Plugin for export full OJS article text to XML

Software Support
1

Is there any plugin to export full OJS article text to XML for apply to PUBMED ?

2

Hi @alabala

Do you want export PDF to XML ? What format is your original manuscript?

Regards,
Israel Cefrin
Public Knowledge Project Team

3

Yes, we have full articles in PDF format. And need to transform this in XML to subscribe to PUBMED.

4

There was a plugin in OJS2 and I think that it is already ported to OJS3 as well: Update PubMed plugin for OJS 3.x · Issue #2101 · pkp/pkp-lib · GitHub

Seems to be available in OJS 3.1. ojs/plugins/importexport/pubmed at ojs-stable-3_1_0 · pkp/ojs · GitHub

5

Yes, but this plugin export just article name, authors and abstract a minimal information to be indexed by PUBMED after you are accepted at PUBMED.

6

You want to transform full article into JATS XML for publishing in PubMed Central?
Inclusion into PubMed doesn’t require XML. Just fill in the inclusion form.

7

Yes. I want to transform full article into JATS XML to be accepted to be indexed by PUBMED
(see technical requirements at How to Include a Journal in PMC)

A journal must provide PMC with the full text of articles in an XML (eXtensible Markup Language) format that conforms to an acceptable journal article DTD (Document Type Definition). PMC does not accept articles in HTML format.

NLM recommends that data be submitted in XML conforming to the NISO JATS Journal Publishing Tag Set, but PMC will also accept data in other full-text article DTDs that are widely used in life sciences journal publishing.

Files required for each deposited article:
1.A separate XML data file for the full text of each article.
… )

8

No no. That’s PMC - PubMed Central. You don’t need to have JATS XML for inclusion to the regular PubMed.

About transformation:
PDF to JATS XML transformation is a quite complicated task. You can look at:
http://pkp-xml-demo.lib.sfu.ca/

For the DOCX to JATS conversion we use: GitHub - Vitaliy-1/DOCX2JATS: Java project, aimed to facilitate DOCX to JATS XML transformation for scientific articles

9

@Vitaliy if I want to use http://pkp-xml-demo.lib.sfu.ca/ what Output Citation Style do I use?

10

For produced JATS XML citation output is irrelevant. You can point there any citation style.

11

I try to use DOCX to JATS conversion tools but when I verify this XML at PMC Style Checker I have an error…“Validation failed: no DTD found”
someone try this conversion and submit full article to PMC ?

Thanks !

12

@Vitaliy How i run this project mean how can i convert my article docx file to Jat XML for pubmed central? Please guide method because i want to convert my full text articles in JAT XML format to submit in Pubmed Central.

13

Hi @hussainyousaf,

I can recommend reading this review of available tools first: https://revistes.uab.cat/web/sites/default/files/documents/2019-pkp-jats.pdf

Just a comment that there aren’t ideal tools for this task.