managing references

Jess and Alick from Mendeley recently visited us at NYU, with Jess leading a discussion on using Mendeley for reference management (slides). She covered these features: (1) adding content; (2) managing content; (3) sharing content; and (4) discovering content. I should say that, considering an analysis of reference management tools that we thought of yesterday, we’re likely to call these functions, with the two other major ‘objects’ being uses and steps. But hold that for another post. I should also say that I’m a Mendeley Advisor and that I think it’s the best tool for reference management. And, as you could guess, everything that follows is ‘all me’.

I think the above features are probably described somewhere on the Mendeley page, and maybe in videos, and if not, then I think they will be soon. Nonetheless, I’d like to textualize some of what Jess discussed, and add some commentary or highlight some stuff.

Adding content

Adding stuff is easy. One route is to drag-and-drop content. You can do that with files or folders. If it can, Mendeley will extract metadata and it’ll sync with online for backup. I think that’s conditioned on your preferences. Another option is to add the stuff to a watched folder and it’ll sync. Third option is to use ‘Import to Mendeley’ from within a browser, which will add the stuff directly.

To me, this seems like a relatively broad set of ways to get stuff in, and my impression is most of it works pretty well. It’d be interesting to know more about how people are differentially using these. For example, is there some clean way to decide that you’re going to use web-based importing for this kind of stuff and watched folders for a different kind of stuff, and drag and drop almost never. It can actually be pretty easy to forget all of your options, and having some bridge to them, like some way of saying what you’d like to do and then it choosing the best option, might be helpful. Another option there might just be for you to be able to visualize how you typically do things. That visualization could be the point at which suggestions are made. Then again, you don’t want to have a modernized-and equally annoying-version of the ‘Office Assistant’ that showed up in some Microsoft product that I’ve pretty much forgotten about.

We have also noted, as you may have, that as acquiring content has gotten easier and easier, our stack of want to read but will never read, has gotten bigger and bigger. You could say that as the efficiency of getting stuff has increased the ratio of read to have has diminished. This suggests that just after addition might be a good time, not only for sorting, but for prioritizing. Like, ‘these are super important and I need to look at them’. This could also be connected to something at intervals, or something preferenced-out, that comes up later and says ‘you marked these as must reads and you’ve done nothing with them, why not read now or archive’.

As is the case with Gmail - Priority Inbox, the obvious way to go about this is for most of it to happen without your input, but in such a way where you’d be able to modify later. An example might be where Mendeley marked a paper as a priority and put it in my must read folder, but it’s actually not important and is more of an optional read, so you change it to that and it goes to a different location. Here too, though, it might be nice to be able to create some rules, or as many conditional rules as you like. These might be things like, ‘if I import something by Steve Jobs, put it in must read’. But even that might be weird since you might import things after reading them.

Managing content

You can search as you type and can do it within documents, meaning as you enter something. Example might be something like ‘protein’, where it’ll pull up stuff that has ‘protein’, and highlight it in yellow. I actually don’t find this terribly useful. I mean it’s obviously important to be able to search for stuff, but I don’t like looking at what comes up, maybe because I’m not familiar with how the stuff will show up and it’s visually complicated. It’s also not clear why this stuff is any more limited than say searches with OS X’s Finder. Like, ‘Kind>Is>Image>JPEG + Last opened date>Is>this month + File label>green’. The equivalent of that could be something like wanting supplemental information that I’ve read in the last six months that has tags for ‘retna’ and ‘graffiti’. How could this be done with what’s there now? If it can be done, is the output easily parsed?

This reminds me that the green dot that shows whether you’ve read something is flawed. You double click something to look at it, and the green dot goes away meaning you read it, but you didn’t, you just looked at it. It seems like opening something doesn’t need an indicator, but reading does. If an estimate can be made automatically of whether a user has finished reading something, why not prompt them and say ‘we think you’ve finished reading this, have you’. Then show the outcome of that. This is weird though because we’re not tied to readable things, so one would hope that wouldn’t show up for things that are just a reference, or an image, for example. But with a video would you like something such as ‘we think you’ve finished watching this, have you’? As it is now, you open something to read the abstract and it’s then marked as read, then you end up putting it back to unread.

You can highlight (but only in yellow) and you can add Post-it Notes, which are called annotations. Not to be inconsistent, these can only be yellow, unlike the ‘real’ ones from 3M. These have an indication of who wrote it, ‘You’, and the date/time, as well as the page. And, something you might struggle to remember, the ‘Notes’ (the text box on the right side) is for your own comments. I find both of these rather limiting. You can’t, for example, outline very well in ‘Notes’ since there are no styles, such as ‘heading 1’. You can’t resize this or reposition it. You can’t have more than one. You can’t make different saves of stuff. I also can’t tell from the main ‘My Library’ which documents have this stuff, or who has added it. I might like to know, for example, that Umesh and I have a bunch of annotations on this document and to be able to see that from ‘My Library’.

We have also thought that in some cases the right model would be to say that this content, such as this PDF, is a master, and all of this stuff is a layer. Then for the layers to be editable and easily visualized. Idea is we modify it so that we have ‘these annotations AND notes are a single layer’, layer 1. This summary and criticisms from our lab is in layer 2. These layers, as in Adobe Illustrator, can be rearranged, meaning we can change what’s in front of what. Also, we can change their permissions and visibility. For example, we might want to say lock layer 1 (James and Umesh notes) and make them visible only to these people: James, Umesh, Rob and Rich. Then keep layer 2 (group summary and criticisms) unlocked, so everyone can edit, and make it visible to all, but invisible on printing. You can imagine this would break down in cases where there is no obvious master and in that way could be connected to the ‘find duplicates problem’.

You can interface with Mendeley in some word processing tools. The known ones are Microsoft Word, OpenOffice and NeoOffice. For our purposes, a much better set would be Pages, Google Docs and LaTeX. Everyone uses these for preparing papers. One preference, which Mike raised, is to separate the compile bibliography step, as in LaTeX with BibTeX. We are all also under the impression that these things are, to the extent that they are there, only halfway there. Having said that, we think this is going to get much better soon. I mean, dump papers in a private group with colleagues working on a paper, read stuff as you go along, have a common set of tags for adding to the paper and to talks (meaning Keynote), add them from within Google Docs, click something there and it compiles a version of the bibliography..

Sharing and discovering content

You can obviously create groups to share references and documents. This is really important, is cool, seems to be defined in a reasonable way and seems like it’ll continue to get better. You can also use Mendeley to connect to others and to share your publications, which happens through your profile. I don’t know if it’s already there, but, assuming it isn’t, it might be nice to have more stuff to mark what is yours, including stuff that isn’t official publications, such as ‘these are my notes on Linear Algebra 314’. This could also be linked to LinkedIn or similar tools. Another thing is to find stuff, such as with ‘Most read articles’ in an area or to do so via groups owned by others, such as the one for ‘Bayesian MCMC’.