The purpose of this project is not to propose a particular upper-level or coding for ontologies, but to demonstrate ontology construction as a general technique for coding ethograms and other descriptions of behavior into machine understandable forms. As such, it is intended to encompass, rather than serve as an alternative to, previous attempts 1,2 at formalizing the description of behavior.
The goals of this project differ from efforts such as those of the Gene Ontology Consortium. This project is more focused on representing and coding descriptions, rather than using ontologies as a semantic level of metadata for linking entities in existing databases. Part of this reflects the small number of data sources in this project. A plan to work on the integration across sources of description is coming in the near future.
I have updated the files for the H. californicus courtship ontology. The generated html, as well as the Protege (frames) source and project files, have been updated to Protege 3.4 (build 519).
Phylontal is a library with a GUI application frontend for aligning phenotype ontologies (e.g., behavior, anatomy) based on a phylogeny. It is still under development, but status updates are available here.
Looking for information about OwlWatcher or EOLite? Try here. Current OwlWatcher status: OSX support still broken, Windows versions 0.036 and 0.04 will work with older versions of Apple's Quicktime for Windows. New version with video support from Xuggler and using the OWLAPI v 3 (with OWL2 support) is in progress.
Substantial updates to the Loggerhead ontology were made during December 2001 and September 2002.
The generated rendition of the ontology begins with an outline of the concepts defined in the ontology, organized by superclass/subclass relations. Within the page for each concept, there is a textual definition, followed by a list of slots for that concept. Each slot specifies a relation that may (or must) exist between instances of the current class and other objects described in the ontology or its associated knowledge base. Each slot is specified by a name, a description, and several other properties (also called facets of the slot). The "Type" property specifies the "data type" of the object that fills it - usually instance, less frequently class or number. The "Allowed values" property specifies the classes that can fill a slot of "Type" instance. This is a more "implementation transparent" notion of type. Finally, the cardinality specifies the number of things that the slot can refer to: the token 0:* means the slot can refer to any number of things.
Loggerhead Nesting Although the coverage of the behavioral terms is complete, this ontology is useful as a test bed for developing software tools and advanced representation ideas, such as prototypes. Prototypes are particularly important in published ontologies since the descriptions represent a summary of multiple events.
Habronattus courtship I am working towards having OwlWatcher in a state to reconstruct the Habronattus ontologies, using OWL and aiming towards OBO-foundry compliance.
Comparative Methods The primary goal of the work described here is to develop comparative methods for ontology-based behavior data. I have discussed issues of alignment and comparative methods in several recent presentations, which are linked here.
1. Golani, I. 1976. Homeostatic motor processes in mammalian interactions: a choreography of display. In: Perspectives in Ethology vol 2. (Ed. by P.P.G. Bateson & P. H. Klopfer), pp. 69-134. New York: Plenum.
2. Schleidt, W. M., Yakalis G., Donnelly M. & McGarry, J. 1984. A proposal for a standard ethogram, exemplified by an ethogram of the bluebreasted quail (Coturnix chinensis). Zeitschreift für Tierpsychologie 64:193-220.
3. Hailman, J. P. & Elowson, A. M. 1992. Ethogram of the nesting female loggerhead (Caretta caretta). Herpetologica 48:1-30.
All ontologies on this site and content of this page (except where otherwise acknowledged) are copyright 2001-2010 Peter E. Midford (firstname.lastname@example.org).
The photo of H. californicus is from a video copyright Wayne Maddison
The Loggerhead nesting picture is copyright Jack P. Hailman