In a morphological ontology the expert’s knowledge is represented in terms, which describe morphological structures and
how these structures relate to each other. With the assistance of ontologies this expert knowledge is made processable by
machines, through a formal and standardized representation of terms and their relations to each other. The red flour beetle
Tribolium castaneum, a representative of the most species rich animal taxon on earth (the Coleoptera), is an emerging model
organism for development, evolution, physiology, and pest control. In order to foster Tribolium research, we have initiated
the Tribolium Ontology (TrOn), which describes the morphology of the red flour beetle. The content of this ontology
comprises so far most external morphological structures as well as some internal ones. All modeled structures are
consistently annotated for the developmental stages larva, pupa and adult. In TrOn all terms are grouped into three
categories: Generic terms represent morphological structures, which are independent of a developmental stage. In contrast,
downstream of such terms are concrete terms which stand for a dissectible structure of a beetle at a specific life stage.
Finally, there are mixed terms describing structures that are only found at one developmental stage. These terms combine
the characteristics of generic and concrete terms with features of both. These annotation principles take into account the
changing morphology of the beetle during development and provide generic terms to be used in applications or for cross
linking with other ontologies and data resources. We use the ontology for implementing an intuitive search function at the
electronic iBeetle-Base, which stores morphological defects found in a genome wide RNA interference (RNAi) screen. The
ontology is available for download at http://ibeetle-base.uni-goettingen.de.