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Plant structure ontology: How should we label plant structures with doubtful or mixed identities?


Kirchoff, B K; Pfeifer, E; Rutishauser, R (2008). Plant structure ontology: How should we label plant structures with doubtful or mixed identities? Zootaxa, 1950:103-122.

Abstract

This paper discusses problems with labelling plant structures in the context of attempts to create a unified Plant Structure Special attention is given to structures with mixed, or doubtful identities that are difficult or even impossible to with a single term. In various vascular plants (and some groups of animals) the structural categories for the description forms are less distinct than is often supposed. Thus, there are morphological misfits that do not fit exactly into one the other category and to which it is difficult, or even impossible, to apply a categorical name. After presenting three studies of intermediate organs and organs whose identity is in doubt, we review five approaches to categorizing organs, and evaluate the potential of each to serve as a general reference system for gene annotations. The five are (1) standardized vocabularies, (2) labels based on developmental genetics, (3) continuum morphology, process morphology, (5) character cladograms. While all of these approaches have important domains of applicability,
we conclude that process morphology is the one most suited to gene annotation.

Abstract

This paper discusses problems with labelling plant structures in the context of attempts to create a unified Plant Structure Special attention is given to structures with mixed, or doubtful identities that are difficult or even impossible to with a single term. In various vascular plants (and some groups of animals) the structural categories for the description forms are less distinct than is often supposed. Thus, there are morphological misfits that do not fit exactly into one the other category and to which it is difficult, or even impossible, to apply a categorical name. After presenting three studies of intermediate organs and organs whose identity is in doubt, we review five approaches to categorizing organs, and evaluate the potential of each to serve as a general reference system for gene annotations. The five are (1) standardized vocabularies, (2) labels based on developmental genetics, (3) continuum morphology, process morphology, (5) character cladograms. While all of these approaches have important domains of applicability,
we conclude that process morphology is the one most suited to gene annotation.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Department of Systematic and Evolutionary Botany
Dewey Decimal Classification:580 Plants (Botany)
Uncontrolled Keywords:Character cladogram, Continuum, Evo-devo, Flower, Flowering plants, Gene ontology, Intermediate organs, Leaf, Morphological nomenclature, Organ identity, Plant ontology, Plant structure ontology, Root
Language:English
Date:2008
Deposited On:23 Jan 2009 11:31
Last Modified:05 Apr 2016 12:52
Publisher:Magnolia Press
ISSN:1175-5326
Official URL:http://www.mapress.com/zootaxa/list/2008/zt01950.html

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