Upgrade Storage[Plugin] Abbreviation Helper - hover over an abbreviation to see what it means
I got tired of scrolling back through papers to find where an abbreviation was first defined, so I made a plugin that recognizes abbreviations in a paper and displays the meaning when hovering over it.
https://github.com/Cydoimos/zotero-abbreviation-helper
Zotero 7 or newer, works on Mac, Windows and Linux, MIT licensed.
It finds definitions using the Schwartz-Hearst algorithm (Biocomputing 2003), and also reads the "Abbreviations" lists some journals put at the front. There's a small built-in glossary for terms like PCR and ELISA that papers use without defining.
I checked it against 357 abbreviations across 22 papers from 12 publishers. It finds 94.7% of them and gets the meaning exactly right for 90.5% of those (97.9% if you count close-enough answers).
It has blind spots: supplier names like NEB that happen to look like abbreviations, gene names sitting next to explanatory text, short peptide sequences, weird stuff with / and - and anything with a space in it like Pol II. You can add those to an ignore list so they stop coming up.
You can also add your own definitions, which override whatever the paper says. There are optional lookup links to UniProt, GeneCards and a few others for gene and protein names.
Nothing leaves your machine and the only network traffic is Zotero checking for plugin updates.
Almost everything I tested it on was molecular biology, so I don't know how it holds up elsewhere. If you try it on something different I'd like to hear how it went.
The plugin was written with AI help. The code is all there if you want a look before installing it.
Feel free to leave feedback!
https://github.com/Cydoimos/zotero-abbreviation-helper
Zotero 7 or newer, works on Mac, Windows and Linux, MIT licensed.
It finds definitions using the Schwartz-Hearst algorithm (Biocomputing 2003), and also reads the "Abbreviations" lists some journals put at the front. There's a small built-in glossary for terms like PCR and ELISA that papers use without defining.
I checked it against 357 abbreviations across 22 papers from 12 publishers. It finds 94.7% of them and gets the meaning exactly right for 90.5% of those (97.9% if you count close-enough answers).
It has blind spots: supplier names like NEB that happen to look like abbreviations, gene names sitting next to explanatory text, short peptide sequences, weird stuff with / and - and anything with a space in it like Pol II. You can add those to an ignore list so they stop coming up.
You can also add your own definitions, which override whatever the paper says. There are optional lookup links to UniProt, GeneCards and a few others for gene and protein names.
Nothing leaves your machine and the only network traffic is Zotero checking for plugin updates.
Almost everything I tested it on was molecular biology, so I don't know how it holds up elsewhere. If you try it on something different I'd like to hear how it went.
The plugin was written with AI help. The code is all there if you want a look before installing it.
Feel free to leave feedback!
https://s3.amazonaws.com/zotero.org/images/forums/u19380537/iyyu66u7y9hmk6qupe7r.gif
What's new since my first post:
- Better detection. I rewrote how definitions are matched. It now also reads methods sections placed after the references (Cell Press STAR Methods, Science) and ignores page headers and footers. On a new benchmark of 39 papers that I didn't use for tuning, it finds 88.6% of defined abbreviations (the previous version found 82.6%), and the meaning is right for 96.3% of them.
- Each tooltip now says where its meaning comes from: defined in this paper, a probable meaning, one of your other papers, a common term, or your own definition.
- Definitions from your other papers: when a paper uses an abbreviation without defining it, the plugin can offer the definition from another paper in your library. This stays on your computer, and you can turn it off in the settings.
- Tooltips work in Zotero 10's Reading Mode.
- A new optional tooltip shows where a word is used: once you switch it on, hold Ctrl (Cmd on Mac) over any word to list its first uses in the paper and jump to them.
- 73 more common abbreviations in the built-in glossary, and five more databases for the lookup links (Ensembl, InterPro, RCSB PDB, RNAcentral, Addgene).
- Lots of bug fixes. The most important one: with several PDFs open in tabs, tooltips could show another paper's definitions. That's fixed.
It's also listed on zoteroplugins.org, which checks the code of Zotero plugins (grade A).
Download: https://github.com/Cydoimos/zotero-abbreviation-helper/releases/latest