Subject: How do you organize your *.pdf files?

From: "Daniel Svozil" <svozil..at..uochb.cas.cz>
Date: Thu, 21 Oct 2004 19:33:23 +0200 (CEST)

Hi all,

though my posting is not only computational chemistry related, I think the
discussion may be of general interest.

I would like to know, if there is any free linux solution that would help
in organizing pdf files with the articles downloaded from the web. I was
looking for some application/script, but I didn't find anything.

My question is, if it is possible to build a database (e.g. BibTeX) of pdf
files (articles) that would include information such as title, author,
journal, abstract etc. + path to the pdf file taken automatically from
*.pdf. It seems to me, that thi is may be even not possible, as pdf format
is not a markup language (as XML) and is not suitable to such a task.
Maybe the best way would be to convert pdf to text (pdftotext in Linux),
and than to parse the text file for the information. But such a script
would be very complicated, as format of text data differs journal from
journal, and many possibilities would have to be taken into account.

I found one free application that makes life with my pdf mess much easier,
it is called Quaneko (http://quaneko.sourceforge.net/), and it is
available both for Linux and Windows. What Quaneko does it takes pdf by
pdf, converts them to text files, and than indexes those, so one can
easily query information using keywords and logical expressions. The
possibility to view a text preview or full pdf by acroread is also
avilable. Quaneko proved to be very useful and I rely on it quite heavy.

And what is the way you organize your pdf articles in computer?

Thanks in advance
  Dan

  P.S.; Please, post your responses to the list, so the whole community
can benefit from them.

-- 
Daniel Svozil, PhD
Institute of Organic Chemistry and Biochemistry
and Center for Complex Molecular Systems and Biomolecules
http://www.molecular.cz/
Czech Republic

phone: +420-220 410 312

---

From: Jeff Nauss <jnauss..at..accelrys.com>
Date: Thu, 21 Oct 2004 13:09:31 -0700

"Computational Chemistry List" <chemistry-request..at..ccl.net> wrote on 

> And what is the way you organize your pdf articles in computer?

For almost 15 years now, I have used a reference manager program.  The 
program indexes each document by a reference number and has associated 
with it information such as author, title, keywords, etc.  I then file 
each document by the index number, whether hard copy or electronic PDF. In 
the reference manager, I can search by keyword, abstract, author, date, 
and so forth.  I get the index number and find the document in my file.

I first used Papyrus which was cheap, easy to use, and pretty good.  But 
it was not maintained well enough with updates to be useful with later 
versions of MS Word.  I switched to EndNote a few years ago and have been 
quite happy with it.

With EndNote I can download PubMed entries directly into the database. You 
can also download information from quite a few other databases as well.

I suppose you could do something similar with a LINUX based database 
manager if not a reference manager program.

Jeff
--
Jeffrey L. Nauss, Ph.D.
Lead Training Scientist

Accelrys
9685 Scranton Road
San Diego, CA 92121-1761

Phone: 858-799-5555
Fax: 858-799-5100
E-mail: jnauss..at..accelrys.com
http://www.accelrys.com/training