See also Scientific publishing.
There are two common ways for academics to write their articles: LaTeX and Microsoft Word. LaTeX is well-suited to heavily mathematical and structured writing: it has extensive equation typesetting that still sets the standard for quality, comprehensive automatic cross-referencing and indexing, high-quality PDF output, support for multiple customizable document styles, and is completely programmable through a (admittedly rather unpleasant) macro language.
Word, on the other hand, is WYSIWYG. That’s about all I’ll say about it.
The problem with both is they’re not well-suited to modern publishing. We don’t just want static PDFs: articles must be presented on the web, archived, searched, reformatted for new devices and apps, cross-referenced, and so on. LaTeX, with its focus on print output, isn’t very good at this, and Word is, well, Word.
JATS XML is a tag suite for tagging journal articles. Meant to provide semantic markup for articles. Publishers typically use a combination of scripts and outsourced labor to convert Word or LaTeX submission to JATS, since articles required to be deposited in PubMed Central have to be provided in JATS.
Because JATS is semantic, it’s easy to extract references, do full-text search, text mine articles, and so on. But it’s XML, so authoring is a pain. Journal publishers use JATS, but editors and authors basically never touch it, so nobody supports JATS submissions yet.
Texture is a web-based JATS editor, using a WYSIWYG system. Initially meant for use by publishers, but eventually could be used by authors for direct JATS submissions.
pandoc-jats, an extension to Pandoc to support output of JATS from anything Pandoc can ingest.
ScholarlyMarkdown was an attempt to expand Markdown (through extensions to pandoc) with cross-referencing, bibliographies, and so on, so it could be useful for academic writing. Had output to Word and LaTeX. Unfortunately, not touched since early 2015.