Paper on Plant Ontology in press

Kirchoff, B. K., E. Pfeifer, and R. Rutishauser. in press. Plant Structure Ontology: How should we label plant structures with doubtful or mixed identities? Zootaxa (as part of special issue on Updating the Linnean Heritage. Names as Tools for Thinking About Animals and Plants)

The paper is a critique of the Plant Ontology, a controlled vocabulary (an ontology) that is intended to describe plant structure, growth, and developmental stages. The Ontology is being developed to prove a framework for gene annotation. It is intended to allow cross-species queries in databases of DNA sequences. Although it has enjoyed some success, the ontology has only been developed for a few species. Our concern is that as the ontology is expanded terms will need to be found for plant organs that are either intermediate in structure, or whose morphological identity is questionable. These plant parts cannot easily be labeled with a single term. The paper reviews five alternative approaches to gene annotation and concludes that, though the plant ontology can be improved, the best method of annotating plant structure and developmental genes is most likely process morphology. Process morphology was developed by Rolf Sattler in the early 1990s and uses sets of developmental processes instead of structural categories to describe plant structures. The method has been made quantitative by a number of authors including Bernard Jeune, Denis Barabé, and Christian Lacroix.