PubMed XML file invalid

Using the PubMed XML export plugin, I am able to export the XML file. However, testing the file on https://www.ncbi.nlm.nih.gov/pmc/tools/article-previewer/ any file I run fails.

What is confusing is the error messages are say that there are undeclared tags, which are in the file. For example, and

ERROR: ERROR :[2018-03-06 14:19:21]: -:8: element JournalTitle: validity error : No declaration for element JournalTitle

Does the export plugin not actually work?

Hi @HeatherO,

I think you’re probably mixing PubMed with PubMed Central. See https://support.ncbi.nlm.nih.gov/link/portal/28045/28049/Article/789/What-is-the-difference-between-PubMed-Central-PMC-and-PubMed for details.

Regards,
Alec Smecher
Public Knowledge Project Team

Hi @asmecher,

Thanks for the quick reply. I’ve only just taken over the management of a journal and they are applying for PubMed Central. Being new, I didn’t realise there was a difference as everyone refers to it as PubMed!

Is there an export tool to create the XML files for PubMed Central?

With thanks,

Heather.

There sure is!

We have a still-experimental new service called the Open Typesetting Stack (demo instance available here: http://pkp-xml-demo.lib.sfu.ca/) which is designed specifically to convert Word and PDF input to National Library of Medicine JATS XML, which you can then use to produce a browser view or an ePub or send it off to Pubmed Central.

It’s hard to produce perfect JATS XML automatically, so OTS is designed to work with the (integrated) Texture editor: http://substance.io/texture/. We also have an OJS plugin for integrating OTS directly into OJS, so it’s easier to suit your workflow: https://github.com/pkp/ojs3-markup.

Officially these are all in the experimental stage, but you should find them fairly usable, and you should be hearing more about them soon!

Hi everybody! I need to export a search strategy from PubMed in the XLM format and I can not do it with the new version of PubMed. can anybody tell me how to do it?