NEW in Version 11.0.8

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

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

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

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

• Microsoft Word scripts are compatible with Microsoft Word 2011

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

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

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

 • Bug fixes

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




NEW in Version 11.0.7

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

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

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

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

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

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

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

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

 • Bug fixes

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



NEW in Version 11.0.6

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

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

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

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

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

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

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

• Bug fixes

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



NEW in Version 11.0.5

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

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

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

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

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

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

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

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

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

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

• Bug fixes

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




NEW in Version 11.0.4

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

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

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

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

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

• Improved pdf download to handle changes made by some publishers

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

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

 • Bug fixes

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




NEW in Version 11.0.3

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

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

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

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

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

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

• Bug fixes

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




NEW in Version 11.0.2

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

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

• Get PDF From Internet is better at finding older biomedical articles

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

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

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

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

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

• Bug fixes

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



NEW in Version 11.0.1

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

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

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

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

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

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



NEW in Version 11

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

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

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

• Modified user interface

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

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

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

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

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

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

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

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

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

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

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

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

• Command-S saves an edited Journal Glossary