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Old 06-26-2011, 09:45 PM   #1
houshuang
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Integrating Kindle clippings, DokuWiki and BibDesk for academic notes

Hey guys. I've tied together a bunch of applications (primarily BibDesk, Skim and DokuWiki in Chrome) to come up with a solution for managing and sharing citation metadata, notes, PDFs, etc for my academic readings. Part of the package is automatic syncing with Kindle - I can take documents in BibDesk and automatically send them to Kindle, reformatted and with nice metadata. I can then take notes and highlights on the Kindle, and once I plug in the Kindle in the USB port, it automatically imports all citations into the wiki, and attaches it to the right articles. (Here's an example of a publication that had its highlights automatically imported: http://reganmian.net/wiki/ref%3Aallen2001getting)

I've tried to document it all here http://reganmian.net/wiki/researchr:start

Stian
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Old 06-27-2011, 02:33 AM   #2
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How is this different from going to https://kindle.amazon.com/?

I have other methodological problems with using ebooks in acadamia though, such as: Is a location # in a academic setting going to hold up? As a masters degree student I haven't tried it (although I've read books for school on my kindle, unfortunately), but I think the prof would want something more accessible than a number that is only available on a certain publication from a certain reader and a certain e-edition (which may or may not be available in the next 6 months because of updates or the book being pulled from e-distribution - which happened to one of the books that I purchased).

Those are the reasons I've never used my kindle for academic purposes.
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Old 06-27-2011, 02:50 AM   #3
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Thanks for sharing this. I'm an undergraduate for now. I hope this would help me in the future.
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Old 06-30-2011, 12:25 PM   #4
davekin
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Organizing Notes

Hello All,

I've found an application that may help you: Klippings Kollector. I have been using it for a few days now and its been extremely helpful for oranizing, sorting and printing notes that i take while reading on my kindle. Curious if others have had experience with this tool?

-Dave
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Old 07-01-2011, 10:23 AM   #5
houshuang
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Quote:
Originally Posted by xnowimcoolx View Post
How is this different from going to https://kindle.amazon.com/?

I have other methodological problems with using ebooks in acadamia though, such as: Is a location # in a academic setting going to hold up? As a masters degree student I haven't tried it (although I've read books for school on my kindle, unfortunately), but I think the prof would want something more accessible than a number that is only available on a certain publication from a certain reader and a certain e-edition (which may or may not be available in the next 6 months because of updates or the book being pulled from e-distribution - which happened to one of the books that I purchased).

Those are the reasons I've never used my kindle for academic purposes.
It's different because Amazon only gives you clippings from books you buy on Amazon, whereas most of what I read is papers I download through my library, and which my scripts automatically convert to mobi with proper metadata etc. THen when you import them, they automatically are assigned to the proper citation information.

Since you also have the PDF, and there is a link to open the PDF directly from the wikipage, it's very easy to find out which page a certain citation comes from when you decide to cite it. I am also working on two approaches:

one - find out how to embed page numbers in mobi files (which Amazon now does) when converting from PDF

two - find a way to convert Kindle clippings to highlights in Skim on the PDF (this is easy, if it hadn't been for the fact that through conversion small artefacts are added, so the clipping usually isn't bit for bit identical. need some kind of fuzzy matching algorithm)

(Also, again as a reader of articles, usually you don't need the page number unless it's a direct quote. This might vary by discipline though)
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Old 07-01-2011, 10:42 AM   #6
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That's really cool. Good job!
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Old 11-26-2011, 11:05 PM   #7
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This I am sure will be much useful to many people (I have no info on bibdesk and devonthink though)...

May I ask whether you made any progress in Kindle notes and Skim highlights integration?
(I just found another thread on this topic today, which sounded great... Yet it was posted quite a while ago and I am not sure whether matthewmhv is still working on that...)
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Old 12-02-2011, 12:40 AM   #8
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No progress

I've improved some other aspects of the system, and made it easier to install (still really hard unfortunately), but not really worked on this. Since I export both Skim notes and Kindle notes to my wiki, it wasn't ever very important. Just would have been neat.

I tried doing what that other link is trying, my problem is that in converting the PDFs to text, the text would often be slightly mangled, page numbers would end up in the middle of the page etc, so the clippings wouldn't match perfectly with Skim. Skim also won't search or create highlights across page gaps... So I was trying to do something quite fancy to get across this with hinged on collapsing all the text, but making note of where the page gaps where, doing a fuzzy search of the clipping, expanding etc. But I could never find a fuzzy algorithm for Ruby that worked (the ones I found all focused on matching a word from a dictionary, not matching a substring and finding its location).

Unfortunately Amazon doesn't seem at all interested in expanding the functionality of the Kindle, unless it makes you buy more books from Amazon.com. A friend of mine is using a Nook with Android to read PDFs, it has Skim on the device. Although I love e-ink screens I think an integrated app that let's you read the PDFs on various devices and keeps track of annotations etc is the future...

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Old 12-10-2011, 02:31 PM   #9
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Many thanks houshang, even if it did not work out, exporting all to wiki is a great "alternative."

What you said about nook and skim is exciting in itself as well! I assume you mean the Nook color/ or tablet; but having Skim on a tablet too sounds wonderful. I never heard that this was possible. May I ask whether you know how he managed to do that?
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Old 12-16-2011, 08:15 AM   #10
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I use the Kindle, and have some scripts converting from the My Clippings file to the wiki. A friend of mine uses a jailbroken Nook which has had "real Android" installed, and uses a tool called RepliGo to read and highlight PDFs - she really likes it. When she transfers files back to the computer, she can use "Convert highlights" in Skim to convert Adobe highlights into Skim highlights that can be exported.
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Old 02-26-2012, 09:09 AM   #11
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in my case, I usually use the export&convert and upload to evernote function combination of http://clippingsconverter.com. well, I'm not a very tech savvy person so I prefer possibly simpler and easier options.
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