Using Zotero as a Robust Research Manager

Recently a friend of mine post­ed about los­ing his entire research library in OneNote, which brought flash­backs to los­ing my entire research library many years ago in the Endnote 7 to X upgrade.

You nev­er want to see this.

As such I am using this as an oppor­tu­ni­ty to briefly review my own research and back­up prac­tices, and run through how I use Zotero as a cloud synced, con­stant­ly backed up, and ulti­mate­ly human read­able research manager.

Zotero

Firstly, I have post­ed about Zotero a few times now, so there are more details in those posts. All avail­able here: http://www.porterblepeople.com/tag/zotero/

Zotero func­tions as the heart of the sys­tem and is used to make access to your research library quick and easy. But it is not the only part of the sys­tem and requires oth­er aspects to func­tion effec­tive­ly. As I go into in one of my oth­er posts the Zotero cloud stor­age capac­i­ty leaves a bit to be desired, so I store all of my PDFs in Dropbox. Zotero makes it easy to rename all the files eas­i­ly and keep soft-links to the database.

Zotero also allows you to keep notes with your doc­u­ments, and those notes are indexable. 

Notes attached to a jour­nal article.

Those notes are also syn­chro­nised across devices using the Zotero cloud, and as raw text they take up very lit­tle space, so no wor­ries there.

Zotero Export (BibTeX)

However, on its own Zotero isn’t great for being human read­able. The last thing you want is for a ser­vice to decide that they are wrap­ping up and then you lose access to all your notes tak­en in that plat­form. I have had this hap­pen with old OneNote, and seen it hap­pen plen­ty of times with oth­er platforms.

Mercifully in the research man­ag­er world there is an open-source stan­dard called BibTeX. Now BibTeX is usu­al­ly used to gen­er­ate ref­er­ences for LaTeX. If you are a LaTeX user then this is great (and this post is unlike­ly to be news to you) but for any­one else who does­n’t use LaTeX then this aspect is like­ly to be some­what moot. Rather we are inter­est­ed in the fact that it gen­er­ates a plain-text human-read­able export of your data­base. In the event of your soft­ware being with­drawn or ren­dered inop­er­a­ble by some­thing (e.g. 64bit upgrades) then you will always have all of your research entries and notes in plain text. 

BibTeX out­put from Zotero

I will be the first to admit that it isn’t par­tic­u­lar­ly pret­ty, but it is human read­able and that is what mat­ters. Plus it is entire­ly like­ly that some­one out there will have writ­ten a con­vert­er to oth­er plat­forms or soft­ware that uses BibTeX as an inter­me­di­ary step, and there­fore you can restore your data some­where else. Absolute worst out­come is that you can still read your data with­out hav­ing to deal with a closed soft­ware for­mat (and you could always learn LaTeX and keep using it). 

To do this Zotero needs a lit­tle plu­g­in called BetterBibTeX, which I cov­er in this post: http://www.porterblepeople.com/2015/06/zotero-addons-extensions/ In that plu­g­in you can export your library (File>Export Library…) and just check the “Keep Updated” box on export. I store my library in my Dropbox fold­er so that it is always cloud synced.

Dropbox

I use Dropbox as my cloud stor­age of choice, but most cloud stor­age will work well enough. I quite like Dropbox though as it also offers snap­shots and the abil­i­ty to roll back and restore files. Anything you use for cloud stor­age should offer those, in case you acci­den­tal­ly delete an entire direc­to­ry. But if the cloud stor­age you choose offers the abil­i­ty to roll back or undelete files, then use that.

Fin

That is it. Expecting more? It is a rather sim­ple and robust back­up sys­tem for a research library. I have had a hard dri­ve die on my lap­top before and it was annoy­ing (down­time) but all of the data was restor­able quick­ly and eas­i­ly (being on 3G made it a bit slow­er). I was back up and run­ning again in about 8 hours. 

tl;dr? Critical things: keep your files backed up, and your research data­base export­ed in a human read­able format.

Appendix A

As some friends have point­ed out using a cloud ser­vice as a back­up is only one lay­er of redun­dan­cy, and may not save you. Especially if you have sync con­flicts or longer offline peri­ods. However, in this I am aim­ing for a bal­ance of automa­tion and sim­plic­i­ty, as com­plex­i­ty often intro­duces bar­ri­ers to adop­tion of new practices.

Personally I have Dropbox set­up for con­stant sync which keeps my 3 machines synced, plus Time Machine back­ing up to a local serv­er, and that doing a night­ly rsync to my US serv­er, and I also take a portable HDD into work that is on month­ly rota­tion. Paranoid? No, I worked for a cou­ple of unis in sup­port roles and have seen first hand the dev­as­tat­ing effects of los­ing research too many times. But it is a lot more to set­up than a cloud service.

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