Mar. 26, 1989

BiblioFile

Version 3.10

PURPOSE:

The Biblio-File system is a citation management system designed to
be used in keeping track of literature references. Biblio-File differs
in approach from other citation management packages by providing you
with the automatic capacity to file citations by subject matter in
addition to using key words. The package is written to accommodate the
way most of us collect and create our journal files. That is, we start
with a broad topic, collect a few citations in this category and then
realize we need to subdivide the file folder into separate and more
precise headings. Biblio-File follows this same concept, and allows
easy reclassification of articles originally filed in a broader
category.

The system is menu driven, and uses multiple windows to provide easy
and consistent entry of information. All key words, subjects, authors
and journals can be added during citation entry, or they can be added
independently using the appropriate utility function included in the
package. Each of the utility functions as well as the set up and use
of the system will be described in more detail below.

BiblioFile uses B+ tree indexes into the citation for authors,
journals, key words and subjects. This provides for unparalleled speed
of retrieval on any combination on these index fields.

NOTE: If you have been using an earlier version of BiblioFile (prior
to 2.51) you MUST run the BIBCONV program on your ".CIT" files
to be able to use them under any version after 2.51. A
description of this program and the procedure for converting is
given in Appendix A.
FILES:

BiblioFile consists of the following programs:

BIB.EXE: The main executable program for the BiblioFile system.

BIB.OVR: The overlay portion of the executable program.

REVISION.HST: Revision history for BiblioFile.

CONFIG.SYS: The configuration file to increase the number of files
and buffers available for BiblioFile.

CONTROL: A user configurable file containing the colors for video
monitors.

CONTROL.MNO: A control file for monochrome monitors. Copy this to
CONTROL if the VSET program (below) doesn't create a
pleasing screen appearance.

BIBUTIL.EXE: The utility program for BiblioFile that contains
modules for listing the index files, setting video
attributes, deleting duplicate citations, and deleting
entire databases. Replaces DELBIB.EXE, VSET.EXE, and
DUPES.EXE.

BIBCONV.EXE A conversion utility to transform the ".CIT" files of
earlier versions into the format needed by Bib251 or
later.CREDITS:

Turbo Pascal and Database Toolbox are trademarks of Borland
International.

IBM, PS/2, and Compaq are the trademarks of the respective
companies.

The windows and the screen writes used in this program are
accomplished using the QWIK and WINDOW routines of Jim LeMay (CIS
76011,217).

Turbo Professional is the trademark of Turbo Power Software.

MedLine and Grateful Med are copyright of the National Library of
Medicine.

DISTRIBUTION RIGHTS

This system is now distributed as ShareWare. The author retains
exclusive copyright to the material.

Users may freely copy and distribute this software and
documentation in its original, unmodified state. Other than reasonable
copying and shipping and handling charges, no remuneration may be
accepted by any party other than the copyright holder.

If you find BiblioFile useful after an evaluation period of one
month, please register your copy by sending $40 to the author. This
registration fee is one-time only, and allows unlimited upgrades to
future versions of the shareware BiblioFile System. Registration fees
will be used to defray development costs and to encourage further
improvements.

The latest version of BiblioFile will always be available on the
Genesis Project BBS, and usually, CompuServe on the IBMAPP forum.

Please direct all inquiries and comments about BiblioFile to

SYSOP
Genesis Project
(505) 843-2389
300/1200/2400 baud,
no parity, 8 data bits, 1 stop bit

Or to

Dean Madar, M.D., Ph.D.
1855 Girard NE, #16
Albuquerque, NM 87106

Or to

Dean Madar
CIS 73210,2741


DISCLAIMER:

BiblioFile and its companion programs are distributed as is without
warrantee of any kind expressed or implied. The author will not be
liable for any damage arising out of their use.


SYSTEM REQUIREMENTS:

BiblioFile will run on IBM PC, PC XT, PC AT, and PS/2. BiblioFile has
also been tested on IBM close compatibles including COMPAQ, UNISYS
(Sperry), Tandy, ARC Turbo 12, and Northgate.

Minimum requirements are:
380 kilobytes of free memory;
MS DOS or PC DOS 2.0 or greater;
Two diskette drives, (although a hard disk is recommended for
performance reasons);
A color or monochrome monitor including CGA, EGA, VGA or Hercules;
A large collection of otherwise unorganized journal citations.
Grateful Med from the National Library of Medicine (if you wish to
use the direct importation facility.

LANGUAGES AND LIMITS:

The current version of BiblioFile incarnation is written in Turbo
Pascal 5.0, with some assembly language assists. Windowing is handled
using the QWIK and WINDW units of Jim LeMay. Some units from Turbo
Power Software's Turbo Professional are also used. The data and index
files use the Turbo Pascal Database Toolbox. The final code has been
analyzed with Turbo Power's Analyst to remove uncalled procedures,
remove unused variables, and pack the .EXE file.

As in any program, there were some design assumptions and limits
made in BiblioFile. Some of the known limits follow.

Your subject tree may have a maximum level of 10. That is, 10
nested levels from parent to last child. Within any level,
though, the only limit on number of siblings is disk space.

Only 20 databases may be active at any one time.

Although the system will run on a dual floppy computer, a disk
cache program would be very useful in speeding up disk input. There is
a LOT of disk activity associated with this program. It is also
written in such a way that the index and data files are flushed with
each new addition to protect against disasters. This is most
noticeable, of course, on a floppy based system.


GETTING STARTED:

If you are currently using a version of BiblioFile prior to 2.51,
read Appendix A: "Converting from BiblioFile Before 2.51". You MUST
convert your data files before using this version of BiblioFile.

One of the files included in the BiblioFile distribution disk is a
CONFIG.SYS file. If you already have a CONFIG.SYS file without the
lines the lines FILES = 20 and BUFFERS = 20, include those lines in
that file. If you do not have a CONFIG.SYS file, copy the CONFIG.SYS
file provided onto your boot diskette, then reboot your computer.


Dual floppy system:

If you will be running BiblioFile from a dual floppy system, the
program disk will be in drive A and the data disk will be drive B.
Create a new formatted system disk in drive A and copy the
following files from the distribution disk to your new system disk:

BIB.EXE
BIB.OVR
CONFIG.SYS
CONTROL
DEFAULT.FMT

Create a second formatted system disk in drive A and copy the
following files on to it:

BIBUTIL.EXE
CONTROL
BIBCONV.EXE (only if you will be converting data files made prior to
version 2.51)

This second disk now contains all of the utilities needed to run
BiblioFile. These modules are used only occasionally, and need not be
present on the main program disk. Remove the distribution disk from
the B floppy drive and replace it with a formatted blank disk.

For hard disk systems:

Create a new subdirectory of your choice and copy all of the files
from the distribution disk into the subdirectory. The CONFIG.SYS file
should be filed to the root directory if you do not already have a
CONFIG.SYS file present there. See above for a more complete
explanation of the use of CONFIG.SYS.


General features:

BiblioFile consists of two main programs: BIB.EXE which contains
the database definition, data entry and search features, and
BIBUTIL.EXE which contains the less commonly used utilities to examine
the index files, change the video colors, delete databases and scan for
duplicate citations.

The main menu of the BiblioFile system consists of eight choices,
with eight more choices in the Utility menu. The selection of the
module to execute is made by the "point and shoot" method. Move the
light bar cursor to the desired activity and press to begin
execution. Alternatively, you may also press the number associated
with the menu choice, or the capitalized first letter of the menu
option.

In most cases, data entry in the BiblioFile system is completed by
pressing the key. The cursor moves from field to field by
pressing either the key or using the up or down arrow keys.
Any field may be visited as often as required prior to pressing the
key. Any invalid data input, or attempts to skip a required
field will result in a message window appearing on the screen.

Context sensitive help is available in many fields by pressing the
key. The active function keys are displayed on the last line of
the CRT on all data entry screens. A prompt which varies from field to
field will appear on lines 19-23 of the CRT as the cursor is moved
between fields.


Umlauts and grav marks:

The valid character string changes as you move between fields. For
alphanumeric fields, you can enter any key from the keyboard, as well
as characters with accent marks, umlauts, etc. To access these special
characters, press and hold the key, and type the ASCII code for
the corresponding character on the numeric keypad. For example: the
character " " is created with 129. See the ASCII table in the
back of any DOS, BASIC or other programming manual for a complete
listing of these characters and codes.


Starting BiblioFile:

Change to the directory containing the BiblioFile system. (Probably
hard drive users only).

From the DOS command line type BIB followed by . If you wish to
use the utility functions, type BIBUTIL followed by . The
primary menu of the program will be displayed.


Making a new database:

The first step in using the BiblioFile system is creating a new
database and telling the system where the data files will be stored.
Select option 6) "Make a New Database" from the main BiblioFile menu.
A database name may be any valid DOS file name up to eight characters
in length. After entering the database name, press to advance
the curser to the data drive field. Enter the drive letter where the
data files will be stored. If the database is already in use, or if
similarly named files already exist on the data disk, a message window
will appear on the screen.

For hard disk systems the data drive may be the same drive that
contains the BiblioFile programs. For dual floppy drive systems, it
is recommended that the second floppy drive be used for data.

After pressing , BiblioFile will create fifteen files on the
data drive. These files all share a common name with different
extensions depending on the purpose of the file. For floppy based
systems it is recommended that only a single database be placed on one
floppy disk. On a hard disk system any number of databases may be
created, up to the capacity of the hard disk. There are no shared
files between various databases. Each of the data files is created in
the directory from which BiblioFile was activated. Paths are
currently not supported.

IMPORTANT: If you are using a dual floppy system, you must copy the
DBLIST file created by BiblioFile onto the second floppy you made with
BIBUTIL.EXE. Some of the utilities require this list of database
names.


Picking a Database:

Whenever you use the BiblioFile system, you will first need to pick
a database from the list of currently active entries. Select option 1)
"Pick a Database" from the primary menu. A list of all currently
available database names will be displayed on the screen. Move the
cursor to the desired database by using either the up or down arrow
keys. Select the database by pressing . Each screen of the
system will display the name of the database in use to guard against
inadvertent corruption of datafiles.


Subject Entry:

Prior to using a particular database for the first time you must
enter the subjects under which you will be filing citations. The
concept of the BiblioFile system is that subjects are arranged in a
hierarchical, or conceptually, as a branching tree structure. Each of
the major subjects can be considered the root of a subject tree which
may have up to 9 sub-headings (branches and leaves).

The first time that subject entry is selected after creating a
database, you will be asked to enter a subject name. After typing the
subject and pressing the key this first subject will be
displayed in a window on the left border of the screen. From this
point on to add a new subject at this level of the tree, simply press
the key on your keyboard. The "Add Subject" window will appear
again and you may enter the new subject.

As entries are made into the primary subject window, they will be
alphabetized and displayed. If there are more subjects than there are
spaces on the screen, you may use the or keys of the
keyboard to display other frames of subjects.


Adding subheadings

To create a subheading under a subject, highlight the desired
subject by using the up or down arrow key, or if required the
or key. To add a new sublevel press at this
point. If a sublevel already exists for the selected heading, a
warning window will be displayed with instructions to proceed to
the lower level by pressing the key. If a sublevel does
not yet exist, you will be asked for the name of the sublevel in
an input window similar to the one displayed for subject entry.

After the first subheading is added to a subject, the parent
window is displayed showing an arrow to the right of the
selected subject, indicating the presence of sublevels. By
moving the highlight to that subject and pressing the or
right arrow key, a secondary window will be displayed. The
title of the secondary window reflects the parent subject and
any available subheadings are printed within the newly displayed
window.

This procedure may be repeated up to 10 levels for each
subject in the first window to create any level of complexity of
the tree structure.

Please note that unlike the primary subject window, using the
"Add Subject" function in any sublevel DOES NOT alphabetize the
subheadings inserted in the windows. Rather, the new subheading
is inserted directly below the highlighted subject at the time
the key is pressed. This is provided as an option for
users who prefer to arrange the subjects by frequency of use
rather than an alphabetical list. You are free to create your
own alphabetical list in any of these subheadings by arranging
the highlighted bar in the appropriate location prior to using
the insert function.

Deleting subject headings

Any subject may be deleted at any level of the tree by
highlighting the appropriate subject and pressing the key.
A warning window is displayed on screen asking for verification
of the delete, explaining the consequences. Any citations which
are contained in the branches of the tree derived from the
deleted subject will be lost.

Editing subject headings

The spelling of any of the subject headings can be modified at
any time by highlighting the appropriate subject or sublevel and
pressing the key. A data entry window will be displayed
containing the current spelling. Changes at this point affect
only the displayed subject and have no effect on any data
contained in the database.


Reclassification of citations by subject:

After citations have been added to any particular subheading
or subject in the database, at some future time you may want to
subdivide the citations into more specific subheadings. At that
time, any citations contained in the parent node may be
reclassified into any of the child nodes if desired. Also, all
citations imported directly from the OUTPUT file of Grateful Med
will require reclassification (see below). The steps involved in
this reclassification are as follows.

Create the new entries to your subject tree using the
procedures described above, or from the Citation Entry
option.

Use the and keys or and keys to
select the subject containing the citations you wish to
reclassify. Press the key to begin reclassification.

The citations currently located in the parent node will be
displayed to the screen, one at a time. At this point the
citation may be skipped and left where it is, or reclassified
to any level of the tree. This is accomplished by pressing
the R key (Case insensitive). The subject window will appear
on the screen. Use the right and left arrow keys to show
other windows of the tree, and the up and down arrow keys to
highlight the new "home" for the citation. Press to
complete the reclassification. The process is automatic from
that point forward, and all associated links are adjusted in
both the parent and child nodes and indexes to accommodate the
reclassification.

In case a mistake is made in reclassification, you can
"undo" it immediately by entering the reclassification
function and pressing "U" with any citation on the screen.
The last reclassification will be reversed, no matter what
citation is displayed on the CRT.

Mistakes encountered later can be corrected by using the
Cut function in combination with Delete Citation, and then
Pasting the entry into the correct place during Citation
Entry.


Listing the subject tree
A visual picture of the subject tree can be printed by
pressing at any level of subject entry. A window will be
displayed, asking if the entire tree should be printed.
Answering "o" will cause only the tree below the current
cursor location to be printed. Otherwise, the entire tree will
be printed, using indentation to indicate child levels.
Siblings subjects will have a similar level of indentation.
NOTE: Some printers cause an error here if they are not turned
on. Other printers allow the program to trap the error and
recover.


Citation Entry, Edit or Deletion

At any time after the subjects have been added to the system,
citations may be added by selecting option 3 from the main BiblioFile
menu.

The first level of subjects will be displayed in the window to the
left of the CRT screen. Select the appropriate subject under which you
wish to enter a citation. Citations may be entered at any level,
depending on the requirements of the citation. If you wish to select a
subheading under a particular subject, you may either press the
key or use the right arrow key to move to the sublevel window. Note
that new subjects may also be added here by pressing .

After you have reached the appropriate sublevel, press the key
to display the citation input template.

The title field is up to 240 characters in length. The first line
is a required field and must contain at least one character. The
second and third lines are optional depending on your needs. Within
these fields, the right and left arrow keys are nondestructive cursor
motion keys as are the home and end keys. The backspace key is a
destructive backspace.

After completing entry in the title field, move the cursor to the
first author field using either the down arrow key or the key.
Both author fields may be filled by either typing the author's name as
desired or using the Help key. Pressing will display a
window asking for a name fragment. Enter the beginning few letters,
and a list of all authors whose names start with these letters will be
displayed. By moving the cursor to the appropriate author and
pressing , the author name will be transferred to the field
underlying the window. This insures uniform spelling of author names
and will improve record retrieval by author in the Extended Search
function.

The first author field is likewise a required field. It must
contain some entry prior to pressing to file the record.

If the author typed into the field is not currently in the author
index file or data file, you will be asked to verify if you wish to add
this author to those files. Pressing "Y" for yes allows you to enter
authors "on the fly" without having to leave the citation entry
function.

The second author field is an optional field and may be filled in
as desired. For complete citation entries, BiblioFile versions after
2.51 offer space to store a total of 20 authors. To enter more than 2
authors, place an "X" in the "et al." field of the citation entry/edit
screen. Moving to the "next" field will open a window that allows
entry of up to 18 additional names. The function key works for
these fields as it does for the previous screen. File the additional
authors by pressing , or return to the previous screen without
saving by pressing .

Move the cursor to the journal field and enter the abbreviation of
the citation. Again this field may be filled by typing an
abbreviation, or by using the help function. You will be asked to
enter a name fragment, then the system will display a window containing
all of the currently available journal abbreviations as well as their
full text translations. Selecting the appropriate journal with the up
or down arrow keys and pressing will transfer the abbreviation
of the journal to the appropriate field.

The journal field is also a required field.

Sentinel articles in any given subject may be indicated by pressing
"Y" with the cursor in the sentinel article field. This is a
searchable criterion and may be used to retrieve important articles on
any given subject.

Move the cursor to the volume field and enter the appropriate
volume number. Valid characters in this field include numbers as well
as characters to allow entry of issue numbers as in: 183(2).

The volume field is a required field.

Move the cursor to the beginning page field with the cursor key or
the enter key. The beginning page number is a required field and may
be any number less than 32767.

The ending page field is an optional field, but if any entry is
made in this field it must be a page number greater than the beginning
page number.

The year field is a required field and the format may be either the
last two digits of the year, or all four digits of the year.
Whichever format is selected, be consistent because this is a sort
criterion for the search module.

Up to six key words may be entered for any article. These key
words may be entered by typing them directly into the field, or by
using the Help function. As above, if you type a new key word
that is not found in the index files, you will be asked to verify if
you wish to add this key word to the index files prior to continuing.
Again this allows you to add new key words to your index list without
exiting the citation entry function.

One important restriction for key word entry is that you must fill
the fields in order. Do not leave a blank in the key word lists.

Comments may be entered at any time by pressing the key. A
window will appear in the middle of the screen and any existing comment
will also be displayed. A comment up to 400 characters in length may
be entered. Within the comment window, the right and left arrow keys
work as nondestructive cursor motion, and Ctrl-right arrow and Ctrl-
left arrow work as expected for a standard word processor. The
key toggles overstrike and the key removes the character at the
current position. Complete the comment entry by pressing the
key.

A cut and paste function is provided to allow easier and faster
data entry. After the desired fields have been filled, press the
key to "cut" an image of the screen to a storage buffer. At any time
during the session when is pressed, a copy of the clipboard will
be pasted onto the screen. If you press , you will be asked to
verify overwriting any data that may be present in the buffer. An
indicator appears on the lower right of the CRT screen whenever
something has been placed in buffer.

Complete the entry of the citation by pressing the key.
Pressing the escape key will open a verification window asking if you
truly wish to escape without saving the current citation.

It is important to realize that the citation is NOT filed until the
key is pressed with the citation input template on the screen.

After is pressed, the blank input template will reappear.

You may escape from the input template and return to the display of
subjects and subheadings by pressing the escape key with a blank input
template.

After the subject headings are redisplayed, you may continue data
entry with a new subject by selecting it as described above.


Editing Current citations:

A current citation may be edited by selecting the appropriate
subject, subheading, etc. and pressing the key. The system will
display the citations one at a time beginning at the first citation
under the subject heading and continuing to the last entry. Move
between citations with the and keys. When a citation is
on the screen, any field may be changed in a manner similar to that
used when originally filling the fields. You may use either the
keyboard or the function key to fill or change appropriate fields.
Notes may also be added or changed at this time. Any changes must be
filed by pressing before leaving the citation or the edit
function.

Exit from the citation edit function by pressing the key or
the escape key as indicated.



Extended Search:

The primary use of the search function is to locate articles
dealing with a particular topic or key word quickly. By selecting
option 4 "Extended Search" in the main BiblioFile menu the search
input screen is displayed. If you wish to search by a particular
subject, place an X in the subject field. The actual selection of the
subject to be used as a search criteria will be selected on the next
screen.

If you wish to select by the sentinel article flag, place an X in
the sentinel article field.

The author fields should be filled using the Help function.
This insures that only authors who are actually in the database will
be scanned. The author search will find an author no matter which
position they occupy in the actual citation (first through twentieth
author). You may search for up to two authors simultaneously.

The journal for the citation may also be entered as a search
criterion. Again using the function key is recommended for
filling the field.

Up to three keys may be also used as search criteria. Individual
keys may also be entered with the help function.

If you wish to sort the retrieved records, place an X in the sort
field. The actual sort order will be specified on a later screen.

If output is to be sent to a DOS text file, place an X in the File
field. All output is sent to a file named SEARCH.BIB. If the file
currently exists, new data will be appended to the existing citations.

If output is to be sent to the printer, enter an X in the printer
field. Output may be directed to both the printer and a text file
simultaneously, but not also to the CRT. The output to the text file
or printer may be numbered if desired by placing an X in the "Number"
field. A window will open asking for the first number to be assigned
to citations found in this search. Any number between 1 and 9999 may
be used.

A logical AND is performed on multiple search criteria. That is, if
you have asked for a search on subject and author and journal, only
citations which meet all three criteria will be listed in the final
output.

For searches that will have output directed to either a text file or
the printer, a window will appear on the screen asking for a particular
format that should be used. Move the light bar to the desired format
with the arrow keys, and press when the appropriate format is
highlighted. These format files are user defined and can be created
using the MAKEFMT utility from the DOS command line. They control
which data are printed from the citations, in what order, and what
punctuation is used between fields.

If you have asked for a search by subject, the primary subject
window will appear on the screen. Select any level of the tree by
using the arrow keys to move the light bar to the appropriate branch of
the tree. Press the key to select the highlighted subject as a
search criteria. If you are asking to search on some node that is not
a leaf of the subject tree, you will be asked to verify that you wish
to search at this level. This is an important advantage of the
BiblioFile system, and provides automatic hierarchical searching.

If you have selected "Sort", the sort criteria screen will be
displayed. You may sort either by search author one, author two,
journal or year. The order in which the citations will be sorted is
displayed at the bottom of the screen as you select. Move the cursor
to the desired field and press to select sort criteria. As the
cursor moves to another field, the selected options will remain
highlighted as the cursor moves. You may select up to four sort
criteria from this frame.

After input of all search criteria, the search is initiated by
pressing . If the data are being sorted, an indicator will appear
on the screen to indicate that some activity is occurring. Any matches
to the search criteria will be displayed, filed or printed. If output
is to the CRT, a screen identical to that used for citation input will
be displayed with all data pertinent to the particular citation. The
and keys may be used to scan through all citations. Any
comments may be viewed by pressing the "Show Comment" key.
Additional authors may be viewed by pressing . After all
citations have been scanned, you may return to the search input
template by pressing .

If output is to the printer, the listing of all matches will be
produced, without any associated comments.


Import data from Grateful Med:

Many users use BiblioFile for tracking citations downloaded from
the National Library of Medicine's Medline computer. NLM offers a PC-
based front end to Medline known as Grateful Med that both simplifies
and streamlines personal use of Medline. The OUTPUT file of Grateful
Med can be directly imported to a BiblioFile database without retyping
any entries. The major restriction to this import is the format of the
OUTPUT file. BiblioFile will correctly interpret the format of the
Medline output only; other databases available through Grateful Med
(e.g. TOXLINE) have a different format and cannot be imported. If
there is sufficient demand for other formats, they will be provided in
future releases.

Grateful Med version 4 no longer requires that the results of a
search go to a file named OUTPUT. BiblioFile 3.10 now allows you to
select the file to be used for importing into your database. More on
this below.

You can also use this facility if you can create an OUTPUT file in
the same format as the Grateful Med file. A description of the
expected format is given in Appendix B.

Create the OUTPUT file by performing a Grateful Med search or by
creating a similar format if you are currently using a generalized
database (See Appendix B for the format). The search may include MeSH
headings, abstracts, and/or extra lines before the source line. Copy
the OUTPUT file to the same subdirectory or disk as the BIB.EXE file,
and keeping the name OUTPUT. The OUTPUT file is read but not altered
during the import.

Start BiblioFile, and select the database that will contain the
imported citations. Select option 5 "Import from Grateful Med" from
the main menu.

Bib will first verify that you intend to do an import. If you do,
the first window of the subject tree will appear. Beginning with Bib
3.10, you can direct the contents of the Grateful Med file to any level
of your subject tree. Select the desired category by highlighting it
with the arrow keys, and press .

Next, you will be asked to indicate what data file the information
should be read from. All available files that have no extension will
be displayed. Select the desired file by highlighting it with the
arrow keys, and press .

From that point on, all operations are automatic. The screen will
display the current operations (Reading, Parsing, and Writing), as well
as the line number of the data file being processed. Any citations
which cannot be processed accurately are appended to a PROBLEMS file,
an error message appears on the screen, and a more specific message is
printed on the printer. Experience has indicated that less than 1% of
the citations will fail importation, but these can be entered manually
after examining the PROBLEMS file.

If any of the imported citations do not properly belong to the
selected subject, reclassify them into their correct locations by
selecting option 2 "Subject Entry" from the main menu, highlighting the
subject containing the imported data, and pressing to begin
Reclassification of the citations. See Reclassification, above, for a
more complete description of the procedure.


Creating a new output format file:

The current version of BiblioFile allows you to control which
fields are printed to a text file, or to the printer. In addition, you
can control what punctuation, words or characters, if any, should be
placed before and after the various fields.

To create the file used to control this output, select option 7,
"Generate File/Printer Format". A window will appear asking for the
name of the new format file. Type the name of a new file, and press
. If the file already exists, you will be asked for a unique
filename. A new window will appear containing all of the field
elements which may be printed. Select which elements you want to
print, in the order in which you want them printed. For example, if
the authors should be printed first, move the cursor to the Author
element and press .

As each element is selected, additional windows will open asking for
any characters or punctuation that should be printed before, and after
the selected element. For authors, there is a third window asking for
the punctuation and characters that should be printed between multiple
authors. Beginning with release 3.10, BiblioFile will now accept a "{"
character in the punctuation field. This will be interpreted as a
carriage return/line feed combination when the citations are printed.
This allows individual fields to be isolated on single lines if
desired.

The Parameter window will reappear to allow you to select the next
element to be printed. If you don't want the output to contain one or
more of the elements, don't select them from the Parameter window.
When all desired parameters have been selected, press the key at
the parameter window to save the file and complete the session.

Any format files which are no longer needed can be deleted from the
DOS command line at any time. All format files end in the extension
".FMT".


Utility programs:
The BiblioFile utility programs are contained in the BIBUTIL.EXE
file. Dual floppy system users should place the second floppy created
during installation into drive A for the utilities. Type BIBUTIL from
the DOS command line and press to begin execution.

Three utility programs are provided to allow primary entry, editing
or deleting of the journal name, author name and key word text
entries. All three of these utilities are similar in function, and
provide the capacity to list, enter, edit, or deactivate entries.

One common feature of these utilities is that entries are in fact
deactivated and not deleted. This provides the capacity to continue
to look up previous data entered using any deactivated entry, but you
can no longer use that entry in a new citation added to the system.

All of these utility functions may be used to enter data into the
system. Although they may be used as stand-alones, you will probably
add entries to all three of these files automatically during citation
entry. The utilities are most useful for editing spelling previously
entered by any mechanism, as well as generating a list of entries in
the file sorted in any of three ways.

In addition, all of these utilities provide the capacity to rebuild
the index files into any of these data files.


Duplicate citation deletion:

Large databases may have duplicate citations in the same subject,
especially if the automatic importation feature is used. BiblioFile
contains an automatic duplicate deletion utility that can be invoked
from the utility menu. As usual, be sure you have a backup copy of
you BiblioFile data files before you begin this procedure.

Invoke the deletion utility by selecting option 5 from the Utility
menu. The screen will display the list of current databases. Move the
light bar to the database and press . The screen will display
each of the subject headings and a series of "."s to indicate records
scanned. Dots displayed in reverse video represent duplicates that are
being deleted.


Deleting a currently active database:

At some point it may be desirable to remove a database from the
active list. To accomplish this two steps are required. First, select
option 6 from the BiblioFile Utilities menu.

The list of currently active databases will be displayed. Move to
the desired database by using the up or down arrow keys, and press
when the appropriate database is highlighted. A verification
window will be displayed at this time. If you press "Y", the database
will be removed from the list of active databases, however the
database files themselves have not yet been deleted.

The second step in the deletion process is to erase all of the data
files for this particular database. On a floppy drive system you will
need to place the data disk in drive B. On the DOS command line type
the word DEL followed by the name of the database to be deleted and
".*". For example if your database was named "PC", you would type
"DEL PC.*" (without the quotes). This will delete all the data files
from the data disk.

This two step process is intentionally designed to make accidental
deletion of data difficult. If you are using a floppy drive system,
you should copy the DBLIST file from this disk to the primary system
disk after completing the deletions.


Changing the colors used by BiblioFile:
(Creating the CONTROL file)

The video colors used by the BiblioFile system may be modified at
any time by the user. This may be accomplished by selecting option 7
from the BiblioFile Utilities menu.

The screen will clear and display an initial blue background with
bright white letters. You should cycle through the available colors of
the foreground by pressing the space bar until the desired color is
displayed on the screen. With each screen pressed, the current
foreground color of text is displayed. When an appropriate color is
displayed, press the C key to continue.

A similar procedure should be followed for selection of the
background color as well as the selected text color. A CONTROL file on
the main program disk will be updated by VSET for use the next time
BiblioFile is used.

This may be used by anyone with a color monitor of any type
including the VGA monitor on PS/2 computers. It may also be necessary
to invoke this function if you are using a monochrome monitor such as a
COMPAQ which displays various shades of green or amber rather than a
particular color. The colors can be reset at any time without damage
to the database.

Invoking the video option on a system with a monochrome text
adapter will create a CONTROL file with "white" letters on a black
background. No color selection will be offered. If the Control file
created does not look appealing, rename the CONTROL.MNO file on the
distribution disk to CONTROL and try that one.

If you are using a dual floppy system, copy the CONTROL file created
by this option to the primary system disk as well.Appendix A
Converting From BiblioFile Prior to 2.51

Beginning with BiblioFile 2.51, up to 20 authors can be included in
each citation. Unfortunately, this meant adding a new data field to
the citation record, and requires a conversion of all data files with
extension ".CIT" from versions of Bib prior to 2.51. The conversion
program, BIBCONV, is included in this package.

To run BIBCONV, copy it to the drive or directory where your
BIB.EXE file is located. BIBCONV must be on the same drive or
directory as your DBLIST file to work correctly.

PLEASE, work from a backup copy of your database !

For floppy system users, note that your data drive must have
slightly more free space available than your ".CIT" file currently
occupies. It may be necessary to temporarily copy the ".CIT" file
(only) to another floppy drive, do the conversion, then copy the ".CIT"
file back to its original floppy. This strategy will give you enough
room on the floppy containing only the ".CIT"; only the one file is
modified during the conversion.

Begin the conversion by typing BIBCONV at the DOS command prompt.
A list of all currently active databases will appear on the screen just
as they do when you are running BiblioFile. Select the appropriate
database by moving the cursor to that name with the arrow keys and
press . The screen will display the number of records to be
translated, and the status of the conversion.

When the conversion has completed, the screen will clear, and the
DOS prompt will appear. Your database is now ready to work with the
latest version of BiblioFile. You can add more authors to current
citations if you wish, or just begin adding more authors from newly
added citations. If you don't put more than 2 authors into a
citation, no additional space is used in your datafiles.Appendix B
Format Required in OUTPUT to use the Import Facility

The Grateful Med citations are always written to a file named
OUTPUT, and that's what Bib expects to find. To use the Import
facility, create an ASCII text file from your current database in the
following format:

1
UI - 88260958
AU - Barnett GO
AU - Justice N
AU - Souder DE
TI - An operational ambulatory medical record system.
SO - Methods Inf Med Suppl 1976;10:41-50

2
UI - 88246180
AU - Grossman JH
TI - An ambulatory medical record system for patient care and health
care management.
SO - Methods Inf Med Suppl 1972;6:375-82

3
UI - 88231910
AU - Shapiro AR
TI - Exploratory analysis of the medical record.
SO - Med Inf (Lond) 1983 Jul-Sep;8(3):163-71

The key features as far as Bib's parsing is concerned are: the "UI
- " that indicates the start of a citation, and the other line
prefixes.

The number after the "UI - " is optional but the dash and spaces
must be there as shown on this and all the lines after the line
prefixes. Bib uses the "UI" line to mark the beginning of a new
citation. The number preceding the UI line doesn't need to be there;
Bib ignores it scanning for UI.

The next most important item is the format of the Source (SO - )
line: Journal abbreviation followed by a space, the year, followed by a
semicolon, the volume (with or without issue, its a text field)
followed by a colon, beginning page, a dash, and ending page. The dash
and ending page are optional.

The title may be more than one line, and spacing (shown in citation
2) is immaterial. Bib deletes all the extra spaces as it imports. You
may have up to 20 authors per citation, each on one line. Punctuation
on the author line optional, and will be retained.

After creating your OUTPUT file, place it in the same subdirectory
as BIB.EXE, start Bib and select "Import" from the main menu.Index

Adding subheadings . . . . . . . . . . . . . . . . . . . . . . . . . 8
Additional authors . . . . . . . . . . . . . . . . . . . . . . 11, 15
BIBCONV . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1, 20
BUFFERS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Changing the colors . . . . . . . . . . . . . . . . . . . . . . . . 19
CIS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Citation entry edit or deletion . . . . . . . . . . . . . . . . . . 11
Comments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
CONFIG.SYS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
CONTROL file . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Converting pre-2.51 datafiles . . . . . . . . . . . . . . . . . . . 20
Cut and paste . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Deleting a data base . . . . . . . . . . . . . . . . . . . . . . . 18
Deleting subject headings . . . . . . . . . . . . . . . . . . . . . . 9
DISCLAIMER . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
DISTRIBUTION RIGHTS . . . . . . . . . . . . . . . . . . . . . . . . . 4
Dual floppy system . . . . . . . . . . . . . . . . . . 5, 7, 8, 18, 19
Duplicate citation deletion . . . . . . . . . . . . . . . . . . . . 18
Editing Current citations . . . . . . . . . . . . . . . . . . . . . 13
Editing subject headings . . . . . . . . . . . . . . . . . . . . . . 9
et al. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Extended Search . . . . . . . . . . . . . . . . . . . . . . . . . . 14
FILES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2, 5
Format File . . . . . . . . . . . . . . . . . . . . . . . . . . 15, 17
General features . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Generate File/Printer Format . . . . . . . . . . . . . . . . . . . 17
GENESIS PROJECT . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
GETTING STARTED . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Grateful Med
Format of OUTPUT File . . . . . . . . . . . . . . . . . . . . . 21
Importing citations from . . . . . . . . . . . . . . . . . . . . 15
Grav Marks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7, 12, 14
Import File Format . . . . . . . . . . . . . . . . . . . . . . . . 21
Import from Grateful Med . . . . . . . . . . . . . . . . . . . . . 15
Listing the subject tree . . . . . . . . . . . . . . . . . . . . . 10
Making a new data base . . . . . . . . . . . . . . . . . . . . . . . 7
Numbering citations . . . . . . . . . . . . . . . . . . . . . . . . 14
OUTPUT file
from Grateful Med . . . . . . . . . . . . . . . . . . . . . . . 15
OUTPUT File Format . . . . . . . . . . . . . . . . . . . . . . . . 21
Picking a Data Base . . . . . . . . . . . . . . . . . . . . . . . . . 8
PURPOSE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Reclassification
Undo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Reclassification of citations by subject . . . . . . . . . . . . . . 9
Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Sentinel article . . . . . . . . . . . . . . . . . . . . . . . 12, 14
Sort criteria . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Starting Biblio-File . . . . . . . . . . . . . . . . . . . . . . . . 7
Subject Entry . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Adding subheadings . . . . . . . . . . . . . . . . . . . . . . . . 8
Deleting subject headings . . . . . . . . . . . . . . . . . . . . 9
Editing subject headings . . . . . . . . . . . . . . . . . . . . . 9
Listing the subject tree . . . . . . . . . . . . . . . . . . . . 10
Reclassification of citations by subject . . . . . . . . . . . . . 9
SYSTEM REQUIREMENTS . . . . . . . . . . . . . . . . . . . . . . . . . 4
Text File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Umlauts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Undo Reclassification . . . . . . . . . . . . . . . . . . . . . . . 10
Utility programs . . . . . . . . . . . . . . . . . . . . . . . . . 17
Video colors . . . . . . . . . . . . . . . . . . . . . . . . . . . 19