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PubMed LinkOut program

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PubMed LinkOut program

Postby mgscano » Thu Aug 13, 2009 2:07 am

I searched the forums, but can't find much about this.

Justa as a reference: http://www.ncbi.nlm.nih.gov/projects/li ... nkout.html

The NIH/NLM/PubMed has this very interesting service, which enables printed or simply not completely digitally archived journals, to link to the full online text of the articles for which they submit citations to PubMed.

This is a great tool for OJS-based journals, which might not have the people resources to face a PMC application, but want to get the best out of the online available resources. Much more this is significant for the OpenAccess journals.

Since my journal eventually falls and totally fits into these parameters, and I was directly invited to participate :) , I was wondering on how to integrate the Import/Export plugin to also generate the necessary XMLs ready to be FTP-ed to the NIH archive.

Now, is there anyone who has taken this into consideration? We might join forces to create the new plugin for the forthcoming 2.3 version (I'm in the beta testing program).

Let me know ....
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Re: PubMed LinkOut program

Postby mj » Mon Aug 17, 2009 9:58 am

Hi Marco,

I've worked fairly closely with NLM/NIH for a number of years with PubMed and PMC and I have to admit I've never been entirely clear on LinkOut. The best analogy I can come up with is that LinkOut is sort of like the "Reading Tools" for PubMed (but this may be inaccurate or plain wrong).

I think it's also worth clarifying again that PMC (PubMed Central) is a very different service and process altogether from PubMed. PMC is a full-text archive, whereas PubMed is "only" an index (though still of enormous value, especially for OA journals).

What I can say is that for journals that have been accepted into PubMed and are submitting indexing metadata directly (ie. from OJS), NLM automatically generates LinkOut information to the original article, whether that's full-text or subscription (and actually identifies in the XML which kind of access it is). So, I'm not completely clear on how a journal that is not accepted in PubMed would be able to participate in LinkOut. But, I would be very curious to learn if you know more and are willing/able to share.

MJ
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Re: PubMed LinkOut program

Postby mgscano » Thu Sep 03, 2009 12:50 am

Hi mj,
the linkout program is not "a sort of reading tools", it's just a way to provide a link to the online article (if there is one), directly from the PubMed citation, via a customizable button.

It requires some data to be provided to the NIH FTP in XML format, in a way they can identify the citation, and link to the proper online resource.

This is why I'm saying it could be integrated as a plugin ... is there any better place to find a link to a published article than the OJS database itself? I'll see what comes out, and eventually publish the results.

[==> OFF TOPIC]

Then, let me go temporarly out of topic just to clarify one more thing: I know in one of my past posts, probably due to my poor english, I wrote a sentence in which it was not clear if I knew the difference between PubMed and PubMed Central. I pledged guilty at that time, now please do not assume every time I post something, I don't know what I'm talking about! :wink:

bye
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Re: PubMed LinkOut program

Postby mj » Thu Sep 10, 2009 5:59 am

Hi Marco,

the linkout program is not "a sort of reading tools", it's just a way to provide a link to the online article (if there is one), directly from the PubMed citation, via a customizable button.

What I mean by "a sort of reading tools" is that Linkout allows the publisher to provide links from the PubMed entry to multiple resources relating to the article, not just the original online source; eg. related definitions, non-expert terminology, thesauri, etc. This is heavily under-used in biomedical literature, but is much more common in Genbank entries, for example. So, most journal entries only point back to the online article, but some have additional links to Pubmed Central, etc.

It requires some data to be provided to the NIH FTP in XML format, in a way they can identify the citation, and link to the proper online resource.

Yes, and this format as far as I'm aware this is the NLM Standard Publisher Data Format that is used to submit items to Pubmed/Medline. This is the format the OJS currently exports using the PubMed export plugin.

I know in one of my past posts, probably due to my poor english, I wrote a sentence in which it was not clear if I knew the difference between PubMed and PubMed Central. I pledged guilty at that time, now please do not assume every time I post something, I don't know what I'm talking about!

Let me clearly say that your English is excellent, and that I'm not making any assumptions whether you know what you're talking about -- quite the opposite, your posts are very insightful and informative. The only reason I raised the issue with PubMed and Pubmed Central is that it is an extremely common mix-up which is the result of NLM/NIH's very poor choice of naming convention. So, it has nothing to do with you at all. :wink:

Hope this helps,
MJ
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Re: PubMed LinkOut program

Postby mgscano » Fri Sep 18, 2009 10:31 am

Okay, I came up with a workaround for this.
While it's not the best thing to do, I use the correspondent PUBMED ID as the OJS Article ID for every article I submit.
This allows me to submit a ultra-simple query-based resource file for LinkOut, since I just have to indicate a base url like
<domain>/index.php/journal/article/view/
and then use the PUBMED ID as the rule to access the correspondent online resource.

Basically, the selecting part of the file should look similar to this:
Code: Select all
<ObjectSelector>
   <Database>PubMed</Database>
   <ObjectList>
      <Query>"journalabbrev" [Journal]</Query>
   </ObjectList>
</ObjectSelector>
<ObjectUrl>
   <Base>&base.url;</Base>
   <Rule>&lo.id;</Rule>
   <Attribute>full-text online</Attribute>
</ObjectUrl>

I say it's not the best thing to do because the pubmed ID is entirely numerical, and this means there's gonna be a day when the OJS article id will start duplicating and crashing the application ... while since the Pubmed IDs are now around the number of tenths of millions, and my journal has a dozen articles a month, I can expect to have that problem by February 139131.
It's going to be a tough will for our descendants :D

Hope it helps
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