The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants
Microsoft Excel 2007
Microsoft Excel 2007
Gkoutos, Georgios V.
de Oliveira, Sylvia Mota
Vos, Rutger A.
KAUST DepartmentComputational Bioscience Research Center (CBRC)
Computer Science Program
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Permanent link to this recordhttp://hdl.handle.net/10754/621835
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AbstractBackground 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.
CitationHoehndorf R, Alshahrani M, Gkoutos GV, Gosline G, Groom Q, et al. (2016) The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants. Journal of Biomedical Semantics 7. Available: http://dx.doi.org/10.1186/s13326-016-0107-8.
SponsorsThe initial draft of the Flora Phenotype Ontology was created at the 2014 Biodiversity Data Enrichment Hackathon (Leiden, the Netherlands), which was sponsored by the the pro-iBiosphere project (Grant Agreement number 312848), funded by the European Commission under the 7th Framework Programme. Funding for GVG was provided by the National Science Foundation (Grant Number: IOS-1340112), the BBSRC national capability in plant phenotyping (Grant Number: BB/J004464/1) and the FP7 European Plant Phenotyping Network (Grant Agreement No. 284443). Funding for MS and CW was provided by the Deutsche Forschungsgemeinschaft (DFG) under grant no. HI 1538/2-2 (GFBio). RH and MA were supported by funding from the King Abdullah University of Science and Technology.
JournalJournal of Biomedical Semantics
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