February 12, 2010

The 3rd OBO Foundry Workshop 2010, Cambridge, UK

Ultrawide Wellcome Trust Genome Campus, Cambridge by Tim NugentThe Open Biomedical Ontologies (OBO) [1] are a set of reference ontologies for describing all kinds of biomedical data shared in a centralised repository called The OBO Foundry. Every year, users and developers of these ontologies gather from around the globe for a workshop at the EBI near Cambridge, UK. Following on from the first workshop two years ago, the second workshop last year it’s already time for the third workshop on February 15th-16th. All the details and agenda are here if you’re interested. This workshop is possible thanks to sponsorship from the BBSRC funds for Workshop on Data Standards and the EU ELIXIR ‘Data Integration & Interoperability’ Package 7.

[Update: outcomes from the workshop are available here, along with a summary of discussion from Monday and a summary of discussion from Tuesday.]


  1. Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L., Eilbeck, K., Ireland, A., Mungall, C., Leontis, N., Rocca-Serra, P., Ruttenberg, A., Sansone, S., Scheuermann, R., Shah, N., Whetzel, P., & Lewis, S. (2007). The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration Nature Biotechnology, 25 (11), 1251-1255 DOI: 10.1038/nbt1346

[Ultrawide panoramic picture of the Wellcome Trust Genome Campus by Tim Nugent, as featured on the cover of the EMBL-EBI Annual Scientific Report 2009. Making those pictures looks like a lot of fun.]

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]

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