title: An ontology of fungal subcellular traits.
abstract: •
  
  
  OBJECTIVE
  The Fungal Subcellular Ontology used in the Assembling the Fungal Tree of Life project is a taxon-wide ontology (controlled vocabulary for attributes) designed to clarify and integrate the broad range of subcellular characters and character states used in higher-level fungal systematics. As in the algae, cellular characters are important phylogenetic markers in kingdom Fungi. The Fungal Subcellular Ontology has been developed primarily to help researchers, especially systematists, in their search for information on subcellular characters across the Fungi, and it complements existing biological ontologies, including the Gene Ontology. •
  
  
  METHODS
  The character and character state data set used in the Assembling the Fungal Tree of Life Structural and Biochemical Database (http://aftol.umn.edu) is the source of terms for generating the ontology. After the terms were accessioned and defined, they were combined in OBO-Edit file format, and the ontology was edited using OBO-Edit, an open source Java tool supported by the Gene Ontology project. •
  
  
  RESULTS
  The Fungal Subcellular Ontology covers both model and nonmodel fungi in great detail and is downloadable in OBO-Edit format at website http://aftol.umn.edu/ontology/fungal_subcellular.obo. •
  
  
  CONCLUSIONS
  The ontology provides a controlled vocabulary of fungal subcellular terms and functions as an operating framework for the Assembling the Fungal Tree of Life Structural and Biochemical Database. An ontology-based design enhances reuse of data deposited in the Structural and Biochemical Database from other independent biological and genetic databases. Data integration approaches that advance access to data from the diversity of biological databases are imperative as interdisciplinary research gains importance. In this sense, the Fungal Subcellular Ontology becomes highly relevant to mycologists as well as nonmycologists because fungi interact actively as symbionts and parasites or passively with many other life forms.
authors.affiliation: Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 USA. thiru014@umn.edu
authors.forename: T K Arun
authors.initials: TK
authors.lastname: Kumar
authors.forename: John A
authors.initials: JA
authors.lastname: Crow
authors.forename: Trevor J
authors.initials: TJ
authors.lastname: Wennblom
authors.forename: Maritza
authors.initials: M
authors.lastname: Abril
authors.forename: Peter M
authors.initials: PM
authors.lastname: Letcher
authors.forename: Meredith
authors.initials: M
authors.lastname: Blackwell
authors.forename: Robert W
authors.initials: RW
authors.lastname: Roberson
authors.forename: David J
authors.initials: DJ
authors.lastname: McLaughlin
mesh_terms: D005658:Fungi / Q000378:metabolism*; D013347:Subcellular Fractions / Q000378:metabolism*