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Journal Articles Journal of Ecology Year : 2016

Towards a thesaurus of plant characteristics: an ecological contribution

1 CEFE - Centre d’Ecologie Fonctionnelle et Evolutive
2 CESAB - Centre de Synthèse et d’Analyse sur la Biodiversité
3 MPI-BGC - Max Planck Institute for Biogeochemistry
4 iDiv - German Centre for Integrative Biodiversity Research
5 UFZ - Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research
6 Bioversity International [Rome]
7 ESPACE-DEV - Département Environnement et Ressources [Montpellier]
8 EEF - Ecologie et Ecophysiologie Forestières [devient SILVA en 2018]
9 Department of Ecology, Evolution and Environmental Biology
10 Frontier Wildlife Conservation [Mumbai]
11 NJIT - New Jersey Institute of Technology [Newark]
12 VU - Vrije Universiteit Amsterdam [Amsterdam]
13 IMBIV - Instituto Multidisciplinario de Biología Vegetal [Córdoba]
14 Department of Ecology and Evolutionary Biology [University of Arizona]
15 IMBE - Institut méditerranéen de biodiversité et d'écologie marine et continentale
16 Institute of Biology and Environmental Sciences [Oldenburg]
17 LECA - Laboratoire d'Ecologie Alpine
18 Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany]
19 Fraunhofer MOEZ - Fraunhofer Center for International Management and Knowledge Economics
20 FZJ - Forschungszentrum Jülich GmbH | Centre de recherche de Jülich | Jülich Research Centre
21 NCEAS - National Center for Ecological Analysis and Synthesis
22 UdeS - Département de biologie [Sherbrooke]
23 UWEC - University of Wisconsin - Eau Claire
24 Leipzig University / Universität Leipzig
25 Dpt Biological Sciences, Macquarie University
Sandra Lavorel
Bill Shipley

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’ of an ‘Entity’ ) 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.
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hal-01460790 , version 1 (14-05-2018)

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Eric Garnier, Ulrike Stahl, Marie-Angelique Laporte, Jens Kattge, Isabelle Mougenot, et al.. Towards a thesaurus of plant characteristics: an ecological contribution: An ecological contribution. Journal of Ecology, 2016, 105 (2), pp.298 - 309. ⟨10.1111/1365-2745.12698⟩. ⟨hal-01460790⟩
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