As an ontologist, one of the most common questions that you get is: where is there a book or a tutorial that I can read which describes how to build an ontology. Currently, there is some tutorial information on the web, there are some books; but there is not a clear answer to the question. Many of the books are collections of papers, or are technologically biased.

If ontologies are to continue in their growth within biomedicine, we need to address this gap; the current process of spending years in the community, reading mailing lists and gathering knowledge from snippets on the web and the many wikis is too slow, too expensive and too difficult; more so, as the ontology community is itself evolving and changing over time; old knowledge made not be current practice, something which the newcomer is hard-pressed to judge.

We believe, therefore, there is a need for a resource to which people can be pointed, that is populated with short, succinct articles describing the different aspects of ontologies, ontology technology and the custom and practice of building ontologies.

A problem

The obvious solution to this problem would be to write a book. However, book writing is time-consuming, tiring and takes a number of years to come to fruition. If the book has one or a few authors, it tends to reflect only a narrow slice of opinion. Multi-author collected work tend to be even harder work for the editor than writing a book solo.

Books do not change very frequently. They are therefore out-of-date as soon as they are available. Authors feel a greater pressure for correctness, as they will have to live with the consequences of mistakes for many years; most scientists welcome feedback, but being asked to justify something you wish you had not said gets tiresome once it happens ten times or more.

Books lack instant gratification for the authors; it may be a year or two before anyone reads their hard work, if at all. Especially for encyclopedia articles, authors rarely see the print copy of their own work, because the books are too expensive to buy for the brief pleasure the hard-copy provides.

A solution

The solution to the problem seems to be to use the web. One suggestion would be to use a wiki; however, for the scientist, the multi-author nature of a wikipage tends to reduce the benefit in terms of recognition. We suggest instead writing an encyclopedia of ontologies by blog technology. The idea is simple; a set of authors will be invited to write short approx 2000 word articles which they publish on an ontogenesis blog; alternatively, if they wished to retain control, they could publish on their own blog and post a short summary. Articles would under go a light peer-review; given that contributions would be invited, this would be more aimed at copy-editing than determining correctness. Submission and publication would be simultaneous; all peer-review would be performed in the open.

When an article is deemed “ready”, it will be recategorised to reflect this change in status; at this point, no further changes will be expected. New articles that act as an update will be possible, and will be linked with existing blog technology.

The advantages of this are straight-forward; the publication will be as close to free as possible; it will cost no more than the authorship. Authors will get immediate gratification and feedback. The blog can grow over time with more knowledge as it becomes available. If the authors wished to retain control over publication, they could simply use their own blog; the ontogenesis tutorial would act as a simple aggregator.

We could generate a static page index, with trails which will help new readers navigate. In practice, this might be unnecessary; one advantage of a web page as opposed to a book is that text search comes for free. This will also encourage authors to contribute directly rather than aggregate as their post would be more like to be found by search. Additionally, while categories will be controlled, tags will be freely open to the authors and maybe the readership to add as they choose. Finally, existing blog technology would allow comments, or trackbacks if others wished to argue or present opposing points-of-view.

In short, blog technology provides most of what we need, and a few hoped for rules-of-practice would support the light-weight, rapid and changing publication environment that we hope to achieve.

Next Steps

To start this process, we propose to gather a number of scientists from field to gather for a short meeting. At this meeting, we would have basic discussions about the process, develop a (very!) light-weight category scheme. We will generate a set of initial topics and discuss potential invited authors. We hope these discussions will be short as most of the meeting will be taken up with individuals writing initial articles; feedback will be immediate and rapid, so that we generate by example, rather than by design, a house-style and other conventions. An additional outcome would be a set of seed articles, so that invited contributers in the future would see what they are contributing to, as well as providing an immediate resource for readers. We also hope that the seed article and growing resource, with its immediate publication and open access will encourage others to offer contributions; after the initial stage, we will in no way limit to invitation only.

Following this initial meeting, we expect contributions to slow, however, given the short and light-weight nature of the articles, scientists will be able to contribute as-and-when, fitting the authoring into their busy schedules, rather than chasing publisher-derived deadlines. This easy publication strategy may well result in far more contributions than a more deadline driven process.

1 Comment

  1. Blogging a Book about Bio-Ontologies « O'Really?

    January 21, 2010 @ 11:05 am

    […] As part of an ongoing experiment, we are posting all this information on a blog called if you’d like to follow, subscribe to the feed and read the manifesto. […]

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