Spys in the Lab: Reference Managers are all spyware

[Blogio]

A reference manager is a conceptually simple piece of software. You need to maintain a database of articles that you have in hand or that you know about, maintain many, many details concerning the article.... because, at some point, you are going to format that information into a citation and bibliography in a book or article of your own.

So, it's a glorified database entry program with a report generator, essentially.

This shouldn't cost a lot of money, nor should it leak what journal articles you have to the internet... but that's exactly what's going on.

These are the two choices: 1) Free web-based software that tracks your every move and will give/sell your data to whoever demands/pays for it and 2) Stand-alone software (usually commercial) that doesn't track your every move, but helpfully offers to retrieve data on your entire collection from the net. Either way, whoever owns the software you use has a pretty good readout on what you're studying, what associations you think exist in the literature, and probably what you're planning to do.

If you're a student... that's no problem. But if you're a professional scientist, that's exactly what shouldn't be happening (assuming you're any good at your job).

I've recently completed a survey of all available reference management software for Linux, and I can say with certainty that it's either bad (as in doesn't work), overt spyware, or covert spyware. You have to pay close attention to the language they use to describe their products. If they say something like "The metadata from your files will be extracted via indexing", that means that it's too much trouble to read your PDF, they're just going to send enough data to a server someplace that will know what PDF you have because they have a comprehensive list. It's not that I don't like the data lookup services. I just want to be able to pick and choose.

Fortunately, some packages are open source and can be rescued.

My bestest reference manager software that actually works is Zotero (https://www.zotero.org/). Now, unfortunately, I'm going to have to do a bit of brain surgery on this software to make it safe and release it under a different name.

It used to be said that if you aren't paying for the product, you are the product. Well, they don't give you the option to not be a product anymore unless you're willing to rewrite their spyware, which I am. Stay tuned.

[Blogio]

I haven't had time to fix Zotero. Maybe in a few months.