New publishing technologies challenge the traditional structure of peer-reviewed scientific journals. For hundreds of years the “article” has been the primary vehicle for conveying scientific information – but semantic markup, tagging, and wiki are reconstructing scientific publications into a flexible and evolving concept. This panel will look at the social and legal implications of “Web 2.0″ and “Semantic Web” as they impact science and scientific knowledge.

Some of this was a bit over my head, but I’m just going to toss up my notes and then follow up with my impressions.

Panelists:

• Moderator: John Wilbanks, Creative Commons
• Matt Cockerill, BioMed Central
• Melissa Hagemann, Open Society Institute
• Timo Hannay, Nature Publishing Group
• Amit Kapoor, Topaz/PLoS One

Notes:

• We used to communicate scientific information by sending it to someone and having them publish it
• Definitions:
  • Timo: Web 2.0:
    • Multi-faceted concept
    • Architecture by participation (network effects, harnessing collective intelligence)
    • The Long Tail
    • Open APIs, Mashups (Open Data and Open Access)
    • Interface Issues (AJAX, web apps)
    • Development process (perpetual beta)
    • Web as a platform
  • Matt: The Semantic Web
    • Web pages no longer electronic paper
    • Robots/machines reading them along with humans
    • Defining standards for allowing computers to read information
    • Flood of data, more info that humans can possibly read
    • Need semantic web tools to sift through it
    • Help scientists publish work in a way that captures semantic structure
  • Melissa: Open Access
    • Free online availability of scholarly content
    • Defined 5 years ago – Budapest open access initiative
    • Open Access Journals are freely available online and don’t rely on subscriptions for revenue
    • Apply combinations of new business models
      • Article processing fee
        • Fee paid by researcher or research grant
    • Many researcher agencies are mandating Open Access for their researchers
• Measure impact of article by citations in other articles (much different than hyperlinking)
  • Citation specifics have been a monopoly, still publish the definitive numbers
    • Starting to become available from other sources (Google Scholar)
  • Scientists don’t blog or comment very much
    • Those things don’t get credit for them
    • Very competitive
  • Connotea: Del.icio.us for scientists
  • Standards are being developed for web usage of scientific sites
  • Citation-based metrics—takes too long to get the data
    • Ancient history by the time everything is published
• Amount of info that has to be dealt with is absolutely amazing
  • Lack of standards, lack of formats
  • Semantic Web played huge role
    • It is an evolving concept
    • Start with a concept, modify it over time
  • Text annotations
    • Attach a note to an article that says specific research is wrong
    • You can later search for all opposing theories
  • Trying to put out a release every two weeks
    • At about version number 0.5 now
• All journals now (whether they like it or not) are databases
  • What is missing is the standards for the different types of data to be interwoven
• No way BioMed science can move as quickly as it could if data is not open
  • OpenAccess makes this possible
  • Facilitates exchange of information
• Nature relies on reader subscriptions
  • Nature rejects 92% of papers submitted
• NatureJobs : Scientific career service
• Web 2.0 science tools don’t generate any revenue yet (like Connotea)
• History of policy pressures from government
  • OpenAccess – government funders didn’t want to pay for information twice
  • One funder provided a grant of 250,000 pounds to pay for research then he himself couldn’t access it
    • Wondered how much impact the research will have if nobody can access it
• Semantic Web
  • Everything needs a permanent URI
  • What is the vocabulary of the community?
    • Bottom up AND top down approach to establish vocabularies
    • Wikipedia approaches have great value because otherwise nothing will ever happen
  • Bookmarking can become much more than keeping a list of favorite articles
    • As someone bookmarks and tags articles of interest, they can assemble a collection of scientific knowledge that is intresting and trustworthy
      • Can be used to recommend other research
  • RDF and ontologies have their place, Tagging and Microformats have their place
    • Tagging gives noisier data
    • Microformats are not the same as a formal ontology, but can be very useful
  • Defining things like what a gene is should be left to scientists
    • Things like defining an author can be done by the community
• Question: Total divergence of solving the same problem (Tagging vs. Semantic Web)
  • Tagging: Assign keywords, let the Googles of the world figure it out
  • Semantic Web: Each document filled with tons of data
  • Amit: Tagging is a way of classifying objects
    • Tagging is a small subset of what the Semantic Web is all about
    • Tagging is the first step
    • The cost of putting in semantic web info is very high
      • Who is going to bear that cost? The author? The distributor?
• Great second question from Amy, but a bit over my head. Must get from podcast when it comes out. The gist was how about how user-generated content can feed The Semantic Web.
  • Very effective ontologies have been extracted from user generated Wikipedia content

I work with many scientists that publish papers, but a lot of this is still so very foreign to me. I personally have a lot of faith in “Web 2.0″ tools such as tags and Microformats. I struggle a bit with some of this Semantic Web stuff.

I guess if I was trying to record my life by using Semantic Web technologies, I’d have to somehow go back and record everything I’ve ever said, where I said it, who I said it to, what they said back, what other thoughts I had without speaking them aloud, etc. If I use “Web 2.0″ technologies to record my life, I’d have my blog posts, Flickr photos, Del.icio.us links, YouTube videos, Twitter tweets, GMail, and any other social tools—plus the tags, timestamps, and (perhaps) GeoCodes that go with each. I could go a step further and do a desktop crawl for files, local photos (I haven’t thrown all 2500+ photos of Ella into Flickr), perhaps POP email, timestamps, folder names, etc.

Would this second approach be perfect? No. But could it be done? Yes. To me, the Semantic Web just feels too much like a dream that is unachievable. The panelists were definitely giving me that vibe, too. There is already so much scientific information out there. You can’t go back and put all this meta info on it. And for all the information that’s coming out, it’s hard to force people to follow a strict process of extracting certain data for the Semantic Web purposes. You can, however, track how that information floats around the web, how it is tagged, sorted, commented, annotated, etc.

One thing that didn’t sit well with me is the fact that scientists won’t blog because there’s no “credit” for that. They need to release their info in an environment that can be tallied up to rank them against their “competition.” Well, does writing a book directly help a blogger’s Technorati ranking? No, not directly. But with that book out there, more discussion about that person will ensue. Even though links are not being made to the book, the book is causing more discussion. I would like to think that a scientist that shares by blogging and commenting would gain notoriety in other ways. Perhaps not, but I’d like to think that.

But what do I know? I’m just a web hippie. I know many Semantic Web folks turn up their noses at things like Microformats. But to me, that feels a bit too much like someone that complains about small size of the in-ground pools that one person is digging as he is trying to dig an ocean. Only problem is, he’s been digging for ten years already and there’s no swimming in sight.

Drew’s talk was one of three related to Microformats. The first was by Mark Norman Francis (of Yahoo) and the second was by Jeremy Keith. Drew’s came third. The theme of the three was a past, present, and future of Microformats and the applications of Microformats.

Drew talked about how simply adding Microformats (the formal name for adding semantic, standardized class names to your HTML, essentially) could open your site up to many of the benefits an API gives. Your plain HTML content then becomes machine readable and agents can use your data with very little difficulty.

I have explained Microformats to colleagues as somewhat of a “band aid” between “semantic markup” and “The Semantic Web” (the latter being Tim Berners-Lee’s vision of a machine-readable and -usable web). But Microformats seems to be encroaching on some of the ground established by the Semantic Web. The first speaker, Mark Norman Francis, gave a compelling and provocative case for adopting Microformats as a replacement for much of what the Semantic Web is trying to accomplish.

First, Mark quoted the Semantic Web’s entry on Wikipedia:

For example, with HTML and a tool to render it (perhaps Web browser software, perhaps another user agent), one can create and present a page that lists items for sale. The HTML of this catalog page can make simple, document-level assertions such as “this document’s title is ‘Widget Superstore’”. But there is no capability within the HTML itself to unambiguously assert that, say, item number X586172 is an Acme Gizmo with a retail price of ‚Ǩ199, or that it is a consumer product. Rather, HTML can only say that the span of text “X586172″ is something that should be positioned near “Acme Gizmo” and “‚Ǩ199″, etc. There is no way to say “this is a catalog” or even to establish that “Acme Gizmo” is a kind of title or that “‚Ǩ199″ is a price. There is also no way to express that these pieces of information are bound together in describing a discrete item, distinct from other items perhaps listed on the page.

Mark immediately follows with:

Those people have never heard of the hListing microformat, which does pretty much exactly that.

This is the problem we have—visible metadata. All of the information on the web should be visible to you as a human. The moment you take this information, whether it is already on the web page or about the web page and put it somewhere else, it becomes invisible to you. You then have to go and use other software to extract it. This is bad, from my point of view anyway.

Mark then continues to go on to slap around the Semantic Web some more, as well as things like XML namespaces. He certainly makes a case. I’m not going to pretend I know enough about the Semantic Web to say all of the associated technologies can be replaced by Microformats, but it seems that some aspects of both the Semantic Web and APIs are simplified by Microformats.

I highly recommend listening to the podcasts. Mark’s is quick—just 21 minutes. Here are the links:

• Mark Norman Francis | audio | slides
• Jeremy Keith | audio | slides
• Drew McLellan | audio | slides

More Microformats resources:

• Official Microformats site and wiki
  • Their post on the WSG meetup
• Microformatique, a blog about Microformats started by John Allsop
• Microformats Primer by Garrett Dimon on Digital Web
• Microformats Search Engine @ Technorati
• Microformats @ Wikipedia
• Dan Cederholm’s use of microformats on Cork’d