How to create and validate JATS/XML?

What is JATS/XML?

JATS (Journal Article Tag Suite) is an XML format used to describe the structure of scientific articles in text format. JATS is designed to facilitate the exchange of information between scientific journals and search engines or databases. JATS contains elements and attributes that describe article metadata, structure, and content.

In recent years, the use of the JATS/XML format in scientific journal publications has increasingly been used as an indexing requirement by some of the leading indexation services, PubMed. JATS/XML helps ease the indexation of articles, and allows researchers and readers to find relevant articles quickly and easily.

Therefore, using the JATS/XML format in scientific journal publications is very important in meeting indexing requirements by leading indexation services. This will also improve the accuracy, completeness, and legibility of scientific article indexation, thereby increasing the visibility and impact of research conducted.

Want to save time and create a high-compliance JATS file?
Access the JATSeditor.com, the FIRST and ONLY intuitive online editor that allows you to create a JATS file with stress-free and built specifically to comply with NCB/PUBMED JATS Standard. Just upload your DOCX file into the editor, and the content of your journal will be loaded to JATSeditor easily.
Check the result with our viewer of JATS with BetterJATS viewer using this link.

What is the relationship between JATS/XML and OJS

JATS has become an international standard format for publication in scientific journals. Therefore, JATS is closely related to journals and scientific journal publications.

In the world of academics and research, journals are one of the important media for publishing research results. Journals also function as a means of scientific communication between researchers, thus facilitating knowledge transfer and collaboration between researchers.

JATS enables researchers and readers to understand the structure and content of scientific articles more easily and quickly, and enables search engines to search for information more accurately and effectively. By using the JATS format in scientific journal publications, journals can be indexed and accessed more easily by search engines and databases, thereby increasing the visibility and impact of published research results.

In addition, many scientific journals are currently adopting the JATS/XML format in scientific article publications, and several leading indexation services also require the use of the JATS/XML format in scientific journal publications. Therefore, the use of the JATS/XML format in journals is very important in ensuring that scientific articles can be accessed easily, accurately, and effectively by readers and researchers.

What types of OJS indexing require the JATS/XML format

Several types of journal indexing services that currently require JATS/XML formats in scientific journal publications are:

1. Scopus

More than 95% of journals indexed in Scopus, metadata is submitted by publishers via e-Feeds, with XML as one of the recommended formats by Scopus. This method allows for quick and efficient processing, ensuring that article data is fully indexed and accessible within Scopus, typically within two to three weeks of its publication on the publisher’s website.

(source: Scopus Content Coverage Guide)
XML formatting is essential for maintaining metadata accuracy and enables streamlined integration with Scopus systems, enhancing discoverability and citation tracking.

2. Web of Science

Web of Science (WoS) has become an essential data source for researchers, scientists, and academics seeking access to scientific publication information. To optimize the available data, WoS offers several data formats for analytical purposes, including XML.

By leveraging XML, research institutions and publishers can improve work efficiency and data accuracy. Data accuracy is critical in editorial selection processes within Web of Science, making XML invaluable for ensuring that high-quality information is readily available for analysis and decision-making. (Guide for Web of Science XML data)

3. PubMed

Pubmed receives citation and abstract data from journals uploaded via Secure File Transfer Protocol (SFTP) in tagged XML format, as only citations that have been approved for inclusion in pubmed can be submitted. Since journal publishers in pubmed must send their citation and abstract data electronically, the XML format is widely used to upload various journal publishing purposes for example like updating citations and downloading PubMed data. They also make specifications for using XML for publication in pubmed.

4. DOAJ (Directory of Open Access Journals)

In the DOAJ context, the implementation of JATS/XML is format required to be indexed in DOAJ. The XML format helps ensure that article data is consistently available and can be distributed to third parties, supporting open access, transparency and global visibility for published scholarly work.

5. Crossref

As a Crossref member, publishers can register a DOI (Digital Object Identifier) which is useful for identifying and sharing their content within the global scientific ecosystem. All metadata deposited with Crossref is submitted as XML. So, JATS/XML is essential in the process of registering content in Crossref as this format allows the metadata of articles and scientific content to be described in a structured standard. 

It is important to note that these are only a few examples of journal indexation services that require publication of scholarly journals in JATS/XML format. There are many other journal indexation services that also require the JATS/XML format, and an increasing number of scientific journals are adopting this format as their publication standard.

What are the steps to create the correct JATS/XML in OJS

Before starting the JATS creation process, first prepare some of the plugin tools needed, such as:

A. docxConverter
B. texture
C. JATSParserPlugin

Another option is using an online tool for creating a JATS file :
D. Using JATSeditor.com

1. Creating JATS using Texture in OJS

1. Make sure before downloading all plugins are compatible with the OJS version you are using
2. The tutorial below is made and simulated using OJS version 3.3.0-14, and using all the latest versions of the 3 plugins above

1. After all the plugins are installed and activated, then please upload the article document format file (docx) into the production menu for one of the articles that has a production status.

2. Then click Convert to JATS XML

3. After a successful conversion, a new file in XML format will appear, then please click edit with texture in the XML file

4. On the texture work editing page, please enter article content data such as abstracts, keywords, and others, including data such as tables and images.

5. To display the data table of content as shown below, please set all heading items in the article content

6. To add a table to the article content, please click Insert -> Table

Note:
Given the limitations of the edit feature on the table in this texture, if the table data you have has a very specific structure then you can take an alternative option by converting the table data into an image.

7. To add a images/figure to the article content, please click Insert -> Figure

8. If you want to add Reference data and make that data hyperlinked automatically with related article content data, like the GIF example below

So please first make a data reference on the menu Insert -> Reference

Then select the type of Journal Article

Then enter the reference data in the form provided, and to save the data that has been submit you only need to close the reference form.

As shown above, we can see the results of the References that have been made. Please make a reference format according to your journal type.

And all reference data created will appear like the following example

9. Next, to create a hyperlink between the article content data and the references that have been made, please specify the location of the reference numbering in the article content data.

Note:
– Arrow 1, is the location for placing the reference data numbering.
– Arrow 2, to display the reference data that has been created.

After that, please select the relevant reference data

After successful reference numbering will appear as follows

10. After all the article content data has been successfully created, please save and close the texture editing page.

11. Refresh the production page, then select Create Galley

The “Create Galley” feature as shown above is only found for the latest texture plugin version and only supports OJS 3.3 version

12. Please enter the type of format such as XML/JATS, and fill in other form data as needed

13. If successful, XML format will appear in the galley production metadata menu

14. Finally, please publish the article to see the results

15. At this stage the creation of a simple JATS/XML has been completed, you can improve or try using other menu tools provided from the texture plugin.

As you can see you can create JATS file easily using Texture as integrated in OJS.

However, based on our experience there are a lot of lack features in Texture those are :
1. Formatting the table is quite challenging as in Texture for example removing borders and text styling
2. Unable to add ORCID and Scopus records for the authors
3. Cannot add correspondent authors
4. Lack of feature of importing doc/docx file into the body section
5. Reference mode only has one styling which is [#REF 1] that is not compliance with other reference styling such as Vancouver, APA, IEEE
6. The Texture actually is an abandoned project so it is not compatible with the latest version of OJS and it only complies with the old standard of JATS.
7. The JATS result does not adhere to the standard from PubMed and JATS4R which will be rejected by PubMed.
8. Those plugins, including texture and jatsparser is not well-maintained and can be considered as an abandoned project. The development and compatibility improvement of this project has been halted.

How to validate the JATS file ?

Validation is the last step of creation process of JATS. This process is crucial as it to make sure that the XML file can be accepted by the indexing service such as PubMed and EBSCO.

Fortunately, there is a public tool to test and validate the JATS file. You can access and should validate your XML file using this site :

1. PMC Style Checker
2. JATS4R Validator tool

For example you will get the “Ok” status when validate using PMC :

You should take attention if the JATS file is not valid as it will be useless for the submission of the XML to the indexing.

2. Using JATSeditor System

Jatseditor.com is the FIRST and ONLY online editor built specifically for JATS that fully complies with PUBMED and JATS4R. It is seamlessly integrated with OJS, it auto-imports essential metadata like DOI, authors, and references. Usable independently, it ensures PubMed compliance with PMC validation. Key features include advanced math support, AI-driven tagging, and one-click JATS export—all at an affordable cost.

Jatseditor.com also adhere the new standard for producing JATS file such as inserting a video from youtube, adding a quote, adding a mathematical equation and other feature.

You have two easy options for using Jatseditor:
a. Integrate with OJS
You can integrate Jatseditor seamlessly with Open Journal Systems (OJS) to automatically pull metadata like journal details, DOIs, authors, and references.

b. As Independent Platform (without OJS)
Alternatively, Jatseditor also functions as a standalone platform, making it a versatile tool for any publishing setup. You can import any of your documents without sync to OJS.

More detail regarding this JATSeditor you can visit this article link: Creating JATS file with ease using JatsEditor
Or visit the official site Jatseditor.com

Advantages using JATSeditor.com
1. Highly comply with EBSCO and PubMed format
2. Complete synchronizing data from the OJS article to the editor (including ISSN, article metadata, reference, abstract, and other crucial metadata).
3. Comply with the latest JATS4R format
4. Included with an exclusive JATS viewer called BetterJATS Viewer Plugin
5. Used by publishers around the world as the best practice in creating JATS.
6. Can be remodified in the future without knowing complex tag.
7. Include file management to manage and organize your JATS file.

Conclusion

The availability of Jats/XML for each article provides convenience to visitors by allowing them to view the article content without the need for downloading. Additionally, it increases the chances of all article contents being indexed by the Google search engine, significantly increasing the likelihood of your article ranking as the top result on search pages for relevant user queries.

Considering the diverse range of OJS versions currently used by OJS users, the tutorial above may not fully align with the explanations provided. However, we highly recommend upgrading your OJS to the latest version, as the automatic generation of XML format in the gallery menu is only available in OJS version 3.3.

Then the results of making the XML above also cannot be validated to be able to support indexing formats such as PubMed and others, this is because the purpose of the tutorial above is only to be able to display the contents of the article on the page menu of each article. To get a Jats/XML file that can be verified in several indexes such as PubMed, you can use the services below:

Muhammad Al Madani

Hello! I'm Almadani, Customer support OJS from Openjournaltheme. Have a passion for helping solve publisher problems, have knowledge and experience related to the use of OJS, OMP and Eprints.