Upcoming Dagstuhl seminar on the development of an environment ontology

Tomorrow I’ll be off to Schloss Dagstuhl for the week-long seminar on “Locating Biology: The Development and Application of an Environment Ontology”, organized by Michael Ashburner, Christian Freksa, Suzanna Lewis, Norman Morrison, and Barry Smith. The aim of the seminar is to “promote new discovery, interoperability and integration opportunities for environmental research data through the uptake, application and development of EnvO (environments) and Gaz (places), including the identification of mechanisms for coordination and dissemination of these artifacts among potential user communities.”

There’s some work to do, to put it mildly, given that (i) there are multiple environment ontologies and ontology-like artifacts in various languages for various purposes, (ii) there are different opinions of what environments are, (iii) there are environments that are underrepresented in EnvO (e.g., agriculture) or can do with a make-over, such as the food section (if one is of the conviction that food science should be part of an environment ontology), (iv) it is neither quite clear who the intended users are, (v) nor which purposes the EnvO has to serve, (vi) nor in which language(s) such an EnvO should be available to serve the widest possible community of users.

This impression has also to do with the discrepancy between the stated aims of an environment ontology and the current version of the EnvO at the Environment Ontology Consortium’s website, even if one were to set aside agriculture and food: “The aims of these efforts [developing an EnvO] are to support the semantically consistent description of, and computational reasoning over, environmental information associated with biological data of any organism or biological sample.”, (copied from the seminar page, emphasis added). The current EnvO is in OBO format, which only meets those aims if they were to be taken in a very minimalist interpretation for a few narrowly defined possible uses, thus missing out on a range of other scenarios.

But challenges are good, especially since there are possible solutions available or around the corner :). I have no doubt it will be an engaging and interesting week with the attendees from a wide range of backgrounds who bring their contribution to this ambitious project. Stay tuned…


Failure of the experiment for the SemWebTech course

At the beginning of the SWT course, I had the illusion that we could use the blog as another aspect of the course and, more importantly, that students (and other interested people) were free to leave comments and links to pages and other related blogs and blog posts that they had encountered. It did not really happen though, so as experiment formulated as such, it failed miserably.

But I can scrape together some data that demonstrate all was not for naught entirely. I have received several off-line comments from colleagues who thought it to be useful, non-SWT-course students who use it to study as means of distance education, or kindly pointed me to updates and extensions of various topics—but the plural of anecdote is not data. So here go some figures.

34 students had enrolled in the Moodle, of which some 10-15 attended class initially, dwindling down to 4-8 the more midterms of other courses and holiday season interfered with their study schedule (and perhaps my teaching skills or the topics of the course), 12 students did a mini-project for the lab within the deadline for this exam session, 12 registered for the exam, and 11 showed up to actually do the exam. FUB strives to have a 1:6 ratio for lecturer:student, so with the SWT course (as well as most other MSc courses) we are at the good end of that.

The aggregated data for explicit blog post accesses (i.e., not counting those who read it through accessing the home page) and slides downloads on 17-2-2010 as sampled during invigilating the SWT exam are as follows: average visit of an SWT course blog post is 112, with OWL, top-down and bottom-up ontology development, and part-whole relations well above the average, and average slide download of 41 with OWL and top-down and bottom-up above average again. At the moment, one can only speculate why.

Clearly, there have been many more people accessing the pages and the slides than can be accounted for by the students only, even if one would take up an assumption that they accessed each of the blog posts, say, twice and entertained themselves with downloading both the normal slides and the same ones in hand-out format. The content of the slides were not the only topics that passed the revue during the lectures and the labs, but maybe they have been, are, or will be of use to other people as well. People who are interested in ontology engineering topics more generally, especially regarding course development and course content, will find Ontolog’s Ontology Summit’s current virtual panel sessions on “Creating the ontologists of the future” worthwhile to consult.

Finally, will I go through the trouble of writing blog posts for another course I may have to teach? Probably not.

A note on the Computer Cooking Contest

Last summer I wrote about a computational analysis of culinary evolution where the mutations of the ingredients of recipes was investigated and modelled. We can speed up the evolution by stirring in some more AI to help you find and adapt recipes based on the ingredients you happen to have. To get to the point, and in the words of the contest organizers, David Aha and Amélie Cordier:

Once upon a time, we wondered whether some software system could help us to make a yummy meal from the contents of our fridge. Given a restricted set of ingredients, the task is to cook something “that tastes good”. More recently, we wondered whether a system could help us to explain our research interests to a broader audience. Given the technological state-of-the-art, the task is to create a problem-solving system. Glue the two together and you get: The Computer Cooking Contest!

There is no restriction on the technology, but the contestants have to start with the basic recipe database, which is available for download from the Computer Cooking Contest website, and it seems that it has to have a web interface. There are four categories in the contest, each with a prize. The “main” one concerns recipe selection and possible modification, the “adaptation” one has to solve specific adaptations of a recipe, the “open” one is, well, open, and scientific originality is the only criterion, and there is a “student” challenge slimmed to solving a chosen subtask. Examples and suggestions are given in the rules & categories page of the CFC. Deadline is 14 April.

Last year’s winner was CookIIS, which is a “recipe creator” using case-based reasoning: you can fill in the ingredients you happen to have, ones that should be excluded, and an additional constraint (such as vegetarian or low-cholesterol), and out comes a list of recipes satisfying the constraints. My “potato, cabbage, beans, cheese”, excluding “olive, banana” and vegetarian had as best suggestion Banda Kopir Tarkari, Chili bean dip, and Dilly Potato Salad (and another 545). After that, I could not play with the recipes; there is an “Adaptation” note at the end of the recipe to change ingredients, but it would be nice if, for instance, I just could click an ingredient (that I did not have and had not specified I did not have…) and see what I could swap it for, or maybe hook up my cupboard and fridge to the computer so the software knows which ingredients I have to begin with.

Either way, CookIIS definitely beats the wine and pizza ontologies in presentability… but then, maybe some of the Semantic Web technologies are just as suitable to excel in any of the four computer cooking challenges.