Supplementary Material for: The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants

Handle URI:
http://hdl.handle.net/10754/624140
Title:
Supplementary Material for: The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants
Authors:
Hoehndorf, Robert ( 0000-0001-8149-5890 ) ; Alshahrani, Mona ( 0000-0002-9848-8248 ) ; Gkoutos, Georgios; Gosline, George; Groom, Quentin; Hamann, Thomas; Kattge, Jens; Oliveira, Sylvia de; Schmidt, Marco; Sierra, Soraya; Smets, Erik; Vos, Rutger; Weiland, Claus
Abstract:
Abstract 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.
KAUST Department:
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division; Computer Science Program
Citation:
Hoehndorf, R., Alshahrani, M., Gkoutos, G., Gosline, G., Groom, Q., Hamann, T., … Weiland, C. (2016). The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants. Figshare. https://doi.org/10.6084/m9.figshare.c.3643244
Publisher:
Figshare
Issue Date:
2016
DOI:
10.6084/m9.figshare.c.3643244
Type:
Dataset
Is Supplement To:
Hoehndorf 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.; DOI:10.1186/s13326-016-0107-8; HANDLE:http://hdl.handle.net/10754/621835
Appears in Collections:
Computer Science Program; Datasets; Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorHoehndorf, Roberten
dc.contributor.authorAlshahrani, Monaen
dc.contributor.authorGkoutos, Georgiosen
dc.contributor.authorGosline, Georgeen
dc.contributor.authorGroom, Quentinen
dc.contributor.authorHamann, Thomasen
dc.contributor.authorKattge, Jensen
dc.contributor.authorOliveira, Sylvia deen
dc.contributor.authorSchmidt, Marcoen
dc.contributor.authorSierra, Sorayaen
dc.contributor.authorSmets, Eriken
dc.contributor.authorVos, Rutgeren
dc.contributor.authorWeiland, Clausen
dc.date.accessioned2017-06-06T07:44:33Z-
dc.date.available2017-06-06T07:44:33Z-
dc.date.created2016-12-16en
dc.date.issued2016en
dc.identifier.citationHoehndorf, R., Alshahrani, M., Gkoutos, G., Gosline, G., Groom, Q., Hamann, T., … Weiland, C. (2016). The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants. Figshare. https://doi.org/10.6084/m9.figshare.c.3643244en
dc.identifier.doi10.6084/m9.figshare.c.3643244en
dc.identifier.urihttp://hdl.handle.net/10754/624140-
dc.description.abstractAbstract 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.en
dc.publisherFigshareen
dc.rightsCC BYen
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectEvolutionary Biologyen
dc.subjectEcologyen
dc.subjectPlant Biologyen
dc.subjectVirologyen
dc.titleSupplementary Material for: The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plantsen
dc.typeDataseten
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.contributor.departmentComputer Science Programen
kaust.authorHoehndorf, Roberten
kaust.authorAlshahrani, Monaen
dc.type.resourceCollectionen
dc.relation.isSupplementToHoehndorf 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.en
dc.relation.isSupplementToDOI:10.1186/s13326-016-0107-8en
dc.relation.isSupplementToHANDLE:http://hdl.handle.net/10754/621835en
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