Utilities Menu

UTILITIES MENU

      JournalGlossary…

      The Journal Glossary provides a rapid means of entering journal names and
      customizing bibliographies.

Entering journal names into the Glossary

      A Journal Glossary entry contains 3 items: the abbreviation for the journal, the
      journal’s short name, and the journal’s full name.

      To navigate the list, use TAB to move from left to right, Shift-TAB to move from
      right to left, and the Up and Down Arrows to move within one column.

      The buttons at the bottom of the dialog let you

      1)
Add Journal—Add a new journal entry.

      2) Delete Journal —Removes the currently selected journal entry.

3) Print …—Prints the list of journals and their abbreviations.

Entering journal names into references

To use the Journal Glossary while entering a reference, you enter the abbreviated journal name (e.g., “ji”, without the quotes) in the Journal category. When you “leave” the Journal category (by pressing TAB, Return, or clicking outside of the field), Bookends replaces the abbreviation with either the short or the full journal name. Preferences contains buttons that tell Bookends which form of the journal name entered in the Journal Glossary, short or full, to use.

Selecting journal names in a bibliography

      In addition to making it easier to enter journal names, the Journal Glossary allows
      you to automatically generate bibliographies that contain either the short or the long
      form of the journal name. In the Order field of each Format, the letter "j" tells
      Bookends to use the short form and the letter "f" the full form of the journal name.
      There, when Bookends is making a bibliography and encounters a "j" or an "f" in
      the Format, it fetches the journal name from the reference and looks in the Journal
      Glossary to see if it is entered there. If the journal name is in the Journal Glossary,
      Bookends selects either the short (if a "j") or the full (if an "f") form to put in the
      bibliography. If the journal name isn’t in the Journal Glossary, Bookends uses the
      name as it was entered in the reference.

      +
The form of the journal name entered in the reference itself (short or full) doesn’t
            matter when a bibliography is being created. If the journal name is in the Journal
            Glossary, Bookends finds it regardless of whether it is the short or the full form.

Adding periods to journal names in a bibliography

      If a journal name in a reference lacks periods (e.g. J Biol Chem, the style used in
      Medline databases) but the Journal Glossary version has periods (e.g. J. Biol.
      Chem.), periods will be added when the bibliography is generated.

      +
Even if the Journal Glossary short journal forms are entered with periods, you
      always have the option of selecting the Remove Journal “.”s in the actual Format if
      periods are not desired.

Transferring Journal Glossaries between databases

      Each database has its own Journal Glossary. You can transfer the Glossary to other
      databases with the Transfer References/Formats option.

      Sort All References…

      You can permanently sort all the references in the database by two fields
      simultaneously. In addition, the order of the sort (ascending, from lowest to highest
      value, such as A to Z) or descending (from highest to lowest value, such as Z to A) 
      can be specified.

+
      If you are using Citation by number in documents to be operated on by the Scan
            a Document option, you shouldn’t permanently sort the database until you are
            finished with the manuscript: the references will have different numbers after
            sorting.

      Show Attachments

      This is the menu equivalent of the Attach button in each reference window. The only
      advantage that it has over the Attach button is that you can select a subset of the filed
      name(s) in the Keywords field (highlight them) and use the Show Attachments menu
      item to bring up these windows (the Attach button will bring up windows of all files
      in the Keywords field).

      Scroll

      Scroll is used when the size of the Bookends window is larger than the monitor
      (screen). In this case, you use the mouse pointer to drag the viewing window,
      allowing you to see the entire Bookends window, even if the monitor is too small to
      display all of the window at once.

      Transfer References/Formats

      This option lets you transfer References, Formats, Journal Glossaries, and Search
      Strategies from one Bookends database to another.

      +
Whenever you receive an update to Bookends, use this option to transfer your
            data from the older to the newer version of Bookends.

      The options are:

Source Bookends Database. Clicking on this button brings up the Open dialog box.
      Choose the Bookends database that you want to transfer information from.
Destination Bookends Database. Clicking on this button brings up the Open dialog
      box. Choose the Bookends database that you want to transfer information to.
Transfer References. If you want to transfer the references between the database,
      this button should be checked. Any references in the destination database
      remain—the references in the source database are appended to the destination
      database. This option will transfer All references or just those in the Hits List. The
      latter is useful when you want to transfer a subset of the references between
      databases. If the with unique ID numbers option is checked, the references will
      retain their original unique ID numbers in the the new database (this is not
      recommended—transfer unique IDs only when you have used these to keep track of
      reprints or to designate references in manuscripts). If Update Lists is checked,
      Bookends will add the Authors, Editors, Keywords, and Journals in the transferred
      references to the Lists in the destination database.
Transfer Journal Glossary. If you want to transfer the Journal Glossary, this
      button should be checked. The entries are appended to any names already in the
      Journal Glossary (if any).
Transfer Search Strategies. If you want to transfer the Search Strategies, you
      should check this button.
Transfer Formats. If you want to transfer the Formats, then this button should be
      checked. You can have all the Formats presently in the new database deleted during
      this process.

      +
If a format you are transferring already exists in the destination database (same
            name and Type), the format in the destination database will be overwritten by the
            format in the source database.

Transfer Labels. Check this button only if you have changed the labels (the names of
      the categories or fields) from the originals supplied with Bookends.
Transfer. Clicking on this button starts the actual transfer. Be sure the source and
      destination database have been selected, and that the other buttons are correctly
      checked. If you are transferring references, you are asked for the name of the
      exported reference file. Normally, you can accept the default name. The temporary
      file is deleted when the transfer is completed.
Done. Returns to the first reference in the database.

User-Defined Imports…

You can create templates that tell Bookends how to import reference information downloaded from a wide variety of on-line services and CD-ROMs. The Utilities menu contains the option User-Defined Imports… When selected, you see the following screen:

 

When filled out, this screen (and the next) will contain all the information Bookends needs to import reference information from text files downloaded from most on-line and CD-ROM sources.

+
For Bookends to import references, the specific bits of information in the file must
      be tagged. Tags are labels that identify the type of information that is to follow. Here
      are three examples of the different ways the Authors field might be tagged:

      AU - Smith AR

      Author(s): Smith AR

      Journal Author
        Smith AR

Designing a new importer

Click on the button New and enter the name of the new importer. Usually, the name will be the same as the information provider (e.g. CD Plus-Medline, ERIC, etc.). If an importer was already selected (i.e. its name was in the pop-up menu labeled Importers:), a duplicate of that importer will be created and given the newly assigned name. This makes it easy to use one template as the basis for creating others.

The user-defined templates are stored in a folder (called ‘User-defined Imports’) that resides in the same folder as the Bookends Plus application. To access a template for viewing, modification, or to make it the basis for a new template, use the Importers: pop-up menu. You cannot delete templates from within Bookends. To delete a template, simply remove it from the User-defined Imports folder and place it in the Trash.

The number of importers allowed is unlimited. To use an already defined importer in Bookends, use the Import References… item in the File menu as you normally would. After you select a file to import, the user-defined importers will appear at the bottom of the menu from which you select the source of the file.

Specifying where the information goes

On the left side of the screen is a column of fields labeled Field tags, each field followed by an arrow and the name of a Bookends reference category. You can tell Bookends what information you want to keep, and where it should go, by entering the tag for each field of interest. Suppose the downloaded file has the following fields:

            UI:
123456789 — unique identifier
            AU:
Jones, Ron — author(s)
            TI:
This is my article — title
            DA:
1995 — date
            PY:
12-24 — page range
            LA:
English — language
            AD:
State University — address of corresponding author

To import the information into the corresponding fields in Bookends, you might fill out the Field tags as follows:

Case matters — ‘AU:’ is not the same as ‘au:’.

Note that in this example you must include the colon in the tag definition. That is because when Bookends analyzes the text for a tag designation, it looks at one word at a time, and a word ends with either a space or a Return character. If the tags are

            UI - 123456789
            AU - Jones, Ron
            etc.

you would define the unique identifier tag as “UI”, without the dash, since UI is immediately followed by a space.

You can import more than one tagged field into any category simply by putting a space between the tag definitions (e.g., importing to the Notes category in the above figure). If the category is a scrolling field, Bookends will put a Return character between the imported tagged fields. If it is not a scrolling field, Bookends will place a semicolon between the imported tagged fields.

What if the tag consists of more than one word? You might encounter a downloaded file that provides reference information like this:

      UI: Unique Identifier
        123456789
      AU: Article Author(s)
        Jones, Ron
      etc.

In this case, enter the last word in the tag. In this example, you would enter ‘Identifier’ and ‘Author(s)’ in the appropriate places in the Field tags portion.

Identifying the beginning of a reference

You must tell Bookends what constitutes the beginning of a new reference in the downloaded file. Typically, this will be a field tag. In the example given above, you would enter

Again, you must enter the entire word, which ends in a space or a Return (so don’t enter the dash here).

There may be cases in which different tags are used to begin different reference types in a single file. You can tell Bookends to look for more than one “new reference” tag by entering the different tags in this field, making sure to separate each one with a space.

+
The tagged field that identifies the start of a new reference will not be imported into
      Bookends unless it is also entered in the Field tags portion of the definition window.

References that begin with numbers
Numbers may sometimes be used to distinguish one reference from another in reference files obtained from on-line services. An example might be:

1
AU Niklinska, B
TI Two years behind the mast
...

2
TI This reference has no author
...

You can indicate that a new reference begins with a number (#) and that a category ends with a Return followed by one or more capital letters. In this case, Bookends will recognize a number following a Return (as well as capital letters) as signifying the end of a category and the beginning of a new reference. When you enter the # symbol as defining a new reference in the User-defined Imports window, this features is indicated with the words "(or a number)" as follows:

+
You must enter just the # symbol. If any other characters are entered Bookends will
      look for the character #, not a number.

+
If a number appears at the beginning of a line of text (that is, after a Return)
      Bookends will assume that this is the beginning of a new reference and import the
      rest of the information accordingly. Therefore, if categories are defined by capital
      letter tags, it is preferable to define the beginning of a reference as a tag (e.g. AU)
      rather than as a number (#).

Although not designed for this purpose, specifying that a reference begins with a number can be useful if you want to import references from an existing bibliography.

Identifying the end of a tagged field

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

All fields end after a Return character, but not all Returns indicate the end of a field! Each time Bookends encounters a Return in the file it is importing, it checks to see if what follows indicates the end of the field.

This is an example of a file in which spaces are used to indent information in a field (the relevant spaces are shown as diamonds (◊), and Returns are shown as ‘¬’):

            ◊TI◊◊- Identification of an Epstein-Barr virus early gene encoding a second¬
            ◊◊◊◊◊◊component of the restricted early antigen complex.¬
            ◊AB◊◊- When the latent Epstein-Barr virus (EBV) genome in B95-8 cells is¬
            ◊◊◊◊◊◊induced into a replicative phase, two abundant early RNAs are…

Note that tags are preceded by a single space and followed by two spaces. Information after a return within a field is preceded by 6 spaces. The correct definition of the “end of field” in this case would be:

In other cases, spaces may not be used to format the output, and all information may begin at the left margin (or indented the same number of spaces in from the left margin). For example:

            TI◊◊- Identification of an Epstein-Barr virus early gene encoding a second¬
            component of the restricted early antigen complex.¬
            AB◊◊- When the latent Epstein-Barr virus (EBV) genome in B95-8 cells is…¬
            induced into a replicative phase, two abundant early RNAs are…

In this case, you can tell Bookends that two capital letters after a Return indicate that the field has ended:

Unlike reference information you enter into Bookends, user-defined importer templates must explicitly be Saved. Bookends will prompt you if you try to leave or quit without saving an importer that has been edited since it was last saved.

Viewing the Text File…

When creating a template, it is helpful to view an example of a downloaded text file from the on-line service or database. To do this, click on the button 

The text file you select from the dialog box will appear in a window above the template.

This window contains up to 20,000 characters from the text file (it is truncated at 20,000 characters if the file is longer than this), and is for display only — you cannot edit the text in this window.

You can, however, Copy selections from this window and Paste them into your template. Bookends will automatically truncate any copied text to the first word in the selection. Thus, if you select the characters ‘structurally related peptides’ and then do a Copy, Bookends will put the characters ‘structurally’ in the clipboard.

Show Invisible Characters is a very useful option that replaces spaces, returns, and tabs with visible characters. Spaces are replaced with ◊, Tabs with ∆, Returns with ¬. This is extremely useful when you are trying to determine how to define the end of a tagged field.

+
 If you Copy from the window with Show Invisible Characters checked ON,
      Bookends will not copy the characters ◊, ∆, and ¬ to the clipboard.

  .                                                          ...Utilities Menu Continued--->