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Re: [O] zotero (or mendeley) integration with org

From: Ramon Diaz-Uriarte
Subject: Re: [O] zotero (or mendeley) integration with org
Date: Sat, 26 Mar 2011 22:06:47 +0100

Dear Stephen,

[My ---long--- comments refer only to Mendeley, not org, so maybe this
should be off-list].

On Sat, Mar 26, 2011 at 4:47 PM, Stephen Eglen
<address@hidden> wrote:
> There was a mail-thread lastyear about zotero and integration with org.
> Now that there is an alpha release of 'org-standalone'
>  http://www.zotero.org/blog/2011/02/
> has anyone looked at whether this helps integrate org and zotero?
> I've not yet switched to a pdf manager (they're all stuffed into a
> folder, with a few subfolders, and the only meta-data is in the
> filename!), so I'd appreciate hearing what others to do to look after
> their pdfs.  Mendeley is a possibility too (although syncing between
> machines is a must, and Mendeley doesn't offer that yet.)

I've been using Mendeley for about 9 months now, after spending a few
weeks examining how Mendeley, Zotero, and some other options, fitted
into my habits. Here are some comments about your questions:

1. Syncing: the "orthodox" Mendeley way allows for two options: a) you
sync the database of the refs (not pdfs) via their servers; b) you
also sync the pdfs, which will most likely require you to pay for
storage in their servers if you have a decent number of pdfs.

However, I do the syncing myself. I've used rsync, then Dropbox, and
for the last four months Wuala. I sync the directory where the dbs are
(~/.local/share/data/Mendeley Ltd./Mendeley Desktop) and the directory
where I store my pdfs. I have had this set up for the 9 months, shared
between four machines, and it works fine (I try not to have Mendeley
open in more than one machine at the same time, to prevent problems,
but have never run into any).

2. All pdfs into a folder with a few subfolders. In Mendeley you can
have each reference under its own subdirectory with some limited
flexibility for the naming of the subdirectories (author, date, title,
etc). Its not ideal (e.g., I dislike spaces in directory names), but I
like it better than Zotero's (names of subdirectories are a random
string). Keeping each ref in its own directory allows me to store
other stuff (e.g., code, suppl. mat, etc) in the same place as the

Now, that said, I am not all that happy with Mendeley.

To begin with, Mendeley is not free software. Zotero is, but the
naming of directories and the lack of a built-in pdf editor were a
no-go for me.

Mendeley's pdf editor allows me to underline and add notes to pdfs. At
least in Linux, adding comments and underlining pdfs is not yet well
solved: evince currently allows comments in the devel. version, but no
underlining. Okular allows comments and underlining, but stores them
in ~/.kde/share/apps/okular, which I dislike (it seems very fragile),
and in okular you cannot underline a single column in papers with
multi-column setup (another no-go for me).

However, with Mendeley's pdf editor/viewer you can only display one
pdf at a time, which is a pain if you want to compare two or more
papers side by side. In fact, Mendely's pdf viewer is rather
under-powered compared to, say, okular (e.g., lack of keyboard
shortcuts for viewing to page or width size, difference between
scrolling and moving to next page, fast searching, etc). If I only
need read-only access to the pdf, even from within Mendeley, I use
another pdf viewer.

I thought about going back to JabRef, and using recoll for searching
over all of my pdf collection (I like recoll's search much more than
Mendeley's one). But that leaves unsolved the pdf commenting issue.
Also, I like the ease of adding papers with Mendeley (e.g., when
searching in the web, or its generally successful extraction of
metadata from a paper's pdf); in fact, I find adding papers is even
easier with Zotero (and friendlier also if you add things like web
pages, etc). I also looked into paperpile, but I find it to be much
more beta than Mendeley, and so far less flexible in almost

So I'd also like to know how others are dealing with pdfs. Anyway, and
in spite of my complaints, since about 9 months ago I have not printed
a single paper. It is great to have all those pdfs synced among my
machines, be able to search them quickly, and not carry around
kilograms of dead trees.



> Stephen

Ramon Diaz-Uriarte
Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)
Phone: +34-91-732-8000 ext. 3019
Fax: +-34-91-224-6972

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