TY  - JOUR
A1  - Hoehndorf, Robert
A1  - Alshahran, Mona
A1  - Gkoutos, Georgios V.
A1  - Gosline, George
A1  - Groom, Quentin
A1  - Hamann, Thomas
A1  - Kattge, Jens
A1  - Mota de Oliveira, Sylvia
A1  - Schmidt, Marco
A1  - Sierra, Soraya
A1  - Smets, Erik
A1  - Vos, Rutger Aldo
A1  - Weiland, Claus
T1  - The flora phenotype ontology (FLOPO) : tool for integrating morphological traits and phenotypes of vascular plants
T2  - Journal of biomedical semantics
N2  - Background: 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.
Results: 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.
Conclusions: 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.
KW  - Phenotype
KW  - Biodiversity
KW  - Flora
KW  - Botany
KW  - Morphological traits
Y1  - 2017
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/45024
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-450249
SN  - 2041-1480
N1  - © The Author(s). 2016 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
VL  - 7
IS  - 1, Art. 65
SP  - 1
EP  - 11
PB  - BioMed Central
CY  - London
ER  -