09 November 2007

Publishing in the New Millennium - Second Panel

(KT: My apologies for not getting these up on Friday. Due to technical difficulties, I'm just catching up now.)

Here are some notes from the second panel (out of two) at "Publishing in the New Millennium" at Harvard Medical School, entitled "Publishing 2.0". Each panelist gets five minutes to introduce themselves and to identify a few key issues.

The panelists:

John Wilbanks - Vice President of Science Commons at Creative Commons

Wilbanks kicked off his 5 minutes by distinguishing the difference between the "social web"/ Web 2.0 and the "research web". This provided a great segue into the Neurocommons work, an open source knowledge management tool. While Science Commons uses a few technologies that fall into the "Web 2.0" category - blogs, tags, comments and feeds - our focus is more on the research web, which Wilbanks succinctly explained.

He started by illustrating how bad the Web works for science. This is where you can start to focus on "research web", in hopes of bringing some of the power of the Web (think of what it did for commerce in terms of eBay, Amazon, etc) to the scientific research cycle. Our Neurocommons project works towards this goal.

His most recent post on Nature Network actually looks at this exact issue, echoing a number of points made on Friday. From his blog:

"We need to start talking about the Research Web, which is the reality of what we’re building here. Just as the Social Web uses, but is more than, AJAX), the Research Web will use the Semantic Web, RDF and other technologies and strategies to accomplish something we deeply care about: Making medical research more effective so that we can cure and relieve the suffering of patients.

We need the Research Web because the existing Web doesn’t work for research. Here’s what I mean: Googling a phrase like signal transduction genes in pyramidal neurons doesn’t get you a list of genes. It should get you a list of genes. No amount of collaborative filtering makes it easy to read 188,000 papers – and this is stuff where you tend to want experts moreso than the “wisdom of crowds” – advice from someone who doesn’t understand signal transduction tends to be less reliable than from someone who does.

The Research Web is about integrating lots of stuff that wasn’t designed to be integrated with anything. It’s about getting precise answers to complicated questions instead of a mess of Web pages. It’s about the move to industrialize the way scientists annotate data. The Research Web is about making the Web work in a complex data environment, where machines make and transmit terabytes of content that humans have to interpret."

Moshe Pritsker - Editor-in-Chief / Founder of the Journal of Visualized Experiments (JoVE)
video publication for biological research

Why did we start publishing this research in video? The idea comes from the lab.

The journal publishes "video articles", documenting how certain biological experiments are conducted. The goal is to make scientific publication usable, adding another layer of functionality to traditional publishing.

Hilary Spencer - Product Manager, Nature Precedings

Precedings is a pre-print server, for prepublication research, preliminary findings and other documents of scientific interest. Spencer provides a bit of background about the server, noting that Precedings does not publish materials regarding clinical trials since the material on the server is not peer-reviewed. Due to that, Precedings does not accept materials that make specific therapeutic claims.

"Web 2.0" technologies employed include a rating system for members of the community, relying on users to rate, filter and flag content of interest. Other 2.0 technologies: comments, "vote to promote", tagging, RSS feeds and e-mail alerts.

Why post research to a non-peer reviewed preprint server? Spencer touches on the following incentives for those in the research community: ability to record the provenance of an idea, Precedings serves as a permanent repository, enables authors to get pre-publication feedback, greater exposure, and authors retain copyright. Content is indexed, as well, in Google Scholar and BASE (an academic search engine).

Bora Zivkovic
- Online Community Manager, PLoS One

PLoS One - now 10 months old. Bora shows some of the tools that PLoS One employs. This journal operates on Topaz software, allowing community members to add content / value to a scholarly work after it's published. This includes a rating system, comments and the ability to post annotations.

A few questions to highlight ...
Q: How much of the community comments on material (directed towards PLoS One and Precedings)?
A: Spencer: Commentary on Precedings is actually quite low. Not sure why. Precedings does not allow anonymous posts, which could be why the numbers are so low. But not sure.
Zivkovic: PLoS One has quite a bit of commentary, 1,000 back in July and growing since then.

Q: There was a considerable amount of work done on the Semantic Web years ago, talk of it being a "cool" technology. What makes you think this will work now?
A: Wilbanks: The SW allows for one to add context to links between two things. The difference this time is that this is a public effort, bringing the power of Metcalfe's and Moore's Law to science. Wilbanks thinks this (being the NC and our SW work at Science Commons) is useful enough to justify the pain of working with RDF. This provides a single point of access to the public domain and information.

Q: Generating and editing all of that video seems like an expensive ambition. What's JoVE's business model?
A: Pritsker: It is expensive and even more so - it's difficult. JoVE employs a distributed production network, minimizing some of the cost through a network of contractors in certain areas. Each of these contractors have not only the skills to film the experiments but backgrounds in the sciences, giving them the knowledge to accurately and thoroughly document the experiments.

Q: I'm curious about the age groups for who uses these services / sites?
A: Wilbanks: The majority of people who use our SW work / NC project are hardcore systems biologists, making this not about the age per se, but more about the willingness someone has to take a risk with a new technology. This skews our demographic.
Spencer: Anecdotally, it's across the board. No formal surveys of the users have been done to date.
Zivkovic: PLoS One is working currently on surveying users to gain a better understanding of the demographic.

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