Progress on the EnvO at the Dagstuhl workshop

Over the course of the 4,5 days packed together at the beautiful and pleasant ambience of Schloss Dagstul, the fourth Environment Ontology workshop has been productive, and a properly referenceable paper outlining details and decisions will follow. Here I will limit myself to mentioning some of the outcomes and issues that passed the revue.

Group photo of most of the participants at the EnvO Workshop at Dagstuhl

After presentations by all attendees, a long list of discussion themes was drawn up, which we managed to discuss and agree upon to a large extent. The preliminary notes and keywords are jotted down and put on the EnvO wiki dedicated to the workshop.

Focussing first on the content topics, which took up the lion’s share of the workshop’s time, significant advances have been made in two main areas. First, we have sorted out the Food branch in the ontology, which has been moved as Food product under Environmental material and then Anthropogenic environmental material, and the kind and order of differentia have been settled, using food source and processing method as the major axes. Second, the Biome branch will be refined in two directions, regarding (i) the ecosystems at different scales and the removal of the species-centred notion of habitat to reflect better the notion of environment and (ii) work toward inclusion of the aspect of n-dimensional hypervolume of an environment (both the conditions / parameters / variables and the characterization of a particular type of environment using such conditions, analogous to the hypervolumes of an ecological niche so that EnvO can be used better for annotation and analysis of environmental data). Other content-related topics concerned GPS coordinates, hydrographic features, and the commitment to BFO and the RO for top-level categories and relations. You can browse through the preliminary changes in the envo-edit version of the ontology, which is a working version that changes daily (i.e., not an officially released one).

There was some discussion—insufficient, I think—and recurring comments and suggestions on how to represent the knowledge in the ontology and, with that, the ontology language and modelling guidelines. Some favour bare single-inheritance trees for appealing philosophical motivations. The first problematic case, however, was brought forward by David Mark, who had compelling arguments for multiple inheritance with his example of how to represent Wadi, and soon more followed with terms such as Smoked sausage (having as parents the source and processing method) and many more in the food branch. Some others preferred lattices or a more common knowledge representation language—both are ways to handle more neatly the properties/qualities with respect to the usage of properties and the property inheritance by sub-universals from its parent. Currently, the EnvO is represented in OBO and modelling the knowledge does not follow the KR approach of declaring properties of some universal (/concept/class) and availing of property inheritance, so that one ends up having to make multiple trees and then adding ‘cross-products’ between the trees. Hence, and using intuitive labels merely for human readability here, Smoked sausage either will have two parents, amounting to—in the end where the branching started—\forall x (SmokedSausage(x) \equiv AnimalFoodProduct(x) \land ProcessingMethod(x)) (which is ontologically incorrect because a smoked sausage is not way of processing) or, if done with a ‘cross-product’ and a new relation (hasQuality ), then the resulting computation will have something alike \forall x \exists y (SmokedSausage(x) \equiv Sausage(x) \land hasQuality(x,y) \land Smoking(y)) instead of having declared directly in the ontology proper, say, \forall x \exists y (SmokedSausage(x) \equiv Sausage(x) \land HasProcessingMethod(x,y) \land Smoking(y)) . The latter option has the advantages that it makes it easier to add, say, Fermented smoked sausage or Cooked smoked sausage as a sausage that has the two properties of being [fermented/cooked] and being smoked, and that one can avail of automated reasoners to classify the taxonomy. Either way, the details are being worked on. The ontology language and the choice for one or the other—whichever it may be—ought not to get in the way of developing an ontology, but, generally, it does so both regarding underlying commitment that the language adheres to and any implicit or explicit workaround in the modelling stage that to some extent make up for a language’s limitations.

On a lighter note, we had an excursion to Trier together with the cognitive robotics people (from a parallel seminar at Dagstuhl) on Wednesday afternoon. Starting from the UNESCO’s world heritage monument Porta Nigra and the nearby birthplace of Karl Marx, we had a guided tour through the city centre with its mixture of architectural styles and rich history, which was even more pleasant with the spring-like weather. Afterwards, we went to relax at the wine tasting event at a nearby winery, where the owners provided information about the 6 different Rieslings we tried.

Extension to the Aula Palatina (Constantine's Basilica) in Trier

Extension to the Aula Palatina (Constantine's Basilica) in Trier

Section of the Porta Nigra, Trier

Section of the Porta Nigra, Trier


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…