Reference management methods for GIS teaching material

I have spent the last couple of days reviewing my reference management system (or lack thereof) and looking for alternatives.  I like to save articles and website links I find online and through journal alerts and blogs so I can use them for case studies and examples in lectures and assignments.  For the last couple of years, I have organized this material by creating a folder for each lecture topic (current and possible new ones), with the intention that when it came time to update a lecture, I could just browse through my files.  The problem is I still manage to forget where I put articles, or duplicate them (sometimes several times), and there is no elegant way to cross-reference them if they are relevant to more than one topic (I use shortcuts, but it’s a clunky method).  So now that the term is over and my study-leave is underway, what better time to take a step back and review my reference management methods?

I have given both Zotero and Mendeley a try and have found both to have their strengths and weaknesses.  I won’t attempt to write full reviews or comparisons of them, as many others have already done this.  My quick analysis is that Zotero’s interface is okay, but limited since it runs inside Firefox (a standalone version is in the works).  Mendeley’s is much better, although it would be so much more efficient if you could see a separate PDF preview pane while looking at your list of articles to review (Zotero has this via the Firefox browser).  Mendeley’s winning feature for me was the easy method for ingesting and renaming my collection of existing PDF files.  With Zotero, I had to select each file individually in order to have the software rename it with a standardized format, which got very tedious, very quickly.  By the way, I should say that I take no sides in the open source vs. proprietary battle – I go strictly on functionality and usability (even just mentioning these two on Twitter triggered a mini debate from adherents on both sides).  For now, I’m going to keep working with Mendeley, as I think it will do what I need and is pretty easy to pick up.  When Zotero releases a standalone version, I will definitely have another look.  I may try some others that have been suggested to me via Twitter, such as CiteULike and, but I really just want to get on with it!    I have dumped all of my PDF files into one folder with the fervent hope that one of these will give me a fast and efficient way to search my collection by keyword and tags so I can pull together a short reading list for teaching and writing purposes.  It’s funny – I feel like I’m late to the whole reference management software party, and yet none of the current crop of solutions strikes me as being fully baked yet.

I am trying OneNote as a repository for making notes on teaching and blog topics.  I gave OneNote a serious try a few years ago, but just couldn’t get into the habit.  At that time I felt that, whatever I produced in OneNote would eventually be transferred to a Microsoft Word or PowerPoint document as a finished product, so why not just start there?  However, I’m finding that there is no easy way to organize a large number of topics, subtopics, pages, web snippets, etc. with that method.  So, it’s back to OneNote once again.  I like the fact that I can sync it with my SkyDrive and access it from any computer or even from their iPhone app (if they ever release it outside the U.S., that is – grrrr).  I have heard of EverNote but have not tried it as, from what I understand, OneNote is better integrated with the Microsoft Office suite, which I use heavily.

I have been amazed at how many files I have, and I’m always looking for better ways to organize everything.  Hopefully all the time I’m spending now reorganizing these files and links and test-driving various software and organizational methods will pay off in the future.  If they do and I adapt/improve my workflow, I will follow up with more details.

What method and/or software do you use to keep track of all your teaching material?






6 responses to “Reference management methods for GIS teaching material”

  1. adam.smith Avatar

    I don’t follow this:

    With Zotero, I had to select each file individually in order to have the software rename it with a standardized format, which got very tedious, very quickly.

    You can put multiple pdfs at once into Zotero, you can use “retrieve metadata” on multiple pdf files, and you can rename multiple files at once. I think Mendeley can watch folders, which Zotero can’t (there is a plugin – Zotfile – that can kind of do that and also allows for more flexible naming of files). (Easier access for plugins is one of the ways in which FLOSS matters directly for getting the job done – another Zotero plugin gives you pdf preview functionality (though it doesn’t work terribly well on windows).

    If you’re on a Mac, Papers is another option. If you’re on Windows, people seem quite happy with Citavi, though I’d be concerned about longtime viability. CiteUlike and are no reference management programs, so those aren’t really alternatives.

    1. Don Avatar

      Thanks for the comments and suggestions – I should have been more specific: the Zotero method I described was done in order to link to the original files, not upload them to the library (I had already hit the limit for free storage and was avoiding having to pay – I’m doing the same with Mendeley). If there is a way to do this automatically, I will certainly think about using Zotero again – I’ve still got a lot to learn on both systems.

      I’m using Windows, so Papers is not an option (too bad, as I hear it’s very good)

      I hadn’t looked at CiteUlike or, so thanks for the comment.

      1. adam.smith Avatar

        ah yes – linking is less comfortable, not possible using drag&drop (unfortunately – it’s been long requested and there is a ticket for it) but still possible in bulk: Under the green plus, select “Link to File” – you can select multiple files in the dialogue that follows. Retrieve and rename then works in bulk, too. I don’t use Zotfile, but my understanding is that it can help to streamline this, so you may want to look into that – as I say above, it also adds flexibility in file naming.
        Also, if cost is the only reason you use links instead of internal storage, you can just turn off file syncing in Zotero.

        1. Don Avatar

          Thanks – I have tried the selecting multiple file method, but have several hundred files, so that’s what I meant by it becoming a bit tedious. I will check out Zotfile. I didn’t know about turning off syncing in Zotero. Thanks again – very helpful!

          1. adam.smith Avatar

            glad that’s useful – as for selecting multiple files – it should be fine to import pdfs in large batches – 50 or so – into Zotero. You can use shift+click to select a large range of files. If they’re in a more complicated folder structure, you can use a saved search/virtual folder (how exactly that’s called depends on your Windows version: for filetype .pdf in the main folder and its subfolders and select the files from the virtual folder.
            Clearly this isn’t as comfortable as in Mendeley, but overall this shouldn’t take more than an hour or so and it’s a one time investment – so if you like Zotero better for other reason – such as FOSS, pdf viewer split screen, better word processor integration, better integration with online databases and other online sources – this shouldn’t really make the difference. Obviously, there are other reasons one might prefer Mendeley – included pdf annotator, stable standalone, maybe stronger social networking component, shinier gui – my point is just that initial costs of adoption should probably not figure heavily for software that you’re likely going to use a lot.

          2. Don Avatar

            You make a good point about looking beyond initial costs of adoption. I think I got impatient and figured there must be a better way. I’ll give Zotero another try. Thanks.

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