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General brainstorming for Note-taking software

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Darwin:
One question about Endnote users:
Would you use Endnote for keeping track of your pdf's and documents if you weren't using it for research?  Like, if you didn't already have Endnote for school purposes (or some other academic application) you wouldn't go out and buy it for it's ability to annotate your documents, right?

I'm just trying to get a feel who is using Endnote this way.  In my case, I'd probably go with Surfulater or something a little less expensive, especially if I didn't it for a properly formatted bibliography. 
-superboyac (June 14, 2007, 10:19 AM)
--- End quote ---

No, you're quite right. If I wasn't using it for academic purposes I probably wouldn't even consider Endnote. Which is not to say that I think it's bad and not to say that I'm going to dump it when (if) the PhD (ever) gets finished.

Nod5:
urlwolf,
A possible solution would be to implement fingerprinting for pdf (like what musicIP does) [---] Now we only need someone to code/maintain a central repository of pdf metadata, and mappings fingerprints -> ids.
--- End quote ---
This is a great idea that completely bypasses the need for DOI extraction. One way I can see it happening would be if some popular application like Zotero implemented this as an opt in feature that works automatic in the background. That is, every time someone downloads both article metadata and a pdf through Zotero, Zotero silently uploads pdf fingerprint and matching metadata to some server. As the database grows, downloading just pdf files will be enough since the metadata is already available in the open archive. Zotero seems like the kind of tool that is innovative and community driven enough to be ready to pioneer something like that.

One problem might be related to protected metadata. Some journals require a login just to see the abstracts for instance. So I'm not sure about the legality of storing such abstracts in an alternative, open archive. One way around that would then be to match and archive only pdf fingerprints and DOI numbers and then let Zotero and so on implement some way to later automatically resolve the doi and grab metadata from the resolved article page (including abstract if the user is authenticated to have that displayed). Another advantage with such piggybacking on the DOI system is that that the archive then never risks having outdated article links. Another problem is if journal publishers change the pdf files from time to time. But perhaps that can be solved just by letting the archive match the multiple fingerprints to the same metadata.

edit: great post on Academic Productivity also

Darwin:
urlwolf - I wrote a lengthy reply here AND then went and read your academic productivity blog on the subject. Wow! All I can say is: "what he said". You covered all the bases, well done!

Nod5:
This might be useable for pdf notetaking and archiving: Adobe Digital Editions. Will try it out later myself.
http://www.adobe.com/products/digitaleditions/

http://www.adobe.com/products/digitaleditions/faq/
What is Adobe Digital Editions? Adobe Digital Editions is a new, exciting rich Internet application (RIA) built from the ground up for digital publishing. Digital Editions is a simplified, engaging way to acquire, manage, and consume eBooks and other kinds of digital publications.

Will a Linux version of Digital Editions be available? Yes, a desktop Linux is under development and a public Beta is expected later this year.

What file formats does Digital Editions support? PDF/A and an OPS (enhanced OEBPS, which is a profile of XHTML 1.1 with OCF packaging) are the two publication-level content types. SWF content and common image file types can be referenced within PDF and XHTML-based publications.

What are the Digital Editions annotations capabilities? Digital Editions 1.0 supports bookmarks, highlights, and text notes via its "bookmarks" panel. These annotations are stored in an open XML format separately from publications, in order to enable seamless annotating across PDF and XHTML-based (EPUB) publications, and to set the stage for future social networking features (e.g. sharing annotations within a community of readers).

Darwin:
Interesting find NoD5 - I'll check it out, thanks!

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