Housekeeping & Self References Meetings & Conferences Science Online Semantics and Ontologies

Ontogenesis: rapid reviewing and publishing of articles on semantics and ontologies

What happens when an ontologist or two gets frustrated at the long-scale publication process that is the norm when publishing scientific books? You get Ontogenesis: a quick-turnaround, low-maintenance solution using WordPress blog software. Next, a bunch of other ontologists are invited to a two-day, intensive writing and peer-reviewing workshop and the initial content is created. Result? Well, my favourite result was Kendall Clark tweeting this: “#Ontogenesis is awesome:“.

What is Ontogenesis?

Phil Lord had the idea, and together with Robert Stevens and others organised the 2-day Ontogenesis workshop that occurred last week, 21-22 January 2010. Why look around for an alternative to traditional publishing methods? When writing a book, accepting the invitation might take 5 minutes, but getting around to doing it can take 6 months or more. You may only spend a couple of days writing the article, but then need to wait months for reviews (and do reviews for the other authors’ articles). Then there is the formatting and camera-ready copy. Then you may wait many months for proofs and then only get a few days to make corrections. Then, you can wait year or so for actual publication, by which time it is possibly out of date. Not ideal, but still necessary for some forms of publishing.

There are a number of benefits to using blog software, and to the Ontogenesis model in general:

  • stable, permanent URLs: Permanent URLs for articles and peer reviews. DOIs have been discussed as well, and are being considered.
  • automatic linking of peer reviews and related online articles. The WordPress software automatically adds trackbacks, pingbacks, etc. as comments on the relevant articles, making it easy for interested readers to visit the peer reviews written for that article.
  • completely open review system. Unlike many peer-review systems in use today, the reviewer (publicly) publishes his/her article in Ontogenesis.
  • less work and quick turnaround time for the editors, reviewers, and authors. Once you have written your article (in whatever format you like, other than a few broad suggestions about licensing and intention), you publish it as “Uncategorised” in the system, and then once reviewers have agreed to look at it, move it to “Under Review”. Once reviews are complete, and the editors have checked everything, it is moved to “Reviewed”. Pretty simple.

A blog that isn’t a blog

But is Ontogenesis a blog? Not really. Is it a book? Not in the traditional sense. While it seems to be correct to call it a blog, how the blog software is being used isn’t the way many people use it. And, though Duncan has called it “blogging a book”, this isn’t quite right either: while content, once completed, will not be changed, new content will be continually added. Phil discussed this point in his introduction to the workshop. He stated that wikis are best suited for certain styles of articles, but not for this sort of infrequently-updated information. Further, in wikis in general, crediting is poor. Google Knol is a nice idea, but not many people are using it. If it’s just a plain website, then there is no real way to have (and to show, more importantly), peer review.

To me, and to the general agreement of the people at the workshop, Ontogenesis can be viewed as a title/proper noun, in the same way as Nature is a title of a journal. Ontogenesis is the first of a class of websites called Knowledge Blogs. It is has more in common with the high-quality, article-style blogging of ScienceBlogs or Research Blogging than it does with the short, informal blogging style that is used by most bloggers. Each article stands on its own, is of a high quality, and describes a topic of interest to both ontologists and novices in the ontology world. Each article is aimed at a general life science readership, ensuring accessibility of knowledge and broad appeal.

My experiences as a contributor

I was lucky enough to be invited to the workshop last week, and had a great time. After an introductory set of presentations, we all got started writing our articles. The idea was that, once written, each article would be peer reviewed by at least 2 others at the workshop. Once the peer reviews were complete, the article would be re-categorised from “Under Review” to “Review”. As Phil said in a recent blog post, we wrote a large number of articles, though the number that have gone through the full review process was not as high. We expect that over the next few days, the number of completed articles will rise.

My article on Semantic Integration in the Life Sciences was the first to come out of peer review. Thanks are very much due to Frank Gibson, Michel Dumontier, and David Shotton for their peer reviewing and constructive criticism: it is a much better article for their input. I also reviewed a couple of articles (1,2) by Helen Parkinson and James Malone, which should be moved to a Reviewed status soon.

Ok, but what’s the downside?

Well, it is new, and there are some kinks to work out. This workshop highlighted a number of them, such as the difficulty people unfamiliar with WordPress had using its UI. Sean has posted a useful summary of his thoughts on the pluses and minuses, which I encourage you to have a read of and comment on. Here are a few thoughts on how to improve the experience in future, as mentioned during the meeting:

  • Enable the plugin for autogenerating related articles to improve cross-links.
  • The Table of Contents has been started, but different “pathways” for different intended readerships to help guide them through the articles would be helpful.
  • Reviewers should be able to change Categories in any article so they can mark when it is Under Review, rather than waiting for the Authors to do this.
  • The article-specific Table of Contents are very helpful, but it might be better to move it to different location in the post (e.g. the top rather than the bottom).
  • Have a way to mark yourself as willing to accept papers to review, for instance if you have some time in your schedule that week: authors could then preferentially choose you.
  • The ability for your name in the byline of an article to link to your profile on Ontogenesis. Currently, the profiles are private and some authors have put their profiles into the article text as a temporary alternative.
  • Add the Stats wordpress plugin.
  • Comments do not have the author of the comment within them, e.g. pingbacks to reviews have to be clicked through to find out who wrote the review.
  • Dealing with references/citations will be done better in future, when an appropriate plugin is found. Currently, basic HTML links to DOIs is the standard way to go.

Conclusions? Be an author yourself, and try it out!

This method of publishing is new, interesting, and quick. If you have a topic you’d like to write about, are interested in peer reviewing, or are just interested in reading the articles then please visit Ontogenesis and have a go, and then let us know what you think!

Please note: as mentioned in the main text, I am one of the authors of articles and peer reviews in Ontogenesis.


By Allyson Lister

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