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

Research output: Contribution to journalArticle

56 Scopus citations

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 (US)
Pages (from-to)298-309
Number of pages12
JournalJournal of Ecology
Volume105
Issue number2
DOIs
StatePublished - Mar 1 2017

Keywords

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

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Ecology
  • Plant Science

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    Garnier, E., Stahl, U., Laporte, M. A., Kattge, J., Mougenot, I., Kühn, I., Laporte, B., Amiaud, B., Ahrestani, F. S., Bönisch, G., Bunker, D. E., Cornelissen, J. H. C., Díaz, S., Enquist, B. J., Gachet, S., Jaureguiberry, P., Kleyer, M., Lavorel, S., Maicher, L., ... Klotz, S. (2017). Towards a thesaurus of plant characteristics: an ecological contribution. Journal of Ecology, 105(2), 298-309. https://doi.org/10.1111/1365-2745.12698