TY - JOUR
T1 - Towards a thesaurus of plant characteristics
T2 - an ecological contribution
AU - Garnier, Eric
AU - Stahl, Ulrike
AU - Laporte, Marie Angélique
AU - Kattge, Jens
AU - Mougenot, Isabelle
AU - Kühn, Ingolf
AU - Laporte, Baptiste
AU - Amiaud, Bernard
AU - Ahrestani, Farshid S.
AU - Bönisch, Gerhard
AU - Bunker, Daniel E.
AU - Cornelissen, J. Hans C.
AU - Díaz, Sandra
AU - Enquist, Brian J.
AU - Gachet, Sophie
AU - Jaureguiberry, Pedro
AU - Kleyer, Michael
AU - Lavorel, Sandra
AU - Maicher, Lutz
AU - Pérez-Harguindeguy, Natalia
AU - Poorter, Hendrik
AU - Schildhauer, Mark
AU - Shipley, Bill
AU - Violle, Cyrille
AU - Weiher, Evan
AU - Wirth, Christian
AU - Wright, Ian J.
AU - Klotz, Stefan
N1 - Publisher Copyright:
© 2016 The Authors. Journal of Ecology © 2016 British Ecological Society
PY - 2017/3/1
Y1 - 2017/3/1
N2 - 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.
AB - 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.
KW - biodiversity
KW - controlled vocabulary
KW - ecology
KW - informatics
KW - ontology
KW - plant characteristics
KW - plant environmental association
KW - plant trait
KW - semantics
KW - thesaurus
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UR - http://www.scopus.com/inward/citedby.url?scp=85009193734&partnerID=8YFLogxK
U2 - 10.1111/1365-2745.12698
DO - 10.1111/1365-2745.12698
M3 - Article
AN - SCOPUS:85009193734
SN - 0022-0477
VL - 105
SP - 298
EP - 309
JO - Journal of Ecology
JF - Journal of Ecology
IS - 2
ER -