bionet.journals.contents to bib reformatting

David Kristofferson kristoff at genbank.bio.net
Tue Sep 3 11:46:29 EST 1991


BIO-JOURNALS/bionet.journals.contents should follow BRS Medline format
(rules below) but unfortunately the ASM journals are in a different
format.  I hope to correct this in the future, but this involves some
wrangling that I don't want to get into at the moment.

				Sincerely,

				Dave Kristofferson
				GenBank Manager

				kristoff at genbank.bio.net

----------------------------------------------------------------------

     Format Rules for BIO-JOURNALS Table of Contents Submissions
     -----------------------------------------------------------

The recommended format for Table of Contents (TOC) submissions to the
BIO-JOURNALS newsgroup is patterned after the BRS Medline format.
First we provide an example and then detailed comments on each field.


AU Santibanez-M.  Rohde-K.
TI A multiple alignment program for protein sequences.
SO Comput-Appl-Biosci.  1987 Jun.  3(2).  P 111-114.


If abstracts are included:

AU Santibanez-M.  Rohde-K.
TI A multiple alignment program for protein sequences.
SO Comput-Appl-Biosci.  1987 Jun.  3(2).  P 111-114.
AB The text of the abstract goes in the AB field and continuation
   lines are formatted like this.


A. Types of Fields
------------------
There are three MANDATORY fields for each reference in the TOC.

	AU - The authors line

	TI - The title line

	SO - The source line

In addition to these fields, the paper's abstract may be optionally
included (AB field).  Comments (e.g., Journal titles, section titles,
etc.) can be included either before or after any reference but not in
between the AU and TI line nor between the TI and SO line of any
entry.

	AB - An optional abstract field.
	CC - An optional comment line

In general, comment lines are for section headings in the TOC, but the
CC identifier must be used to denote any text that is not part of one
of the fout types of fields above.

Each field is defined by its identifier (AU,TI,SO,AB,CC) starting in
column 1 (the left hand column) followed by a space in column 3.  The
text for the field starts in column four and extends no further than
column 80.  If a continuation line(s) is/are needed for the AU, TI,
SO, or AB fields, the text continues in the next line beginning in
column 4.  The AU, TI, SO, and AB identifiers are NOT used on
continuation lines, and the field continues until the following
delimiters are reached:

Field			Delimiter
-----			---------
AU			TI found in columns 1&2 on a later line
TI			SO found in columns 1&2 on a later line
SO			A blank line (<cr> in column 1) OR
			  AB found in columns 1&2 on a later line
AB			A blank line (<cr> in column 1)

CC lines do NOT have continuation lines in the sense defined above.
Any text which is not part of an AU, TI, SO or AB field must be
preceded by CC in columns 1 & 2 regardless of whether or not it is a
continuation of the line immediately above it.


The AU Field.
-------------

Example:	

AU Santibanez-M.  Rohde-K.  Smith-Jr-T-F.  Freeworth-III-F-W-H.
   Santo-Domingo-J-F.  van-Neuman-A-E.

Authors are listed in the order given in the publication.  Last names
are printed first and hyphenated names are allowed as illustrated by
Santo-Domingo above.  Non-hyphenated last names such as van Neuman
above most include a hyphen between the parts of the surname.
Instances of Junior (Jr), Senior (Sr) or II, III, IV, etc., are placed
after the surname and separated by a hyphen from the last name (NOT by
a space; no spaces are allowed within the name of any individual).
Initials come next, and each initial must be separated by a hyphen.
For example, T. F. Smith must be Smith-T-F.  and not Smith-TF.  This
insures that any single character preceded and followed by hyphens (or
followed by a period) is an initial.  Finally, the last initial is
followed by a period ".".  If another name follows, it should be
separated by two spaces from the preceding period.


The TI Field.
-------------

The TI title field contains the title of an article formatted within
the line length and continuation line constraints mentioned above.
The TI field must end with a period ".".  Note that ALL characters in
the TOC (not only in the TI line) must be in the standard 128
character ASCII character set.  Special characters such as Greek
letters must be spelled out whenever possible.  Accent marks such as
umlats over u's should be omitted and the closest ASCII
representation, e.g., a u in this example, should be used.


The SO Field.
-------------

Example:

SO Comput-Appl-Biosci.  1987 Jun 15.  3(2).  P 111-114.

The standard journal abbreviation begins in column 4.  For
abbreviations, see the "Chemical Abstracts Service Source Index" or
"International Serials Catalogue."  Hyphens are used in place of
spaces to connect the various parts of the journal name abbreviation,
and a period is used ONLY at the end of the abbreviation.  Two spaces
are placed after the period at the end of the abbreviation, and then
the complete year (not abbreviated, e.g., 1988, not 88 or '88) is
given.  The year is followed by a single space and then the three
letter abbreviation for the month (Jan, Feb, Mar, Apr, Jun, Jul, Aug,
Sep, Oct, Nov, or Dec).  If only one issue of the journal in question
appears during each month, then the month is followed by a period.  If
multiple issues occur during a month, then the month abbreviation is
followed by a space and then the numerical day of the issue.  The
numerical day is followed by a period.  The period terminating the
date of the issue is then followed by two spaces and then the volume
number.  The volume number is followed immediately by a "(", then the
issue number, and then a ")" and a period.  The period terminating the
volume/issue entry is then followed by two spaces and then a "P", a
space, and then the beginning and ending page numbers of the article
separated by a hyphen as illustrated above.  The ending page number is
terminated by a period.

If abstracts are included, the AB field follows the SO field on the
next line, otherwise a blank line should then follow the SO field
before the start of either the next AU field, or before any CC field,
or before the end of the file.


The AB Field (optional).
------------------------

There are no formatting restrictions on the text of the abstract in an
AB field other than the requirement that each such field begin with AB
in columns 1&2 of the first line, followed by a single space, and then
text (standard ASCII) starting in column 4 and not extending past
column 80.  Continuation lines are blank in columns 1 through 3 with
the characters continuing in columns 4 through 80.  The text in the AB
field must end with a period.


The CC Field (optional).
------------------------

There are no formatting restrictions on text in a CC line other than
the requirement that each such field begin with CC in columns 1&2,
followed by a single space, and then text (standard ASCII) starting in
column 4 and not extending past column 80.  If the CC text must
continue on the following line, this line must also begin with CC in
columns 1&2 and the text continues starting in column 4.  If a CC line
follows an SO field, a blank line should separate the SO field from
the CC line.




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