Comments on: Organizing PDFs & Papers http://www.thepowerofgoo.net/2007/05/20/organizing-pdfs-papers/ exploring high-performance soot and other interesting polymers Sat, 19 Jul 2008 07:48:04 +0000 http://wordpress.org/?v=2.5.1 By: Simon Gadbois http://www.thepowerofgoo.net/2007/05/20/organizing-pdfs-papers/#comment-3230 Simon Gadbois Sun, 02 Mar 2008 00:55:37 +0000 http://www.thepowerofgoo.net/2007/05/20/organizing-pdfs-papers/#comment-3230 <p>Hi,</p> <p>The link for MacScience seems broken: here is the address:</p> <p>www.macscience.net</p> <p>Cheers,</p> <p>S. Gadbois MacScience.net</p> Hi,

The link for MacScience seems broken: here is the address:

http://www.macscience.net

Cheers,

S. Gadbois
MacScience.net

]]> By: kayesdee http://www.thepowerofgoo.net/2007/05/20/organizing-pdfs-papers/#comment-1785 kayesdee Tue, 09 Oct 2007 18:30:15 +0000 http://www.thepowerofgoo.net/2007/05/20/organizing-pdfs-papers/#comment-1785 <p>Check out http://sararah.livejournal.com/294817.html for some more takes on this, especially some notes about the mac software "papers".</p> Check out http://sararah.livejournal.com/294817.html for some more takes on this, especially some notes about the mac software “papers”.

]]> By: kayesdee http://www.thepowerofgoo.net/2007/05/20/organizing-pdfs-papers/#comment-592 kayesdee Mon, 21 May 2007 18:14:12 +0000 http://www.thepowerofgoo.net/2007/05/20/organizing-pdfs-papers/#comment-592 <p>Kutti: done. Sorry for the confusion. Long live the typo!</p> Kutti: done. Sorry for the confusion. Long live the typo!

]]> By: Kutti http://www.thepowerofgoo.net/2007/05/20/organizing-pdfs-papers/#comment-591 Kutti Mon, 21 May 2007 18:11:09 +0000 http://www.thepowerofgoo.net/2007/05/20/organizing-pdfs-papers/#comment-591 <p>@kayesdee: Would you kindly change my name from "Kutto" to KUTTI in your post? I don´t want this typing error to spread (see entry in Mining Drug Space). Aarrghh! ;)</p> @kayesdee: Would you kindly change my name from “Kutto” to KUTTI in your post? I don´t want this typing error to spread (see entry in Mining Drug Space). Aarrghh! ;)

]]> By: Mining Drug Space http://www.thepowerofgoo.net/2007/05/20/organizing-pdfs-papers/#comment-585 Mining Drug Space Mon, 21 May 2007 08:59:21 +0000 http://www.thepowerofgoo.net/2007/05/20/organizing-pdfs-papers/#comment-585 <p><strong>Literature management...</strong></p> <p>...</p> Literature management…

…

]]> By: kayesdee http://www.thepowerofgoo.net/2007/05/20/organizing-pdfs-papers/#comment-584 kayesdee Mon, 21 May 2007 08:56:54 +0000 http://www.thepowerofgoo.net/2007/05/20/organizing-pdfs-papers/#comment-584 <p>CiteULike is great, too! Especially since you can import and export to bibtex! I believe the bookmarklet assists you in filling in the meta-data, but does it work with all journals? Maybe there are some problems with SciFinder-setups that don't work via the publisher's web pages, but rather directly link to the pdfs.?!</p> CiteULike is great, too! Especially since you can import and export to bibtex! I believe the bookmarklet assists you in filling in the meta-data, but does it work with all journals? Maybe there are some problems with SciFinder-setups that don’t work via the publisher’s web pages, but rather directly link to the pdfs.?!

]]> By: sam http://www.thepowerofgoo.net/2007/05/20/organizing-pdfs-papers/#comment-582 sam Mon, 21 May 2007 05:38:36 +0000 http://www.thepowerofgoo.net/2007/05/20/organizing-pdfs-papers/#comment-582 <p>I like <a href="http://www.citeulike.org/" rel="nofollow">CiteULike</a> for organizing my references. Then I just redownload the PDF whenever I want to read the paper. This may be a problem if someday I no longer have institutional access to journals, but at that point, I probably won't want to read the papers anymore anyway1 ;)</p> I like CiteULike for organizing my references. Then I just redownload the PDF whenever I want to read the paper. This may be a problem if someday I no longer have institutional access to journals, but at that point, I probably won’t want to read the papers anymore anyway1 ;)

]]> By: kayesdee http://www.thepowerofgoo.net/2007/05/20/organizing-pdfs-papers/#comment-572 kayesdee Sun, 20 May 2007 18:18:54 +0000 http://www.thepowerofgoo.net/2007/05/20/organizing-pdfs-papers/#comment-572 <p>Well… you have to switch your specialization then ;)</p> <p>BibDesk has some import features that are 'a bit' useful, but in the end you always have to do some work yourself. Since so many publishers out there just produce crappy PDFs (they consider the PDF as just a copy of the papoer version - i.e. no extra markup) you are left looking for extra help. As long as Scifinder is about the only way to access chemistry related databases you are also out of luck, as this app is just a rudimentary version of what it could be on the mac. (Its UI might not stand out as that bad on windows…). Feature-wise there is nothing that I know of that can do what you want.</p> <p>Maybe Endnote (terrible and expensive). JabRef can import some of the exported citations from some publisher's webpages and from scifinder, but still you have to look up the reference and import by hand. In that time you can also just enter the data yourself. In the meantime you learn the names of the folks out there ;)</p> <p>What <em>could</em> be possible is a script that looks up bibliographical data on the web, possibly via google scholar. It could be written in ruby or python… but someone has to do it ;)</p> <p>Again: this is what we have got on the mac so far. It is not perfect, but definitely workable. It takes about 30 seconds per paper to enter the metadata. Is that not worth it?</p> Well… you have to switch your specialization then ;)

BibDesk has some import features that are ‘a bit’ useful, but in the end you always have to do some work yourself. Since so many publishers out there just produce crappy PDFs (they consider the PDF as just a copy of the papoer version - i.e. no extra markup) you are left looking for extra help. As long as Scifinder is about the only way to access chemistry related databases you are also out of luck, as this app is just a rudimentary version of what it could be on the mac. (Its UI might not stand out as that bad on windows…). Feature-wise there is nothing that I know of that can do what you want.

Maybe Endnote (terrible and expensive). JabRef can import some of the exported citations from some publisher’s webpages and from scifinder, but still you have to look up the reference and import by hand. In that time you can also just enter the data yourself. In the meantime you learn the names of the folks out there ;)

What could be possible is a script that looks up bibliographical data on the web, possibly via google scholar. It could be written in ruby or python… but someone has to do it ;)

Again: this is what we have got on the mac so far. It is not perfect, but definitely workable. It takes about 30 seconds per paper to enter the metadata. Is that not worth it?

]]> By: Kutti http://www.thepowerofgoo.net/2007/05/20/organizing-pdfs-papers/#comment-571 Kutti Sun, 20 May 2007 18:06:08 +0000 http://www.thepowerofgoo.net/2007/05/20/organizing-pdfs-papers/#comment-571 <p>Thx kayesdee for this great post! I have been looking at several of the links you posted and I found that Papers seems to be a great piece of software. The thing is that it only supports Pubmed but as chemists, we usually use Scifinder and download the papers directly from the source (e.g. webpage of JACS, Tetrahedron etc.) so this might be the sticking point.</p> <p>About Bibdesk: you know that I used Bibdesk during my Bachelor´s Thesis but I didn´t like the fact that I had to fill in all the information about the paper (author, title etc.) by myself. I am still looking for an application, that automatically names the file after dropping it into the application.</p> Thx kayesdee for this great post! I have been looking at several of the links you posted and I found that Papers seems to be a great piece of software. The thing is that it only supports Pubmed but as chemists, we usually use Scifinder and download the papers directly from the source (e.g. webpage of JACS, Tetrahedron etc.) so this might be the sticking point.

About Bibdesk: you know that I used Bibdesk during my Bachelor´s Thesis but I didn´t like the fact that I had to fill in all the information about the paper (author, title etc.) by myself. I am still looking for an application, that automatically names the file after dropping it into the application.

]]> By: kayesdee http://www.thepowerofgoo.net/2007/05/20/organizing-pdfs-papers/#comment-569 kayesdee Sun, 20 May 2007 16:50:02 +0000 http://www.thepowerofgoo.net/2007/05/20/organizing-pdfs-papers/#comment-569 <p>Just found this link for further mac tools: <a href="http://www.macscience.net/MacScience/Reference%20management.html" rel="nofollow">MacScience: Reference management tools</a></p> Just found this link for further mac tools:
MacScience: Reference management tools

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