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Internet citations

Clint Chapple chapple at biochem.purdue.edu
Tue Aug 13 16:20:45 EST 1996


For those of you who might be interested in the question I recently posted
to the newsgroup concerning whether it is acceptable to reference WWW sites,
here is a summary of the very helpful responses I received.  Apparently, it
seems only to be a question of how to do it (i.e. punctuation) rather than
whether or not you CAN do it.

Also, for those of you who might be specifically interested in the issue of
intron/exon boundaries in Arabidopsis, you might like to check John Brown's
response, which is the last response included.

Thanks to all of those who responded.

Clint Chapple

*******************

My understanding is that journals are accepting URLs as
references to pieces of information that are only distributed
electronically. My impression has been that the references
to electronic information are written in the same way as a personal
communication ie in brackets after the statement about the
information, rather than as a reference per se.

However, that is not true in all cases. For instance, if you were
to site something from Weeds World, since it has an ISSN
number it would be written in the reference section with
year, Vol and page numbers.

Best wishes

Mary Anderson
Editor, Weeds World

********************

Dear Clint - 

I'm in the same situation - I recently wrote a manuscript in which I cited
Caroline Dean's lates RI map on the Web.  We'll see what the editors think
about it.

Daphne

=======================================================================
 Daphne Preuss                                 Tel: (312) 702-1605
 University of Chicago                    Fax: (312) 702-9270
 Department of Molecular Genetics and Cell Biology
 1103 E. 57th Street - EBC Room 304
 Chicago, IL  60637             dpreuss at midway.uchicago.edu
=======================================================================

********************

I referenced the map postition of two new genes I isolated and mapped on
the Lister and Dean RI lines as an internet address.  I used the wording
"accessible at
http://probe.nalusda.gov:8300/cgi-bin/dbrun/aatdb?find+Map+Recombinant_Inbre
d*)"   Despite this long gory address, the Plant Cell let me do it!  (PC 8,
241-249)  I think such references will be necessary more and more often, as
more large data compilations are available only on the Web.

Lynne Reuber

********************

We have a paper coming out in next month's Plant Phys in which we cite a 
"paper" in Weeds World (on the TIGR database).  We treated it like a 
regular journal citation, and apparently Plant Phys was OK with that.

Julia Frugoli
Dartmouth College

visiting grad student at
Texas A&M University
Department of Biological Sciences
College Station, TX 77843
409-845-0663
FAX 409-847-8805

********************

Dear Clint,

Personally, I like your suggestion of citing the Stanford http site.  I did so
myself in a chapter I just wrote for a book.  

I also cited Rounsley et al's Weeds World paper in a paper I have in press at
Plant Physiol.  I was tickled to have an excuse to cite Weeds World.  I don't
know if it is legitimate, but no-one has complained or suggested otherwise (and
the proofs have gone through), so I guess one can do it.

Rob McClung

********************

I have seen a few URLs citations in Science papers, I cannot remember 
which but I think it is becoming a norm.
DB

----------------------------------------------------------------
Dmitry A. Belostotsky
Assistant Professor

Department of Biological Sciences
State University of New York at Albany
1400 Washington Ave.
Albany NY 12222
Tel. (518) 442 4368
FAX  (518) 442 4767
E-mail dab at cnsvax.albany.edu
http://barbara.bio.albany.edu/~dab/
----------------------------------------------------------------

********************

Dear Clint,

Thanks for the ad for AtDB!  Just a few quick points:

The splice-site consensus data in AtDB is somewhat out-of-date. It was
generated from all Arabidopsis data in GenBank at that time. (I'm sure
Mike Cherry could give you more details, should you require them, as he
construted the tables. Mike can be reached at cherry at genome.stanford.edu)

We, and other Arabidopsis Web-sites, such as the Nottingham Arabidopsis
Stock Centre, have already been used as citations for data relating to
papers, notably the two chromosome four physical-mapping papers from
Renate Schmidt, Caroline Dean, et al. Indeed, for their Science paper, it
is my understanding that they were forced into doing this as the journal
wouldn't allow them the space to publish all the data. 

I agree that the potential ephemeral nature of Web sites presents a
problem, but this something that is going to have to be faced by the
scientific (and other) communities in general. As information becomes
easier and quicker to distribute it expands and "keeping track" becomes a
problem. 

As to Weeds World, Mary Anderson had the foresight to get an ISSN number
for it. This makes it an "official" publication. As it's non-refereed, I
would say that this makes it equivalent to say, a book chapter, but I'm
sure you'll hear more details from her. 

Best regards

David F.

-------------------------------------------------------------------------------
David Flanders                   flanders at genome.stanford.edu
AtDB Curator			 http://genome-www.stanford.edu/
Dept. of Genetics                FAX: +1-415-723 7016
School of Medicine               Tel: +1-415-725 3062 (direct)
Stanford University
Stanford
CA 94305-5120			 
U.S.A.				 
-------------------------------------------------------------------------------

********************

Dear Clint,
To get around your question you might be interested to know that a 
corrected version of the Arabidopsis intron consensus sequences will 
appear in Plant Molecular Biology soon.  The consensus on the 
database contained numerous errors which we and another group 
realised.  I haven't looked recently at the consensus so I don't know 
if it has been changed yet.  If you wish I can send you a reprint of 
our paper.

Yours,

John
Dr. John W. S. Brown,
Cell and Molecular Genetics,
Scottish Crop research Institute,
Invergowrie,
Dundee DD2 5DA,
Scotland, UK.

E-mail:  cmgjb at scri.sari.ac.uk
FAX:     +44-1382-562426
Tel:     +44-1382-562731   Ext. 2004

*********************

Clint Chapple
Department of Biochemistry
Purdue University
West Lafayette, IN
47907-1153

TEL:	317-494-0494
FAX:	317-496-1641 or 317-497-7897




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