Semantically marking up JATS bibliographies using meTypeset and Zotero

Originally published on eve.gd on 5 July 2014, last updated 6 September 2026.

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A couple of weeks ago I wrote about the potential for producing semantically rich JATS element-citations by using Zotero's built-in CSL engine. A short while after writing that post, I wondered whether it might, instead, be possible and better to directly link my typesetter to a Zotero database. I quickly mocked up a prototype using an improved version of the libzotero library in Qnotero for the Zotero interaction.

potential for producing semantically rich JATS element-citations by using Zotero's built-in CSL engine
my typesetter
mocked up a prototype
libzotero library in Qnotero

A full initial implementation of this, which replaces the original meTypeset internal bibliographic database, is now available in the zotero branch of meTypeset.

available in the zotero branch of meTypeset

The process for Zotero typesetting in meTypeset is now, as follows:

• meTypeset classifies bibliography entries and places them inside mixed-citation elements
• If the Zotero flag is passed to meTypeset ('--zotero' or '-z') then the bibliographic database kicks in
• The Zotero handler sanitizes input through a series of regex replaces (special characters, digits etc.)
• The Zotero handler searches the local database iteratively reducing the search string by one word from right to left until it finds a unique hit
• If a unique hit is found, the original mixed-citation string is transcribed into a comment and a semantically rich JATS element-citation is inserted

References

This reference list has been generated, in many cases, through an automated process and may therefore contain errors or incomplete metadata. It is provided purely as assistance for finding the items mentioned within this post.

1. ‘GitHub - MartinPaulEve/meTypeset at zotero’, GitHub <https://github.com/MartinPaulEve/meTypeset/tree/zotero>

2. ‘GitHub - MartinPaulEve/meTypeset: meTypeset is a tool to convert from Microsoft Word .docx format to NLM/JATS-XML for scholarly/scientific article typesetting.’, GitHub <https://github.com/MartinPaulEve/meTypeset>

3. ‘Standalone sidekick to the Zotero reference manager (Qt4 version)’, GitHub <https://github.com/smathot/qnotero>

https://github.com/MartinPaulEve/meTypeset/tree/zotero
https://github.com/MartinPaulEve/meTypeset
https://github.com/smathot/qnotero