Refs Menu:   ...New Reference
                   ...Insert Reference
                   ...Duplicate This Reference
                   ...Delete Reference
                   ...Remove Duplicates
                   ...Choose
                   ...Search
                   ...Find
                   ...Find in This Reference
                   ...Find and Replace
                   ...Change All
                   ...First
                   ...Prev
                   ...Next
                   ...Last
                   ...Go to Reference #

REFS MENU

New Reference

Creates a new empty reference at the end of the database.

Insert Reference

Creates a new empty reference immediately after the reference begin viewed.

Duplicate This Reference

Creates a new reference containing an exact copy of the reference being viewed. The new reference can be placed immediately after the existing reference, at the end of the database, or after any reference you specify in this dialog box:

Select where you want the duplicate reference to go, and click OK. If you use after reference number… to select an arbitrary position in the database, the next time you select Duplicate This Reference, the number in this field will be incremented by one so that the placement of the next copy will occur after the previous one (unless you type in a new number). 

This feature useful when you are entering multiple references from the same source (e.g. multiple chapters from a single book).

Delete Reference

Permanently deletes the reference being viewed from the database. Selecting this option (or pressing Command-E) will bring up a warning dialog box unless you have elected to turn the warning off (in Preferences).

Remove Duplicates…

This menu item brings up the Remove Duplicates option:

In large databases, especially those acquired by downloading from national on-line services, it is likely that multiple copies of the same reference exist. You can choose which fields must match for two references to be considered duplicates. Be sure to choose enough fields to guarantee uniqueness. 

In addition to specifying the fields that must be examined to determine if references are duplicates, in some cases you can control what information in each field is used. 

       

Ignore periods when comparing references

When this box is checked, Bookends will not use periods when determining if two references are duplicates of one another. For example, when when this option is checked, two references with this Journal entry might be considered duplicates:

       

J. Biol. Chem.

    and 

       

J Biol Chem

       

       

Authors last names only

When this box is checked, Bookends will consider only the last names of the authors when comparing two references. When this option is checked, two references with these authors might be considered duplicates:

       

Smith, TR

       

Houghton; Jr., John

       

Hyman, D.R.

and

       

Smith, Teddy Roosevelt

       

Houghton, D

       

Hyman, DR

       

       

Volume ignore issue number

When this box is checked, Bookends will not use an issue number, if present, when comparing the Volume field. When this option is checked, two references with these Volumes might be considered duplicates:

       

125(12)

and

       

125

       

       

Pages first page only

When this box is checked, Bookends will only use the first page number when comparing the Pages field. When this option is checked, two references with these Pages might be considered duplicates:

       

13-26

and

       

13

Here are some important things to know before you use this option:

•
Punctuation is considered in the comparison, but spaces and the case of the letters are ignored.

•
If two references are the same, as defined above, the one with the shorter Abstract field is removed.

•
If two references are the same, including Abstracts, the one that occurs later in the database is removed.

+
Since reference removal is irreversible, it’s wise to perform the process on a backup
      copy of the database. Once you have verified that the procedure went smoothly, you
      can delete the original.

+
Selecting this option clears the Hits List.

The database is examined. This may take some time with big databases, especially if  running on slow computers. Next, the number of duplicates is reported:

You can have the duplicates automatically removed. If you choose to Manually Verify Duplicates, Bookends will display all of the references that meet the criteria you set for defining a duplicate. You can move between the duplicates by using the Next and Prev buttons in this dialog box:

To identify a reference as a duplicate, mark it by clicking on the Mark button (all references are initially unmarked). If the reference you are viewing is already marked, the Mark button will change to Unmark, and you can use it to deselect the reference. When you are satisfied with your selections, click on the Delete Marked button. After answering the confirmation dialog box affirmatively, Bookends will proceed to delete the marked references from the database (you can Cancel this process at any time up until that point).

The status of a reference, marked or unmarked, is displayed in the upper right hand corner of the dialog box. In addition, the appearance of the Marked button in each reference window (checked or unchecked) will reflect the status of the reference.

+
No references will actually be deleted from the database until you press the Delete
      Marked button and click OK when asked to confirm your decision.

+
All the references in the possible duplicates list will be shown. Since Bookends can't
      decide beforehand which version of a duplicated reference you will want to keep, be
      sure not to mark all the possible duplicates, or you will delete all copies of the
      reference from the database (the duplicate and the "original").

Choose…

You can generate a Hits List by specifying reference numbers. Each reference is numbered sequentially as it is entered. Once a number has been assigned to a reference you can retrieve that reference by using this number. This feature is particularly useful when constructing a bibliography.

+ Choose is used to create a Hits List in which references are arranged in an arbitrary
      order. This is usually used only for creating a list of references to be cited in a
      bibliography. Since this is typically done automatically by the Scan a Document for
      Citations function of Bookends, you will rarely need to use the Choose function
      yourself.

On the right side of the screen is the Choices field. Here you enter the numbers of the references you want in the Hits List. You can choose more than one reference at a time by separating the numbers with Returns. For example,

      1
      5
      3
      15
      32

selects 5 references from the file, to be displayed in the order given. A range of references can be chosen by using a dash:

      3-9
      15-12

This picks references 3, 4, 5, 6, 7, 8, 9, 15, 14, 13, and 12. To view all references above 35, you enter could enter 36-9999

The other buttons provide these functions:

Get Choices. Click on this button when the numbers of the references you want in the
            Hits List have been entered in Choices. Bookends collects the references and
            places them in the Hits List. It exits to the references.
Choose All. This button places all the references in the Hits List. It exits to the
            references.
Clear Numbers. This empties the Choices.
Cancel. This returns you to the references without modifying the Hits List.
Storage Fields. To the left of the Choices field are two smaller Storage fields. By clicking on the appropriate arrows, you can move the numbers in the Choices field back and forth from the Storage fields. This lets you work on more than one bibliography at a time. Above each storage field is a text field where you can enter a phrase that describes the purpose of the reference numbers you are storing there.
Hits List -> Choices. This button is near the bottom of the screen. Clicking on it
            places the numbers of the references in the Hits List into Choices. It is possible
            to construct a Hits List with Find..., Search…, or the Marked button, and then
            display it for storage or editing Choices.

+
This is the only way you can actually see the numbers of the references in the Hits
      List. The Show Hits List in the Hits menu provides a scrolling list of information
      from each of the references in the Hits List.

Search…

The Search… option provides a way to look through a reference file and select a subset of references based on criteria that you define.

First, you specify what you want to Search for. This collection of characters is called the Search Word or Search Item. Search Object refers to the characters in the reference.

To begin a search, enter one or more “search words” or “search items”. For example,

Individual search words (items) are entered on separate lines. The number of search words is limited to 10 at one time. The “OR” and “AND” between lines are actually pop-up menus with which you can specify boolean “AND”, “OR”, and “NOT” searches (see below).

+
Short cut: if the Shift or COMMAND key is held down while a boolean option
      (AND, OR, or NOT) is being selected from one of the pop-up menus, all of the
      pop-up menus will be set to the same boolean search option.

To delete items (words) that have already been entered, click on the Clear Search Items button.

How a Search is done
The Search function now allows up to 10 independent boolean AND, OR, and NOT searches to be done at once. Bookends uses either a whole word search or a word beginning with  search, depending on your selection in this window. 

A word search for

      Search Word
            Matches
            Doesn’t Match
      cat
                            cat
                     catsup
      blue paint
                 blue paint
          blue (or paint)
      Smith, AB
               Smith, AB
         Smith
      Smith,
                     Smith, Allan
      Smith
      Smith
                      Smith, AB
         Smithson

A word beginning with search for

      Search Word
            Matches
            Doesn’t Match
      cat
                            cat and catsup   
meercat
      blue paint
                 blue paint
          blue (or paint)
      Smith, AB
               Smith, AB
        Smith
      Smith,
                     Smith, Allan
     Arrowsmith

+
Searches are not case sensitive.

Selecting Categories to Search
There are check boxes that represent the categories in each reference to be Searched. For example, checking the boxes Authors, Keywords, and Abstract causes Bookends to look in just these three categories for possible matches. Checking the All button causes every category to be searched. To specify individual fields, uncheck the All button and check the fields you want to search.

Searching the Database or the Hits List
Two buttons let you search the database or the Hits list. When the Entire Database button is selected, all categories in the database are searched for the desired information. If the Hits List button is selected, the search operates on only the references you have already put in the Hits List. This allows you to do a series of searches, sifting through the Hits or each Search to obtain the desired information.

Every time a Search is done, the existing Hits List is replaced by the new Hits List. If you want to save the Hits List prior to a new Search, you can do so in the Choose window.

Saving and Recalling Search Strategies
You can save and restore the search strategies that you create. Whenever you’ve created a search that you would like to save, click on the Search Strategies pop-up menu:

In the Search Window you are presented with the following pop-up menu:

Selecting Save This Search Strategy… brings up this dialog box

The search information is saved under the name you enter. Not only are the present search words saved, but the settings of all the buttons are saved.

What are Search Strategies good for? Two examples are:

1)
If you download from on-line databases routinely and want a uniform search done
    after each download. Save searches you use regularly as Search Strategies, with the
    Search confined to the Hits List. After importing references into the Hits List,
    invoking that Search Strategy will search only the newly imported references.

2)
This is an excellent way to provide a “synonym library”. For example, say you want
    to frequently search a database of references for diseases of the heart. You might save
    the following search strategy:

        heart
        coronary
        coronaries
        bypass
        atherosclerosis
        artereosclerosis
        myocardial
        myocardium
        pericardium
        infarction

searching “All” fields with an “OR” search. A search of this type (tailored to the user’s individual needs) should find all of the references dealing with heart disease. Note the use of singular and plural forms of the same word, to ensure that all references will be found

To recall a strategy that you’ve saved, pull down the pop-up menu next to Search Strategies and choose the strategy you want.

To remove a strategy that you’ve saved, choose Delete Strategies… from the bottom of the Search Strategies pop-up menu:

Highlight the search strategy that you want to delete and click on the Delete button. When you’re through deleting strategies, click on the Done button.

When to Search and When to Find
Both Search… and Find... allow you to examine a database and extract references based on specific information. Bookends includes both because each has an advantage in certain situations.

Search is more flexible and powerful than Find. It lets you look for large character sets, has AND, OR, and NOT options, and allows searching in multiple fields. You can search the entire database or just the Hits List. Also, you can save Search Strategies that you use regularly.

Find is usually faster than Search. Find allows AND searches, which are often sufficient (OR Finds are possible by repetitively Finding and appending each result to the Hits list)..

Show Hits List After Search
If Show Hits List after Search option is checked, Bookends will bring up a window containing the list of references that matched the search criteria (Hits List). This window will not appear if no references are found.

Find…

This is functionally identical to clicking on the Find button that is above each reference, with one difference: if a word or phrase is selected (highlighted) when the Find menu item is selected, that word or phrase will be automatically placed in the Find dialog.

Find in This Reference…

You can have Bookends find and highlight a word or phrase in a particular reference. When Find in This Reference is is chosen from the Refs menu (or Command-T is pressed), the following dialog box appears:

When you click on OK, Bookends will search the displayed reference for the words or characters entered in this dialog box. The search begins from the current insertion point in the reference. If no match is found, Bookends will simply beep. A whole word search ensures that the characters you enter constitute a word (or words). For example, a whole word search for "red pony" will find and highlight the matching words in

"I saw a red pony in the yard"

but not

"I saw a reddish pony in the yard"

or

"I saw red when I saw a pony in the yard"

A character search will find the matching characters anywhere in a word. For example, a character search for "ion" will find and highlight these three letters in

"ion"
"cation"
"perception"

This function is useful if you have done a Find or a Search and want to see the location of the word(s) you searched for in the resulting hits.

+
To do repetitive finds within a reference without bringing up the dialog box, press
      Command-Shift-T (Find in This Reference Again). This will search the reference
      for the same whole word or characters that were previously used.

+
Words or characters entered into the Find dialog box or the first item of the Search
      window will automatically appear in the Find in This Reference dialog box when it
      is opened, and vice versa.

Find and Replace…

With this option you can quickly find and replace text in any reference (or all references) in a database or in the Hits List. Two searches are supported:

whole word
The entire word (including spaces) must match. This is a very fast search.

characters
Will match if the characters appear anywhere in the word. For example, “ion” would match with its counterparts in “ionophore” and “information”. This is slower than a whole word search.

It there are no Hits, the Hits List button will be dimmed.

If a word in a reference is highlighted (selected) when you type Command-R, it will automatically be placed in the Find editable text box as the word to be searched for.

Short cut: Find and Replace can also be invoked by clicking on the Find… button with the Shift key held down.

+
The Find function is case insensitive. Replace inserts the text just as you typed it,
      including case.

Carriage returns can be inserted in the replaced word(s). A Return character will be inserted in place of the characters “^M” (caret-M, without the quotes). For example, if you have multiple authors separated by semicolons rather than returns, searching Authors for “;” and replacing with “^M” will place each author on a separate line.

+
You cannot use ^M in the search word(s).

Change All…

This menu item brings up the dialog box:

Any word(s), spaces, and punctuation marks entered in the editable text field will be placed before, after, or into the specified category in each reference that is in either the Hits List or in the entire database, depending on the options that are selected. Placing words into a category will replace any text that may exist in that field.

Words placed in the Authors, Editors, Keywords, or Notes category will be entered on a separate line. Words placed in any other field will be added immediately after the existing text.

You can insert a Return character in the text by entering ^M; Bookends will replace these two characters with a Return.

+
To delete an entire field, don’t enter any text in the dialog box and then choose to put
      the (empty) text into the field to be deleted.

Warning: This operation is NOT undo-able!

First, Prev, Next, Last

Move you to the first, previous, next, or last reference in the database. Alternately, you could hold down the Shift key while clicking on the Left Arrow or the Right Arrow above each reference will take you to the first or last reference in the database, respectively. Similarly, clicking on the Down or Up Arrow in the Hits Box takes you to the first or last Hit, respectively.

Go to Reference #…

This option displays a dialog box asking for the number of the reference you want to view. Enter the number of the reference and press Return or click on the OK button.