✨ Italicize genus and species names in Zotero ✨

This repository present a procedure to automatically italicize the species names (or any other word) in the titles of your documents in the Zotero library.

Introduction

Zotero is a very useful and powerful tool for managing bibliography. However, when the titles of the documents contain a genus or a species name, many of us struggle because:

• the nomenclature standards require that genus and species to be written in italic
• depending on how the document is imported, the genus and/or species name are rarely already in italic
• it's boring and fastidious to go through the references section of a documents to manually italicize all the genus and species names

The way Zotero manages the rich text formating is with HTML tags. So to italicize a part of the title, it needs to be enclosed by the following HTML tags: <i> Genus species <i/>. So one solution is to go across all the references items in our database and add manually theses tags in the titles, but this is long and tedious.

But lucky for us, since the release of Zotero 5.0.73, it is possible to directly script into Zotero. So here is a script for automatically add the <i> html tags around a list of user define genera and species names.

The step-by-step procedure

• Backup your Zotero data (just in case; it's pretty simple, see here how to do that)
• Open the zotero_italicize_species.js script in any text or script editor (Gedit, Notepad).
• In the toModify variable, insert the list of words (or character strings) you want to have in italic. Each character string is enclosed by quotation marks ("), seprarated by a comma (,).
  Important: in the character strings, you have to separate the genus and the species, e.g. var toModify = ["Quercus", "pubescens", "Homo", "sapiens"]; and not var toModify = ["Quercus pubescens", "Homo sapiens"]; (see the explanation below).
• Select the whole script and copy it.
• Open Zotero, in the menu, go to Tools > Developper > Run JavaScript.
• Paste the script into the code box of the Run JavaScript window, and tick the 'Run as async function' box.
• Click Run or press Ctrl + R.

That's it! Enjoy the time you saved from manually editing all these titles ;)

Explanations

The script will go through every character string in the toModify variable with regular expression to add HTML tags around the character strings.

The toModify variable has to contain every single character string separated from each other.
Depending on the documents you have in your database, genus and species names can occur in different ways. In some titles you will have only the genus name, e.g. Quercus, and in other titles you will have both genus and specific epithet, e.g. Quercus pubescens:

• if your toModify variable only contains genus names (var toModify = ["Quercus"];), the specific epithet will not be italicized (ending up with "Quercus pubescens");
• if it only contains the genus + species name (var toModify = ["Quercus pubescens"];), then all the occurrences of "Quercus pubescens" will be italicized, but not the occurrences of "Quercus" alone;
• and if it contains both (var toModify = ["Quercus pubescens", "Quercus"];), then all the "Quercus" in the occurrences of "Quercus pubescens" will be de italicized 2 times (2 HTML tags: <i><i>Quercus<i/> pubescens<i/>), which will "cancel" the italic formatting around the genus name (ending up with "Quercus pubescens").

That is why the toModify variable has to contain genus and species names separated (var toModify = ["Quercus", "pubescens"];). Note that this will add a HTML tag around each string (<i>Quercus<i/> <i>pubescens<i/>), which might seem a bit messed up. That is why the script contains an extra step of cleaning (see line 36) that removes all the "<i/> <i>" patterns (thus transforming <i>Quercus<i/> <i>pubescens<i/> into <i>Quercus pubescens<i/>, that is Quercus pubescens). However, in case you still want to put the full Genus species string in the toModify variable, the script will still work. It is even recommended in case the genus name or species epithet is ambiguous with non-Latin language, e.g. you might want to put "Gorilla gorilla" instead of "Gorilla" alone, otherwise all the occurrences of Gorilla as the common name will be italicized.

Note that the script is designed such that substrings are not italicized, e.g. if you have "Annona" in your toModify variable, "Annona" will be italicized but not "Annonaceae", although "Annonaceae" does contain the substring "Annona".

PDF file renaming

If you use the function Rename File from Parent Metadata (default Zotero renaming function), Zotero will automatically not include the HTML tag in the .pdf file names.

However, if you are using the Zotfile extension for renaming, it will include the HTML tags in the file name.

To get rid of the tags in the filename with Zotfile, there is a trick. You first have to add a user defined wildcard for the title:

• Go to Edit > Preferences > Advanced > General
• Go to Config Editor > I accept the risk!
• Change the extensions.zotfile.wildcards.user value to {"1": {"field": "title", "operations":[{"function":"replace","regex": "(\\<.*\\>\\b)|(\\b\\<.*\\>)", "replacement": ""}]}}
  You have now defined the new wildcard %1 for Zotfile file renaming.
• Now go to Tools > ZotFile Preferences > Renaming Rules
• Use %1 wildcard instead of %t wildcard for renaming the title, e.g. {%a} - {%y} - {%1} will rename the files like "Author - YEAR - Title" with the title removed from any HTML tag.

Ressources

• https://www.zotero.org/support/dev/client_coding/javascript_api#batch_editing
• Note that this could also be probably achieved in R using Zotero API (see e.g. https://github.com/mbojan/zoterro, https://github.com/giocomai/zoteror), although no ready-to-use function for modifying existing items has been implemented yet
• See also Mazospega that also intends to italicize species names in Zotero, but in a different way (with Python and interface).