January 21, 2010

Blogging a Book about Bio-Ontologies

Waterloo Station Ultrawide Panoramic by Tim NugentIf you wanted to write a guide to Biomedical and Biological Ontologies [1], especially the what, why, when, how, where and who, there are at least three choices for publishing your work:

  1. Journal publishing in your favourite scientific journal.
  2. Book publishing with your favourite academic or technical publisher.
  3. Self publishing on a web blog with your favourite blogging software.

Each of these has its own unique problems:

  • The trouble with journals is that they typically don’t publish “how to” guides, although you might be able to publish some kind of review.
  • The trouble with books, and academic books in particular, is that people (and machines) often don’t read them. Also, academic books can be prohibitively expensive to buy and this can make the data inside them less visible and accessible to the widest audience. Unfortunately all that lovely knowledge gets locked up behind publishers paywalls. To add insult to injury, most academic books take a very long time to publish, often several years. By the time of printing, the content of many academic books is often very dated.
  • The trouble with blogs, they aren’t peer-reviewed in the traditional way and they tend to be written by a single person from a not very neutral point of view. Or as Dave once put it “vanity publishing for arrogant people with an inflated ego“. Ouch.

So the people behind the Ontogenesis network (Robert Stevens and Phillip Lord with funding from the EPSRC grant ref: EP/E021352/1) had an idea. Why not blog a book about Ontology? As a publishing experiment – it might just work by combining the merits of books and blogs together in order to overcome their shortcomings. This will involve getting a small group of about twenty people (mostly bio-ontologists) together, and writing about what an ontology is, why you would want to a biomedical ontology, how to build one and so on. We will be doing some of the peer-review online too.

As part of an ongoing experiment, we are posting all this information on a blog called http://ontogenesis.knowledgeblog.org if you’d like to follow, subscribe to the feed and read the manifesto.


  1. Yu, A. (2006). Methods in biomedical ontology Journal of Biomedical Informatics, 39 (3), 252-266 DOI: 10.1016/j.jbi.2005.11.006

[Ultrawide panoramic picture of Waterloo station by Tim Nugent]


  1. There’s another approach you didn’t list, which is writing a book but also releasing it as an open-access online version. This has the benefit of having a state of ‘finished-ness’ which an evolving resource like a blog might not ever reach, so one can cite a particular section or page [in a particular edition if necessary] and know that it won’t have changed when the time someone chases that link.

    See e.g. http://nlp.stanford.edu/IR-book/information-retrieval-book.html which is published by CUP — a good sign that trad publishers are open to this sort of thing.

    Which approach is better? Well, there’s probably no fixed answer to that. Horses for courses, etc. Your approach has the benefit of transparent peer review, and people getting to see and comment on the material as it’s written.

    Question: is it getting published as a proper book when it’s complete? Because that would give the best of both worlds.

    Comment by Andrew Clegg — January 21, 2010 @ 12:40 pm | Reply

    • Actually, one of the reasons for using a blog rather than a wiki is that the pages don’t change after they have been published and have permalinks. Of course, this isn’t an absolute, as the authors can change things, but essentially, we are working on the basis that once an article has hit the virtual shelves, it will remain essentially unchanged. In time, I expect we will just uncover the version history of the articles.

      For my mind, the state of “finished-ness” of a book is not an advantage. Every book publication process I have ever been involved with “finished” means 2 or 3 years out-of-date. Most of the time, when I have a book chapter finally published, I can barely remember having written it, yet alone what’s in it. Why replicate this? The articles, when published, are peer reviewed and finished.

      I agree with the ISBN or, better, a DOI, though. I don’t think these actually are any better technically, but from a social point of view they add something.

      Comment by Phil Lord — January 27, 2010 @ 1:12 pm | Reply

  2. PS… Another advantage of books over blogs is permanence. Even if only a handful of copies are printed, if you’ve got an ISBN, and got into the British Library and the Library of Congress, then that’s a fair bit more stability than a collection of potentially transient URLs.

    Not that I’m a particular advocate of turning trees into low-density non-searchable storage 🙂

    Maybe online writing and review + limited print run + open access digital edition = publishing sweet spot.

    Comment by Andrew Clegg — January 21, 2010 @ 12:47 pm | Reply

  3. […] I’m participating on an experiment about using blogs to create a book about bio-ontologies. Duncan Hull has a more in depths explanation. Dejar un […]

    Pingback by KnowledgeBlog: bloging a book about ontologies « Mikeleganaaranguren's Blog — January 21, 2010 @ 4:47 pm | Reply

  4. Wikibooks seems like another good alternative:

    Comment by Paul Gardner — January 22, 2010 @ 8:44 am | Reply

  5. […] 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 […]

    Pingback by Ontogenesis: rapid reviewing and publishing of articles on semantics and ontologies « the mind wobbles — January 25, 2010 @ 1:08 pm | Reply

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