Full article in xml with e-Lens

Good day.
As I see from the demo journal OJS3 currently supports an eLens software that can display xml in goodlooking html without direct transformation.
Our journal would like to publish the fulltext articles in such way.
I would like to learn more about supported xml format. Is it JATS xml?
Is therr anywhere a typical schema of such xml that I could use for quick understanding of this format?
And Is there a need for specific modifications of this xml format (JATS?) to be made for displaying article by eLens?

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Same question from my side too.

Hi guys,

OJS 3.0 ships with the Lens Viewer (GitHub - elifesciences/lens: A novel way of seeing content), which provides a nice, interactive interface for natively rendering and navigating JATS (National Library of Medicine) XML, without needing to worry about HTML transformations.

If you want to see some JATS examples, it’s used across Pubmed Central, and the most recent (I believe) schema is available here: Journal Archiving and Interchange Tag Library NISO JATS Version 1.1 (ANSI/NISO Z39.96-2015)

Additionally, we’re continuing to improve our Open Typesetting Stack, which automates the transformation of Word or PDF articles to JATS format (and also generates a new HTML, PDF, and ePub layout from that JATS) – there’s a demo instance available at http://pkp-xml-demo.lib.sfu.ca/2 and an OJS 3 plugin coming soon.

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Thanks for information.

I have already tested Open Typersetting. But as for cyrillic (Ukrainian language) it works but with issues.
For example I get this code as a part of an article:

 <sec>
        <title>&#x41E;&#x431;&#x433;&#x43E;&#x432;&#x43E;&#x440;&#x435;&#x43D;&#x43D;&#x44F;</title> 

        <p>	&#x423; &#x434;&#x43E;&#x441;&#x43B;&#x456;&#x434;&#x436;&#x435;&#x43D;&#x43D;&#x456;<ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://www.ncbi.nlm.nih.gov/pubmed/?term=Okken V%5Bauth%5D" ext-link-type="uri" xlink:type="simple"> Okken</ext-link> V. S. (<xref rid="IDa1142ef6-a1bc-47eb-bb5d-661db35b28fa" ref-type="bibr" id="ID0059d84f-c8e9-47f6-99dd-07d44a10abe4">20</xref>08) &#x432;&#x438;&#x44F;&#x432;&#x43B;&#x435;&#x43D;&#x43E;, &#x449;&#x43E; &#x442;&#x430;&#x43A;&#x456; &#x43F;&#x441;&#x438;&#x445;&#x43E;&#x43B;&#x43E;&#x433;&#x456;&#x447;&#x43D;&#x456; &#x447;&#x438;&#x43D;&#x43D;&#x438;&#x43A;&#x438;, &#x44F;&#x43A; &#x432;&#x456;&#x434;&#x441;&#x443;&#x442;&#x43D;&#x456;&#x441;&#x442;&#x44C; &#x43F;&#x43E;&#x447;&#x443;&#x442;&#x442;&#x44F; &#x43F;&#x440;&#x43E;&#x432;&#x438;&#x43D;&#x438;, &#x436;&#x430;&#x43B;&#x44E; &#x442;&#x430; &#x441;&#x43E;&#x440;&#x43E;&#x43C;&#x443; &#x449;&#x43E;&#x434;&#x43E; &#x43D;&#x435;&#x434;&#x43E;&#x442;&#x440;&#x438;&#x43C;&#x430;&#x43D;&#x43D;&#x44F; &#x43F;&#x440;&#x438;&#x437;&#x43D;&#x430;&#x447;&#x435;&#x43D;&#x43E;&#x433;&#x43E; &#x440;&#x435;&#x436;&#x438;&#x43C;&#x443; &#x443; &#x442;&#x430;&#x43A;&#x438;&#x445; &#x43F;&#x430;&#x446;&#x456;&#x454;&#x43D;&#x442;&#x456;&#x432;  &#x454; &#x43E;&#x434;&#x43D;&#x456;&#x454;&#x44E; &#x437; &#x43E;&#x441;&#x43D;&#x43E;&#x432;&#x43D;&#x438;&#x445; &#x43F;&#x440;&#x438;&#x447;&#x438;&#x43D; &#x43D;&#x438;&#x437;&#x44C;&#x43A;&#x43E;&#x457; &#x43F;&#x440;&#x438;&#x445;&#x438;&#x43B;&#x44C;&#x43D;&#x43E;&#x441;&#x442;&#x456; &#x434;&#x43E; &#x43B;&#x456;&#x43A;&#x443;&#x432;&#x430;&#x43D;&#x43D;&#x44F; [20]. </p>
 </sec>

It looks like a cyrillic at front end (because cyrillic alphabet is codding accordingly by these symbols) but I cant edit it manually. And I dont know if cyrrilic will be supported in the future.
So I think about editing DOC to XML manually (except bibliographic). For easing the process I will be appreciated for the typical article XML JATS schema, supported by eLens. Which will contain for example , title, authors, abstract, typical section, several citation, table, figure, reflist and needed head <!Doctype>.
Is there such example in the web?

As additional info: our journal is planning to use metadata, abstract, bibliographic in English and article body in Ukrainian. Full English text articles would be in minority. So this issue is important for us.

Lens Viewer is really great!

Hi Vitaliy,

Thanks for this. We haven’t done extensive testing with non-Latin scripts but in principle all of the libraries we’re using support full unicode, and we’ve deliberately avoided using English language cues in the parsing so that we can provide better multilingual support. We’ll be looking into better non-Latin script support eventually.

As for Ukrainian JATS, you’re probably better off contacting the NLM developers directly.

Greetings.

And as for typical JATS XML example schema?
Have you met in the web such examples of xml supported by eLife Lens? Without formulas and ingested tables. Only with several simple tags. I would be very appreciate for the link.

For example like this link eLife Lens
But with addition of citation in text. And with visible source xml code.

We’re currently working with Substance (the developers of eLife Lens) on a new JATS editor called Texture (GitHub - substance/texture: A visual editor for research.) which can be expanded to support as many different element types as are currently in the JATS schema; Texture will eventually be a part of the OJS3 plugin to our Open Typesetting Stack so that authors and editors can clean up the JATS output directly within OJS.

There are plenty of examples of articles embedding citations, formulas, tables and so on using JATS in PubMed Central; I’m not sure whether the existing release of eLife Lens supports formulas (though I’m fairly certain it supports both citations and tables), nor whether there are any public examples of it displaying complex articles like that, but you should probably take a look at eLife :slight_smile: https://elifesciences.org/

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I have tried to make XML format article that could be uploaded to Galleys and viewed with Lens.
The simplest variant includes:

<?xml version="1.0" encoding="UTF-8"?>
<article>
 <front>
   <journal-meta>
		<publisher>
                <publisher-name>eLife Sciences Publications, Ltd</publisher-name>
                </publisher>
    </journal-meta>
    <article-meta>
	         <article-categories>
		        <subj-group subj-group-type="display-channel">
		               <subject></subject>
		        </subj-group>
	         </article-categories>
                 <title-group>
                        <article-title>
                         Article Title
                         </article-title>
               .......
               <abstract>
               </abstract>  
 </journal meta>
 ........

And then goes standard JATS XML with body and back.
As I tested, without lines:
<publisher-name>eLife Sciences Publications, Ltd </publisher-name>
and
<subj-group subj-group-type="display-channel">
article is not displaying by Lens in OJS. It throws an error.
Why is that?
Maybe I don`t understand something?

You’re missing a JATS DTD, though I don’t know offhand if this is an issue for Lens; we aren’t really providing support for the viewer directly.

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