Full-text HTML article publishing in OJS based on JATS XML: what will be the future of JATS Parser and Lens Galleys plugins?

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In my work I provide technical support to many OJS sites of scientific journals that publish full-text HTML articles based on the Jats Parser plugin made by Vitaliy Bezsheko (Thanks again @Vitaliy for the great work you did).
At the time I chose JATS Parser because, unlike Lens Galleys, it provided greater compatibility with JATS XML TAGs and because it provides a static HTML version of the article.

The journals I manage use an external service to convert articles from PDF (or InDesign) to JATS XML. The JATS-converted articles are then entered into OJS and converted into a high-quality HTML version using the JATS Parser plugin.

The sites are all on OJS 3.3.0 LTS for which, as is well known, the support period included in the LTS will end before long.
I have to plan to upgrade to OJS 3.5 LTS for all these journals since, in agreement with the journals, we decided to skip version 3.4.

I am trying to figure out how to do the upgrade to OJS 3.5 without losing all the work done to convert the articles to JATS-XML format (we are talking of hundreds of articles for each journal) and then continue to use the JATS XML files for publishing the full-text HTML.

In recent years I have read on the PKP forum and website that JATS XML integration was planned in version 3.5.
More recently, looking the PKP Forum and attending the PKP Sprint in Turin of October, I understood that this integration will not be done in this version of OJS because it turned out to be too complicated in relation to the available resources.
If this is confirmed, I see two possibilities to upgrade to OJS 3.5 and continue to use JATS XML files for publishing the fulltext HTML version of articles:

  • the version for OJS 3.5 of JATS Parser will be released (this would be the ideal solution)
  • the Lens Galleys plugin will be updated for OJS 3.5 (in which case I would use this plugin instead of JATS Parser)

So I have 2 questions that I hope to find an answer to on this forum, especially from @asmecher and @Vitaliy

  1. are there plans to release a version of the JATS Parser plugin compatible with OJS 3.5
  2. are there plans to release a version of the Lens Galleys plugin compatible with OJS 3.5

Regarding Lens Galleys there would be an additional complication.
I read that the Lens Reader, the javascript library on which Lens Galley is based, is no longer maintained ( see: Where is full-article HTML and sources of JATS XML? - #2 by asmecher)
Can someone who is using Lens Galleys confirm whether this is still the case?
In that case there would still be problems with the limitations on JATS tags supported by Lens and it might be a solution for us that is not usable.

I have a few more questions for anyone who is using the JATS Parser, Lens Galleys or any other plugins for publishing full_text HTML article galley based on JATS XML (@ajnyga ??) :

  • do you have the same problems that I wrote above?
  • how are you coping with the transition to OJS 3.5 LTS version?
  • if you have identified a solution, can you share it?
  • if you have not found a solution, can we try to collaborate to find it together?

Thank you in advance for any feedback you can give me

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I add an additional critical point regarding the possible use of Lens Galleys Plugin:
as far as I know, at present it does not handle responsive and cannot be used on smartphones.
Therefore, for it to become a viable option we need to understand if there is an update to the Lens Viewer that includes responsive.

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Hi all,

We’re doing quite a bit of work internally with our “Production Workflows Working Group” (previously the XML working group) on defining a streamlined production/typesetting workflow for inclusion in OJS (and likely OPS) 3.6. Stay tuned for more information on that.

For now, I can give a partial answer: the status quo is likely to continue for 3.5, with some improvements:

eLife has long ago stopped development on the Lens Reader product, so I would recommend against its use. It will not be getting enhancements e.g. to responsive design.

Regards,
Alec Smecher
Public Knowledge Project Team

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Hi @asmecher and thanks for your feedback.
According to what you wrote,
the only way I can continue on OJS 3.5 to create a full-text HTML version from the large archives of JATS-XML files that my journals have, is to have a version of Jats Parser compatible with OJS 3.5.
@vitaliy : is upgrading Jats Parser to OJS 3.5 in your plans?

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Hi @razzi,

Answering on Vitaliy’s behalf – JATS Parser Plugin is one of the plugins that gets updated with each release, and we haven’t made any plans to stop updating it. It may take a little bit of time after 3.5.0 comes out for us to get through all the plugin updates. So yes, you can count on that plugin being available soon after 3.5.0 is released if not at the same time.

Regards,
Alec Smecher
Public Knowledge Project Team

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Hello @razzi

Thank you for sharing some comperhensive challenge on JATS used as standard publishing in your journal.

Let me share the experiences we have gained from the many users we have managed whether they are creating XML with texture plugins in OJS or using third party vendor services, and also answer some of your questions and concerns.

As a result of this experience, several challenges and limitations emerged in the XML creation process, such us:

  1. Conversion costs using third party vendors are very expensive.
  2. Difficulty to modify or reuse due to dependence on vendors in making JATS
  3. Limited user interface that is difficult for journal managers in making JATS through the editor
  4. The elife lens feature is no longer developed, for example, it does not support complete latex on the text-math tag even though it is needed by the validator, does not support view for subtitle appearance, there is no feature to display long desc in the table in JATS and its issue with responsiveness of the display.

As we aware some of this challenge, our team decide to overcome various challenges and limitations as above.
Here is our solution for that issue :

  1. Developing the Jatseditor.com, built with Svelte and integrated with AI, with a focus on ease of use (reuse and creation is simplify) and the creation of the JATS can be done by anyone as simple as modify anything on online text editor. The result of this editor (JATS file) is also focus on PMC validation and jats4r.niso.org.
  2. JATSImporter plugin in OJS that will automatically send the journal and article metadata to be used in Jatseditor.com
  3. Create BetterJats Viewer plugin to overcome some limitations of eLifelens. (We will release it for free)

The tool is in the final stages of development, with a planned completion date of the end of this month and an expected launch in early December or early next year. However, we still have one more step to go, which is to test the tool on non-technical users. Our goal is to make sure the tool is simple and easy to use, even for those without a technical background.

Therefore, on this occasion, I think you are one of the right people to be the first to test and provide feedback on this tool, and if you are willing, please contact me, and I will create and send you a login account to test and give us feedback about it.

Thank you
Alma
Openjournaltheme.com

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Hi @asmecher
Thanks for the very quick feedbak.

This is a great news!

Best regards

Rino Razzi

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Could you please tell what kind of services you use?

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Hi @Garant
We do not use automatic convertion tools.
We buy convertion services provided by companies focused on this topic.
We just send them articles in PDF or InDesign format and get back the JATS XML version.
I guess that they perform a semi-manual work on the files to produce the XML. The quality of the provided XML is very high. It includes also structured XML for the article’s citations.

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We are currently updating to 3.3 (we’re behind, unfortunately). We depend on the JATS Parser plugin for two book review journals. One peer-reviewed journal has XML encoded by a 3rd-party and relies on the Lens reader. We are similarly looking forward to seeing improved support for XML & JATS in 3.5 and moving away from the Lens reader.

It is very important to us that the JATS Parser Plugin is updated in 3.5 and able to run on PHP 8.x +.

There’s is one thing that we’ve been testing internally that may be different from what @razzi has outlined wrt to JATS publishing: encoding articles in plain text manuscript form to JATS using GenAI tools. We have an article coming out in Journal of Librarianship and Scholarly Communication shortly with our preliminary, mostly positive results.

Richard Higgins
Indiana University Libraries

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@Richard-Higgins
With regards to the use of Jats Parser Plugin with OJS 3.3, there are some minor annoying issues while publishing articles’ references.
We were able to afford them in the time.
If you face similar problems, do not esitate to ask me how we solved them.

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@Richard-Higgins,
thanks for sharing your experience with JATS-XML management in your journals.
I’m very interested on your testings with GenAI tools. Please advice here when the article is available.

According to the state of @Muhammad_Al_Madani below here, there might be a new plugin available for JATS-XML to HTML publication.

So, probably, we will soon have again an alternative option to JATS Parser plugin.

@Muhammad_Al_Madani :
do I understand well that your new plugin “BetterJats Viewer” will be an updated version of Lens Galleys plugin that removes some limitations o eLife Lens libraries?
Will your plugin work in the same way Lens Galleys does?
May you tell us what limitations are going to be overcome?
The main limitations I know of Lens Galleys plugin are:

  • missing responsive layout
  • issues with some type of references

Will they be both solved?

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Hi @razzi

do I understand well that your new plugin “BetterJats Viewer” will be an updated version of Lens Galleys plugin that removes some limitations o eLife Lens libraries?
Yes, the “BetterJats Viewer” plugin can be a replacement solution for the previous plugin (eLife Lens)

Will your plugin work in the same way Lens Galleys does? and, May you tell us what limitations are going to be overcome?
Yes, the “BetterJATS Viewer” plugin is propose to solve the following issues:

  1. Responsiveness
  2. Better User Interface as it will list all the reference, table of contents, table of figures and list of tables
  3. Compatible with DOAJ requirement as it is need to have subtitle for multilingual journal in English or other languange
  4. Add complete affiliation view for each author
  5. Add corresponding author in the jats view
  6. Allow to view a video with youtube or other external video (as current JATS editor and Lens is not available)

Then there is one limitation you mentioned that makes us curious, namely “issues with some type of references”, does this limitation refer to not supporting reference style formats such as APA style or others? or if this is not what you mean can you provide more details and examples of this case.

Regards
Almadani

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Thank you Almadani for your effort and your promising work.
Besides the well known problem of references, there is another problem in JATSParser concerning the mathematical formulas that cannot be easily rendered. I’m wondering if you also covered that point with your new viewer?

Best regards,
Jean-Blaise

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Hi @Muhammad_Al_Madani

I’m speaking of various issues discussed in this thread, some related to references, other to footnotes:

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Hi @claivaz

Yes, BetterJATS Viewer has fixed this issue. See the preview below.

image
image917Ă—576 170 KB

Hi @razzi

Thanks for your detailed information.

Regards
Almadani

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