Zotero Kindle workflow?

mangen
I love Zotero and am thinking about getting a new Kindle. Anyone have a Kindle, and willing to share some insight on the workflow of syncing files between the Kindle and Zotero?

Is batch syncing possible? Will it have to be done manually, file by file?

Being able to use Zotero is a core consideration for which reader I ultimately purchase...

Thanks!
  • noksagt
    Zotero, itself, does not interact with e-readers. It is not likely to in the near future either.

    Zotero, itself, has a unique directory structure to store PDFs. You can use searches and virtual folders to place ALL of your PDFs in a single directory to place on your kindle or can export a subset of your collection manually. There is no automated way now to export a subset of your library in a way that would be easy to place on the device, but one might imagine a future (probably third-party) extension to Zotero that would allow this.

    I am not sure how you'd get that folder of PDFs onto the Kindle. You can certainly do it manually, but I don't know if there is a kindle utility that would let you do it in an automated way. The popular 'calibre' has a separate library structure & database structure, for example.
    Is batch syncing possible? Will it have to be done manually, file by file?
    You could initiate a transfer of multiple files to the device manually (which is a bit better than file-by-file), but I have no clue if you can automate it.
  • mangen
    Thanks for the info.

    "There is no automated way now to export a subset of your library in a way that would be easy to place on the device, but one might imagine a future (probably third-party) extension to Zotero that would allow this."

    I'm not a programmer, but am very interested in helping create such a Zotero extension. What might I be able to do to help such development along? Reading the forums, etc. I get the sense that there is a widespread desire for this kind of extension for multiple platforms...

    The Kindle is not ideal, but it does work on several fronts. Open is always preferable and the e-book DRMs are maddening. The Adam looks good, but who knows when that is coming out, and how much it will cost...

    Anyone have strong opinions on what's the best reader to use with Zotero?
  • adamsmith
    about reader - as much as it pains me (as a dedicated apple un-enthusiast) to say, people seem quite happy combining the ipad and iAnnotate with Zotero. There is a thread on the forum and a blogpost about that somewhere. Obviously no e-ink there, though.

    about plugin development - the problem is that there is probably no way such a plugin could earn money worth the developer's time, so the likely solutions are a) a developer who would like the functionality for him/herself (cf. e.g. the awesome Zotero Quicklook plugin) or the makers of the device themselves - I think that's looking bad for the Kindle because they don't have an app concept if I understand that correctly.
  • noksagt
    I'm not a programmer, but am very interested in helping create such a Zotero extension. What might I be able to do to help such development along?
    It depends on what level of interest you have and what you are able to give. Offhand, I'd say you have two obvious choices. You can either try to learn how to program it yourself or try to recruit someone who already knows how to program to do this for you (either by providing a financial incentive or by showing them that there is some other incentive (such as the potential use by enough people who would express enough gratitude)).
    Anyone have strong opinions on what's the best reader to use with Zotero?
    I'm a huge fan of Zotero & a moderate fan of e-readers, but I would not personally order a device based on the use with Zotero. This is because I don't want to sync my entire library of PDFs with my Kindle, am not motivated to write or wait for a Zotero extension that would manage a subset of the PDFs in an automated fashion, and figure that having to handle this manually makes other factors more important. Another good reason is that the content I have had on my previous Reader has not been a subset of my Zotero library. There is some overlap, but most content is exclusive to one-or-the-other.

    However, assuming you wanted to choose a reader based on Zotero and assuming that you did have some extension that would automatically sync a subset of Zotero documents with a separate directory to sync with your ebook reader, you could choose the reader based on a few things: the ability to read the formats you keep in your library (for me, this would mean the reader that was best able to support PDFs (though some users may prioritize HTML or even other formats to have greater performance)) and the ability to automatically sync that with your device. For this latter point, you'd look for a device with software that could have one or more "watch folders" (and I haven't a clue which do) or perhaps one that had superior support for some open distribution format, such as OPDS (which I think the Kindle lacks).
  • noksagt
    edited August 5, 2010
    I think that's looking bad for the Kindle because they don't have an app concept if I understand that correctly.
    Just to be clear: I was encouraging the writing of a Zotero-specific plugin, since that would have the benefit of supporting the users of many different devices (and others who may want to sync/manage only a subset of their attachments) & because I really see no other way you'd be able to define the subset of references from zotero. In such a case, I think there is nearly equal (and ZERO) motivation for any developer of reader software to do this: again, the overlap of their specific-device-using customers and zotero-users is small.
  • mangen
    Yeah, I've read the raves about the iPad. I just don't want to get stuck in the stack. And, until the price comes down...

    Maybe once the Zotero standalone app is released, something will give. I'm in Android on my mobile and am very pleased with the apps that have come from that space. I'm hopeful that a standalone Zotero app + an Android reader will spur some development that will erase (or at least ease) all the workflow roundabouts.
  • mangen
    Watch folder! That just might be an answer...
    Thanks!
  • novosad
    I currently use the Kindle to read pdf files, and Zotero for citation management. I don't think it would be too difficult to make these work together, although I don't have the time or experience with extensions to do it myself.

    The functionality I desire would be to send pdf files from Zotero to Kindle, and then sync notes taken on the Kindle back to the Zotero citations.

    Kindle -> Zotero
    The Kindle stores annotations in a plain text file "clippings.txt" which is in a standard folder when the Kindle is attached to the computer. It would be relatively easy for Zotero to parse this file and add the notes o the appropriate citations.

    Zotero -> Kindle
    To get pdf files from Zotero to Kindle, they can be copied into a folder when the Kindle is attached, or emailed to <username>@kindle.com. I haven't found a Zotero option to export pdfs from a bunch of selected citations (either into a folder or by email), but I'm sure this would be easy to implement.

    Clearly one could do a lot more with these two applications, but the above would be pretty simple to code and would add a lot of functionality.
  • noksagt
    edited November 18, 2010
    It would be relatively easy for Zotero to parse this file and add the notes o the appropriate citations.
    How would Zotero know which reference to add which annotation to?
    To get pdf files from Zotero to Kindle, they can be copied into a folder when the Kindle is attached
    Click-and-drag would work then.
    or emailed to <username>@kindle.com
    Cross-client/platform email is not easy (and has been discussed previously). Assuming gmail may be easier.
  • novosad
    > How would Zotero know which reference to add which annotation to?

    Zotero already can name pdf files based on the parent reference. Zotero could either assume that the pdf filename matches a citation, or it could search for a matching filename. (The former seems a better approach since many documents default to names like "JSTOR Document1.pdf".)

    > Click-and-drag would work then.

    Indeed.
  • playagiron
    I know this is an old thread but I am surprised there is not much interest in makine ebookreaders work with zotero.

    I just got my Kindle and its really nice, and feasible with academic papers to some point.

    So far I export them manually and use BRISS (http://sourceforge.net/projects/briss/) to automatically cut the margins so it is much more readable on 6 inch.

    What I could imagine to be a perfect workflow (IMHO obviously) would be an option to

    1) select a subcollection or collection
    2) Export the pdfs in a new folder whereby they get renamed by the parent data
    3) run the command line version of BRISS to automatically remove the white borders

    This would give an awesome way of getting all the papers you need for a given project at once and have them on your kindle.

    Any other ideas or experiences of how to improve the workflow? WOuld be interested to hear other users best practices!!!
  • adamsmith
    see this:
    http://groups.google.com/group/zotero-dev/t/a4dd735780524305
    and also see the newest version of Zotfile reader, either of which should make this much easier.
    Neither includes BRISS, but that could likely be added with relative ease to the workflow.
  • Nosnorad
    Hi,
    I know this is a very old post, but I wonder if anyone has worked out a good add on to make kindle reader work with zotero, along the lines of what Novosad suggested.
    Thank you for any information.
    David
  • adamsmith
    edited September 20, 2012
    Look at this - it has an option to push files to/from a tablet that doesn't require anything on the tablet's side, i.e. would work with Kindle et al.
    http://www.columbia.edu/~jpl2136/zotfile.html
  • Nosnorad
    Amazing! At first glance this looks exactly like what I'm looking for. Thank you Mr. Smith!
  • svidd
    As far as I understand, Zotfile does not work with Kindle e-readers (only Fire tablets). Does anybody know of something similar for Kindle?
  • adamsmith
    well, you can set a folder on the Kindle as the ZotFile Tablet folder - you just have to have it connected when you push the files to the tablet.

    AFAIK there is no easy way to syncronize PDFs with the Kindle reader via the internet (along the lines of dropbox, sugarync, etc.), so it lacks even the basic infrastructure to automate this.
  • svidd
    Interesting. But is that push only, or can it also sync the annotations I make on Kindle?

    If it can't sync annotations, I'd still be interested in alternatives, so I can get that functionality.
  • adamsmith
    no, it can't sync or read kindle annotations. I am not aware of any tool that syncs or reads Kindle annotations.
  • duncdrum
    http://michaelhyatt.com/how-to-get-your-kindle-highlights-into-evernote.html

    Not sure if this will do. I use this method to copy my annotations into Zotero. A not too cumbersome way to get all my annotations and quotations into zotero.

    Maybe in the long run, based on the id of the kindle version of a book, and personal log-in info, it could be streamlined further?
  • playagiron
    Hi,

    just if someone is interested: As for optimizing the workflow zotero => zotfile => Kindle I needed to integrate BRISS into the equation since the 6 inch readers get too cumbersome to read with the borders. Since I cannot seem to find a way to include it directly into zotfile, I went with a small batch script.

    Let's say you have a folder /Kindle which you set in zotfile options as your table (be it on the table directly or on your PC still, one folder above I put the briss-09 folder and the following file named briss.sh

    ls Kindle/ > files.txt
    cat files.txt | while read k1; do
    java -jar briss-0.9/briss-0.9.jar -s "Kindle/$k1" -d "Kindle/$k1"
    done


    Basically it creates a list of all PDFs in the directory and runs the briss command saving it under the same name (if you leave out the -d.... option, it will be as standard saved as filename_cropped.pdf


    So now my workflow is
    1) Select files in zotero, Send to Tablet
    2) Under Windows, use Cygwin, in Linux just the console, launch the script via "sh briss.sh"
    (I created an alias in the .bashrc configuration file as
    "alias briss="cd /cygdrive/d/Dropbox/Professional/zotero | sh briss.sh"
    soi I only need to type briss.
    Then finally move the files from the folder onto the Kindle.
    Just in case it halps someone to do batch briss pdf cropping.
  • Armaydie
    edited February 17, 2015
    Zutilo seems to do things with pdf read on kindle.

    "I think that's looking bad for the Kindle because they don't have an app concept if I understand that correctly."

    actually apps can be installed on a (jail-broken) kindle https://www.youtube.com/watch?v=46Ygh1cUXAA but unfortunately I did not find any app that would allow to synch kindle highlights to Zotero and to tag the highlight while reading on kindle (that one would be crazily awesome !).

    Since I did not find any solution working with my kindle (Paperwhite 2nd generation) I sold it, and read directly on my computer using adobe digital edition reader (on which it is possible to retrieve the annotation files). I'm still looking for an open source epub reader that would provide a standard way to make its annotation, and that would offer the possibility to synch the book and its annotation between devices.

    --Inconvenient:
    ○ computer reading is not that fun.
    ○ I still have to copy-past the highlights into new Zotero notes and tag them.

    --Advantage:
    ○ I copy past my highlight into Zotero and tag my notes while reading (with the kindle I had to read again everything once in a while to sort and tag my highlight. That was a huge waste of time)

    I have seen several projects on Github that work with RDFa (it allows to store highlights inside an epub3 instead of a separate file), that would maybe be easier for zotero to extract the highlights. But the tag problem remains. A solution would be to incorporate in zotero an epub reader, to be able to tag-sort the highlights.

    EDIT: it is possible when you buy your book through amazon for your kindle to export your highlights to zotero, but not not if your highlights are made on personal documents (in this case this won't work https://tubarks.wordpress.com/2013/01/10/kindle-and-zotero-a-great-match/ )
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