Citation Management and Interfacing with RefWorks
Background: Dr. Tung-Tien Sun of NYU gave a fantastic presentation last month teaching us poor souls how to do (experimental) science. I'd like to thank Dr. Sun for allowing grad students from surrounding universities to attend his talk, as otherwise I would've been left out. I recommend Dr. Sun's advice to every new scientist.
One of Dr. Sun's suggestions for writing papers is to keep a three-ring binder divided by subject area, with a page for each topic you work on. Within each section is a description of what's known, the central claims, central questions, etc with references to the relevant papers. There's also a protocols section so you can easily find citations for the protocols you use and the advantages of each -- even if you don't currently use them. Within this context, you also jot down you ideas, experiments to try, or the hidden information you see.
I see this as genius advice. I've never been able to keep straight the details of the papers I've read. Even putting down notes within my citation manager wasn't enough. So I've taken up this method, but in wiki form.
Problem: I want to implement the above three-ring binder as a wiki (as DokuWiki) with links to RefWorks so I can get at the paper/abstract/etc easily and also copy these into a paper for automated citation management. Each major field (smFRET techniques, photophysics, the ribosome, protocols) is a separate page, with subheadings for each topic.
Solution: The central problem is making it easy to cite papers quickly and be able to access them as a link. I use RefWorks as my citation manager (because it works with Linux), so I needed to interface DokuWiki with RefWorks.
Accessing RefWorks: DokuWiki needs to link directly into RefWorks. I accomplished this by sharing my account via RefShare and using the provided link. The format is:
http://www.refworks.com/refshare/?site=####/RWWS#####/#####&rn=4
The ###s in the middle are share-specific and the last number is the RefID number (4 here).
I created a DokuWiki Syntax model that replaces {{ID Desc.}} with a link to a my RefShare and that particular article. I can even replace a list as: {{ID Desc.; ID2 desc; ID3;}}. The best part is that I can copy these references directly into the paper as I'm writing and then use RefWorks to build the bibliography automatically -- it recognizes the format. The descriptions can be anything. I usually put the PI's name and year (Green&co 99) so I know who's lab it's from. Otherwise, I put the authors I know. This helps me remember the paper better.
The plugin (rename to .php) should be installed under dokuwiki/lib/plugins/refworks. You will have to change the RefShare address to your account in the code. In principle, I should set it up to use the DokuWiki configuration, but this works for now.
One of Dr. Sun's suggestions for writing papers is to keep a three-ring binder divided by subject area, with a page for each topic you work on. Within each section is a description of what's known, the central claims, central questions, etc with references to the relevant papers. There's also a protocols section so you can easily find citations for the protocols you use and the advantages of each -- even if you don't currently use them. Within this context, you also jot down you ideas, experiments to try, or the hidden information you see.
I see this as genius advice. I've never been able to keep straight the details of the papers I've read. Even putting down notes within my citation manager wasn't enough. So I've taken up this method, but in wiki form.
Problem: I want to implement the above three-ring binder as a wiki (as DokuWiki) with links to RefWorks so I can get at the paper/abstract/etc easily and also copy these into a paper for automated citation management. Each major field (smFRET techniques, photophysics, the ribosome, protocols) is a separate page, with subheadings for each topic.
Solution: The central problem is making it easy to cite papers quickly and be able to access them as a link. I use RefWorks as my citation manager (because it works with Linux), so I needed to interface DokuWiki with RefWorks.
Accessing RefWorks: DokuWiki needs to link directly into RefWorks. I accomplished this by sharing my account via RefShare and using the provided link. The format is:
http://www.refworks.com/refshare/?site=####/RWWS#####/#####&rn=4
The ###s in the middle are share-specific and the last number is the RefID number (4 here).
I created a DokuWiki Syntax model that replaces {{ID Desc.}} with a link to a my RefShare and that particular article. I can even replace a list as: {{ID Desc.; ID2 desc; ID3;}}. The best part is that I can copy these references directly into the paper as I'm writing and then use RefWorks to build the bibliography automatically -- it recognizes the format. The descriptions can be anything. I usually put the PI's name and year (Green&co 99) so I know who's lab it's from. Otherwise, I put the authors I know. This helps me remember the paper better.
The plugin (rename to .php) should be installed under dokuwiki/lib/plugins/refworks. You will have to change the RefShare address to your account in the code. In principle, I should set it up to use the DokuWiki configuration, but this works for now.
posted by rrowv at
2:50 PM
1 Comments:
Very useful idea, but unfortunately your code breaks the built-in links to attached files.
Try someting like "{{attached_file.pdf}}": You'll only see "[]" on the rendered page.
(You may have to refresh the page before you see the effect after adding/removing your syntax.php to the plugin directory)
-- Jörg
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Anonymous, at 12:06 PM
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