NEW in Version 10.6.4

See autotitles in attached Mellel documents in the List View display

Improved built-in software updating mechanism

Updated the download pdf function to deal with changes made by several publishers

Bug fixes
Fixed a problem where accented characters in groups could be rendered incorrectly. Fixed several issues dealing with scanning of Pages documents. Fixed a bug where text styles might be removed when editing a notecard in the note stream. Improved handling of certain threaded functions when Bookends is in the background.



NEW in Version 10.6.3

Updated Google Scholar search to deal with changes made by Google

Modified the APA 6th format to output an article's URL (if available) if the doi field is empty

Bug fixes
Fixed a bug where clicking on a field in the Concise View would fail to allow editing of the text. You can drag and drop a term from the Term List window into its corresponding field in a reference.


NEW in Version 10.6.2

Import references and pdfs from PubMed On Tap (an iPhone/iPod Touch app)
PubMed On Tap is a product of References On Tap, which can be purchased from the iTunes App Store. PubMed On Tap lets you search PubMed and store reference information and downloaded pdfs on the device. If the iPhone/Touch is on the same local network as Bookends, you can view the references in the PubMed On Tap library and transfer them, with pdfs if present, to your Bookends library. Bookends will display the references you already have in your library in yellow, or filter the references so that you see only those you don't already have. Here is a link to PubMed On Tap in the iTunes App Store.

Copy Attachment Path
You can copy an attachment’s full pathname to the clipboard by right-clicking on it in the List View window and selecting "Copy Attachment Path" (this will not work if you use WebKit to display pdfs). You can also use the Action gear in the Attachment Inspector.

Downloading pdfs from online sources works with more journals

Search the Notes tab in the reference window with "Find In This Note" and Find In This Note Again"

Improved formatting of date-only citations
If a date-only citation is included in a citation group and scanned with custom citation format, Bookends will use a comma to separate the reference from a preceding reference, regardless of what character is normally used to separate references. This means that if you create a citation like {Smith, 2005 #12324; %Smith, 2009 #3434; Jones, 2006 #23243}, Bookends might output (Smith 2005, 2009; Jones, 2006).

Improved BibteX scanning
If you have BibTeX enabled and Copy Citation is set to copy the Key field, when scanning Bookends will only check to see if a temporary citation is present in the Key field. This will prevent Bookends from misidentifying temporary citations as ambiguous when the citation's text is present in other fields in other references.

Improved notecards
Rendering and saving a notestream is orders of magnitude faster, meaning that it is now feasible to have hundreds of notecards in a stream.

Citations created during a scan of a Word document will not change subsequent text to the style of the style sheet

Improved import of XML files exported from Papers

The default Type of an imported reference can be set in the import filter (Misc tab)
This was previously possible only for references output as MARC records, and the default import Type for others was the same as the default Type for a new reference. Now the default Type for a new reference and for an imported reference can be different.

Improved Change Case -> Title Case
If there is a period, colon, question mark, or exclamation point followed by a space, the character after the space will be output in uppercase even if the word is in the "do not change" list. Thus, a title might look like "Ben Hur: The Sequel".

Bookends Tutorial.pdf and the video tutorials available on the Sonny Software web site are accessible from the Help menu
Bookends Tutorial.pdf must be in the same folder as Bookends.

The preferred location for Bookends User Guide.pdf is now in the Bookends 10 Folder
This is where Help -> User Guide will look for it. If not found, Bookends will look in the alternative location, ~/Documents/Bookends/ folder (for backward compatibility).

Added Cut/Copy/Paste to the right-click (contextual) menu for text fields

Bug fixes
Find In This Reference works when the reference window is in front. Japanese and other Unicode characters in a Google Scholar search result are now rendered properly. Corrected formatting problems when names with suffixes (e.g. Jr.) are being output in small caps, or when first names/initials are surrounded with parentheses or square brackets. Fixed a bug where a scanned document could be truncated after a citation if the final citation was numbered and in styled text. Fixed a bug in the Attachment Inspector where renaming an attachment would always apply to the first attachment even if another was selected. Authors/editors names imported from MARC records will retain a period after the last initial, if present in the record. Fixed a bug where accented characters in some Google Scholar imports could be scrambled. Fixed several issues dealing with fonts. Fixed a bug that would cause final citations in a scanned Word document to not adhere to the local style sheet settings. Various fixes for scanning citations in Pages footnotes. Fixed a bug in the Online Search data detector display where line spacing was too narrow, making it difficult to read the reference titles. If requested in the Online Search window, Bookends will attempt to download the pdf for an imported reference even if the reference isn't shown in the List View (e.g. if there is text in the Live Search textbox and the imported reference didn't meet that criterion). When a reference is being formatted with the Book Chapter[Book] metaType, the format setting for "Replace repeated authors with" will apply only to the Book Chapter, not the Book. Fixed a formatting bug with author names when only editors were to be output with "et al.".



NEW in Version 10.6.1

Nisus Writer Pro integration
Bookends now communicates directly with Nisus Writer Pro (NWP) 1.4 for citation insertion, scanning, and rescanning (or unscanning). NWP 1.4 has an Edit -> Insert -> Bibliography menu, and the options therein initiate interactions with Bookends: 1) Switch To Bookends, 2) Find Reference (in Bookends), 3) Insert Citation (from Bookends), 4) Insert Bibliography Placeholder, 5) Scan Document (with Bookends), 6) Unscan Document (with Bookends). If you choose to retain hidden citations when you perform the scan, you can rescan the document (or unscan it) at any time. The macros that were previously provided for interaction with Nisus Writer Pro and Express are no longer supported.

Improved importing of reference metadata from Bookends Browser
If you drag and drop the pdf proxy icon onto a Bookends database window, you'll have the option to import the pdf (or web page) to a new empty reference and automatically initiate the Autocomplete Paper process. You can also right-click on the pdf proxy icon and select "Attach To New Empty Reference And Autocomplete Paper". Use these methods to download pdfs or webarchives and allow Bookends to try to find and import the reference's metadata from the Internet.

Press Escape to clear the text in any Search field

The Action menu or a right-click lets you deselect all unpinned terms in a Term List window

Use Shift-Option, not just Option, to highlight in yellow the groups to which the selected reference belongs
This was previously accomplished by pressing the Option key alone.

Automatic downloading of the User Guide
The User Guide is included in the manual Bookends download. When Bookends is run, it will move the file "Bookends User Guide.pdf" to ~/Documents/Bookends, where it will be found if you use the Help menu.

Improved MLA formatting
If consecutive citations are from the same work, only the cited pages will be used in the second case.

Updated autocomplete paper using Google Scholar
Accented characters are displayed and imported correctly,

Bug fixes
Find In This Reference works when the reference window is in front. Japanese and other Unicode characters in a Google Scholar search result are now rendered properly. Corrected formatting problems when names with suffixes (e.g. Jr.) are being output in small caps, or when first names/initials are surrounded with parentheses or square brackets. Fixed a bug where a scanned document could be truncated after a citation if the final citation was numbered and in styled text. Fixed a bug in the Attachment Inspector where renaming an attachment would always apply to the first attachment even if another was selected. Authors/editors names imported from MARC records will retain a period after the last initial, if present in the record. Fixed a bug where accented characters in some Google Scholar imports could be scrambled. Fixed several issues dealing with fonts. Fixed a bug that would cause final citations in a scanned Word document to not adhere to the local style sheet settings. Various fixes for scanning citations in Pages footnotes. Fixed a bug in the Online Search data detector display where line spacing was too narrow, making it difficult to read the reference titles. If requested in the Online Search window, Bookends will attempt to download the pdf for an imported reference even if the reference isn't shown in the List View (e.g. if there is text in the Live Search textbox and the imported reference didn't meet that criterion). When a reference is being formatted with the Book Chapter[Book] metaType, the format setting for "Replace repeated authors with" will apply only to the Book Chapter, not the Book.



NEW in Version 10.6

New update notification mechanism in Snow Leopard
Sparkle automatic updating is disabled when running in Snow Leopard because of incompatibilities. Bookends will still provide automatic checking for updates and the Check For Updates menu will function. If a newer version of Bookends is found, a dialog will offer to take you to the download page on our web site, where you can download the new version and install it manually (which means simply replacing your old Bookends 10 Folder with the new one).

Resize the list of terms and display of matching references in a Term List

Term List filters
Filter which terms you see in real-time by typing in characters in the term list filter. Bookends performs character matching, so that the characters "cog" will match the keywords "cognitive science" and "neurocognition".

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

The AND/OR setting for finding multiple selections in Term Lists is remembered between launches

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

Create a hypertext link from more than one notecard
Select the notecards you want then use Edit -> Copy Notecard As Hypertext Link, or drag and drop them with Option-Command held down.

Add text to a new reference directly from a pdf when using Autocomplete Paper
If you cannot find the reference online when you choose Autocomplete Paper, you can fill in the reference fields using the Action pop-up menu. Select the text and use the pop-up menu to tell Bookends which field it should be placed in. The selected text will replace any text that might already be in that field. If the text is sent to the Authors, Ser. Editors, or Translator field, Bookends will assume it contains names and will rearrange it accordingly. It will assume that words separated by commas represent names, and that the names are surname-last. Bookends will also remove punctuation not normally association with names, as well as numbers and common superscript symbols. Click the Close button when finished.

Copy Citation And Modifiers menu
When you invoke Edit -> Copy Citation And Modifiers (Control-Command-Y) or click on the Copy Citation button with the Control key held down, Bookends will prompt you for the page or page range you want to cite, and other possible modifications to the temporary citation. If there is any selected text in the frontmost window, Bookends will use that as the default value for Cited Pages. If you click OK or press Return, Bookends will switch to your linked word processor and insert the temporary citation with the cited pages at the end, e.g. {Carpenter, 2008, #12343@12-14}. You can also tell Bookends what text (if any) you want to precede the citation or if you want the citation treated in a special manner after the scan (such as show date only, excluded the cited reference from the bibliography, etc.). If more than one reference is selected, cited pages will be applied to the first citation in the group.

Italicize 'et al.' in citations created with an Author-Date scan
Enabled in the format definition window, Citations tab.

Generate Subject Bibliographies based on smart groups
When you select Group while creating a subject bibliography, both static and smart groups will be shown. Both types of group can be used in the same subject bibliography.

Formatting examples update automatically when a reference is edited and then the format window is brought to the front

APA 6th Edition format

Refs -> Global Change -> Remove Orphaned Attachments
Removes an attached file from a reference if the file cannot be located. It can be applied to the selected references in the List View, the Hits List, or the entire database. This is not undo-able.

If the List View has a DOI column, it will be instantly updated after performing a Get DOI

The Preferences settings for font sizes are comboboxes
You can enter a point size not listed in the pop-up display.

Bug fixes
Fixed a screen refresh issue that could cause a pop-up menu in the list view to flicker. Fixed errors that could occur when scanning when the format definition window was in front. Fixed a bug that could result in incorrect Book Chapter [Book] metatype output if two or more such citations were found in the same citation group. Fixed a bug that allowed unnumbered bibliographies to have a hanging indent only when scanning Word documents. Fixed a bug with the Book chapter [Book] metatype where a hanging indent could cause a return character to be added to the bibliography entry when scanning with Word. Fixed a bug that could make it seem that unlinked references that had nested unique ids were actually linked. Fixed a bug that caused umlauted characters in temporary citations in Nisus Writer Pro documents to be duplicated. Accented characters in subject bibliographies generated by scanning from Word are rendered correctly. Fixed a situation where trying to download a pdf from a Springer site without access privileges would result in an error message rather than failing silently. Fixed several small cosmetic issues in the Preferences window. Updated Amazon.de search so that it works after changes made by Amazon.



NEW in Version 10.5.6

Amazon searches are now signed
After August 15th, 2009, this is required to search Amazon.

Updated Online Search to deal with changes made by Google Scholar

Upgraded database engine
Note that if you perform an SQL/Regex search for pages, the field name must be enclosed in brackets: [pages].

The Bookends Browser data detector sheet indicates which references you already have
This works with JSTOR and CiteULike, which provide their own unique identifiers, and with COinS sites for references that have a doi (not all do).

View and sort references by the last modification date
If a reference has not been edited since entry, the modification date is listed as "Never".

If a reference's first attachment is a folder, Bookends will initially display the first item in the folder

Copy notecards as Hypertext links
You can paste into compatible applications, such as Scrivener and Textedit, and click on the hypertext link to open the reference in Bookends. This can also be done by dragging and dropping the notecard with the Option and Command keys held down.

Bug fixes
Fixed a bug that could prevent the pages from begin imported from CiteULike. When you right-click on a reference field, Bookends will show any URIs in the field even if they don't contain periods. Fixed a situation where the vertical scroll bar in Bookends Browser would not appear. Improved handling of COinS imports that have multiple authors. Fixed a bug that could cause an error when performing a Global Change -> Change Case using Title Case. Fixed a bug in a Pages scan where temporary citations in footnotes could be missed, and another that could result in portions of text after a footnote not being displayed until the screen is refreshed.



NEW in Version 10.5.5

Updated Google Scholar online search and autocomplete paper
Changes made by Google required an update in the parsing engine.

Updated the Get PDF feature to deal with changes made by certain publishers

Improved detection of doi's in pdfs when attaching files

Select and manipulate multiple notecards at once
This can be particularly useful if you want to copy multiple notecards at one time to another application, such as a word processor or email application.

Improved MLA format
If a Book short title is required to disambiguate citations, it will automatically be output in italic (if there is no short title, the title will be used).

When importing pages, Bookends will strip out certain trailing characters
These are " p", " p.", " s", and " s."

The ambiguous citation/citation not found window is a regular document window
Unlike the old floating palette, this window will be visible if you switch to your word processor to locate the temporary citation in the document.

Reference metadata copied to the clipboard from OpenOffice Writer can be imported into Bookends

Global Change -> Change Case will properly apply Title Case to words having an apostrophe near the beginning
For languages such as French, contractions such as d' and l' in front of a noun should be left as lower case. When using Title Case, Bookends will treat the apostrophe as a word break character unless it occurs prior to a word-terminating letter "s" (the possessive case). This is already handled properly when a reference is formatted for a bibliography or footnote (see what’s new in version 10.5.4, below).

Improved handling of footnotes in Pages ’08 and ’09 documents
Bookends will find and insert footnotes in scanned Pages documents if they are reset at the beginning of each page or section, and if they are denoted by Roman numerals or symbols rather than Arabic numerals.

Bug fixes
Fixed a cosmetic bug affecting the List View scrollbar refresh. Fixed an error that could occur when printing a bibliography directly to a pdf. Fixed an issue where editing a format in the Formats folder would actually update a format of the same name in the Custom Format folder. Fixed a bug in a Pages '09 document scan where a temporary citation in a table was recognized but not replaced. Suggested file names when rebuilding or repairing databases will take into account the database extension, if any. Spotlight searches in the List View window work again.



NEW in Version 10.5.4

Book chapter [Book] metatype
This “metatype” allows you to combine information from a book chapter and book in a single footnote and/or bibliography entry. Such a citation might look like "Smith, The way things are, In: Jones (ed.) 2009. p. 12-34", where the first third is taken from the book chapter, the second from the book that contains it, and the last from the book chapter again. You can tell Bookends to use the metatype when a certain number of chapters cite the same book. Bookends will automatically add the book to the bibliography if it is not explicitly cited in the text (it is implicitly cited when the book chapter is cited).

Exclude citations from the bibliography
If you place a $ immediately after the open temporary citation character (usually the open curly bracket), after a scan the final citation will will appear in the text or a footnote, but not the bibliography.

COinS metadata will be embedded in the bibliography returned by Bookends Server, if selected in Preferences
This means that those using Firefox to access your database will be able to directly import the references from the browser into their Zotero databases.

Option-double click on citation group in Mellel will cause all members of the group to be made hits and shown in the Bookends List View window

Get PDF From Internet works with more publishers

If you right-click on the Title field and it has a selection, Bookends will offer to put the selected text in the Short Title field

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

Increased the time Bookends will wait for a DOI to be returned (Get DOI) before it stops trying, resulting in a greater success rate

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

When creating a new Bookends database, the suggested name will include the extension .bdb

Minor cosmetic changes

Bug fixes
Fixed a bug that could cause some custom citation formats to use the secondary order when the reference was being cited for the first time. Fixed a problem whe using Title Case in a format where a word's case is mistakenly change when it follows certain punctuation, such a period or semicolon. Fixed a bug in smart search where searching for empty DOI or PMID fields, or for a reference's unique id, would fail. Fixed an error that occured when getting a DOI based on a book's ISBN. Doing an advanced PubMed search restricted to Random Controlled Trials works again. Fixed several bugs in Finding references but not putting the results into the Hits List. Fixed a bug that would cause scanning of the open Pages '09 document to fail. Scan Open Apple Pages Document now works on PPC Macs. The metacharacter for "don't include final citation in the bibliography" (!) works with Pages '08 and '09 documents. Fixed a bug that could cause a crash when scanning with a format that groups references that are always cited together. Fixed a rare bug where a spurious character could be introduced into Japanese Word 2008 documents after a scan. Fixed a problem where files not on the startup volume were left on that volume after being copied to the Trash (e.g. when automatically trashing an imported file, deleting a format, or deleting an import filter).



NEW in Version 10.5.3

Nested group folders
Create a group and folder hierarchy in the List View window with unlimited sublevels. If a folder or a group is selected, a newly created group will be placed in that folder or after the selected group. A new folder folder is created at the end of the Groups list. Hold down the Option key when clicking on a folder's expand/collapse triangle and all subfolders in that folder will be expanded or collapsed. This is a convenient way to quickly show or hide all of the items a folder contains. Older databases are updated automatically to the new groups structure (internally) when opened in Bookends 10.5.3 or later. If these updated databases are reopened in older versions of Bookends, the groups will appear outside of any folders they may have been in.

Flatten groups list hierarchy
The List View action pop-up menu under the groups list (or a right-click in the groups list) allows you to "Flatten Groups List Hierarchy". This will cause all of the groups and folders to be listed at the root level (that is, no subfolders). This may be useful if the groups list becomes disordered and you want to reveal all of the items in it so that you can rebuild the hierarchy. This function is not undo-able.

Automatically obtain a reference's doi
The menu Refs -> Get DOI will request the reference's digital object identifier (doi) from CrossRef. If found, the doi will be added to the selected reference(s) in the List View window or to the reference showing in the Reference Window. CrossRef requires that some reference fields have accurate information, including author, journal or book title, first page, year of publication, and article title. The doi can then be used for features such as Autofill and Get PDF From Internet.

Indicate JSTOR references already in your database
After performing a JSTOR online search, any references that you already have in your database will be highlighted in yellow. Bookends uses the JSTOR URL to identify references.

After an Online Search, quickly go to a reference you already have in your database
Select a reference that is highlighted in yellow (meaning it already exists in your database) and right-click. Select Find Reference In Database (Shift-Command-J) from the contextual menu to have Bookends locate that reference.

Increase/decrease HTML text size in Bookends browser

Use a pop-up menu in access bookmarked sites in Bookends browser
The “bookmark” icon (a small blue ribbon) brings up a list of sites you have bookmarked so you can quickly reference surf to them. You can edit/add bookmarks with this menu. The same functionality can be accessed with File -> Go To URL, but the local pop-up menu is more convenient.

Scan an open Apple Pages '08 or '09 document from within Bookends
If Pages is open, Bookends will enable a menu Biblio -> Scan Open Apple Pages Document. If the document has never been saved, Bookends will offer to switch to Pages so you can save it. If the document has unsaved changes, Bookends will offer to save the file before doing the scan. If you choose not to have Bookends do this, the scanned and formatted document will not include the unsaved changes.

Automatic update of User Guide when using Sparkle
When using Sparkle to update Bookends, the new User Guide will be downloaded replace the old (if present) in ~/Documents/Bookends/

Open online references with a right-click from the reference window
Right-clicking in the doi or pmid fields in the reference window drawer will allow you to select a url that will open the article or PubMed entry in your browser.

If you invoke Autocomplete Paper in the List View and don't find a match, Bookends will open the (usually empty) reference in the reference window for manual data entry

If you click the Attachment tab in the Inspector floating window, Bookends will display the attachments of the currently selected reference

Best-guess detection of ambiguous citations during a scan
If a temporary citation is ambiguous, Bookends will assume the first word is an author's name and scroll to and highlight the first match in the ambiguous citations dialog. For example, if the citation is (Smith 2009} and there are two possible matches, one where the first author is Smith and another where the second order is Smith, Bookends will highlight the former. You can of course then select either.

The ability to save searches from the SQL/Regex search window has been removed
This function was superseded by SQL smart groups.

Bug fixes
Fixed a bug that caused JSTOR searches to behave erratically. Fixed a bug that could cause Bookends to crash when scanning some Pages documents containing complex images. Fixed a bug that interfered with scanning when "group references always cited together" or "sort groups by year" is enabled. Fixed a bug in scanning of Pages and Mellel documents where quoted text in one citation could be placed in a succeeding one if the temporary citation didn't have a match. The sort direction arrow indicator is now set correctly in the List View if you are sorting the [Date] Added column. Fixed a bug where the Rename Attachment feature in the List View window would suggest a name derived from a reference other than the the first selected. Disambiguated MLA citations using the short title will enclose it in quote marks if the reference is a journal article or book chapter but not if it is a book. Fixed several issues with finding the correct reference when Option-double-clicking on a temporary citation in Mellel.



NEW in Version 10.5.2

Modified Get PDF from Internet to deal with changes made by some publishers
Get PDF works again with many more publishers.

The About Bookends window is now a regular document window

Bug fixes
Fixed a cosmetic issue affecting redrawing of popup menus at the bottom of the List View window. Fixed a bug where cancelling from the ambiguous citation window during a scan of a Pages '09 flat file and would result in the document's parent folder being moved to the Trash. Adding references to a static group via the contextual menus now works. Fixed a refresh bug that would cause a reference that was autompleted from a pdf to appear as a blank line until the List View changed. Fixed a bug in autofill from Google Scholar that could result in the incorrect information being downloaded for a reference that had no match.


NEW in Version 10.5.1


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

Import a reference from the Internet by drag and drop of a doi
If you drag and drop the doi of an article on a database window, Bookends will create a new reference and search PubMed and Google Scholar to find it and import the metadata. The doi *must* begin with the characters "10." (without the quote marks), and only the doi can be present in the drag.

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

Export references and their attachments
When you use File -> Export References (Hits), a checkbox gives you the option to export any attachments they contain as well. Export rules are the same as for Refs -> Export Attachments.

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

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

Color labels can be applied to the text or the background
The colors in the color label designations can be used to color the text or to color the background of the references in the List View. This choice can be set in Preferences. The default for existing users is color text, and for new users is color background.

The date or date and time format used by the import filters matches that of Refs -> Insert Date

Attach and display password-protected pdfs

New link type: Original:Translation
This will appear only when for new installations of Bookends. For existing Bookends users, you can enter this relationship in Preferences (Links tab).

Increased minumum database cache to 10 MB

Added a warning when the user tells Bookends to use a format to create temporary citations (Preferences)

The setting of the "Trash after import" checkbox in the import dialog window is remembered between launches

If you attach a .zip file, Bookends will not unzip it when you choose "Open Attachment"

Improved citation disambiguation for the MLA format
When scanning with a format such as MLA that disambiguates citations by short title, the short title will appear without surrounding quote marks and in italic, if you have set it to italic in the reference. If there is no short title, the full title will be output in quotes.

Bug fixes
Fixed a rare instance in which scanning a Pages document that has Section Breaks and has been edited and then imported from Microsoft Word on Windows would result in an unreadable formatted document. Fixed bugs that prevented Bookends from coming to the front when a dialog scan was initiated in Word or Mellel and that could cause problems when Ibid. was used in some formats. Periods terminating abstracts are no longer removed when importing MARC records. FIxed a bug where the progress dialog would not close after rebuilding an empty database. Fixed a few problems with some formats would cause the addition of disambiguating information to citations to fail or be incorrect. Fixed a problem with scanning a Pages document where control symbols (%, -, etc.) immediately after the opening citation delimiter weren't recognized. Bookends will attach a pdf to an empty reference and perform an autocomplete paper correctly even if a group is selected or there is text in the live search box. Using a dash (-) in front of a temporary citation to exclude authors in a citation group works on a citation-by-citation basis (just like % does to show date-only). You can no longer delete the group "Attachments". Fixed a bug in scanned Pages documents where the tabs in lines with multiple tabs could be out of order.



NEW in Version 10.5


Note streams and notecards
The contents of the Notes field can be divided into virtual notecards that can be displayed and manipulated separately. Create a stream in the Notes field by separating individual notes with two Returns (a single empty line between the notes). In the List View window you can show the note stream by clicking on the Note Stream icon at the bottom right or by appropriate menu/contextual menu. Each notecard will be displayed in a scrolling list. Use the + button (or Shift-Enter) or the - button (or the Delete key) to add or remove a notecard in the note stream list (hold the Command key to avoid the warning dialog). Edit a notecard by double clicking on it or selecting it and pressing Enter. Save the edited notecard by clicking the Close button or pressing Enter. To abort press the Cancel button (bottom right) or press Escape. Reorder notecards by drag and drop. Copy a notecard's contents along with a temporary citation to the reference with Edit -> Copy Note And Citation. You can also drag and drop the notecard with the Option key held down into a word processor window. If you use Copy Citation or Copy Note And Citation and the notecard begins with cited pages (@ followed by the page(s)), Bookends will include the cited pages in the temporary citation. For example, if the notecard is "@7 This is my note.", Bookends might create a temporary citation like this: {Smith, 2009, #123432@7}. If you are using Copy Note And Citation, the cited pages will be removed from the beginning of the note. A contextual menu let's you access many of these functions with a right click, as well as select any URIs/email addresses in the notecard. You can even paste a “hypertext link as text” from one reference into a notecard of another and right-click to navigate between them. If you drag and drop text from a pdf or any application onto the notes stream, Bookends will create a new notecard for it. Set the font, font size, and color for notecards in Preferences.

Use EZProxy with Bookends browser and reference surfing
If your institution uses EZProxy you can access restricted web sites even if you are off campus. Enter the EZProxy URL in Bookends Preferences (Internet tab)—it must end in %@ or it won’t be recognized. To start an EZProxy session, open Online Search and either perform a search in Bookends browser or with Google Scholar or PubMed (not JSTOR or Web Of Science, which require ip authentication) and then click on the Web toggle icon to surf references. You will be asked for your name and password, and then taken to the article's web site. You can navigate to the article's pdf and use the Import With PDF import option. For direct download of pdfs from these sites (that is, without using Bookends browser/reference surfing), you still require ip authentication. If you leave the proxy space (the URL doesn't include the proxy information), you can start it again by clicking in the URL field and pressing Return, or press Option-Command-L. Note: EZProxy is for HTML-based access. It will not allow you to perform direct searches of restricted sites—you need to be on campus or have a VPN client for that.

Live e-mail address links in the concise view
Clicking on such a link will open your e-mail client and insert the address. In the reference window, right-click on a field containing an e-mail address to display it in a contextual pop-up, preceded by "mailto:". Selecting this will open your e-mail client as well.

Display files inside an attached folder in the Attachment Inspector

Import references/pdfs from the Online Search window with a right-click contextual menu

Bookends will strip any trailing non-letters from names when importing

Updated Bookends browser JSTOR data detector

Show all chapters in the same book
If a Book Chapter is selected in the List View or shown in the Reference Window, Refs -> Show With Chapters will show all of the chapters from the same book. This already works with Books, Edited Books, and Conference Proceedings.

Bug fixes
Fixed a bug that could cause scanned citations in Mellel documents to be incorrect. Dragging and dropping a reference from the online search window onto a static group once again adds the reference to that group. FIxed a bug in which final citations in footnotes of scanned Pages documents could appear more than once. Fixed a bug that could cause an error when copying and pasting text from one field to another. Fixed a rare bug that could cause an error when scanning with a format that alphabetized grouped citations. When moving a file to an attachments folder on a server, a copy of the original will not be left behind. Fixed a bug that caused an error to be thrown if you edited a format with an unregistered copy of Bookends (i.e. the demo).



NEW in Version 10.4.4


Scans will find citations in tables in Pages '09 documents
Scanning already works with Pages '08 tables.

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

Copy/paste smart groups
In the List View, select a smart group and click on the Action pop-up menu or right-click on the group list to bring up then contextual menu option "Copy Smart Group". Chose the Action pop-up menu or right click again and the option to "Paste Smart Group" will appear. The smart group may be pasted into the same database to duplicate it, or into another database to copy it. If the group name is already used, a number will be appended to the name of the pasted version to make it unique.

Edited formats and filters are automatically moved to their custom folders
If you modify a filter or format, it will be immediately moved to the corresponding custom folder in ~/Library/Application Support/Bookends. This ensures that your modified filter or format will be retained when you upgrade to a new version of Bookends. If a filter or format with the same name is already in the custom folder, the modified file will not be moved.

The names of the static groups to which the references belong will be shown in the manual remove dups side-by-side comparison

Preferences -> Override system proxy settings
Bookends normally accesses System Preferences to get your proxy settings (if any). If you want Bookends to use a different proxy setting from the rest of your applications, check "Override system proxy settings" in Preferences (Internet tab) and enter the proxy server address and port that you want Bookends to use. This setting will be used by Online Search but not by Bookends browser (reference surfing), which always uses the settings in System Preferences.

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

Bug fixes
Fixed a bug that could cause scanned citations in Mellel documents to be incorrect. Dragging and dropping a reference from the online search window onto a static group once again adds the reference to that group. FIxed a bug in which final citations in footnotes of scanned Pages documents could appear more than once. Fixed a bug that could cause an error when copying and pasting text from one field to another. Fixed a rare bug that could cause an error when scanning with a format that alphabetized grouped citations. When moving a file to an attachments folder on a server, a copy of the original will not be left behind.


NEW in Version 10.4.3

Bookends can scan Pages '09 documents saved as flat files (the default) or as packages

Automatic updating of Bookends works again if you have Bookends 10.4.2 or later

Open URLs or URIs linking to other applications from within Bookends
Right-click on any field in the reference window that contains a URL/URI to bring up a contextual menu containing that hyperlink. This will allow you to, for example, use links to items in Devon Think 2 and access them while you are in Bookends. If the URI is in a field that normally contains multiple lines of text (e.g. the Abstract field), it must reside on its own line or Bookends won't recognize it. Application URIs (e.g. to DevonThink 2) will also appears as live links in the concise view pane.

Attachment subfolder hierarchy is cached
The list of attachment folders/subfolders shown in the Attach Dialog pop-up menu is cached after the first time the window opens. If you have a complex attachment subfolder hierarchy, this will make subsequent openings of the window considerably faster. If you create a new subfolder, the cache will be automatically updated. If you bypass Bookends and add/delete an attachment subfolder the Finder, use the menu item "Rebuild Folder List" to update the pop-up menu.

Send your documents to Bookends as pdfs to be attached
A menu item "Bookends" will be added the Print -> PDF pop-up menu of all applications. The “printed” pdf will sent to Bookends, which will allow you to attach the reference to the first selected reference or a new empty reference (if the List View is in front), or to the reference showing in the Reference Window (if it is in front).

Bug fixes
Citations in Pages and OpenOffice documents beginning with modifiers such as *, %, and - are now processed correctly. Fixed a cosmetic bug where editing a reference in the right pane of the List View window would generate an error message if the List View contained a Links column. The Attachment Inspector now shows the the selected reference's attachment, if there is one, when it opens. Fixed a bug that affected the ability of the up and down arrows to display all the relavent terms when using text autocomplete in the reference window. The Online Search text search field is no longer disabled when switching from a boolean search to a Google Scholar search. Fixed a bug in scanning an Apple Pages document with a format that uses year-only to disambiguate two citations. The concise view scrollbar resizes correctly when changing references in the List View.


NEW in Version 10.4.2

Automatic updating (Sparkle) updated for Mac OS X 10.5.6
Bookends' automatic updating was broken by the Mac OS X 10.5.6 update. A new Sparkle framework and the addition of security features has resolved this problem. Note that it is the Bookends update after 10.4.2 for which you will be automatically notified.

Updated BibTeX format
The BibTeX format has been modified to be compatible with the conditional grouping feature introduced in Bookends 10.4.1.

Automatic book chapter links
When using Refs -> Replicate As Book Chapter, the new reference will be automatically cross-linked to the book with a link type of "Book:Book Section".

Sort by label
In the List View window, the action pop-up menu or a right-click on the reference list has a Sort By Label option. The sort is descending, so unlabeled (uncolored) references are listed at the end, and there is a secondary sort based on the first column (usually Authors).

When you rename an attachment in Bookends, the suggested new name will reflect your settings in Preferences (e.g. Author Date, or based on a format)

Bug fixes
Fixed an error that could be generated when scanning with a custom citation format that called for the references in groups to be sorted by date. Fixed a rare error that could interrupt the scan of a Pages document.



NEW in Version 10.4.1

Reference cross-links (links)
Establish relationships between references with the Links Inspector. The selected reference in the List View (or the open reference window) will be made the "parent" and appear in an image well above the linked list. To add a link, drag and drop one or more references from the List View (or the unique ID in the reference window) onto the Inspector link list. Choose a link relationship with the parent (e.g. Review and Work Reviewed) as well as add comments. Double-click on a linked reference or the parent reference to select it in the List View. Use the checkbox next to the reference to add or remove the reference from the Hits List. If you have viewed more than one parent, forward and back arrows let you scroll through the viewing history. You can define up to 20 link relationships in Preferences and indicate which is to be used by default (if any). You can see which references have links, and how many, by selecting "Links" as a List View column in preferences. The reference window has a Link icon which will be enabled if the reference has links. Click on the enabled icon to open the Link Inspector and make this reference the parent.

Control format output with conditional groups
You can tell Bookends to use the information in a given field in the formatted reference, and if that field is empty to use another field. "Conditional groups" are enclosed by curly brackets, and the conditional fields are separated by the caret, ^. You can place as many conditional separators as you want, and you can include punctuation and quoted text in the conditional statements. For example, if you wanted the title output in quote marks, and
if no title was present the journal name output, and if neither are present the publishers name preceded by the label "Published by", you could use this construct: {"t"^j^`Published by `u}. The logic is: if there is a title output it in quote marks, if there is no title output the journal name, if there is no journal name output the words "Published by " followed by the publisher's name. If there is more than one field in a conditional group, *all* must have data or that group will be ignored.

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

Bibliographies will be placed at the end of scanned RTF file after the first scan
If you are doing a rescan of an RTF document and retain hidden citations was enabled, the bibliography will be placed wherever you had previously moved it. Subject Bibliographies are placed in the clipboard, to be pasted into the scanned RTF file after opening it in your word processor.

Word RTF documents can be rescanned
You can choose to "Retain hidden citations" when you scan an RTF file. If you do, you can rescan the document and Bookends will incorporate any changes you have made and generate new final citations and a bibl
iography. Note: this option only works with RTF files created by Microsoft Word. If you open and save the scanned RTF file with another word processor (e.g. Nisus Writer, Mellel, etc.) the hidden citations will be discarded.

Unscan a Word RTF document
You can unscan Word RTF file that you have previously scanned with "retain hidden citations" enabled. The result of the unscan will be an RTF file in which final citations and the bibliography have been removed and temporary citations have been restored. Note that you can rescan without doing an unscan first.

Attachments can be placed in an unlimited number of subfolders in the default attachments folder
To create new subfolders, when adding an attachment select the "parent" folder from the folder pop-up menu and then select "New Folder". The default subfolder (if any) will be saved and restored per database (that is, you can configure different databases to use different default attachment subfolders).

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

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

Improved Bookends' ability to correctly identify DOIs embedded in pdfs

You can have grouped citations ordered by date when scanning with a custom citation format

If the final citation contains no text before a cited pages entry, any spaces or punctuation at the beginning of the "before cited pages" text will be suppressed

Show books with their book chapters
If the reference window in front, or the first selected reference in the List View is a book, edited book, or conference proceedings, the menu Refs -> Show With Chapters will be enabled (in the List View you can also right-click or use the Action menu pop-up). When selected, Bookends will find and list the book and any chapters it has (they are identified as such if they are of Type Book Chapter and have the book’s title in their Book Title field).

Bug fixes
Fixed a bug that could cause the scan of a Pages or OpenOffice document to hang if there are cited pages in a citation and no "before" cited pages punctuation entered in the format. Fixed a bug where right-clicking on the proxy icon in Bookends browser could return an error. Modified the JSTOR data detector in Bookends browser to account for changes made by JSTOR. Fixed a bug where pressing the Option key would fail to identify smart groups that contained the selected reference when the smart group specified which other groups the reference belonged to. Fixed a bug introduced in 10.4 where the name punctation for a custom citation was taken from the format used for scanning, not the custom format. Fixed a bug where double-clicking on an attached folder could create a copy of the folder. Fixed an SQL error that could occur when selecting an empty group with the Attachment Inspector open. Fixed a rare occurrence in Bookends Server that could result in incorrect parsing of browser requests and a bug in handling of accented characters in SQLQuery searches. Fixed a problem that could cause an error when syncing a Mellel document containing Bookends citations. Updated Amazon Online Search because of changes at Amazon that caused the spinning wheel to continue after finding and displaying less than 10 references. Fixed a bug where the pdf would not be downloaded from the data detector if the reference didn't appear in the List View window (i.e. a group was selected or there was text in the live search box). Improved error detection so that if you have designated a default attachments folder and it no longer exists, you will receive a intelligible error message when trying to move attachments to that folder. Fixed problems in the creation of MLA citations that could cause error messages to be generated during a scan. Fixed a number of problems with creating a new format when Bookends had been removed from the Bookends 10 folder.




NEW in Version 10.4

Improved MLA citations
Resolve ambiguous citations in a custom format by appending a letter to the year or adding the author's initials/ full name/short title until the citation is unique (the full title will be used if there is no short title). The latter is used in the MLA citation style.

Expanded format options
There is one group of settings for author and editor punctuation in a format (Name Punctuation tab), and the settings apply to all Types. Author and editor names can now have different settings.

Improved format definition window
The window has four sections (tabs) to better distinguish the options. Formatted examples are automatically shown and updated as the format is modified.

Redesign of the boolean online search interface
The boolean search fields and options appear in the main search window, not a drawer, and a number of improvements have been made in usability. Saved Amazon power searches from older versions of Bookends will not work with this version of Bookends and will need to be recreated.

Live feedback showing the groups to which a reference belongs
Hold down the Option key to highlight in yellow the groups (static and smart) to which the selected reference belongs. If more than one reference is selected, groups containing all will be highlighted. The reference or group list must have the focus when the Option key is pressed.

Autocomplete paper using ISI Web of Science
Requires access privileges and ip authentication.

Automatically move attachments to the Trash when a reference is deleted
The confirm deletion dialog has a checkbox "Move attachments to the Trash". Use this carefully, because it is possible to have more than one reference, perhaps in more than one database, attached to the save file. Note that this setting is ignored when you remove duplicates or delete references from the List View without the confirm dialog (that is, with Command-Delete).

Perform boolean NOT live searches
Exclude refere
nces containing given words by placing a dash (minus sign) before a word in the live search textbox. For example, "shakespeare -william" will find references containing the word "shakespeare" but not the word "william". The minus sign must precede each word that is to be excluded.

Edit references from a remote location using Bookends Server
You can use a browser on any platform to edit references in databases made available via Bookends Server. The syntax is detailed in the User Guide.

Smart group searches can be restricted to references that are or are not in any static group

References imported into Bookends by syncing with Papers, a Mellel document, or by drag and drop from another Bookends database are highlighted in the destination database

After online search, select references to import that are not in your database
After searching PubMed or Web of Science, right-click on the reference list and tell Bookends to select just the references that are not already in your database (the ones you have will be highlighted in yellow). This is handy if you want to quickly select and import the references you don't already have.

Display names in the list view as surname-only

Use the keyboard shortcut Option-Command-I in Term Lists to insert the selected terms into the corresponding field in the selected reference

Window -> Minimize Window works with any window in the Window menu

When attaching and autocompleting from Google Scholar based on the doi, Bookends will retrieve the most complete information available

Bug fixes
Fixed an error that could arise when finding text in a reference. Fixed a rare error in the Find dialog Spotlight search where nonmatching references were found. Performing a Find from a Term List no longer generates an error. Fixed a bug where an ampersand in an attached file's name might not show up in the Bookends attachment pop-up menu. Word 2004 scans work properly when the insertion point is in a footnote when the scan is initiated (for users of older versions, they must replace the old Bookends Word X Template in Microsoft Office 2004 -> Startup -> Word with the new one). Fixed some rare cases when virtual groups could give incorrect results. Fixed a bug on Intel Macs where colored text settings were sometimes not saved correctly. Fixed an issue where an incomplete and invalid doi could be obtained from an attached pdf.



NEW in Version 10.3.4

Scan OpenOffice 3 Writer documents
Bookends can scan files saved in OpenDocument format (with the extension .odt). Bookends will add the bibliography at the end of the document or at a location of your choosing. If set as your default word processor, Copy Citation will switch to OpenOffice but you will have to paste in the temporary citation yourself, because at this time OpenOffice lacks AppleScript support.

Automatic downloading of pdfs works with more journals
Includes PNAS and Cell Cycle.

Ambiguous citations in scanned Pages documents are shown in context

Improvements in the sort “ignore” function
You can specify that "words" ending in an apostrophe in the first author's name or at the beginning of the title be ignored when sorting bibliographies. This means, for example, that if you were ignoring "L'", "L'enfant" would sort with the "e"s.

Bug fixes
Bug fixes: Importing BibTeX accented characters works with more variations. The direction of the sorting arrow in the "Added" column in the list view is now correct. Fixed a problem where printing references could result in a crash in Leopard. Fixed a bug where adding a new reference with the list view window closed would make Bookends quit. Fixed a problem in which footnotes in a scanned Pages document could have incorrect sytled text offsets.


NEW in Version 10.3.3

Autocomplete Paper
When you attach a pdf, Bookends will search it for a doi. If present, and the paper can be located on PubMed or Google Scholar, Bookends will offer to attach the pdf and then import the reference automatically. If no doi is found, Bookends will offer to attach the pdf to an new reference and then autocomplete it. This option opens a dialog that displays the pdf and provides several fields in which you can enter information from the pdf (author, title, year, etc.). A pop-up action menu in this dialog copies selected text from the attached pdf to the search fields, and in the case of authors or year will attempt to clean up the raw text to a form suitable for submission to the search engines. Bookends will use the information to search PubMed, Google Scholar, or JSTOR, and give you a list of the first 20 references that match. You can refine the search, if necessary, until you find the reference. Select it from the list, click on Import, and it will be downloaded to your database and the attachment associated with it. Note that you can also perform a Refs -> Autocomplete Paper on any reference already in your database that has a pdf or webarchive attachment.

Improvements in locating matching pdfs on the local hard drive

One-click import of online search results
In the online search window the Import button will require one click if only one database is open and you are not reference surfing. Otherwise, the Import button will present a pop-up menu allowing you to select the database and/or whether to download and attach the current pdf/web page.

Assign hypertext links to groups
Use the Edit -> Copy Hypertext Link menu (which lets you copy the link as plain text as well) to copy a link to a group, to be pasted into a compatible application (like Scrivener, DevonThink, and TextEdit). Clicking on that link the application will take you to the corresponding group in the Bookends database. When using a hypertext link to a reference or group in Bookends, the list view will be set to show all references if it's not already.

Improved remove duplicates
The logic for automatic removal has changed slightly. Now if two references have identical based on the match criteria, Bookends will keep the one with more attachments. If the number of attachments are the same, Bookends will keep the one with the longer Notes.

Help -> FAQ… takes you to the Sonny Software FAQ (Frequently Asked Questions) web page

Improved format Show Example
In the format definition window, Show Example will use the information in the selected reference if the Types match (the reference Type and the Type selected in the format window). If they don't match, Bookends will use default reference information to create an example.

Bug fixes
Improved conversion of smart groups from pre-10.3.2 databases to the new format. When outputting as BibTeX, en dashes are correctly converted to two hyphens (--). The modification date is now updated when a reference is altered by a Global Change operation. Fixed a problem with direct z39.50 searches failing to return accented characters correctly even when the text encoding was set correctly. Changed the escaped sequences for accented characters exports as BibTeX to match those used when importing BibTeX. Fixed a rare occurrence in which exporting references with a very large field that contained the super- or subscript character could cause a crash.

NEW in Version 10.3.2

Redesigned Find and smart group interfaces and more flexible searches
Smart groups saved by this version of Bookends cannot be read by older versions.

Improved smart group searching of static groups
Smart searches can be restricted to references that do or do not belong to particular static groups.

Full-window integrated browser
In the online search window, select Bookends Browser from the pop-up menu to bring up the built-in browser in the entire window.

JSTOR reference data detectors in the Bookends browser
This means that you can use Bookends browser to navigate to JSTOR if you have ip authentication or username/password access and import references you find into Bookends. The automatic pdf download from the browser still requires ip authentication, but drag and drop import and attaching of pdfs via the proxy icon will work with username/password access.

JavaScript is enabled in Bookends browser
This improves certain interactions on the Web of Science, PubMed, and other sites. It is selectively turned off at sites that are known to be problematic when JavaScript is enabled. If you encounter a problem with JavaScript, please contact us and provide the URL of the affected web page.

Database cache size settings have been moved to the .plist
If you are upgrading from an older version of Bookends, the database cache will be set to 8 MB regardless of what it was previously. If you had changed that setting, you must restore it in Preferences and then relaunch Bookends.

Download pdfs automatically from PLoS Biology
We have worked around an error on the publisher’s servers that prevented this in earlier versions of Bookends.

Bug fixes
Fixed a problem with some complex images in Pages that could cause a crash when scanning. Fixed a Spotlight error that could occur when looking for local pdfs for many files at once. Virtual groups containing the Hits and Attachments groups work properly. Fixed an error that could occur when importing a COinS reference and the doi was not supplied. Fixed a bug that could in some circumstances cause an attachment to be assigned to an apparently random reference instead of a new empty reference.

NEW in Version 10.3.1

Web page reference metadata detectors
When you use Online Search and reference surf to a web site, Bookends will automatically detect the presence of embedded reference metadata. You will be alerted by the appearance of a green icon that, when clicked, will present a list of the references. Check the references you want to import (Bookends will offer to import the assocated pdfs, too, if it can find them). Web sites that embed such reference information include CiteULike (http://www.citeulike.com), Copac (http://copac.ac.uk/), and OCLC's Open WorldCat (http://www.oclc.org/worldcat). These sites are automatically added to your Bookends bookmarks list.

Embed reference metadata in Bookends bibliographies
If enabled in Preferences, Bookends will add COinS (ContextObject in Span) reference information to bibliography files generated as HTML, or bibliographies that are delivered dynamically by Bookends Server. This means that anyone who accesses bibliographies on your web site or Bookends server will be able to see and download the references if they are using a browser that can detect COinS, for example Firefox (http://www.mozilla.com/en-US/firefox/) and the free Zotero plug-in (http://www.zotero.org/).

Automatic pdf download from Web of Science with one click
Check "Download pdf" in the Online Search window and use the Import pop-up menu or drag and drop the reference(s) onto a Bookends database window (access privileges required).

Open a reference's full text or pdf in the Bookends browser
In the Online Search window, double clicking on a reference will open the reference’s full-text (if available) in the built-in Bookends browser (reference surfing). If you want to open it in your default browser, hold down the Shift key when double clicking. This works with PubMed, Web of Science, Google Scholar, JSTOR, Amazon, and arXiv.

Use File -> Go To URL to access any web site in the Bookends browser
When the Online Search window is in front, File -> Go To URL will use the Bookends browser to display the web site. Hold down the Shift Key to force the default browser to be used.

Improved importing from Google Scholar
When using Online Search with Google Scholar, Bookends will attempt to locate and import the most complete information Google Scholar offers. If no additional information can be found, Bookends will import the information available on the web page. Note that if you import by drag and drop (rather than with the Import pop-up menu) Bookends will import the information from the web page. The Google Scholar import filter is now obsolete.

The Online Search "download pdf" setting is remembered between launches

Import references from a text file by dropping the file onto the Bookends icon in the dock

Bug fixes

Fixed a bug where the online search window would open when an automated PubMed search was performed. Fixed Amazon.fr searches to ignore accented characters. Em dashes in temporary citations are handled properly during a scan. Improvements in unscanning Word 2008 documents. Fixed several problems with scanning of Pages documents, one which could cause the scan to abort with a error message. Find/replace correctly finds the return character (¬) if it's in the search string.


NEW in Version 10.3

Google Scholar Online Search

Download pdfs from JSTOR with one click
Check "Download pdf" in the Online Search window, then use the Import popup menu or drag and drop the reference(s) onto a Bookends database window (access privileges required).

The Get PDF menu option searches a broader range of sources
If the reference contains a PMID Bookends will search PubMed. If there is a stable JSTOR link in the URL field Bookends will fetch the pdf from JSTOR. If neither are present but there is a an entry in the doi field, Bookends will use that to locate the pdf.

Automatic download of a reference information from Google Scholar when attaching a pdf
When attaching a pdf that contains a doi, Bookends will search PubMed and then Google Scholar, and offer to import the reference information if it is found on either site.

Automatic database synchronization (Auto Sync)
In the Sync -> Configure menu you can tell Bookends to sync your database automatically on database open, database close, or both. Regardless of these settings, you can always perform a manual sync whenever you want.

Improved handling of Ibid.
When Ibid is called for in a footnote, any cited pages following will be suppressed if the previous reference used the same cited pages

You can tell Bookends to create a Subject Bibliography when initiating a document scan

The List View groups pane has a permanent listing named Attachments
This group will show all references that have at least one attachment.

Smart searches can be restricted to references in one or more static groups you specify

DOIs will appear in the Concise View as active hypertext links to the article
Requires access privileges.

Calculate an author's h-index (Hirsch number)
After performing an Online Search of the Web of Science or Google Scholar, you can have Bookends calculate the h-index of the selected references. A discussion of the h-index, and its limitations, can be found here: http://en.wikipedia.org/wiki/Hirsch_number

Copy Citation will work with Nisus Writer Express and Pro on non-English systems
Requires NWE 3 or NWP 1.0.1 or later.

If BibTeX styling is selected for formatting, smart closed quotes will be output as '' (two apostrophes)

Bug fixes
Dragging and dropping Safari proxy icons for links that have "pdf" at the end onto a Bookends database window will result in an offer to attach the pdf. Attaching files using the reference window attach button work again. Remove duplicates no longer makes mistakes when there is very little text to be compared. Fixed a problem with JSTOR where an empty reference would cause Bookends to hang. Fixed several formatting issues with using Unicode "thin spaces" in references. Fixed a bug when searching the local hard drive for pdfs that would bring up the Online Search window if more than one pdf matched. Fixed a problem where the BibTeX enable checkbox in preferences was unresponsive. When attaching a pdf and downloading the source from the Internet, the rename option will be honored. Fixed a bug that could cause the wrong reference window to come to the front when replicating a reference in a group as a book chapter. Modified the EndNote XML import parser so that a journal full title, if provided, will be imported instead of the secondary title. Fixed a bug where text entered in the reference window drawer enlarged view might not be saved.



NEW in Version 10.2.1

Reference surfing
Online Search contains a WebKit-based browser. After searching for references on web-capable sites (such as PubMed, Web of Science, JSTOR, arXiv, and Amazon) you can toggle the reference view from Text to Web. The built-in browser will take you to the reference on the web site, where you can navigate to the full text article or pdf (if available and you have access privileges). You can import the reference information and web pages/pdfs directly into Bookends with a click on the Import button. You can also attach the web pages/pdfs to an existing reference by drag and drop onto a Bookends database window (or save to disk by dropping on the Finder). Right-clicking on the web proxy icon brings up a contextual menu that lets you create a new empty reference and attach a web page/pdf, or attach the web page/pdf to a newly created Internet reference in which the title, URL, and date and year accessed are automatically entered. A URL field in the Online Search window lets you navigate to pages at any site you choose, where you can obtain pdfs or save the web pages. When the Online Search window is in front and the URL field is enabled, the File -> Go To URL menu will use the Online Search browser instead of your default browser. Note: the pdf download/import will not work if the Adobe or Schubert pdf plug-in is installed.

Live web pages/pdfs in the List View
You can copy text from pdfs attached to references, and hypertext links in attched web pages are live. A toggle in the Action pop-up menu lets you display pdfs with WebKit (links active, text selectable) or in the Bookends pdf viewer (links inactive, text not selectable).

Copy selected text from an attached pdf/web page to the reference
If you are using WebKit to display pdfs, select text and use the Action pop-up menu to "Copy selected text to" any field. If the field is authors or editors, Bookends will attempt to parse the names, assuming that they are surname last and separated by commas. Limitations: Bookends will remove non-letters from the names (e.g. superscripted numbers specifying footnotes), but will not remove superscripted letters. Also, pdfs often have spurious characters (often spaces) that you can't see but that are copied to the clipboard. Bookends will not remove these.

Attach a file to a new empty reference
If you have pdfs with no corresponding reference information, you can choose to have Bookends create a new empty reference and attach the pdf to it.

Searching JSTOR works again
This was broken by changes made in the JSTOR gateway

A BibTeX @collection reference will be imported as an Edited Book Type

Improved Change Case
Global Change -> Change Case -> Title Case will uppercase words that begin with punctuation (e.g. quote mark, bracket, etc.).

Color labels can be displayed and edited in the concise view pane

Book images obtained from Amazon will always be the highest quality available

Highlighting of a drag to a static group is much more obvious

Import article numbers from Web of Science
Some journals covered by the Web of Science use article numbers instead of page ranges. These are now displayed in the search window and imported to the Pages field in Bookends (using the AP tag). The doi for such articles, if present, will also be resolved properly.

Press Command-S to save an edited import filter

Don't Change Case can be applied to words containing hyphens
This means that words like X-ray can be added to the Don't Change Case list.

The virtual "issues" field can be used with the binding command in a format

The User16 field for Journal Articles is now used to store the PubMed Central ID number
This field has been renamed PMCID. The PubMed import filter has been modified to import the PubMed field containing the PMC into PMCID. If you have an older version of Bookends and renamed the User16 field for Journal Article, your label will be left intact.

Bug fixes
Fixed several problems with Word 2008, including failure to remove an old bibliography when unscanning, unintended substitution of accented characters that followed a citation, and failure to recognize control characters like % or * or unicode characters immediately after the opening citation punctuation. Invoking the Word 2008 Scan and Unscan AppleScripts works when the cursor is placed in a footnote. Control-Command-1, 2, and 3 now corretly changes the label in the reference window rather than changing the tab selection. The items in an attached Mellel or Pages document bundle will not be listed in the attachment pop-up menu or in the list of subfolders in the attachment dialog. Fixed a bug that prevented Bookends from importing an existing bibligraphy if the references were preceded by numbers. PDFs imported from a browser by drag and drop will be renamed correctly. Fixed a problem in which a temporary citation without a closing citation delimiter (such as a curly bracket) would cause Bookends to abort a Pages scan. Fixed a problem where scanning of some Pages documents could result in truncated citations. Fixed an out of bounds error that could happen when opening a database created with a version of Bookends prior to 10.1.4 and selecting an unused Type of 11 or higher when creating a reference. Fixed a problem where replicating a book as a book chapter would open the wrong reference window if the list view live search box has text in it. Fixed a bug in which two citations containing a year and distinguishing letter would be incorrectly grouped when "Letters for repeated years" was checked in the format. Fixed a bug in Online Search where the filter in the Bookends/Import Filters folder would be used even if there was a filter with the same name in the Custom Import Filters folder. Fixed SRU search for the British Library (broken in the last update by changes made to accomodate JSTOR).


NEW in Version 10.2

Apple Pages '08 compatibility
Bookends can scan Pages '08 files and replace temporary citations with final citations. Use the Biblio -> Scan A Document menu, select a Pages '08 document, and then scan. A new Pages document will be created, and after the scan is completed it will be opened in Pages and the formatted bibliography pasted in (either at the end or or a location you have indicated by entering "" in the document). If there is an AppleScript error during this phase, you can still perform a manual paste to place the bibliography where you want it. If the final citation contains styled text (e.g. a superscripted number or a custom citation as in a footnote), the font will be the default font for the text element. You can change this for one or all elements in the document by using the Pages '08 Styles drawer. Although Bookends can scan Pages documents saved with track changes active, the results may be unpredictable and it is strongly recommended that you turn off track changes and then save the document prior to a scan.

Scan RTF documents saved from Scrivener that have accented characters

The enlarged view in the reference window has a Cancel button

Copy/paste a bibliography honors hanging indents
If a bibliography with a hanging indent was sent to the Bibliography window, the hanging indent will be preserved when you copy and paste it into a word processor.

Find/Replace in Term Lists finds terms with punctuation

Files lacking file type metadata but having the extension .cgi will be recognized as text files when you import

Import to Hits List default behavior has changed
In the Online Search window, if Import to Hits List is checked Bookends will add the imported references to the current hits list. If you want to have Bookends clear the hits list first so that the hits list contains just the more recently imported references, hold down the Option key when clicking on Copy To button or dragging and dropping the references to be imported.

The Nisus Writer Pro/Express "Scan a Doc" macro works on non-English systems
This requires NWP 1.0.1 or NWE 3.0. Prior versions will generate an error.

Shift-Command-O opens attached files when the reference window is in front

A static group's name will temporarily highlight when a reference has been added with Command-#

Bug fixes
Fixed a crash that occurred when formatting a references whose journal name was > 255 characters. Fixed a problem with the incorrect reference being copied when using the Copy Hypertext Link menu with a format. Fixed a rare crash that could occur when some pdfs were attached and checked for the presence of a doi. It is once again possible to undo a paste into an empty reference field. Fixed a rare crash that could occur if an author's name had a comma followed by numbers. Fixed an error message that occurred when editing a reference in the list view while the Notes field was displayed in one column.


NEW in Version 10.1.4

Term List enhancements

There is an action button that contains the following: Insert, Find…, Save…, Replace…, Update
, and a boolean setting that tells Bookends what to display when multiple terms are selected (AND/OR). Right-click in the term list to see these options as well. The option "Replace" is the same as performing a Global Change -> Find And Replace on the entire database, but with fewer options. The advantage it offers is convenience if you simply want to correct a misspelling in a term or want to normalize the spelling of a term, such as a journal name.

The minimum widths for the reference and list view windows is smaller

This may useful if you are using a Mac with a small screen, such as an iBook.

Ten more unused reference Types have been added

The total number of Types you can assign is 20.

Spotlight searches in Leopard are case-insensitive

This makes Spotlight searches in Leopard behave as they did in Tiger.

Better handling of "Ibid." in footnotes

If Ibid. appears in a series of references in a footnote, the trailing period will not be removed before the separating comma or semicolon.

Boolean NOT searches are much faster

Phrases can be entered in the "Don't change case" list

Bookends will accept phrases in the list of words whose case should not be changed when using Sentence case or Title Case. This means proper nouns like American Revolutionary War Society can be entered and the case will be preserved.

Search for references edited within a defined interval

In the SQL/Regex search box enter the following

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

where X is
the number of days prior to the present you want to retrieve. For example,

dateModified > datediff( now(), '01/01/1904 00:00:00', 'second' )
- (7 * 24 * 60 * 60)

will find all references edited in the
last week. This includes references entered manually, as well, but not references added to the database by importing and never edited. This can be saved as an SQL smart search.

Pressing Command-M in a Term List will add/remove the selected references to/from the hits list

Bug fixes

Fixed a bug that caused incorrect subject bibliography output if a format that didn't sort references was used. Fixed a bug in subject bibliographies where styled text runs could be correctly offset if there were non-ASCII characters in the format. Fixed a problem in which scanning Word 2008 files and not saving citations as hidden text resulted in the bibliography not appearing at the end. Fixed a problem with Word 2008 where some documents would not unscan. Fixed a problem in Bookends Server that would prevent the default.html page from being found. Fixed a crash that could occur if the styled text information for a reference was mangled. When a database is rebuilt, the last modification date of each reference is retained. Consecutive spaces in an custom citation format will be reduced to one space, just as it is for bibliography entries.


NEW in Version 10.1.3

Word 2008 compatibility

A Bookends hierarchical menu under the Word 2008 menu Script icon contains five scripts: Find In Bookends, Go To Bookends, Insert Citation, Scan Document, Unscan Document. They provide the same functionality as the corresonding options in the Tools menu of earlier versions of Word. You can move these scripts out of the Bookends hierarchical menu and/or rename them, and they will still work.

Update to future versions of Bookends automatically using Sparkle

This means
that updates will occur automatically and will not require you to move files or folders manually.

Directly search Web of Science

You can search the ISI Web of Science via Online Search (requires access privileges and ip authentication). You can search any Web of Science database edition for which your institution has a license: Science Citation Index, Social Sciences Citation Index, Arts & Humanities Citation Index, Index Chemicus, and Current Chemical Reactions.

Import PubMed references dragged and dropped from a browser

This was broken in earlier versions by changes made in PubMed.

Column width settings for Online Searches are remembered between launches

Improved algorithm for correctly oriented pdfs that were scanned in

Bug fixes

The unique id is preserved when a reference is exported to a tab-delimited text file and then imported to a new database. The Biblio -> Default Format menu now updates correctly when formats are checked or unchecked in the Formats Manager window
. Performing an automated PubMed search no longer generates an error. Fixed a bug where adding/deleting Types in a format would fail. Fixed a problem with MLA bibliographies where a letter would be appended to the year if there were two or more citations from the same author. Fixed a crash that occurred when creating a formatted reference where a field had more than 32K characters. Fixed a crash that occured with using only the Source parser to import references and the reference was followed by a return character.


NEW in Version 10.1.2

Sync databases

Synchronize Bookends databases across a network or the Internet. Sync can be configured to work for individuals who use Bookends in more than one location as well as groups that want to sync personal databases with a master copy. Sync will keep references (additions, deletions, and modifications) and groups up to date. Individual sync options will be shown before they are performed and can be denied on an ad hoc basis. Ancillary files, such as attachments, must be synchronized separately.

Enabled formats and filters are remembered after a Bookends update

The list of formats and filters you have enabled is stored in preferences and won't be reset when you upgrade Bookends.

Replicate As Book Chapter is enabled for Conference Proceedings

Duplicating a reference is faster when the unique id is in a numeric sequence

The date and time of duplication will be used as the date added for duplicated references

Improved show example for formats

If the example drawer in the format window is open, it will automatically update when you switch references in the List View.

More versatile bibliography sorting

You can
specify that citations in a group can be sorted or not for both author-date and custom citation formats.

Improved Amazon searches

Bookends will remember the Amazon search category (Author, Title or Keywords, etc.) between launches. Amazon searches for 13 digit ISBNs work.

The ability to sort the physical order of references in the database has been removed

Bug fixes

Fixed a bug that prevented non-pdf images from being displayed in the list view. Updated the JSTOR import filter so that it downloads references properly. Fixed a bug in the info pane where pressing the return key in a field with a term list would enter two returns. Fixed a bug in the format examples where "Journal of Biological Chemistry" would be used for the full title even if a reference was selected. Double-clicking on a Bookends database with the extension .bdb will open it in Bookends regardless of the file type metadata. Retrieving a reference from PubMed when attaching a pdf works in Leopard. The punctuation after the last author that is ouput will be suppressed when using "et al.".


NEW in Version 10.1.1

Perform online searches of SRU-compatible libraries

New import filters have been added for JSTOR, British Library, and COPAC. Simple searches treat spaces like a boolean AND. To look for phrases, enclose them in quote marks. If "boolean search" is selected, the entries in one of the three fields are treated as if they are within quote marks.

Perform online searches of arXiv

arXiv (http://www.arXiv.org) is a premiere open access site for e-prints in physics, mathematics, computer ccience, quantitative biology, and statistics.

Smart attachment folders

You can attach folders to a reference. Bookends will list all the items in the attached folder and you can select any to view, reveal in the Finder, etc. Any files added to the folder in the Finder are automatically made attachments (and if you remove a file from the folder it is no longer treated as an attachment). Attachments in such a folder are one level deep (that is, a subfolder in the attached folder will be shown, but not any files in it). If you add/remove files from an attached folder, the list view will need to be refreshed to see the change (just click on the reference is sufficient for this).

Searches ignore diacritics

For example, searching for "Schütz" will find both "Schütz" and "Schutz". The exception is a Find search by character, in which case searching for "ü" will not find "u". This applies to all new databases you create. You must Rebuild (Keep User Info or not) databases created with prior Bookends versions to have diactric-insensitive searches.

More versatile example display in the Format Manager

Clicking on the Example button will use the information (authors, title, etc.) from the reference window (if open) or the first selected reference in the List View (if open). If neither are
open, default example information will be used. The example will update automatically when a different format is selected. Pressing Command-E when the formats manager is in front will toggle the example pane open and closed.

Replicate as Book Chapter works with Book as well as Edited Book

Sending attachments with e-mail works in Mac OS 10.5 (Leopard)

Hypertext links in the display pane in the Online Search window are live

Improved handling of non-Roman characters in Live Search

Improvements in Spotlight accuracy when matching references with local pdfs in Mac OS 10.5 (Leopard)

Bug fixes

Fixed a bug where sorting on the Added column in the List View could cause an SQL error. Fixed a nil object error when editing a reference with the List View closed. Bookends cleans up HTML entities from attachment names when importing XML from EndNote 9. Fixed a bug where the appearance of some pdfs would be incorect on PPC Macs. For the unmatched or ambiguous list after a scan, the type ahead function works even if an author's name begins with a unicode (accented) character. Fixed a bug in subject bibliographies where style runs in the first reference could be offset incorrectly. Edit -> Special Characters now works on Intel Macs. Fixed a bug that caused an error when importing references from Bookends 7.x that had fields with non-Roman characters and styled text.


NEW in Version 10.1

A highly configurable, interactive, and editable concise view

Two views, Summary and All, let you view the fields you want in the List View. These views are "live", meaning that you can click on the fields to edit them, assign ratings, go to linked URLs, and more.

Display up to seven columns in the List View

Redesigned Import Filter and Formats Manager windows

These windows have a unified look,
with a list of filters/formats on the left and the settings on the right.

Text in a reference window tab indicated with an asterisk

In the reference window, an asterisk
will be appended to the Notes or Keywords tab caption if that field contains text. This allows you to see if the field has information while you are viewing the main tab.

PDF orientation corrected if necessary

The List View display pane will always show a pdf in a readable orientation even if it was scanned in as a vertical image.

PDF viewer will skip damaged pages

It will write a message to the Console telling you which pages it couldn't read.

Improved DOI lookup from PDFs

Bookends works with more pdfs (for example those from PNAS and J Exp Med) to locate the citation information on PubMed when they are attached.

Automatic proxy server configuration

Bookends gets the HTTP proxy server and port information (if any) from System Preferences. If you are using an authenticating server, you still need to enter you user name (id) and password in Bookends Preferences, Internet tab.

Smarter Global Change

When doing a Global Change -> put after, if the word being inserted begins with a return character, the return will be suppressed if the receiving field is empty.

Include the list of static groups a reference belongs to in a formatted reference

Upload to Refbase using either XML or RIS output

Replicate as book chapter is enabled when the List View is in front

Bookends will offer to move format or filter you delete to the Trash

Improved BibTeX escaping of reserved and accented characters

References exported as XML retain full links to attachments

This means that if you import these into EndNote 9 or later the attached files will retain their links.

Bug fixes

Bookends will recognize attachments with the extension ".htm" as html files. Fixed a bug where Find PDF on the local drive would result in a list of possible hits but no pathnames visible. Fixed a bug where a new, not upgraded, Bookends Preference file would list duplicated column options for the List View. Fixed a bug where accented characters in the subject bibliography subject lists were not rendered properly. Fixed a bug where importing styled text from an EndNote 7 XML export file could cause an error on Intel Macs. Fixed a bug where a find/replace restricted to a field in the main tab could also finding matching text in a drawer field. Fixed a bug where the new name of a renamed SQL smart group wasn't shown. Fixed a bug where sorting by date added didn't work. Fixed a rare bug where a global change -> insert for a large number of references could corrupt the database. A cosmetic bug in which the List View fields could be drawn on top of one another after a rebuild was fixed.


NEW in Version 10.0.3


View attachments in a tab in the reference window

A pop-up menu at the bottom of the window lets you switch between multiple attachments. A contextual menu lets you manipulate the attachments.

More versatile display of attached files

Bookends can show the textual contents of attachments of many different file types: .doc (Microsoft Word), Mellel (XML), RTF, RTFD, Nisus Writer, and HTML. The display contains the main body of the text only (no text styles or images, and in the case of Mellel no note streams or footnotes). The Bookends Spotlight search will find text in these attachments if they are in the default attachments folder (or subfolders). Note that to find Mellel file attachments you must have installed the Mellel Spotlight plug-in. PDFs and images can be zoomed up to 300%.

Improved Remove Duplicates

If two duplicates are indistinguishable, the older one (the one with a lower sequential number) will be marked for deletion. The manual verification shows duplicate references side by side. Only fields that have information (in either reference) will be shown, and any fields that differ will be highlighted in red. Field names will be preceded by a clickable symbol. When clicked, a dialog containing that field from both references will allow you to copy/paste or drag and drop text from one to the other, so that you can merge the reference information into one reference and then mark the other for dele
tion. Navigation arrows let you move amongst duplicate pairs, or you can click on particular references to examine.

Compare references

If more than one reference is selected in the List View, you can use Refs -> Compare References to view the first two selected references side-by-side in a new window. Only fields that have information (in either reference) will be shown. In this window you can move between references using a stepper control or enter the numbers of the references you want to compare. You can mark/unmark the references in this window to add/remove them from the hits list, and assign ratings. Field names will be preceded by a clickable symbol. When clicked, a dialog containing that field from both references will allow
you to copy/paste or drag and drop text from one to the other.

Show PubMed references you already have

When doing an online PubMed search, Bookends will highlight in yellow any retrieved references that are already in your database (determined by matching PMIDs). The database must be open. If more than one database is open, Bookends will examine the database nearest to the Online Search window.

Bookends will refuse to open a database located in the same folder as itself

This is done so that users won't inadvertently delete their databases when replacing the older with the newer Bookends Fold
er when upgrading Bookends.

Switch to a linked word processor with a menu command

Don't clean up consecutive spaces in formatted references

This format option tells Bookends to allow runs of spaces in a formatted reference. This is useful, for example, for formats like RIS that require two spaces between each field tag and the following hyphen.

Z39.50 Default connections assume returned text is encoded as UTF-8

Deleting a reference in the reference window has been simplified

You can delete references when a smart group is selected

The List View window title is the name of the database

Bug fixes

Fixed several cosmetic bugs where the width of the keywords or notes field in the main tab could be wider than the reference window, or the width of the keywords field in the second tab could be too narrow. Multiple OpenURL servers are now shown correctly in the list view contextual menu. You can now open attachments with long names via the display pane contextual menu. Fixed a problem where incorrect styled text data could result in a nil object error. Fixed a bug where creating a new reference when there was text in the live search box and one of the columns contained reference numbers would open a new reference window with text already entered from another reference. Edited styled text with unicode characters in the Notes field tab is saved correctly. Fixed a bug where a Mellel verify scan using a format with styled text to replace temporary citations would result in the RTF formatting commands being embedded in the citation object. Changes to the pdf zoom value using the contextual menu are now saved.


NEW in Version 10.0.2


Configurable display of keywords and notes

The reference window can be configured to display the notes or the keywords in the main tab (set in Preferences).

Scan .rtfd documents exported from Pages '08

This means that even if you have graphics embedded in your Pages file it can be scanned by Bookends (export it from Pages as "rtf"). Note that graphic placement may be altered by exporting/importing as rtfd, and certain metadata such as track changes and comments will not make the round trip.

Lookup from DOI

If the selected reference has a doi, this menu option will open your browser and go to the address pointed to by the doi resolver at http://dx.doi.org/.

Update references listed on Pubmed

If the selected reference(s) has a PMID entry (either in the drawer or in the URL field), selecting the menu Refs -> PubMed -> Update From PubMed will fetch the reference again from PubMed. If the information in any field you are importing differs from the current entry, the newer information will replace the old. Fields that aren't identified in the PubMed import filter will be untouched. This is useful if you import pre-publication reference information from Pubmed and want to update the record once the paper is published. It also means that if you enter just the PMID, Bookends can download the entire reference for you.

Choose the application to open an attachment on-the-fly

Open an attachment in any application that can handle it by dragging and dropping the image from the display pane onto the application icon in the Dock or in the Finder.

Manipulate an attachment even if its contents cannot be displayed

You can drag and drop, open with a double-click, or right click to open a contextual menu a attachment the display pane whose contents cannot be displayed (e.g. a Word .doc file).

Improved list view updating

If the reference Type is shown in a List View column, it will be updated immediately if the Type is changed in the reference window.

Rename local pdfs on Find & Attach

If this Preferences option is checked, Bookends will rename the pdfs found with Get PDF -> local hard drive as specified in the popup menu (by author date or according to a format).

The default status of the "rename attachment" option is remembered between launches

The PubMed filter distributed with Bookends imports the DOI (digital object identifier), if available

Output reference ratings in a bibliography

The letter to use in the format's order field is 'r'. The result will be 0 (unrated) to 5.

Bug fixes

Shift-Command-U opens the correct URL when two or more databases are open. Editing the keyords in reference window no longer causes a subsequent Command-W to close the List View window. Fixed a bug in which a new Bookends 10 Preferences file (not an upgraded file) would not remember certain settings between launches. BibTeX acronyms in the title will be completely surrounded by curly brackets (if elected in preferences) even if they are the last word in the title. Fixed a bug in which importing references with extremely large abstracts could cause the import process to stop. Corrected a situation where a graphic attachment with the file type incorrectly set to TEXT would be opened as a text file in the Attachment Inspector. Journal Glossaries created on Intel Macs now have the file type set correctly. Fixed a bug where invoking Quit with a reference window open just closed reference window but did not quit. Fixed a bug where outputting authors in Small Caps in styled text could create a RTF file that couldn't be opened by a word processor. The "Reveal in Finder" contextual menu in the display pane now finds files with very long names.


NEW in Version 10.0.1


Bug fixes

Fixed: sorting the Date Added column didn't work and could cause an error when adding references with the column selected. Fixed: bibliographies can be sorted again. Fixed: the keyboard shortcut for OpenURL is shown only once even if there are multiple OpenURL servers. Fixed: a bug in Subject Bibliographies that could result in an out of bounds error. Subject bibliographies can now be sorted. Fixed: the size of the display pane is remembered between launches, as is the size and position of the List View if it was closed while maximized. Fixed: automated PubMed searches work again. Reference files created with a "Bookends" export are selectable in the Import References Get File dialog. An attached pdf or image file can be opened by double-clicking on it in the display pane. Fixed a bug where spurious characters would be output if a title began with a smart quote and the format called for Title Case (like Chicago 15th).



NEW in Version 10


Bookends 10 requires Mac OS X 10.4 (Tiger) or later

Revamped user interface with integrated pdf/image/text file viewer

The List View contains four panes, three of which can be open or closed (they can be toggled with icons, a View menu, or the keyboard). The panes are: groups, references, info (concise summary or Notes), and display (formatted reference or pdf/image/text file attachments). PDFs in the display pane are shown in their entirety, and can be zoomed or scaled to fit. The reference window has a tabbed interface. The main page contains most fields, including resizeable Abstract and Notes. The second tab contains Keywords, and the third has an enlarged Notes field. You can select the tab with the mouse or keyboard (Command-1 = main, Command-2 = keywords, Command-3 = notes).

Direct Z39.50 access to online libraries

Access libraries using UNIMARC or OPAC. Text encoding can be specified, allowing accurate retrieval of accented and non-Roman characters from many non-English sources. Direct Z39.50 access supports userid/password and proxy servers, but not an authenticated proxy servers. The Library of Congress gateway is available if an authenticated proxy server support is needed.

Two new user-defined fields

Default values are DOI (Digital object identifier) and, for journal articles, PMID (PubMed ID). DOI has been added as a criterion in the advanced PubMed search.

Reference ratings

Ratings, from none to 5 stars, can be set by clicking on the rating icon in the reference window, or in the List View with the action button or a contextual menu.

Subject bibliographies

In a subject bibliography references are grouped under a subject heading. Subject bibliographies can be made for references in the hits list based on any of these criteria: authors, editors, authors and editors, journal, keywords, reference type, color label, or static group.

Direct export of references to Refbase

Refbase is an open source online reference repository. Bookends can automatically upload references to Refbase. Refbase can be searched via a browser, and references downloaded as files and imported into Bookends or any other reference management application. The Refbase organization has created a public Refbase server for Bookends users. In addition, any institution can install their own (free) Refbase servers for internal use.

Add references to Bookends databases via Bookends Server

Remote users can upload references to a database by submitting them in a tagged format that a Bookends import filter can parse (e.g. RIS, PubMed, EndNote Refer, BibTeX, etc.). An example web page that demonstrates several very flexible techniques to do this is included in "Serve a Bookends database in 5 minutes (or less)".

Send a text file containing references to others via Bookends Server

You can have Bookends send the results of a remote search to a text file. This allows you to send reference in a tagged format (like RIS or EndNote Refer) that remote users can import into their reference manager. A format to output RIS files is included.

User-defined attachment names

The suggested name for a Bookends attachment can be author-date or defined in a format.

User-defined temporary citations

You can cite by Content, Author/Date/unique ID, or any format.

User-defined hypertext link text

You can use the title (default) or define the visible portion of a hypertext link that you create in Bookends via drag and drop or copying to the clipboard.

User-defined Concise View

The concise view in the List View info pane can be the default provided by Bookends or contain information specified by any format.

Append letters-only to repeated dates

For author-date citations and repeated authors, you can tell Bookends to output repeated years and distinguishing letters (2006a, 2006b) or simply the letters (2006a, b).

Improved Word and RTF document scanning

Bookends will consider adjacent temporary citations to belong to the same group. For example, {cite1}{cite2} is the same as {cite1; cite2}. If any characters or style changes occur between the citations they will be treated as different goups.

Open URL is a hierarchical menu

This allows quick access to your favorite web sites. If you have entered a URL for Refbase in Preferences, it will appear in the Open URL list as well.

Import tagged information into two fields

Omit authors from final citation

If the first character of a temporary citation is a - (hyphen or dash, such as {-author, date, citation info}), Bookends will omit the authors (or editors) from the final citation. When used with an author-date format, this is identical to using a % (show date only). When used with a custom citation format, all the elements in the final citation will appear except authors/editors.

Use Spotlight for attached pdfs or text files when doing a Find or searching with a smart group

Bookends will look for pdfs that match the query and are in the Bookends attachments folder (or subfolder). The results of this search are combined with any other criteria in the Find or smart group dialog.

Spotlight searches are faster

Improved BibTeX output

Acronyms in the title can be output between curly brackets to preserve their case, e.g. {DNA}.

Display the date a reference was added in the List View

Sorting of this column is by the date.

Bookends will offer to rename attachments even if they are not moved to the attachments folder

Set the format for Inserted Date

Use System Preferences setting or yyyy-mm-dd

Bookends will automatically check for and alert you of new versions on launch

User-defined fields have a maximum of 2044 characters

The text used to substitute for repeated authors can be styled (italic, bold, etc.)

Improved bibliography sorting

If all the sort fields are the same (i.e. author, editor, title), Bookends will order them as they are entered in the database

Automatic backup is turned on by default when the Preferences file is first created

Internet Search has been renamed Online Search and moved to File. Utilities is now Extras

Use Command-1 through Command-8 to select the corresponding tab in Preferences

The Attachment Inspector will display the text at the beginning of a text file

The encoding will be set that that specified in File -> Import Text Encoding at the time the file is shown

A text file dropped on a window with the Command key held down can be attached

More than one OpenURL server can be stored and accessed with OpenURL Search

Bookends will show all files if the Shift key is held down when telling Bookend to import from a file

This allows you to select text files downloaded from the Internet that lack the usual identifiers (like a .txt extension).

Bug fixes

Bookends will not append a letter to "In press" in a reference in a bibliography if there are two "in press" citations by the same author. Fixed a bug where moving a database between two computers with two monitors each, in different configurations, could result in the reference window opening off-screen. Double-clicking on a PubMed reference in the Online Search window takes you to the full text in your browser (if available). Fixed a bug in which the Bookends Spotlight search would fail to find attachments whose name contained certain punctuation characters. Fixed a problem where a damaged or inaccurate Mac OS X Spotlight index could cause Bookends to report an error when doing a Spotlight seearch. When you export a reference directly from Papers to Bookends (File -> Export), the location of an attached PDF is imported into Bookends. When performing an OpenURL search for a book chapter, the volume title is used instead of the chapter title. Fixed a bug in some Preferences updated when moving from Bookends 8 to Bookends 9 which would prevent Bookends from finding attachments outside of the default attachment folder. Fixed a bug where a new reference displayed the information from an existing reference when it was created as part of a static group and the Live Search textbox had text. Fixed a bug where the last letter of a custom citation ending in a quote mark could be removed when using cited pages.