Introduction

The JATS (Journal Article Tag Suite) is an XML-based format for tagging and describing scientific articles. Developed by the National Library of Medicine (NLM), it has been widely adopted by publishers and archives as a standard for scholarly article markup.

Usage

Use the .jats.xml file extension, or the --to jats or --from jats options, when converting to/from JATS e.g.

stencila convert doc.smd doc.jats.xml

By default, the encoded JATS XML is un-indented for compactness. Use the --pretty option for indented output, but note that this can introduce whitespace that may affect rendering in some XML processors.

Implementation

Stencila supports bi-directional conversion between Stencila documents and JATS. Parsing of JATS XML uses the roxmltree Rust crate with encoding powered by quick-xml. Per-node-type JATS encoding is derived via the codec-jats-trait and codec-jats-derive crates.

Limitations

JATS is designed for scholarly articles. Non-article document types may not map well to JATS structure.

Stencila-specific node types (e.g. executable code chunks, parameters, styled blocks) have no JATS equivalent and are lost during export.

Some JATS elements (e.g. <supplementary-material>, <ext-link> with custom types) may not be fully mapped during import.

Using --pretty can introduce significant whitespace in mixed-content elements.