail. If Ibid appears in a citation group, the group will not be sorted, to ensure that the Ibid follows the correct reference. Fixed a bug where renamed field labels were not instantly updated in the library window reference pane. Fixed a bug were the modified date was not being set for references transferred between libraries by drag and drop. Fixed a bug where performing an autocomplete paper when a tag cloud item was selected could result in an error message although the autocomplete worked. Fixed a problem where some groups would not sync with Bookends On Tap. Fixed a cosmetic bug in Lion and Mountain Lion where groups didn't appear after a rebuild until the library was closed and reopened.

NEW in Version 11.3
(June 23, 2012)

Direct PubMed searches and using PubMed for autocomplete paper restored
These functions were broken by changes at PubMed.

Bug fixes
Fixed a bug where a period following cited pages would not be removed before semicolons in grouped footnotes after a Mellel scan. Fixed a rare bug where secondary Ibid. citations could have misplaced style information with formats containing a secondary order. Fixed a bug where Word and NWP scans would output Ibid in formats with secondary orders even though the preceding matching citation was in a group. Fixed a bug where the first reference would always be used to display an Author-Date citation example in the Format Manager, regardless of which reference was selected.

NEW in Version 11.2.9
(May 16, 2012)

Import Bookends references into Tinderbox
Option-Command-drag a reference onto a Tinderbox document and it will be imported, creating a link and a formatted version of the reference, as well as populate the Reference prototype attributes with reference metadata. Requires Tinderbox 5.11 or later.

Updated the Google Scholar online search to account for changes made by Google

AppleEvent support for obtaining formatted references from Bookends
Users can use Script Editor, and developers can use an IDE, to create scripts or code that asks Bookends to return formatted references on demand. The User Guide has complete details.

Unicode normalization includes all reference fields

Modified Bookends Spotlight searches
The search is by word, with spaces between words treated as "AND"s. To do a boolean OR search, separate works with the word " or ". This replaces the old behavior, which was to treat the words entered in the search field as a phrase.

A confirm dialog will appear you edit a field in the enlarged view and press Cancel
This is a change in previous behavior, when the confirm dialog appeared when you pressed Save.

Bookends is now signed for Mac OS 10.8 (Mountain Lion) Gatekeeper

Bug fixes
Uncommitted text edits will be automatically saved when you Duplicate a reference. Fixed a bug in the format's bibliography example where the user16 and user18 default text was not correct. Show book with its chapters works again. Fixed a hang that could occur when editing additional fields in a standalone reference window. Fixed an error that could sometimes be thrown when the menu was used to bring the already opened format window to the front. Fixed an error message when importing jpgs from Amazon that would appear if the user had defined his own default attachment folder and it was subsequently renamed or trashed. Fixed a bug in the Nisus Writer Pro scan where an en dash in cited pages would not be rendered properly. Fixed a problem in Word and Nisus Writer Pro scans where an en dash in cited pages was replaced with an em dash and vice versa.

NEW in Version 11.2.8
(April 18, 2012)

Updated the Google Scholar online search to account for changes made by Google

Scripts for Word 2011 SP2 (version 14.2) will be installed in the new Office scripts folder
Microsoft changed the location of the scripts folder in this version of Word.

URIs in the notes pane are active
Right-click to see the list of URIs (e.g. links to items in DevonThink or other apps). This already works in the reference fields in the Main tab.

Citation groups containing literal text will not be sorted when scanned
If any citation in a group has leading quoted text (e.g. \See also\), the entire group will not be sorted even if the format calls for it. This ensures that reference order won't be altered in a nonsensical way.

Find dialog improvement
You can now choose to search for a Unique ID directly (not as an option in text searches). The search type changes to "is", reflecting that only exact matches will be found.

Option to suppress a warning when Bookends database sync can't find the remote library
In the sync configure sheet you can turn on (default setting) or off a warning that the remote library is unavailable. Turning off this warning may be useful because it is redundant if the remote library is on a server that can't be mounted (Mac OS will display a warning in that case). If this is a common scenario for you, turn off the warning generated by Bookends.

View the references in the Hits List in their order in the library window
If you turn off sorting of the reference list in the library window (in preferences), clicking on the Hits group will show the references ordered by their position in the Hits List. If you use Hits -> Sort Hits List, the library window will be updated immediately.

The formatted reference display in the library window will update automatically when leaving edited fields

Bug fixes
Fixed a problem with spurious characters sent to Bookends by Mellel when syncing. Fixed a rare problem that could occur if the reference Type was set incorrectly. Fixed a bug that caused incorrect scanned citations when using the 'et al. in italics' feature with cited pages. Fixed a bug where adding a reference to a static group via the menu option would cause any edited text not yet saved to be lost. The live search for "all fields" will now find entries in User19 and User20 (you'll have to Reindex any libraries made with previous versions of Bookends for this to work). Fixed a bug where the Edit menu was not refreshed properly in some cases when the note stream was closed. Fixed a bug where the ¬ character in the Misc tab text fields in an import filter was not being converted to a Return. If you limit Finds to "Any Groups", Bookends will now only show matching references that belong to one or more static groups.

NEW in Version 11.2.7
(March 25, 2012)

Improved scanning
When scanning a Word document, placing adjacent citations in a single group is more reliable.

Drop files on the Bookends icon in the dock
Drop on the dock icon to open a library, import references from a text file, or attach a pdf.

The 1Cate OpenURL service has been removed
To use UpenURL, get the URL from your institution's library.

Bug fixes
Fixed a bug where importing "Bookends" files exported from Bookends 9.x or Bookends 10.x would fail. Fixed a bug that could cause references already in your library to be reimported when syncing with a Mellel document. Fixed a bug that could cause assigned text colors in a reference field to revert to black. Fixed an encoding issue that would cause notecards to redraw erratically if they contained accented characters. Fixed a rare bug that could cause an error when a library couldn't be located from the Open Recent menu. Fixed a bug that could cause an error message when attaching a pdf in the library window's browser. Fixed a problem where importing references without authors from a Mellel document or from a direct export from Papers would yield an error. Eliminated some rare errrors that could occur when importing from the Online Search window. Fixed a problem that could result in an error message when opening the Online Search window. The percent character (%) is now be displayed properly in a notecard if it is not part of a tag. Subject Bibliographies for author and editor now work.

NEW in Version 11.2.6
(February 15, 2012)

Notecard tags
Each notecard can be assigned one or more tags. Tags must be entered on one line (before or after the note) and preceded by a % symbol. You will be able to distinguish tags from text in the note stream because they will be displayed in gray.

Notecard search
You can select Notecard in the Live Search box. A notecard search will find references that having matching text in the Notes field, and if the note stream is showing in the right pane, only the notecards that match will be shown. You can search for a tag by preceding the search term with the % symbol. Note that notecards found as a result of a notecard search cannot be edited, deleted, or rearranged until you exit the notecard search. You can, however, Copy Citation, Copy Notecard And Citation, etc.

Updated the PubMed parser to deal with changes made by NCBI

The Keywords or Notes field sizes in the standalone reference window will be remembered between launches

Bug fixes
Fixed a bug where Bookends wouldn't find the linked word processor in some cases. Fixed a bug that could cause PubMed automated searches to fail.

NEW in Version 11.2.5
(February 11, 2012)

Notecard headers
You can create notecards that consist of a header or have two parts, a header and content. The header will have a slightly darker color than the content and will be displayed in bolded and enlarged text. A header is created in the Notes field by placing the # character before the text (Bookends takes care of this for you if you use the command "Add Notecard With Header" (or with the note stream showing, click on the Add pop-up menu or right-click on the note stream itself). If the header has no content (that is, nothing in the line below it), it will be centered in the listbox cell. If it has content associated with it, the header will appear in the top half of the cell and the content in the lower.

New error reporting mechanism
If you encounter an error unrelated to the database engine, you will be offered the chance to create a message in your e-mail client that contains your comments (e.g. what you were doing when the error occurred) and diagnostic information that will help Sonny Software determine the cause of the problem. Only the information you see in the e-mail message will be sent to Sonny Software.

Keyboard shortcut to add a notecard
When the note stream is showing, Command-[ will add a new notecard and open it for entering text. The Shift-Enter shortcut has been removed.

Optional .fmt and .fltr extensions for format and import filter files
If you use unix-based methods to transfer files between computers, the file metadata (file type and creator) will be stripped off and Bookends will not be able to recognize format and import filter files (and the file icon will be blank in the Finder). You can restore recognition by adding the extension .fmt or .fltr to the format or import filter file name, respectively, in the Finder. These extensions are optional, and for backward compatibility will not be automatically added to the format or filter names distributed by Sonny Software.

Bookends will display pdfs even if they lack a file type and/or .pdf extension

Mark/unmark all linked references in the Link Inspector at once
Shift-click on the checkbox next to any reference or right-click and select Mark All or Unmark All from the contextual menu.

Use the down arrow key to change the search field in the Live Search box
This is handy if you want to quickly change from one field (or All Fields) to another. Press Return or Enter to accept the new field to search (Esc or click outside the menu to cancel).

Bug fixes
Fixed a bug in scanning Word or Nisus Writer Pro files where the open parenthesis of a citation output as a bold or bold and italicized number would assume the style of the number. Improved handling a dropped pdf proxy icon from Bookends browser on an empty reference list. The concise view background color will not revert to white when you edit a field. Importing to a specific static group by dragging a pdf from the Finder onto that group works again (was broken in a previous update). An active edited field in the reference pane is saved if the window is closed. Fixed a bug that could cause a spurious number to be output after the year when using the MLA format and final citations consisting of only the year. Fixed a bug where a notecard added to one reference could be appended to a different reference. Fixed a bug in cross-links where the default parent-child relationship was not saved correctly if it wasn't the first option (users who have set this to another option will have to check it again in preferences for the fix to work).

NEW in Version 11.2.4
(January 14, 2012)

Updated Google Scholar direct search and Autocomplete Paper to deal with changes made by Google

Import abstracts from Google Scholar
Note that the abstracts Google Scholar provides are incomplete, but still may be helpful.

Type ahead search works in the single column reference list
The search is always for the author, regardless of the sort status of the list. It will only jump to an exact match of the typed characters.

Bug fixes
Fixed a bug where the pathname to attachments was not being output when exporting as XML. The preference option to insert COinS into HTML-formatted refs is saved between launches and COinS are suppressed if it is unchecked. Fixed a bug that caused Refs -> Insert Date to insert the date in the Authors field if a standalone reference window was being used. Fixed a bug that could cause invisible folders to be listed in the subfolder pop-up in the attach dialog. On attaching, a file name is checked for uniqueness and modified if necessary even if the file is not being moved to the attachment folder. Precaution: if the Desktop is selected as the default attachment folder, subfolders will not be shown.

NEW in Version 11.2.3
(January 8, 2012)

Increased speed of many operations

See example citations in the Format Manager
Citation examples are shown in the Citations Options tab, and automatically update as you edit the format.

Improved sorting of the reference list
Sorting uses the contents of the Date column (if present) for a secondary sort. Assuming that the Date column is set to show year only (that is, no month or day), any primary sort will also be sorted by year.

Added right-click option to open a pdf in Adobe Reader
The other options are Preview and Skim.

Shift-Command-O opens attachments when the edit pane is active

Updated direct pdf download for site that use ScienceDirect

Bug fixes

Fixed a bug where an open and edited text field in the edit pane was not saved if you used the View menu to switch to another view. Fixed a bug that caused a long delay when attaching a file if you already have many (thousands) of attachments. Fixed a bug where repeated opening of the Import References dialog would cause replicated entries in the import filter pop-up menu. OpenURL works again. The text style of fields in the Additional Fields tab now conforms to the preferences settings. Fixed a delay in keyboard access to the attach dialog that appears after a drag and drop. Fixed a bug with drag and drop pdf and Autocomplete Paper that caused a delay in text entry in the autocomplete dialog and often a crash when adding a second or third pdf this way. Added a check to make sure that the right pane widths are not corrupted, and to reset them to the factory defaults if they are. Fixed a rare bug that could cause a Mellel scan to hang. Fixed a rare bug that could cause a crash when editing a format.

NEW in Version 11.2.2
(December 18, 2011)

View attachments in the library window editing pane (on the right)
The Attachments tab in the reference editing pane lets you view attachments (e.g. pdfs) on the right side of the library window. This may be preferable to the lower display pane for those with wide screen displays. If there is an attachment, it will be indicated by an asterisk in the tab panel caption (i.e. Attachment*). Note that the setting "Use WebKit to display pdfs" only applies to pdfs in the lower display pane only; the Bookends pdf viewer is always used in the editing pane.

The standalone reference window drawer has been removed
It is replaced with the same Additional Fields tab used in the library window reference pane.

There are more ways to add attachments
Refs -> Attach menu, right-click in the reference list, or use the Action pop-up menu in the library window.

The height of the lower display pane will be saved and adjusted independently for each view
This means, for example, that you can have different heights for the pdf display and the formatted reference display.

Detach has been added to the library window Action pop-up menu

The Bookends browser data detector will check for COinS references before other types
This means that it will find all references embedded in Web pages at sites like CiteULike, not just those with DOIs.

Copy Citation button added to the library window toolbar
It works just like the Copy Selected menu: hold down the Shift key to copy without delimiting punctuation (e.g. curly brackets), the Command key to Copy Formatted, or the Control key to Copy With Modifiers.

The maximum number of references returned from Google Scholar limited to 1000
This limit is imposed by Google.

Imports from Google Scholar are limited to 50 at a time
If you try to retrieve too many references at once, Google will think you are an automated service and block your ip address. To prevent this, Bookends limits the number of references you can import at once to 50. If you have more than 50 references to import, select and import blocks of 50 or fewer. Note that this limitation does not apply to the number of references that can be displayed (the limit is 1000), just the number that can be imported into your library at a time.

New Bookends Server options
A new parameter, HTMLOutput, lets you specify how you'd like the results of your searches returned. If it is undefined or 0 (default), full HTML output is returned. If it is set to 1, Bookends will return the results as HTML, but references, omitting the wrapping , content description data, and tags. If it is set to 2, Bookends will return the results as plain text (UTF-8) with no HTML markup. The new options may make it easier to post-process the results with your own scripts.

Bookends Server doesn’t check for libraries outside of the Server folder
You can open and work on a copy of your library that has the same name (and thus cannot be in the Server folder).

Ad hoc control of the "before text" in cited pages
You normally tell Bookends what to output before cited pages (for example ", p. ") in the format. However, there may be times where you want to change this for a particular reference. Do this by using quoted text (text surrounded by backslashes) in the cited pages, like this: {temp cite@\: \3}. This will tell Bookends to ignore the Before text specified in the format and use a colon and space, for example: (Smuth, 2011: 3). Note that the quoted text backslash must be placed immediately after the @, and if there is no closing backslash the results will be unpredictable.

Choosing Right-click -> Copy Notecard will switch to your linked word processor and insert the selected notecards as plain text
Use Edit -> Copy Notecard to just copy the selected notecard styled text to the clipboard).

Bug fixes

Fixed a bug where using the Attachment Inspector to attach a pdf to an empty reference and autocomplete opened the reference window and did not perform an autocomplete. Fixed an error that occurred when changing the color label in the All concise view. Bookends can display the body text of Pages documents again. Fixed a bug introduced in 11.2.1 where the pop-up menu listing available formats didn't appear in the library window when viewing a formatted reference. Fixed a bug that caused erratic drawing of the browser view in the library window lower pane when window height was at its minimum limit. A standalone reference window will be refreshed once again to show a newly imported reference. Fixed a bug where an extra Enter character would be inserted in front of a Mellel temporary citation after a Verify. Fixed a bug in syncing of smart groups with Bookends On Tap.

NEW in Version 11.2.1
(November 20, 2011)

Bookends Browser: detect and import references from Web pages that display a PMID or DOI
If a PMID or DOI is detected when reference surfing with Bookends Browser, the green import icon will be displayed, allowing you to view the titles of the detected references and download them. This works on any Web page that displays PMIDs (e.g. PubMed) or DOIs.

Updated direct downloads of pdfs from Nature journals and JSTOR
These fixes deal with changes made by the publishers.

Sort the single column view in the library window
Right-click, or click on the Action pop-up, to sort by the following fields (secondary sort in parentheses): Author (Date), Title (Date), Date, Date Added, Date Modified, Type (Date). The Date Added and Modified sorts are descending (i.e. most recent at the top).

The library window title will not show the .bdb extension if it is hidden in the Finder

The library window will scroll to the reference you are entering or editing if it changes position

Updated Autofill From Internet imports reference metadata from Amazon if you have the ISBN
This was broken by changes made by Amazon.

Copy Selected without delimiters
If you hold down the Shift key when pressing Command-Y or choosing Edit -> Copy Selected, the temporary citation that is inserted in your word processor document will not have delimiters (i.e. no curly brackets). This is useful if you want to insert a temp citation into an existing citation group.

Cosmetic improvements to the dialog window that lists multiple hits with Get PDF from local hard drive

Autosync with Bookends On Tap
This preference, set in the Bookends On Tap Settings screen, causes syncs to begin without waiting for the confirm dialog. If you have Autosync on and want to change options in that dialog (e.g. to sync particular groups rather than all references), turn Autosync off and sync. After changing the settings in the Bookends confirm dialog and completing the sync, you can turn it on again in Bookends On Tap. Requires Bookends On Tap 1.0.2 or later.

Bug fixes

The PubMed automated search listbox is no longer invisible. Fixed an error generated by clicking the cross-link icon in the standalone reference window. Fixed a bug where normalizing unicode in certain fields failed. Fixed a bug that could cause Bookends to crash when syncing with Bookends On Tap. Fixed a bug where clicking on the image of a Mellel document in the Attachment Inspector caused a crash. Fixed a bug that caused an error message when editing a field in the Addition Fields tab whose name had been changed. Fixed a bug where attaching of pdfs or Web pages from the Online Search window would fail if the browser was open in the lower pane. Fixed a cosmetic bug where the field labels would not be updated properly when a new reference was created with the Add pop-up menu. Fixed a cosmetic bug when the library window reference pane wasn't updated immediately after doing a Global Change -> Restore Default Font And Styles. Fixed a cosmetic issue with overdrawing of the text indicating the number of references in the library window. Fixed a bug where edited text in a field in the reference pane was not saved if the pane was closed with the View menu or keyboard equivalent. Refs -> Go To Reference # works again when the reference window is in front. Fixed a cosmetic bug when resizing the standalone reference window with the drawer open. Fixed an error in Google Search in which an author name consisting of three words or more could be displayed without spaces between the first names. Fixed a bug where a NOT search (-) in the live search box would fail in some cases when a specific field to search was specified. Fixed a bug where dropping the pdf proxy icon from Bookends Browser onto a library window would fail to import the pdf or web archive. The "date added" of a reference you duplicate is now set to the current date. Fixed a problem where Replicate As Book Chapter would give a "reference locked" error if All was not selected in the groups pane. Fixed a cosmetic issue where the reference number shown in the reference list could be incorrect.

NEW in Version 11.2
(October 28, 2011)

Bookends 11.2 requires an Intel Mac
Bookends 11.1.7, which runs on both Intel and PPC Macs, is still available from our Web site (, but will receive no further updates or bug fixes.

Sync with Bookends On Tap
Bookends On Tap is our new app for iOS devices, and is available on the iTunes App Store. You can wirelessly sync references and pdfs between Bookends and Bookends On Tap, ensuring that your desktop and portable libraries are up-to-date.

Reference entry/editing pane integrated in the library window
The editing pane can be opened in a variety of ways (Refs -> New, double-clicking on a reference or selecting a reference and pressing Return, clicking on the Edit Reference button at the lower right, and the Views menu). A Preferences setting allows you to revert to the old behavior, opening references in a separate window.

New browser pane in library window
If the selected reference has an entry in the URL field, clicking on the URL icon (globe) at the bottom of the library window opens a browser in the lower pane showing the corresponding Web page. The browser is active, meaning you can follow links and navigate to the full text or a pdf of the reference. You can attach whatever you are viewing (a pdf or a web page as a webarchive) by clicking on the attach icon (paper clip) associated with the browser.

Single column reference display
A "column" control lets you display the reference information in multiple columns or a single column. The single and multi-column views are functionally identical (i.e., mark references, drag and drop, right-click contextual menus, etc.).

Two new fields: Medium and User20
These are available in the Addition Fields tab (or the drawer in the reference window). The Medium field is intended to hold the type of publication (Print, Video, Internet, etc.), which is required for the MLA 7th edition format.

Attach folder contents with drag and drop
Drag and drop folders on a library window with the Command key down attaches any files in them (and in any subfolders).

Window -> Reset Window Position
Although Bookends tries to ensure that the library window is visible when you move from a two display setup to one display, sometimes the window is drawn off screen. If this happens, use Window -> Reset Window Position to move the main window (or the reference window, if it is not integrated into the main window) to the top left corner of the main screen.

If Bookends doesn't find a recently opened library on opening, it will ask you if you want to create one
You can always create a new library at any time with File -> New Library.

Indicate references that have orphaned attachments
When you right-click on the references list or click the Action pop-up button, you can choose to indicate references with attachments that can no longer be located. Bookends will indicate these with red paper clips. The next time the reference list is redrawn the paper clips will be drawn normally.

Open an attachment in Preview or Skim
These options are in an "Open Attachment With" hierarchical menu generated by right-clicking on an attachment in the lower display pane ("Use WebKit to display pdfs" must be unchecked). The default option opens the attachment in the application the Finder chooses.

Each library window remembers its own settings when reopened
As a result, Bookends works more smoothly with the Lion option to restore window positions when re-opening apps.

Library Maintenance -> Verify checks for unnormalized Unicode and offers to normalize and reindex
Unicode normalization is performed if necessary when you do a Database Maintenance -> Rebuild or Repair. Unicode normalization is also performed if necessary when older databases are converted to 11.2. Normalize for Pages, Volume, Date, Location, Publisher, User 1-4.

Improved Remove Duplicates
If two references are otherwise identical, the reference that belongs to a static group will be retained.

Improved Find and Replace
This function (in Global Change) no longer opens the reference window to allow find/find next/replace next, but works globally on the selected references, the Hits List, or the entire database. You will be told how many references will be affected before confirming the replace operation.

The factory default link type is Book : Book Chapter
This can be changed in Preferences. Undefined link types are no longer allowed.

Many small cosmetic changes

Library window nomenclature
To simplify documentation and comparisons between Bookends and Bookends On Tap, your collection of references will be referred to as a library, not a database, throughout the documentation.

Smart scanning of UTF-8 encoded text files
Bookends will recognize a UTF-8 BOM at the beginning of a text file and correctly interpret accented characters. If no BOM is detected, Bookends assumes the file is encoded in MacRoman.

You can create sql searches for Date Added (example in User Guide)

Create final superscripted citations that have a closing but no opening parenthesis
This format is used by journals published by the Japan Society for Bioscience, Biotechnology, and Agrochemistry (JSBBA). This feature is not yet available for Mellel documents.

The Refs -> Find Again menu has been removed
All Finds result in putting the matches in the Hits List. The option to replace or append to an existing Hits List remains but the popup menu giving the choice will be disabled if there are no hits, in which case there is nothing to append to.

The Go To Reference menu and keyboard shortcuts work when the library window is in front
Note that First, Last, Next, Prev refer to the actual reference number in the database, not to the place in the sorted list of references.

Removed menus: Peek, Insert Reference, Hits navigation when the library window is in front

Removed controls: the library window View pop-up and the + add reference button

Removed features: BibTeX option to underline labels of required fields (color field is still available)

Bug fixes

Fixed an issue with how an ellipsis is displayed in Google Scholar online searches. Fixed a bug that caused excessive CPU use when the List View window was open. Bookends will no longer generate an error message if text is mistakenly entered when searching for a reference by a unique id. Fixed an incompatibility with Lion that caused an error when trying to scan an OpenOffice .odt document. Fixed a bug where autocomplete paper with JSTOR would not import the metadata. Fixed a rare error that could occur when scanning with metatypes and a reference has an undefined link type. The default attachment subfolders popup menu is now updated correctly if the subfolder has been deleted in the Finder. Fixed a bug where proofreading a Word document would remove a leading ^ in a temporary citation. Fixed a bug where author names placed in front of the final citation by using the ^ metacharacter didn't obey the name formatting rules if a custom citation format was used. Fixed a bug that could cause conversion of author names to Normal case to fail in some cases. Fixed a bug where cited pages following styled text would assume that style. Fixed an error that could occur when the reference list was unsorted and a key was pressed. Links to DevonThink records now work in the reference pane URL field after a right-click.

NEW in Version 11.1.7
(August 28, 2011)

Direct searches of Amazon Italy and Amazon China

Import total pages and edition from Amazon, if present

Amazon will allow you to retrieve no more than 100 references for a given search
If a search finds more than 100 hits and the book you wanted is not in that list, you must refine the search. This is a new limitation enforced by Amazon, not Bookends.

Normalize Unicode
Bookends stores text as composed Unicode. If you enter decomposed characters (for example, by copy and pasting text from the Web), indexed searches (such as Live Search or Find Words Beginning With) can fail to find some or all of the matching references because the decomposed characters interfere. Database Maintenance -> Reindex, Rebuild, and Repair functions will now normalize any decomposed characters found in the following fields: Authors, Editors, Title, Keywords, Notes, and Abstract.

New smart quotes: Swedish Print
Example: »double quote» and ›single quote›

Words with embedded apostrophes can be added to the list of words whose case should not be changed

Output a close parenthesis after scanned citations
Some publications require citations consisting of a superscripted number followed by a close parenthesis. This option is available in the format definition "Enclose citations with" pop-up menu.

Bug fixes

Fixed a rare bug where an attachment could be attached to the wrong reference. Fixed a first-run installation or update bug where the Formats folder could be empty. Fixed a cosmetic bug where the fomat pop-up at the bottom of the lower pane could disappear. Fixed a rare bug that could cause quoted text from the last citation in a paper to be inserted in the first citation after a scan. Changed the cited pages function so that it will not try to expand or contract a page number in a range if more than one page range, separated by a comma, is entered in the pages field. Fixed a bug in scanning Pages documents with annotations that could result in a hang. Fixed a bug that caused some unicode characters to be displayed incorrectly in a bibliography after scanning.

NEW in Version 11.1.6
(July 24, 2011)

Globally remove terms in Term Lists
In the Terms List window, select the term and right-click or use the Action pop-up and select Replace. Delete all characters in the replace text box and press Replace. Bookends will remove the selected term from the corresponding field in every reference in the database and update the Term List.

Use the pipe character ( | ) as a citation delimiter
Set in Preferences.

Direct online search for missing citations after a scan
If a citation doesn't have a matching reference after a scan, you can choose "Search Online", which will open the Online Search window with the citation in the text search box. The last used search engine will be selected by default unless it is Bookends Browser, in which case PubMed will be selected. You can edit the search text and change search engines before performing the search.

Updated JSTOR import in Bookends Browser to deal with changes made on their server

Bug fixes

There is no longer an error message when renaming a dropped attachment that had a slash in its name. Fixed a bug in a Pages scan that would cause a self-deleting temporary citation (beginning with an !) to be shown by mistake if it contained styled text. Fixed a bug that could cause incorrect text to be included in a citations "quoted text" when scanning a Word document. Fixed a bug in Word and Nisus Writer Pro scanning where a citation with an author name that contains a smart apostrophe could not be matched. Bookends will leave a trailing comma in an imported author's name (the institutional name indicator). Fixed a problem with Pages scans where some citations following annotated text might not be recognized. Fixed a bug where garbage characters could be inserted into a Word or Nisus Writer Pro citation if there was quoted text that contained Unicode characters. Fixed a bug in Global Find/Replace where the ¬ character in the Find field was not being recognized as the metacharacter for Return. When you click on a hypertext link in the concise view, trailing periods will be ignored. Fixed a bug in scanning text documents where some formatting metacharacters in the temporary citation were ignored. Fixed a bug in Pages scans were a tab in the middle of a paragraph could cause Bookends to skip over any following citations in that paragraph. Fixed an encoding issue with some Google Scholar references containing accented characters. Fixed a problem where the list of formats or import filters in their respective Manager windows could be truncated. Fixed a rare bug where unscanning a Word or Nisus Write Pro document with consecutive citations delimited with tildes would fail. Fixed a cosmetic bug where the attachment inspector image wouldn't clear when you imported a new reference. Fixed a problem with some installations from the Mac App Store where the Formats folder would be empty. Fixed a bug where a live search for more than one term would fail if a group was selected.

NEW in Version 11.1.5
(May 14, 2011)

A new metacharacter to automatically change parentheses to square brackets
If a citation begins with a square bracket, Bookends will replace any internal parentheses with square brackets when scanning with a custom citation format. This is useful for formats such as SBL, where footnotes following quotes are surrounded by parentheses, and the parentheses that would normally be used inside the footnote should be changed to square brackets. This feature does not work yet with Mellel.

Updated the JSTOR Bookends Browser importer to be compatible with changes made by JSTOR

Access Google Scholar Related articles in Online Search
To see Related articles, hold the Option key down when you select a reference in the Online Search window and you have toggled to the Web view (lower pane). This can be useful if you have access privilege for the pdf from some sources and not others. In the Related articles web page you can chose to get the article from a source for which you have privileges.

Cited pages are ignored when a format calls for numbered citations

Use literal text with more than one citation in a citation group in Word and Nisus Writer Express
Previously this was only possible with Mellel and Pages.

If a citation group contains literal text at the beginning, the group will not be sorted during a scan
This prevents the leading literal text from (such as "See also") from being moved in the final formatted citation group.

You can now access formats in the Custom Formats folder when running in the demo mode
Note that if you currently use Bookends 9 or earlier, any format you open or use will be automatically updated to the Bookends 11 schema and can no longer be used by the older version.

Bug fixes

Fixed a bug where "Ibid." was left out when scanning with a custom citation format. Fixed a bug where an error could occur for some author-date scans. Fixed a bug that could cause incorrect footnote citations with cited pages, and failure to make a range of consecutive number citations, in Word and Nisus Writer Pro scans. Fixed some issues where punctuation preceding cited pages was not trimmed properly. Fixed a bug where an error could be thrown if PubMed or Library of Congress search contained certain punctuation marks. Fixed a bug where cited pages used with numbered citations could result in incorrect output. Fixed a bug in the JSTOR import filter that prevented it from importing journal name and volume. Fixed a bug that caused the second of two consecutive citations to the same work with different cited pages to be empty when scanning with the MLA format. Fixed a bug where unmatched citations would not be listed after a Word or Nisus Writer Pro scan and the unmatched citations would be emptied. Fixed a bug where dropping the pdf proxy icon from the Bookends Browser window on the Finder didn't create a copy of the pdf or webarchive. Fixed a rare bug that could result in ∆ to appear at the beginning of references in bibliographies. Fixed a bug that could cause a Word or Nisus Writer Pro document to be truncated after scanning with a format specifying "Use year-only for repeated authors".

NEW in Version 11.1.4
(March 31, 2011)

Expanded support for APA 6th
For references with 8 or more authors, Bookends will output an ellipsis after the sixth author and follow it with the name of the last author, as required for the APA 6th style. The placement and composition of the text can be modified for other styles if needed.

Copy notecards
Use the standard Edit -> Copy (Command-C) to copy the text of the selected notecards to the clipboard. This is useful if you want the notes but not the temporary citation. Copy Notecard is also available via the right-click contextual menu.

New location for formats from Sonny Software
The factory-supplied Formats folder will be moved to ~/Library/Application Support/Bookends/ with each update. When Bookends is updated, the contents of the old Formats folder will be replaced with the latest versions shipped by Sonny Software. Any formats you have created or modified will not be touched (they will be in the Custom Formats folder). This change was introduced to make Bookends compliant with Mac App Store rules.

Automatically rename an attachment with the reference title
This setting is in Preferences, Refs tab. If the reference has no title, the author and date will be used.

The file format of the Microsoft Word 2008/2011 script files has changed

Improved importing of references from CrossRef
Worked around a problem in CrossRef where the text encoding of the reference metadata from CrossRef was misrepresented to Bookends.

Bookends will prompt you to create a database on first run
The prompt will appear when you click on the Continue Demo button and there are no databases in the Open -> Recent Database menu.

Increased font size in Format Manager examples
The styled citation example in the format definition window will be 2 points larger than the bibliography default, to make small characters like punctuation easier to read when creating/editing formats.

Bug fixes

Fixed a bug in import and attach from a pdf's doi if the metadata was provided by CrossRef. Fixed a bug where an extra parenthesis was output when scanning an RTF file with citations beginning with quoted text. Fixed a bug where drag and drop importing of a Google Scholar reference could result in appearance of garbage characters if the default import encoding wasn't set to UTF-8. Fixed a bug where a Find for characters in a specific field could return incorrect references. Fixed a problem with rename attachment where the presence of certain characters in the name could cause a crash. Fixed a bug that could cause incorrect MLA citations with some word processors when the same reference was cited consecutively. Fixed a bug that could result in failure to update the "Save PDF to Bookends" option for new versions (does not apply to Bookends bought from the Mac App Store, which does not allow automatic creation of these files). Improved algorithm to display the number of references in the subset when doing a live search. Fixed several issues where some footnotes in a Pages document would be overlooked during a scan. When creating a new virtual tag with a right-click, pressing Cancel exits without creating a virtual tag.

NEW in Version 11.1.3
(Februrary 27, 2011)

Search for phrases, including punctuation, with Live Search
Live Search normally searches for indexed words, which is very fast but doesn't allow searching for phrases or punctuation. If you enclose text in the Live Search box with quote marks, Bookends will search for an exact character match. For example, searching for "United States" will not match a reference that has the words "United Kingdom" and "altered states", only ones with the exact proper noun (the search is still case-insensitive). You can mix indexed and non-indexed searches. To perform a NOT search, place a minus sign immediately before the opening quote mark, for example: cancer -"B cell lymphoma" will find references with the words "cancer" but not "B cell lymphoma". Once you type in a quote mark, Bookends will wait until you've entered a closing quote mark before performing the search (that is, Bookends won't perform a search if there are unbalanced quote marks). Note that non-indexed searches are slower than indexed searches, which you will notice if you have many references. Bookends will display a spinning progress wheel to indicate that a non-indexed search is being performed.

Insert a notecard's content and its citation in Mellel
Requires Mellel 2.8.1 or later.

Improved PubMed automated search
Any references found by the search that you already have in your database will be colored yellow. Various cosmetic improvements were made to the automated search window.

Import text encoded as UTF-16
Set this in the File -> Import Text Encoding menu.

Updated functions that use CrossRef, such as importing from existing bibliographies
Deals with changes made by CrossRef.

Display text of attached Mellel 2.8 and later documents
Works with the compressed file format introduced in Mellel 2.8.

Changes in Import Filter and Formats Manager windows
If there are two formats or import filters with the same name (one supplied by Sonny Software, one in the Custom Format folder), only the custom format will be shown in the corresponding manager window.

Bug fixes

Fixed a bug where updated Word 2011 AppleScripts would failed to install automatically. Fixed a bug that prevented COinS from being detected. Fixed a bug in author-date scans using ibid when consecutive citations of different references were output as year-only and were from the same year. Fixed the JSTOR filter and reference detector. Fixed several problems in Bookends browser. Fixed a bug in PubMed automated search that caused a crash if no Bookends database was open. Fixed a bug were some attachments with Unicode characters were not found by the "Reveal In Finder" function.

NEW in Version 11.1.2
(January 30, 2011)

Bookends will replace missing Word and Pages add-ins and scripts on launch, if necessary
For non-English systems, it may be necessary to replace or update them manually.

New file/folder locations
The files/folders Bookends 11 Preferences, Backup, and Bookmarks are now in ~/Library/Application Support/Bookends/. The Bookmarks file has been updated to contain current URLs. If you added URLs to the old Bookmarks settings, you will need to add them again.

Updated the JSTOR import function in Bookends Browser to deal with changes made by JSTOR

E-Mail… has been added to the Refs menu

Newly created formats are automatically enabled (checked)

Bug fixes

Fixed a bug where attaching a folder or Mellel file would result in an error message, and the folder and contents would be moved to the Trash. Fixed a bug where the letter appended after a year to disambiguate a citation could be incorrect. Fixed a bug that would cause a crash when printing. Fixed a scanning bug where the setting for citing multiple references in a group under one number was affecting author-date and custom format citations. Fixed a bug in the Online Search window where double-clicking on a reference found in Amazon would not launch Bookends Browser. Updated Autocomplete Paper to deal with changes in Google Scholar and fixed a bug that could result in the wrong reference being imported from Google Scholar.

NEW in Version 11.1.1
(December 19, 2010)

Bookends is a self-contained application package
There is no longer a Bookends Folder. The folders for the factory default Formats, Import Filters, and files for documentation (Read Me, Bookends Tutorial.pdf, and User Guide.pdf) are in the Bookends app package itself. The documentation can be accessed via the Bookends Help menu. The various folders for tutorials and word processor add-ins and scripts are in ~/Library/Application Support/Bookends/. These changes are being made to comply with requirements of the Mac App Store. Upgrading to future versions of Bookends will be done by simply replacing the old Bookends application with the new one.

Malformed pdf warning
You will receive a warning if you attach a file with a length of 0 bytes. This can happen if the Adobe pdf plug-in is installed.

Virtual tags are sorted
Virtual tags will be sorted alphabetically in Preferences and in the tag cloud contextual menu.

Lookup Article From DOI using Bookends Browser
The menu Lookup Article From DOI is hierarchical, letting you view the article using your default standalone browser (e.g. Safari) or Bookends Browser. The latter is useful if you want to import reference information from an Internet source that has embedded COinS, for example, or a pdf.

Bug fixes

Improved algorithm for removing periods in front of or trailing a word when creating tags.

NEW in Version 11.1
(November 26, 2010)

Introducing virtual tags
Virtual tags allow you to group tags words in titles, abstracts, and/or notes under a term of your choosing. For example, you could create a virtual tag Colors and include in it the terms red, green, and blue. The size and color of the virtual tag Colors would reflect the frequency of all of these tags, and when you click on Colors… in the tag cloud pane Bookends will display all the references that have any of those words in the corresponding fields. You can also use virtual tags to aggregate words with the same basic meaning but differ in tense or spelling, such as computer, computers, computerized, etc. You can tell Bookends to hide or show individual tags that are included in a virtual tag. You can manage virtual tags in two places, Preferences (Tags tab) and in the tag cloud pane (via contextual menus). In the latter, select and then right-click on a virtual tag to see the tags it contains, remove an individual tag component, or delete the virtual tag. Select one or more real tags and use a right-click to add the selected tags to an existing virtual tag or to a new virtual tag you create on-the-fly.

Attach a PDF only if reference metadata is found online
This option is available when attaching PDFs in bulk by dropping them on a database window with the Command key held down. If the box “Attach PDF only if reference metadata are found online” is checked, Bookends will only attach a pdf (and move or copy it to the default attachments folder if requested) if Bookends can locate the reference metadata on the Internet. This is useful if you want to have Bookends automatically download reference data for pdfs you already have, but don't want the pdf attached if Bookends can't locate it.

Amazon online searches will display book descriptions, if present
These will be imported to the Abstract field.

A sortable publication date column has been added to the Amazon search display

Set the maximum number of recently opened databases Bookends will display (Preferences)

Get PDF works with more publishers

Get DOI was updated to work with changes made by CrossRef

Improved handling of Ibid. citations
To avoid ambiguity, if a citation is the last member in a group and then is cited immediately after that group, Ibid. will not be used even if the format calls for it.

Database Maintenance -> Rebuild (Keep User Settings) has been named Rebuild
The old Rebuild function, which deleted all database-associated information and groups has been removed. If there are problems with database tables, you can use Database Maintenance -> Repair instead to fix them.

Bug fixes

Fixed a bug in the Mellel scan where Ibid. could be incorrectly used for identical consecutive citations to different references, or an error message could appear. Fixed a bug in the Pages scan where text could be mistakenly repeated in the scanned document. Fixed a scanning bug where an open parenthesis could be mistakenly be output when citation enclosures were suppressed and the citation began with quoted text. Fixed a bug that could cause a letter to be appended to the year after scanning with Word or Nisus Writer Pro if a document had only one citation. Fixed a minor bug where Live Searches could result in a list of references where none was selected. Fixed a bug in groups where renaming a folder could result in failure to update its subgroups. Fixed a bug in Mellel scans where using Ibid. could result in an error. Fixed a bug in which a proofreading scan of a Word or Nisus Writer Pro file could introduce a spurious open parenthesis. Fixed a rare bug that could result in the inclusion of spurious unicode characters or punctuation in a citations after a scan. Fixed a bug where incorrect groups could be listed in formatted references. Fixed a bug where "et al." could sometimes be output with the wrong text style. Fixed a bug that could in some cases cause a scanned NWP document to be truncated after an inserted pdf image.

NEW in Version 11.0.9
(September 19, 2010)

Perform an Autocomplete Paper using CrossRef as a source of reference metadata
This is in addition to the other sources (Pubmed, JSTOR, Google Scholar, and Web Of Science), and requires that the reference have a doi.

Updated JSTOR reference detector
This was broken by changes made by JSTOR. Note that automatic downloading of JSTOR pdfs still requires ip authentication.

Bug fixes

Fixed two bugs that could prevent Bookends from finding some citations in Pages footnotes. Fixed a bug introduced in v11.0.8 where automatically finding reference metadata when attaching a pdf with an embedded doi failed. Fixed a bug that could cause Bookends to fail to append a letter to the years of ambiguous author-date citations. Fixed a bug in Mellel and Pages scans where having an Ibid. in a group would suppress the output of subsequent citations in that group.

NEW in Version 11.0.8
(September 6, 2010)

Direct JSTOR searches and using JSTOR for autocomplete paper restored
This was broken by changes made by JSTOR. Note this still requires ip authentication.

Searching for and importing JSTOR references and pdfs with Bookends Browser restored
This was broken by changes made by JSTOR. Note that automatic downloading of JSTOR pdfs still requires ip authentication.

CrossRef added as a source for Autofill
Bookends will attempt to autofill a reference (Refs -> Autofill From Internet) based on a doi from Internet sources in this order: PubMed, CrossRef, Google Scholar. Because CrossRef is usually a better source than Google Scholar, this should improve the completeness and quality of the metadata.

Korean and other Asian characters returned with a Google Scholar online search are rendered correctly

Microsoft Word scripts are compatible with Microsoft Word 2011

Revised handling of modified journal glossaries
If you modify a journal glossary that's in Bookends 11 Folder/Journal Glossaries, Bookends will ask you to rename it when it is saved. The renamed copy will be saved to ~/Library/Application Support/Bookends/Custom Journal Glossaries and be set as the default journal glossary. This ensures that the glossary will not be overwritten when you upgrade Bookends.

Improved handling of selected references
Bookends will remember the last selected references when you move away from a group and then return to that group. This does not apply to the group Hits or to virtual groups (made from selected multiple groups).

Smart quote options now include German Guillemets
Examples: »double« ›single‹

Bug fixes

Fixed a bug in Term List where updating the list would ignore any text in the search filter. Fixed several cosmetic errors in the standalone Term List window. Fixed a bug where an opening citation parenthesis would not be output when scanning a Word document with a format calling for italicized numbers, and where using the "don't enclose citation" metacharacter, *, would result in the inappropriate output of the open parenthesis. Removed the "Show Examples of All Formats" button from the format window (use Biblio -> Create Format Catalog).

NEW in Version 11.0.7
(August 8, 2010)

Create a catalog displaying all your formats
Biblio -> Create Format Catalog will generate a file containing examples of each Type from each format. The catalog can contain all formats, only formats marked in the Formats Manager, or just the default format. The catalog will automatically be opened in the application used to open RTF files (usually TextEdit). Format catalogs are especially useful for finding a format whose output is similar (or identical) to one you need but for which a specific format does not exist. Note that unlike most real-life examples, the example references used by Bookends have no empty fields, so the output may contain reference information that you won't usually see with your own references. Also note that hanging indents will not be shown in the format catalog, and that metatype formats will output example fields from the same reference regardless of any parent/child (i.e. square bracket) indicators.

If the temporary citation delimiter has been set to comma for use with BibTeX, it will be reset to semicolon if BibTeX is disabled
This ensures that you won't get spurious citations when scanning temporary citations with commas, such as {Smith, 2010, Nature}.

Improved attachment indicator
Multiple attachments are indicated by two paper clips in the List View. This replaces the red paper clip that was introduced in Bookends 11.0.6.

Allow selection of any file when importing references
The File -> Import References dialog allows you to view text files or all files. This is useful if you have downloaded a file from the Internet that cannot be identified as a text file (e.g. it doesn't have a .txt extension or the TEXT file type metadata). Note that you can also import such a file by drag and drop with the Shift key held down.

Drag and drop multiple files change
The default behavior is now to attach each file to the selected reference. If the Command Key is held down, Bookends will offer to attach each file to a new reference.

Footnotes created with a custom citation format and that contain super- or subscripted characters will be displayed correctly in scanned Pages documents

Link Inspector change
The parent : child relationship is now only based on the settings in Preferences (Links tab). That means that the reference you display in the Link Inspector "dock" can be either a parent or a child, and relationships you set with references in the link list will act accordingly.

Use drag and drop to import PubMed references from Google Chrome
This feature has always been available for Safari.

Bug fixes

Fixed a bug that could insert a space before the title in some references imported from JSTOR via Bookends Browser. Fixed a bug that could affect formatting of conditional groups that contain the issue field. Fixed a bug in scanning where letters were sometimes not added to the year to disambiguate identical citations referring to different references. Fixed a bug in Sync where specifying Use Last Sync Dates could result in the wrong Client/Master relationship. Improved the reliability of of Spotlight searches within Bookends. Fixed a bug that could cause an existing attachment to be detached when copying a new file with the same name to the attachments folder. Fixed a bug where an extra parenthesis could be output when using quoted text with a citation that is output as an italicized number.

NEW in Version 11.0.6
(July 11, 2010)

Attach multiple files to the same reference in one drag and drop
Press the Command key when making the drop. If you don't press Command, Bookends will offer to attach each file to a new reference.

Import multiple text files with one drag and drop
Press the Shift key when making the drop. If you don't press Shift, Bookends will offer to attach each file to a new reference.

Automatically rename attachments by title
If selected in Preferences, Bookends will use the first 220 characters in a reference's title when it automatically renames an attachment.

Improved author "ignore list" for sorting
The author "ignore list" used for bibliography sorting can include punctuation marks used for grouping: (, [, and {. For example, you can enclose an author's name in parentheses, such as (Smithy, JR) and the reference will sort with others that have author names beginning with 's'.

Drag and drop import to a specific group
If you drag a text file to a static group and import the references, those references will be automatically added to that group. If you drop a pdf on a static group and chose to Autocomplete Paper, the imported reference will be added to that static group. If you drop a pdf on a static group and do not autocomplete paper, the pdf will be attached to the selected reference in the list, as usual.

Footnotes created with a custom citation format and that contain super- or subscripted characters will be displayed correctly in scanned Pages documents

Improved attachment indicator
A red paper clip will be displayed in the List View to indicate that a reference has more than one attachment (otherwise a grayscale paper clip will be used).

Bug fixes

Fixed a bug in which styled text could be incorrectly formatted in footnotes inserted in a scanned Nisus Writer Pro document. Now you can search Google Scholar for exact text by surrounding multiple words with quote marks. Fixed a rare problem where an extra space could be output after a surname when using a format calling for "et al." to be inserted. When Copy Formatted is used with a linked Pages document, the formatted reference will be automatically inserted but in plain text — manually paste if there is styled text in the formatted reference. Fixed a bug where bibliographies generated from scanned OpenOffice documents could only be created with plain text.

NEW in Version 11.0.5
(June 6, 2010)

Globally rename attachments
Refs -> Global Change -> Rename Attachments will automatically rename any attached files in the selected reference, the Hits List, or the entire database according to the specifications defined in Preferences. This is similar to the rename attachment option available in the Attachment Inspector or right-clicking on an attachment in the List View window, but can be applied to many references at once. This operation is not undo-able. Note that if an attachment is shared by two databases, changing its name will make any links to it in other databases orphans.

Automatically rename the pdf after autocompleting a paper
The autocomplete paper dialog sheet has an option "Rename pdf after import". If checked, after importing a reference Bookends will rename the attachment according to the specifications you defined in Preferences.

Attach multiple files to new references in one step
If you drag and drop more than one file onto the List View or reference window, Bookends will offer to attach each one to a new reference. This is a convenient way to populate your reference database with pdfs you already have. Bookends will look for an embedded doi in any pdf you drop, and if found will try to download the reference metadata from PubMed or Google Scholar. You will be able to specify if they will be moved or copied to the default attachment folder (or subfolder) or left in place, and if they should be renamed. Names will be generated according to your preference settings. Note that the reference's metadata, if found, will be used to create the name. If not found, generic placeholder names will be created.

The ~/Documents/Bookends folder can be deleted by the user if it is not being used
It will be automatically recreated if you use the Bookends automatic backup feature (highly recommended!) or move attachments to the default attachments folder. This is intended for those few who don't use these features and who want to keep their Documents folder "tidy".

Extended the ability to exclude particular titles from title-case rules
To exclude a Series Title, Short Title, or Book Title from the title-case rules for a format, end the text with a comma (this already works for the Title field).

Footnotes created with a custom citation format and that contain super- or subscripted characters will be displayed correctly in scanned Pages documents

Improved List View sort
Bookends will use the first author for sorting if only the first author's name is shown (set in Preferences). This means that the references will appear in first author-date order.

Restored the ability to import references from existing bibliographies via CrossRef
This had been broken by changes made by

File -> Import From Existing Bibliography is a menu item
This will take you to CrossRef Simple Text Query, just as Online Search -> Bookends Browser does. It has been added as a menu item for convenience and visibility.

Improved handing of text files after import
If you have checked "Move to Trash after import", Bookends will move the file to the Trash only if at least one reference was imported. Therefore, if you use the wrong import filter by mistake, you don't have to recover the file from the Trash to try again.

Bug fixes

Choosing Mark/Unmark All when the Terms List is being viewed in the List View will only affect the references showing in the reference list (the same behavior as when Groups are showing). Fixed a problem in Snow Leopard that caused Bookends to fail to display pdfs in the List View window when WebKit was turned off or in the reference window. The Term List filter textbox is now cleared when the Term List to be displayed is changed. Fixed a bug that would cause link relationships to not display in the Inspector in certain circumstances. Fixed a bug in HTML export that would trigger an error message if the first author position of a paper was an empty line. Fixed a bug where dashes could be inappropriately substituted for an authors name if it was from a chapter in an edited book and the edited book was included in the bibliography just before it. Eliminated a leading space that could be present when adding a term from a Term List to an open reference window. Fixed a bug where a citation could be garbled when scanning a Mellel document and output "et al." in italics turned on in the format.

NEW in Version 11.0.4
(May 5, 2010)

Display Term Lists in the List View window
The Groups pane header is now a pop-up menu from which you can select Groups or a Term List (Authors, Keywords, etc.). Clicking on a term will show all the references in which it is contained, and selecting multiple terms will show the references that contain all of the terms (AND) or any of the terms (OR), as specified in the Action pop-up or a contextual menu. The Term List window still exists, but now is just a single column that can be used to rapidly add one or more terms to many references at once, change a term's spelling, be saved as a text file, etc.

Updated database engine
Some operations are faster than in previous versions. Custom formats created in Bookends 7 and never modified in a later version will not be recognized by the newer database engine.

Journal Glossary and Term Lists menu items have been moved to the Window menu
The Extras menu has been removed.

Bookends creates a new alias in the PDF Print Services folder each time it is launched
This means that the alias won't be broken by upgrading to a new version of Bookends.

Restored Get DOI functionality
This was broken by changes made by CrossRef.

Improved pdf download to handle changes made by some publishers

Keyboard shortcuts let you add/change reference ratings
Using Shift-Option-Command-# to assign ratings (0 through 5 stars).

The Find and Find In This Reference dialogs are now sheets rather than windows

Bug fixes

Fixed a rare bug that could cause custom citations to be malformed if they contained Unicode text. Fixed a bug in Autocomplete Paper that could result in an inappropriate error message. Fixed a problem introduced in 11.0.2 where Bookends would not match temporary citations containing accented characters. Fixed a bug where filling in the PMCID from the PMID on multiple references at once could result in incorrect pairing. Fixed a bug that could cause the "get references from existing bibliography" to hang. Fixed a minor bug involving color labels. Fixed a bug in scanning .odt files created by NeoOffice. Fixed a bug that could prevent syncing of a Mellel document with a Bookends database. Other minor fixes.

NEW in Version 11.0.3
(April 11, 2010)

Add terms (keywords, authors, etc.) to multiple references in one step
Open the Term List window and drag one or more terms onto the List View window. Bookends will offer to add those terms to the selected references. If the term is an author, editor, or keyword, Bookends will check to see if it is already in the corresponding field of each selected reference, skipping over it if the term is present. This operation can also be invoked with the Action pop-up menu or right-click contextual menu "Add Term To Selected References". If the reference window is open, this option will be worded "Add Term To Open Reference".

Better identification of references you already have when performing an Online Search
Bookends will use the doi (if present) in addition to the pmid to determine if you already have a reference when searching PubMed.

Run attached QuickTime movies (.mov) in the List View window display panel

Right-click on Online Search references to select those you do or don't have
You can then import or delete the selected references.

Easily add tag cloud words to the "stop list" list of words to exclude
Add selected tag cloud words to the stop list via the Action pop-up menu or right-clicking and selecting the corresponding contextual menu choice. This works with Title, Abstract, and Notes tag clouds.

Improved pdf download to handle changes made by some publishers
Previous versions could return a "103" error in some cases.

Bug fixes

Fixed a rare bug that could cause custom citations to be malformed if they contained Unicode text. Fixed a bug in Autocomplete Paper that could result in an inappropriate error message. Fixed a problem introduced in 11.0.2 where Bookends would not match temporary citations containing accented characters. Fixed a bug where filling in the PMCID from the PMID on multiple references at once could result in incorrect pairing. Fixed a bug that could cause the "get references from existing bibliography" to hang. Fixed a minor bug involving color labels. Fixed a bug in scanning .odt files created by NeoOffice. Fixed a bug that could prevent syncing of a Mellel document with a Bookends database. Other minor fixes.

NEW in Version 11.0.2
(March 20, 2010)

Import journal articles in existing bibliographies
In some cases Bookends is able to locate and download articles (and pdfs) listed in existing bibliographies. To do this, use Bookends Browser to go to the bookmarked CrossRef simple text query page ( Paste in a bibliography copied from a word processor document or pdf, one reference per line. If PMIDs or DOIs for one or more reference is identified, Bookends will show a list of the titles and you can choose to import them (with or with looking for the pdf) into your Bookends database. Bookends will attempt to retrieve the reference metadata from PubMed or Google Scholar. Because the process only finds references that have a DOI or PMID listed in PubMed or Google Scholar, the chances of success are much greater for journal articles, especially those in the biomedical literature, than for other reference types. Even for these, you should not expect 100% efficiency. This is especially true of older articles in the biomedical literature that do not have their DOIs entered in PubMed, which means that Bookends relies on Google Scholar for the metadata, which unfortunately sometimes returns the wrong article.

Retrieve PubMed Central ID (PMCID)
If a reference has a PMID, you can use the menu Refs -> PMID -> Fill In PubMed Central ID (PMCID) to have Bookends search for the PMCID. This can be done in batch by selecting multiple references in the List View (the first must have a PMID for the menu to be enabled). There is a limit of 2000 PMIDs that can be processed in a single query. When used in the List View, Bookends will report the number of PMIDs that were submitted and the number of PMCIDs that were found.

Get PDF From Internet is better at finding older biomedical articles

The Links button in the reference window is always enabled
If there are no links the color is dark gray, if there are links the color is blue. Clicking on the Links button toggles the Links Inspector.

Output page ranges with "Last page as entered"
If this is selected in the format (Bibliography tab), Bookends will not try to parse non-standard page ranges. For example, 5.14-15 would be output as is, not expanded to 5.14-5.15. You can have Bookends output the "Last Page As Entered"on an ad hoc basis if you terminate the pages in the Pages field with a comma. In this case, Bookends will always output the page range exactly as it was entered regardless of how page ranges are set to be handled by the format (Bookends will still output just the first page if the format uses "p" rather than "p-").

Exclude a title from the format's case rules on an ad hoc basis
If a title ends in a comma it will be output as entered regardless of what case rules (Title Case, ALL CAPS, Sentence Case) are specified in the format.

Output square brackets ( [ and ] ) in metatypes by entering them as quoted text (i.e. surrounded by two dollar signs, backquotes, or tildes)

PDFs are displayed in the reference window with Bookends’ built-in controls, and the reference window appearance has slightly changed
As a result, the text cursor will no longer submarine (disappear for a short period of time) when using the arrow keys to navigate in text fields.

Bug fixes

Fixed a bug where accented characters at the beginning of a source field could be mangled when imported. Fixed a bug in which the italic style could be incorrectly offset within a citation group in a scanned Pages document. Fixed a bug where renaming a group in a folder would cause it to disappear when the folder was closed and reopened. Fixed a rare problem where importing multiple references at once form some sites (e.g. ICCU) could fail. Fixed a bug in metatypes where the pages for the first (child) reference might be output even though the temp citation contained cited pages. Fixed an issue when scanning Mellel documents where special citaiton formatting instructions, such as output date-only, were ignored if the citation was to have no enclosing punctuation. Fixed a problem where the live search textbox would lose the focus after a few keystrokes if "Use WebKit to display pdfs" was enabled.

NEW in Version 11.0.1
(March 6, 2010)

Use WebKit to view attached pdfs in the reference window
This means that, for example, you can see annotations made in Preview. How pdfs are displayed is determined by the List View window's "Use WebKit to display PDFs" setting.

Configure the tag cloud display
Set the smallest and largest font size used, as well as the background color.

The font for the groups pane is the same as the reference list

Metatypes will be recognized when generating a bibliography with the Bibliography Formatter

Minor cosmetic changes
Removed the Add pop-up menu button in the lower left hand corner of the List View window and the Delete option in the Action pop-up menu because they were redundant with other UI elements. The minimum width of the groups pane has been reduced.

Bug fixes
Fixed several bugs with the creation of final citations in scanned Word documents (where literal text of a Word temporary in-text citation would be placed outside of the enclosing punctuation, and where the citation could begin with two parentheses instead of one). Fixed a problem that could cause a reference Type to be undefined if the import filter Misc tab setting instructed Bookends to insert literal text. If a temporary citation begins with literal text, Bookends will keep it at that position even if the citations in the group are sorted by author or date. The ability of Bookends to detect temporary citations in Pages footnotes has been improved.

NEW in Version 11
(February 13, 2010)

Tag clouds
A tag cloud is a visual depiction of the user-generated terms or words in your references. Bookends will generate a display of tags from the references in the List View window (the "reference set"). You can tell Bookends to limit the number of tags to the top 50, 100, 200, 500, 1000, or All. There are two kinds of tag cloud. One, used for Keywords, Authors, and Editors, makes each line in these fields a tag, so a tag may consist of more than one word. The other, used for Title, Abstract, and Notes, displays individual words from these fields. Tags are displayed in alphabetical order, with the size and color of the text being proportional to the number of times the tag is used. When you hover the mouse over a tag, its frequency will appear at the bottom of the tag cloud display. Bookends will show the full dynamic range of a particular reference set, so a word that may be a minor tag in the context of all references may be a major tag for a particular subset. Clicking on a tag will cause the list of references to update to show only matches. You can select multiple tags by Shift-clicking or Command-clicking (you can deselect a tag by Shift-clicking or Command-clicking on a selected word, or all tags by clicking in empty space). The tag cloud will refresh whenever you change the reference set, such as by clicking in the Groups list or doing a Find. Otherwise the tag cloud will remain as you "tunnel down" through the references by clicking on tags or using the Live Search textbox. You can also switch the bottom view pane to see attached files or the formatted view of the selected reference without disturbing the tag cloud. An editable list of “stop words” and one character words are filtered out of tags generated from the Title, Abstract, and Notes fields. Use Refs -> Create Tag Cloud From This Reference Set to make and show a tag cloud from the references on display. This lets you drill "down" but not "up" through the references—to return to the original tag cloud you must recreate the reference set, for example by clicking on a group or All. Note: Bookends tries to isolate "whole words" from the Abstract, Notes, and Title fields, but depending upon the use of punctuation marks and other non-letter characters you will sometimes see partial words or words that, when you click them, don't match a "whole word" in the reference.

Unlimited and configurable metatypes
A metatype is a virtual Type that lets you combine outputs of two different references in one footnote or bibliography entry. Previously this was limited to Books and Book Chapters. Now you can define a metatype for any pair of linked references, regardless of their native Type. For example, you can have two journal articles that are defined in the Link Inspector as Argument and Rebuttal. If you create a Rebuttal [Argument] metatype in the format, citing the rebutting article will automatically cite portions of the original article (e.g. author, title, etc.) in the footnote and/or bibliography.

Improved notecard display
Characters in the Notes field that are in styled text (italics, bold, underline, and color) will be displayed as such in notecards. This means that you can create bold titles, italicized comments, etc. that can be seen in the note stream. Spacing between notecards has been improved, and notecard text that is too long to be seen in its entirety will end in an ellipsis (…).

Modified user interface

Smart quotes
If selected in Preferences Scan & Bib tab, Bookends will replace straight quote marks and apostrophes (" and ') with smart ones when formatting. Smart quote choices include English, Dutch, German, Guillemets , Guillemets With Spaces, and Scandinavian (English is enabled as default).

Improved scan algorithm
If the unique id is included in a temporary citation, any other text will be ignored during the scan. This means, for example, that if you cite by Author, Date, Unique ID and then correct a typo in the author's name in the database, Bookends will still find the correct reference when the scan is performed.

Refs -> Make Parent In Link Inspector
This command will change the parent in the Link Inspector (if showing) to the selected reference in the List View. Previously this was only possible by drag and drop. If the Link Inspector is not showing, use Window -> Show Inspector to accomplish the same thing.

File -> Set Default Attachment Subfolder
When you perform a Refs -> Get PDF -> From Internet, the pdf is placed in the last used default attachment folder or subfolder. You can use this menu option to set the default subfolder prior to performing the download.

Normalize unicode when importing
Bookends will normalize unicode characters (converting composite to precomposed) for imported references. This means that you can import accented characters from sites that output composite unicode and they will be indexed correctly (and searchable) in Bookends.

BibTeX scanning enhancements
During a scan, if Bookends finds a temporary citation in the form \citeNP{key} it will omit the enclosing punctuation from the final citation. If it encounters \citeyear{key}, it will output only the year in the final citation. Text in square brackets prior to the key will be appended to the end of the final citation, after a comma and a space. For example, \cite[p. 12]{key} might resolve to (Johannson, 2009, p. 12).

Mix formatting instruction and literal text in the same temporary citation
For example, {%\See also \Smith, 2009} will output a citation preceded by the quoted text and containing the year-only: (See also 2009). The Copy Citation With Modifiers dialog allows you to enter both preceding text and special formatting instructions.

More versatile Author-Date citations
The built-in Author-Date citation method can output "Ibid." (or another word or phrase of your choice) if consecutive citations refer to the same reference. You can change the text that Bookends uses after the first author when there are more than two authors in an Author-Date citation (the default is " et al."). You can tell Bookends to automatically italicize the authors' names and associated text, such as "and" and "et al.".

Automatically generate citations such as 'Carpenter (2009)'
If you place a caret immediately after the temporary citation opening delimiter (usually a curly bracket), Bookends will extract the author and place the name(s) in front (if there is no author, the editor's name(s) will be used). The name(s) will be output in the Author-Date style. That is, one author results in a single surname (Jobs), two authors gives two surnames (Jobs and Cook), and three or more authors results in the first surname followed by 'et al.' (or whatever you have told Bookends to output in the Author-Date style). Bookends will use whatever word you have entered to use between two authors for Author-Date citations (usually 'and'). If a citation group contains more than one reference, the author(s) of the work will be placed in front, and the authors of the other works will not be displayed (e.g. Franks (2000, 2003) ). If you are using Mellel, this feature requires Mellel version 2.7.3 or later.

Reveal a format or import filter in the Finder
Right click on a format or import filter in the respective manager and Bookends will offer to show it to you in the Finder.

Designate text to be output in front of numbered citations
This is useful, for example, for scanning Science supplemental text, where the citations must be preceded by the letter S. You can already tell Bookends to output an S before each number in the bibliography.

Sparkle is discontinued
This automatic update process was removed due to repeated compatibility problems with Mac OS X updates. A new check-for-updates feature will notify you of updates and offer to download them directly with your browser. To install a downloaded update, quit Bookends, drag the Bookends 11 folder into the Application folder, then relaunch Bookends.

Command-S saves an edited Journal Glossary