Towards a thesaurus of plant characteristics: an ecological contribution

Eric Garnier*, Ulrike Stahl, Marie Angélique Laporte, Jens Kattge, Isabelle Mougenot, Ingolf Kühn, Baptiste Laporte, Bernard Amiaud, Farshid S. Ahrestani, Gerhard Bönisch, Daniel E. Bunker, J. Hans C. Cornelissen, Sandra Díaz, Brian J. Enquist, Sophie Gachet, Pedro Jaureguiberry, Michael Kleyer, Sandra Lavorel, Lutz Maicher, Natalia Pérez-HarguindeguyHendrik Poorter, Mark Schildhauer, Bill Shipley, Cyrille Violle, Evan Weiher, Christian Wirth, Ian J. Wright, Stefan Klotz

*Corresponding author for this work

    Research output: Contribution to JournalArticleAcademicpeer-review

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    Abstract

    Ecological research produces a tremendous amount of data, but the diversity in scales and topics covered and the ways in which studies are carried out result in large numbers of small, idiosyncratic data sets using heterogeneous terminologies. Such heterogeneity can be attributed, in part, to a lack of standards for acquiring, organizing and describing data. Here, we propose a terminological resource, a Thesaurus Of Plant characteristics (TOP), whose aim is to harmonize and formalize concepts for plant characteristics widely used in ecology. TOP concentrates on two types of plant characteristics: traits and environmental associations. It builds on previous initiatives for several aspects: (i) characteristics are designed following the entity-quality (EQ) model (a characteristic is modelled as the ‘Quality’ <Q> of an ‘Entity’ <E>) used in the context of Open Biological Ontologies; (ii) whenever possible, the Entities and Qualities are taken from existing terminology standards, mainly the Plant Ontology (PO) and Phenotypic Quality Ontology (PATO) ontologies; and (iii) whenever a characteristic already has a definition, if appropriate, it is reused and referenced. The development of TOP, which complies with semantic web principles, was carried out through the involvement of experts from both the ecology and the semantics research communities. Regular updates of TOP are planned, based on community feedback and involvement. TOP provides names, definitions, units, synonyms and related terms for about 850 plant characteristics. TOP is available online (www.top-thesaurus.org), and can be browsed using an alphabetical list of characteristics, a hierarchical tree of characteristics, a faceted and a free-text search, and through an Application Programming Interface. Synthesis. Harmonizing definitions of concepts, as proposed by TOP, forms the basis for better integration of data across heterogeneous data sets and terminologies, thereby increasing the potential for data reuse. It also allows enhanced scientific synthesis. TOP therefore has the potential to improve research and communication not only within the field of ecology, but also in related fields with interest in plant functioning and distribution.

    Original languageEnglish
    Pages (from-to)298-309
    Number of pages12
    JournalJournal of Ecology
    Volume105
    Issue number2
    Early online date5 Nov 2016
    DOIs
    Publication statusPublished - Mar 2017

    Funding

    E.G., U.S., M.-A.L., J.K. and I.M. designed the study and were involved in the main stages of the thesaurus development. B.L. is in charge of the maintenance of the web site hosting the thesaurus. All authors contributed to the choice of terms and definitions. E.G., U.S., M.-A.L., J.K. and S.K. wrote the manuscript with contributions from all authors, who gave final approval for publication. This work was partially funded by the following grants: GDR 2574 (‘Traits’) of CNRS (France); the TraitNet Research Coordination Network (US National Science Foundation Grant No. 0639161); the SONet effort (US NSF Grant No. 0753144); the project ‘Towards a unifying system of plant trait definition and measurement’ (the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig/Deutsche Forschungsgemeinschaft via Grant No. 50170649_#16); the German Federation for Biological Data - GFBio (Deutsche Forschungsgemeinschaft via Grant No. KA 3323/2-2); FONCyT, CONICET, Universidad Nacional de Córdoba and Inter-American Institute for Global Change Research (CRN 2015 and SGP-CRA2015, supported by NS grants GEO-0452325 and GEO-1138881), which supported the collaboration with the Plant Trait Handbook. Marie-Claude Quidoz, from the ‘Système d'Information en Ecologie’ platform at CEFE made possible preliminary work on the ThesauForm tool on the web.

    FundersFunder number
    German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig/Deutsche Forschungsgemeinschaft50170649_#16
    Universidad Nacional de Córdoba and Inter-American Institute for Global Change ResearchGEO-1138881, SGP-CRA2015, GEO-0452325
    National Science Foundation
    Directorate for Biological Sciences0753144, 0639161
    Deutsche ForschungsgemeinschaftKA 3323/2-2
    Consejo Nacional de Investigaciones Científicas y Técnicas
    Centre National de la Recherche Scientifique
    Fondo para la Investigación Científica y Tecnológica

      Keywords

      • biodiversity
      • controlled vocabulary
      • ecology
      • informatics
      • ontology
      • plant characteristics
      • plant environmental association
      • plant trait
      • semantics
      • thesaurus

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