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PubMed export plugin

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PubMed export plugin

Postby mrich » Mon Jan 02, 2006 5:49 pm

A colleague and I are plan to start publishing an online radiology journal this month using OJS. Once we have published a sufficient number of articles, we hope to have our journal indexed in the U.S. National Library of Medicine's PubMed database.

In order to submit citation data to the NLM, we need to send them appropriately-formatted XML files. This brings up a few questions:

  1. Has anyone else already written a plug-in that will export OJS citation data in the PubMed format?
  2. Would the OJS Development Team consider adding such a plug-in? Besides my own selfish need for such a plug-in, I'm sure it would be a huge plus for any other prospective OJS medical publishers out there.
  3. Does anyone write such plug-ins for hire?

If options 1 - 3 above fail, I'll have a go at it myself, using the sample OJS plug-in code, though my plate is already fairly full, getting this journal started. :wink:

Regards and Happy New Year to all!
Posts: 12
Joined: Thu Dec 08, 2005 12:43 am
Location: University of Washington, Seattle, Washington

Postby asmecher » Mon Jan 02, 2006 6:01 pm

Hello mrich,

There isn't currently a PubMed export plugin for OJS, but writing one would be fairly easy. OJS 2.0.2-1 ships with an Erudit export plugin, which has the same rough requirements as PubMed's XML format; the code for the Erudit export plugin would make a good starting point. (See plugins/importexport/erudit/* for the implementation.)

We might eventually write such a plugin, as it would be a useful addition, but we don't currently have plans to. If you do write a plugin, I'd encourage you to contribute it back to the OJS codebase so we can distribute it in the future. We have at least one other user who has inquired about interoperability with PubMed.

If you have questions about the process of writing an export plugin for OJS, please post them here; in addition to helping you through the process, this would provide a valuable resource for anyone else who wanted to do something similar.

Alec Smecher
Open Journal Systems Team
Posts: 10015
Joined: Wed Aug 10, 2005 12:56 pm

PubMed plugin

Postby mrich » Tue Jan 03, 2006 3:27 am

Hi Alec,

Thanks for the quick response.

I'll have a look at the erudit example and see what I can do with it. If I can make a workable plugin, I'll be happy to share it with you and other OJS users.


Mike Richardson
UW Radiology
Posts: 12
Joined: Thu Dec 08, 2005 12:43 am
Location: University of Washington, Seattle, Washington

Postby John » Thu Jan 05, 2006 12:20 am

I would add to Alec's comments that MJ Suhonos <mj@robotninja.com> has developed an elegant system for implementing the NLM's DTD for the OJS journal, Journal of Medical Internet Health, http://www.jmir.org/ms/index.php.

MJ is planning to develop a generalizable version of this XML setup as a module for OJS, and it might be worth contacting him on this.

We do see this as an important development for the system.
Posts: 89
Joined: Tue Oct 14, 2003 9:15 pm
Location: University of British Columbia

JMIR's implementation of NLM's DTD

Postby mrich » Sat Jan 07, 2006 11:21 pm

Thanks very much for the suggestion, John.

I'll e-mail MJ and see if he has anything I can use for our system.


Mike Richardson
UW Radiology
Posts: 12
Joined: Thu Dec 08, 2005 12:43 am
Location: University of Washington, Seattle, Washington

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