PubMed (Not PubMed Central) Experience

Has anyone successfully indexed their journal using OJS 3.1.1 and the PubMed plugin in PubMed database. Can someone share their experience? Specifically I am looking for the following inputs:

  1. Is PubMed plugin in OJS 3.1.1 fully functional? We keep on getting random XML invalidation errors?
  2. How do you integrate PubMed ID in your articles in OJS. I don’t see a place in metadata form to enter and display PubMed ID when assigned.
  3. The PubMed requirement is to submit citations also. The PubMed plugin doesn’t extract the same. Does it have to be done manually?
  4. How do you integrate LinkOut service since this is one of the mandatory requirements LinkOut: General Information

Thank you.

1 Like

you have passed technical evaluation step ?

No. We have not. With the current limitations in the PubMed plugin, it’s not possible unless we do it manually.


are there any updates on this? Are you still working to have your journal indexed by the NML in PubMed? We are currently applying. In addition to your four points, I have a fifth:

  1. How do you handle the required longtime archiving? Do you plan to use PubMed Central (and thus need full text xml) or one of the CRL certified archives (Canadiana(dot)org, Chronopolis, CLOCKSS, Hathitrust, Portico, Scholars Portal?

No we didn’t get any further. For long-term archiving also we are awaiting the release CLOCKSS plugin to be functional in OJS3.

Ah, ok. I just submitted our application for NML indexing. It will probably be reviewed in the LSTRC meeting in February 2019. So now I have 6 months to figure out how to do all of the above, in case we get a positive reply.

  1. Short answer is no. However, you can fix some missing tags here and there to get a compliant XML. The devs are working on a better integration which should be available with the 3.2 (there’s a post on github)

  2. That’s what I’m trying to find out. Better start another thread

  3. Seems the same question as of 1. Plugin is not perfect, but saves you some work.

  4. You should provide them with a consistent link structure, which should include the pubmed id. In OJS 2.x it used to be a breeze, where you only had to paste the pubmed id into the Public URL field. See my point 2.

Good luck for your application. I was forced to do it again a few years ago, and it took me one whole year to finalize it.

The CLOCKSS integration do works pretty well.
Start the application process with them, and declare you want to use the harvest mode. The process is long (it took me more than six months), they will nonetheless pester you with new requests of adding text snippets here and there, but in the end everything works.

We also have someone who is interested in getting a journal indexed in Pubmed. I checked the current information that is available especially at

We noticed this requirement as well (“Provide NLM with XML-tagged data of bibliographic citations”) and i am not sure if I get it right. Does this mean, that you have to deliver the bibliographic data for all the references, that are cited in an article, as an standardized xml-file? Or does it mean that you have to deliver the article data (and not the references) as such an xml file?

As far as I can see the latter one is done by the existing OJS-export plugin. But getting all the bibliographic reference data as a standardized xml-format would require processes that are probably outside of OJS or that require a highly specialized xml-manuscript workflows so that such a file is created as byproduct during fulltext preparation.

Has anyone experiences in Pubmed delivery from OJS?