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PubMed Central (PMC) Export Plugin

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PubMed Central (PMC) Export Plugin

Postby thebigaym » Sun Jun 26, 2011 4:13 am

Our journal has been accepted into PubMed Central (PMC).

My understanding is that the PubMed export plug-in produces XML files for inclusion in PubMed which is different from PMC.

I used the OJS articles export based on the native.dtd Document Type Definition and the PubMed XML export.

Each has some fields that can be used for the PMC XML format. Both lacked tags for references and a URI back to the OJS page for the article. Page numbers defaulted to the article ID number.

I'm not sure how to handle page numbers. Our journal has been printed for 20+ years, and we want to include page numbers for the print version. In all likelihood we'll drop the print version soon, so I'm not sure how to handle something like page numbers at that point. I did not see anywhere where the editor could enter page numbers.

Regarding references, some PMC articles allow the user to see a list of references used in the article. Currently, our only galley format is PDF. Does anybody know how PMC gets the references from the article? Is it pulling from the PDF with tags embedded in the PDF, or are there separate tags for references? I did not see anyplace where the editors or authors could enter references.

I'm sure there are many other potential options to consider. So is there any plan to produce a PubMed Central export feature?
thebigaym
 
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Re: PubMed Central (PMC) Export Plugin

Postby jmacgreg » Tue Jun 28, 2011 4:47 pm

Hi Thebigaym,

Regarding the page number question: you'll find an option to enable a page number field in Journal Management -> Setup Step 4.3. After you enable this, Editors will be able to enter page numbers for each article from the Issue's Table of Contents management page. This page information will subsequently be displayed in the Article & Issues XML export file, in the <pages>...</pages> tag for each article.

Recent versions of OJS (2.3.3+, IIRC) also include a Citation Markup Assistant that can be used by Editors to extract, parse, and edit reference lists/citations included by Authors. More information on this feature can be found from the third point here. Most importantly, you can use this feature to semi-automatically convert your articles' reference lists to NLM 2.3 or 3.0 XML, which can then be copy&pasted into any NLM file going to PubMed/PMC. We'll be planning better integration with our various export plugins in the future.

Otherwise ... we'd definitely like to support PMC deposit more fully. I'll be asking our lead developer what we're planning in that regard in the future, and will try to get back to you soon.

Cheers,
James
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Re: PubMed Central (PMC) Export Plugin

Postby thebigaym » Thu Oct 20, 2011 9:21 am

Ok, I've gotten our hosting service to enable citation extraction.

I logged in as editor and entered references for an article whose landing page is visible at:

http://jima.imana.org/article/view/8276

To my surprise, the references appear below the abstract.

Which export plugin exports the references? I'm particularly interested in submitting the references to CrossRef. Note that the CrossRef plugin exports article and issue information, without references.

http://pkp.sfu.ca/ojs/docs/userguide/2.3.3/journalManagementSetup3.html

the citations will be subsequently available in a variety of export formats including NLM XML and citation-style-specific formatted text.
thebigaym
 
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Re: PubMed Central (PMC) Export Plugin

Postby jmacgreg » Mon Oct 31, 2011 1:32 pm

Hi thebigaym,

You may be interested in the following: http://pkp.sfu.ca/bugzilla/show_bug.cgi?id=6615 (nothing yet implemented) and also viewtopic.php?f=28&t=7566, which implements Cited-By linking as a plugin.

Cheers,
James
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