Abstract Detail

Developmental and Structural Section

Zapata, Felipe [1], Stein, Lincoln [2], McCouch, Susan [3], Rhee, Seung [4], Jaiswal, Pankaj [3], Stevens, Peter [7], Ware, Doreen [2], Vincent, Leszek [5], Polacco, Mary [5], Reiser, Leonore [4], Sachs, Marty [6], Kellogg, Elizabeth [1], Avraham, Shulamit [2], Ilic, Katica [4].

Developing the Plant Ontologies: examples and computational tools.

The Plant Ontology Consortium (POC) (www.plantontology.org) is a collaborative effort of workers in pant systematics, development and genomics. The goal of POC is to standardize a descriptive terminology for anatomical and developmental studies in plants. The POC follows an existing structure and set of rules already developed by the Gene Ontology Consortium (www.geneontology.org). It includes a set of terms arranged in a structure called Directed Acyclic Graph (DAG), in which parent terms can have multiple children (like a conventional hierarchy), but child terms can also have multiple parents (unlike a simple hierarchy or classification). Also, children are not allowed to be their own ancestors; hence cycles are forbidden. For example, gynoecium (parent term) is composed of carpel, ovary, style and stigma (all child terms). Carpel is also a particular kind of modified leaf, a megasporophyll. Hence, carpel, a child term, has multiple parents: gynoecium and megasporophyll. The resulting structure is quite flexible and can accommodate plant morphological data that are not strictly hierarchical in nature. For instance, some wholes cannot be defined exhaustively by their parts; not all embryos have cotyledons, and the only thing common to all embryos would be a mass of four cells. We use the ontology-editing tool, DAG Edit (available from SourceForge.net), for creating and editing plant ontology files in a standard flat file format. Individual members of the POC are assigned particular sets of terms (nodes) in the hierarchy. All members of the Consortium review and discuss the structure created for each node, in terms of biological and computational correctness and functionality. The hierarchy is not intended to be exhaustive even for the organisms currently under focus, but care is taken not to label nodes in such a way that subsequent inclusion of plants with very different morphologies will necessitate a restructuring of the hierarchy.

1 - University of Missouri-St. Louis, Biology, 8001 Natural Bridge Road, St. Louis, Missouri, 631321, USA
2 - Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724
3 - Cornell University, Department of Plant Breeding, Bradfield Hall, Ithaca, New York, 14853
4 - Arabidopsis Information Resource, 260 Panama Street, Stanford, California, 94305
5 - University of Missouri-Columbia, Department of Agronomy, 215 Curtis Hall, Columbia, Missouri, 65211-7020
6 - University of Illinois, Department of Crop Sciences, Maize Genetics Cooperation - Stock Center, Urbana, Illinois, 61801-4798
7 - Missouri Botanical Garden, PO Box 299, St. Louis, Missouri, 63166-0299, USA

Keywords:
anatomy
bioinformatics
comparative genomics
comparative plant morphology
development
morphology.

Presentation Type: Paper
Session: 1-13
Location: Alpine A (Snowbird Center)
Date: Monday, August 2nd, 2004
Time: 11:30 AM
Abstract ID:351