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

Handle URI:
http://hdl.handle.net/10754/621835
Title:
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 V.; Gosline, George; Groom, Quentin; Hamann, Thomas; Kattge, Jens; de Oliveira, Sylvia Mota; Schmidt, Marco; Sierra, Soraya; Smets, Erik; Vos, Rutger A.; Weiland, Claus
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:
Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Citation:
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.
Publisher:
Springer Nature
Journal:
Journal of Biomedical Semantics
Issue Date:
14-Nov-2016
DOI:
10.1186/s13326-016-0107-8
Type:
Article
ISSN:
2041-1480
Sponsors:
The 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.
Is Supplemented By:
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; DOI:10.6084/m9.figshare.c.3643244; HANDLE:http://hdl.handle.net/10754/624140
Additional Links:
http://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0107-8
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC); 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, Georgios V.en
dc.contributor.authorGosline, Georgeen
dc.contributor.authorGroom, Quentinen
dc.contributor.authorHamann, Thomasen
dc.contributor.authorKattge, Jensen
dc.contributor.authorde Oliveira, Sylvia Motaen
dc.contributor.authorSchmidt, Marcoen
dc.contributor.authorSierra, Sorayaen
dc.contributor.authorSmets, Eriken
dc.contributor.authorVos, Rutger A.en
dc.contributor.authorWeiland, Clausen
dc.date.accessioned2016-11-17T09:00:09Z-
dc.date.available2016-11-17T09:00:09Z-
dc.date.issued2016-11-14en
dc.identifier.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.en
dc.identifier.issn2041-1480en
dc.identifier.doi10.1186/s13326-016-0107-8en
dc.identifier.urihttp://hdl.handle.net/10754/621835-
dc.description.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.en
dc.description.sponsorshipThe 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.en
dc.publisherSpringer Natureen
dc.relation.urlhttp://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0107-8en
dc.rightsThis 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.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectPhenotypeen
dc.subjectBiodiversityen
dc.subjectFloraen
dc.subjectBotanyen
dc.subjectMorphological traitsen
dc.titleThe flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plantsen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.identifier.journalJournal of Biomedical Semanticsen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionCollege of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birminghamen
dc.contributor.institutionInstitute of Translational Medicine, University Hospitals Birmingham, NHS Foundation Trusten
dc.contributor.institutionInstitute of Biological, Environmental and Rural Sciences, Aberystwyth Universityen
dc.contributor.institutionRoyal Botanical Gardens, Kewen
dc.contributor.institutionBotanic Garden Meiseen
dc.contributor.institutionNaturalis Biodiversity Centeren
dc.contributor.institutionMax Planck Institute for Biogeochemistryen
dc.contributor.institutionGerman Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzigen
dc.contributor.institutionSenckenberg Biodiversity and Climate Research Centre (BiK-F)en
kaust.authorHoehndorf, Roberten
kaust.authorAlshahrani, Monaen
dc.relation.isSupplementedByHoehndorf, 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.relation.isSupplementedByDOI:10.6084/m9.figshare.c.3643244en
dc.relation.isSupplementedByHANDLE:http://hdl.handle.net/10754/624140en
All Items in KAUST are protected by copyright, with all rights reserved, unless otherwise indicated.