title: The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants.
abstract: The systematic analysis of a large number of comparable plant trait data can support investigations into phylogenetics and ecological adaptation, with broad applications in evolutionary biology, agriculture, conservation, and the functioning of ecosystems. Floras, i.e., books collecting the information on all known plant species found within a region, are a potentially rich source of such plant trait data. Floras describe plant traits with a focus on morphology and other traits relevant for species identification in addition to other characteristics of plant species, such as ecological affinities, distribution, economic value, health applications, traditional uses, and so on. However, a key limitation in systematically analyzing information in Floras is the lack of a standardized vocabulary for the described traits as well as the difficulties in extracting structured information from free text.
  
  
  
  We have developed the Flora Phenotype Ontology (FLOPO), an ontology for describing traits of plant species found in Floras. We used the Plant Ontology (PO) and the Phenotype And Trait Ontology (PATO) to extract entity-quality relationships from digitized taxon descriptions in Floras, and used a formal ontological approach based on phenotype description patterns and automated reasoning to generate the FLOPO. The resulting ontology consists of 25,407 classes and is based on the PO and PATO. The classified ontology closely follows the structure of Plant Ontology in that the primary axis of classification is the observed plant anatomical structure, and more specific traits are then classified based on parthood and subclass relations between anatomical structures as well as subclass relations between phenotypic qualities.
  
  
  
  The FLOPO is primarily intended as a framework based on which plant traits can be integrated computationally across all species and higher taxa of flowering plants. Importantly, it is not intended to replace established vocabularies or ontologies, but rather serve as an overarching framework based on which different application- and domain-specific ontologies, thesauri and vocabularies of phenotypes observed in flowering plants can be integrated.
authors.affiliation: Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955-6900, Kingdom of Saudi Arabia. robert.hoehndorf@kaust.edu.sa.|Computer, Electrical and Mathematical Sciences & Engineering Division (CEMSE), King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955-6900, Kingdom of Saudi Arabia. robert.hoehndorf@kaust.edu.sa.
authors.forename: Robert
authors.identifier: 0000-0001-8149-5890
authors.initials: R
authors.lastname: Hoehndorf
authors.affiliation: Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955-6900, Kingdom of Saudi Arabia.|Computer, Electrical and Mathematical Sciences & Engineering Division (CEMSE), King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
authors.forename: Mona
authors.initials: M
authors.lastname: Alshahrani
authors.affiliation: College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham, B15 2TT, United Kingdom.|Institute of Translational Medicine, University Hospitals Birmingham, NHS Foundation Trust, Birmingham, B15 2TT, United Kingdom.|Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 2AX, United Kingdom.
authors.forename: Georgios V
authors.initials: GV
authors.lastname: Gkoutos
authors.affiliation: Royal Botanical Gardens, Kew, Richmond, Surrey, TW9 3AB, United Kingdom.
authors.forename: George
authors.initials: G
authors.lastname: Gosline
authors.affiliation: Botanic Garden Meise, Nieuwelaan 38, Meise, 1860, Belgium.
authors.forename: Quentin
authors.initials: Q
authors.lastname: Groom
authors.affiliation: Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands.
authors.forename: Thomas
authors.initials: T
authors.lastname: Hamann
authors.affiliation: Max Planck Institute for Biogeochemistry, Hans Knoell Str. 10, Jena, 07745, Germany.|German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany.
authors.forename: Jens
authors.initials: J
authors.lastname: Kattge
authors.affiliation: Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands.
authors.forename: Sylvia Mota
authors.initials: SM
authors.lastname: de Oliveira
authors.affiliation: Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, Frankfurt am Main, 60325, Germany.
authors.forename: Marco
authors.initials: M
authors.lastname: Schmidt
authors.affiliation: Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands.
authors.forename: Soraya
authors.initials: S
authors.lastname: Sierra
authors.affiliation: Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands.
authors.forename: Erik
authors.initials: E
authors.lastname: Smets
authors.affiliation: Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands.
authors.forename: Rutger A
authors.initials: RA
authors.lastname: Vos
authors.affiliation: Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, Frankfurt am Main, 60325, Germany.
authors.forename: Claus
authors.initials: C
authors.lastname: Weiland
mesh_terms: D064229:Biological Ontologies; D010641:Phenotype; D010944:Plants / Q000033:anatomy & histology* / Q000235:genetics
keywords: Biodiversity; Botany; Flora; Morphological traits; Phenotype