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…