Online collaborative manuscript annotation

While at the inaugural AMIA Summit on Translational Bioinformatics the first half of this week (stay tuned for another post summarizing that), I started thinking about some ideas for tools that could help make discussion of papers easier and more productive.

Currently, it seems that there are a few avenues for discussing a paper: 1) have an informal conversation in person, 2) hold a journal club where one person presents the paper and discussion ensues, or 3) blog about it and hope others comment. (You could argue that another avenue exists through some journals - especially open access ones - allowing comments on published articles, but this hasn't caught on as far as I can tell.) There are several disadvantages of the current systems. In-person conversations or journal clubs can be stimulating as they happen, but are transient and usually go unrecorded, resulting in little tangible benefit to others (or often even the participants); they also usually preclude remote participation without some sort of audio-visual setup. Going the blog route allows anyone to participate, but it's difficult to connect the comments back to the paper and the discussion may be less productive than hoped.

A group of students in my human-computer interaction class a few years ago developed an idea called Collaboread for their final project. In essence, it allowed multiple online users to markup a document, enabling collaborative annotation. I'm sure there are several products out there that allow either online markup of documents (Adobe, for one) or collaborative editing (Google Docs), but I haven't seen anything that resembles exactly what I envision.

Suppose you are viewing a document on the screen - maybe a full-text articles at BioMed Central, or a PDF. Clearly, things like web URLs and references should be hyperlinked already. But suppose you could create additional hyperlinks, such as to wikipedia pages, other papers that were not referenced but are relevant, blog posts, etc. You can also start individual discussion threads attached to a particular results, claims, or points made in the paper, or to tables or figures. Mousing over or clicking on the icon indicating such a thread would bring up a summarized view of the thread overlaid on the screen which you could browse more deeply or hide if you decide you're not interested. The idea is to make a richly annotated document that is easy to read but at the same time make it easy to see what other people thought or were confused by and respond if so inclined without too much disruption. When I envision this, I see a Google Maps-like navigation and manipulation style with lots of linked text, little colored balloons at the POIs - the discussion threads, and liberal use of tags to help with filtering and searching of the document and annotations.

A tool like this would be useful not just for journal club-style discussion of papers, but also as a teaching and editing tool. Authors could collaboratively comment on a paper, or learn from others' comments after it is published and made the focus of such a discussion. Readers and students would benefit from the additional linked resources and learn from the discussions how to critique a paper. And the annotated document would be available to everyone long after discussion has tapered off.

Of course, there are potentially many technical, legal, social, *al issues surrounding this, but I think some kind of tool along this vein would be useful and interesting. Does anyone know of any tools that do these things already? If not, I am already looking into what it would take to develop it, and would appreciate tips, suggestions, warnings...

Science journal feedmixes

The topic of literature review came up at a recent group meeting. Our advisor receives a number of print subscriptions to journals, but these often languish in some forgotten corner. Even when they are brought out of the depths, it seems a daunting task to leaf through them to find articles of interest to each student. Since everyone is on the interwebs, it is much easier (and complete) to get updates on relevant articles through a website or email, peruse the titles and blurbs online, and then decide what to actually sit down and read. There are a few problems with this, however.

1. Getting alerts from journals, search engines, or aggregators like Faculty of 1000 still usually produces too many articles to sift through.
2. To limit the amount of junk you get, you provide keywords - but, if you're like me, you will browse through unlikely articles in Science or Nature or PLoS ONE on a regular basis because they look interesting, so keywords will filter these out.
   

I've set up a feedmixer for science journals and related information using Feed Digest. It's little more than an aggregator right now so it doesn't really address those problems. If anyone knows of any cool tricks to help sift through the ridiculous amounts of information we're supposed to keep up with, without losing the unexpected gems, I'd love to hear it!

Update: A new tool called Persai claims to learn your preferences through what you accept and what you reject (review on Slate), and filters your feeds accordingly. I'm not sure it will help with issue #2, but it's probably just an irreconciliable trade-off between #1 and #2. Perhaps the solution is to have a couple different pages set up with Persai - narrow ones for specific fields or interests, and broader ones for the science "pleasure reading"!

Review on open source CMS for bioinformatics

An alum of my lab recently published a review on open source content management systems and their uses in bioinformatics.